diff options
| author |   Julien Roy <julien@jroy.ca> | 2024-02-22 19:46:50 -0500 |
|---|---|---|
| committer | Julien Roy <julien@jroy.ca> | 2024-03-25 12:28:56 -0400 |
| commit | a6b3f15b1a76a2b066f9ff763fab5588bab902c6 (patch) | |
| tree | 86f32d7074d66c79409440a9426b97d7efaf5df8 /sys-cluster | |
| parent | profiles: Unmask treecleaned packages (diff) | |
| download | guru-a6b3f15b1a76a2b066f9ff763fab5588bab902c6.tar.gz guru-a6b3f15b1a76a2b066f9ff763fab5588bab902c6.tar.bz2 guru-a6b3f15b1a76a2b066f9ff763fab5588bab902c6.zip | |
*/*: treeclean stale/unmaintained packages
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Closes: https://bugs.gentoo.org/800076
Closes: https://bugs.gentoo.org/921884
Closes: https://bugs.gentoo.org/822456
Signed-off-by: Julien Roy <julien@jroy.ca>
Diffstat (limited to 'sys-cluster')
92 files changed, 0 insertions, 4506 deletions
diff --git a/sys-cluster/AXL/AXL-0.5.0.ebuild b/sys-cluster/AXL/AXL-0.5.0.ebuild deleted file mode 100644 index d43d456a8..000000000 --- a/sys-cluster/AXL/AXL-0.5.0.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit cmake - -DESCRIPTION="AXL provides a common C interface to transfer files in an HPC storage hierarchy." -HOMEPAGE="https://github.com/ECP-VeloC/AXL" -SRC_URI="https://github.com/ECP-VeloC/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="test" - -RDEPEND=" - dev-libs/KVTree - sys-libs/zlib -" -DEPEND="${RDEPEND}" - -RESTRICT="!test? ( test )" -PATCHES=( - "${FILESDIR}/${P}-no-static.patch" - "${FILESDIR}/no-install-readme.patch" -) - -src_configure() { - local mycmakeargs=( - -DAXL_LINK_STATIC=OFF - -DBUILD_SHARED_LIBS=ON - -DENABLE_CRAY_DW=OFF - -DENABLE_IBM_BBAPI=OFF - -DENABLE_TESTS=$(usex test) - ) - cmake_src_configure -} - -src_install() { - cmake_src_install - dodoc -r doc/. -} diff --git a/sys-cluster/AXL/AXL-0.7.0.ebuild b/sys-cluster/AXL/AXL-0.7.0.ebuild deleted file mode 100644 index 3edcf9df4..000000000 --- a/sys-cluster/AXL/AXL-0.7.0.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit cmake - -DESCRIPTION="AXL provides a common C interface to transfer files in an HPC storage hierarchy" -HOMEPAGE="https://github.com/ECP-VeloC/AXL" -SRC_URI="https://github.com/ECP-VeloC/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="test threads" - -RDEPEND=" - dev-libs/KVTree - sys-libs/zlib -" -DEPEND="${RDEPEND}" - -RESTRICT="!test? ( test )" -PATCHES=( - "${FILESDIR}/${PN}-0.5.0-no-static.patch" - "${FILESDIR}/no-install-readme.patch" -) - -src_configure() { - local mycmakeargs=( - -DAXL_LINK_STATIC=OFF - -DBUILD_SHARED_LIBS=ON - -DENABLE_CRAY_DW=OFF - -DENABLE_IBM_BBAPI=OFF - -DENABLE_PTHREADS=$(usex threads) - -DENABLE_TESTS=$(usex test) - ) - cmake_src_configure -} - -src_install() { - cmake_src_install - dodoc -r doc/. -} diff --git a/sys-cluster/AXL/Manifest b/sys-cluster/AXL/Manifest deleted file mode 100644 index 834a1db4c..000000000 --- a/sys-cluster/AXL/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST AXL-0.5.0.tar.gz 47792 BLAKE2B acc82ac512f2e598bd0f11b9e762b9aad618a50e38b3e3f117232b9c94efa444b39ed8d8923278a18db39ba4db46fc95867a3c9efaa7a38ed9a5280649d8ceae SHA512 81d9bb0c5cd100dee8bc813f7f39ad8c7f18ed6415525845bf6d79ccfe6e84c00d0660e0621ad9458522826068fbbb8cbf4680abc5b23cd4da058ce9f5482a4d -DIST AXL-0.7.0.tar.gz 48339 BLAKE2B 57525b6288617f0f9b2d4fcbe653a2bdc312d81a9b00671d79f625a8ea9b8b79dcfc3122acf2d27fc60c5f1d04b4f90d688fe9e1441fa3f9a44575cac9056318 SHA512 5d57f1dd60dfe8ceb27348a1c0389291a3cac6d909514fdbd6fdf31eeaba974a0b5aca23e7de35fea63585485c841622f4993cf0b3a060aa54af532728fc826d diff --git a/sys-cluster/AXL/files/AXL-0.5.0-no-static.patch b/sys-cluster/AXL/files/AXL-0.5.0-no-static.patch deleted file mode 100644 index f75d0976d..000000000 --- a/sys-cluster/AXL/files/AXL-0.5.0-no-static.patch +++ /dev/null @@ -1,16 +0,0 @@ ---- a/src/CMakeLists.txt -+++ b/src/CMakeLists.txt -@@ -30,13 +30,3 @@ - SET_TARGET_PROPERTIES(axl PROPERTIES OUTPUT_NAME axl CLEAN_DIRECT_OUTPUT 1) - INSTALL(TARGETS axl DESTINATION ${CMAKE_INSTALL_LIBDIR}) - ENDIF() -- --ADD_LIBRARY(axl-static STATIC $<TARGET_OBJECTS:axl_o>) --IF(AXL_LINK_STATIC) -- SET_TARGET_PROPERTIES(axl-static PROPERTIES LINK_SEARCH_START_STATIC 1) -- SET_TARGET_PROPERTIES(axl-static PROPERTIES LINK_SEARCH_END_STATIC 1) --ENDIF(AXL_LINK_STATIC) --TARGET_LINK_LIBRARIES(axl-static ${AXL_EXTERNAL_LIBS}) -- --SET_TARGET_PROPERTIES(axl-static PROPERTIES OUTPUT_NAME axl CLEAN_DIRECT_OUTPUT 1) --INSTALL(TARGETS axl-static DESTINATION ${CMAKE_INSTALL_LIBDIR}) diff --git a/sys-cluster/AXL/files/no-install-readme.patch b/sys-cluster/AXL/files/no-install-readme.patch deleted file mode 100644 index 40876175d..000000000 --- a/sys-cluster/AXL/files/no-install-readme.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -125,9 +125,6 @@ - SET_SOURCE_FILES_PROPERTIES(config.h.in PROPERTIES GENERATED FALSE) - SET_SOURCE_FILES_PROPERTIES(${PROJECT_BINARY_DIR}/config.h PROPERTIES GENERATED TRUE) - --# Special Install Files --INSTALL(FILES README.md DESTINATION ${CMAKE_INSTALL_DATADIR}/axl) -- - # Package - SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Asynchronous Transfer Library") - SET(CPACK_PACKAGE_VENDOR "Lawrence Livermore National Laboratory") diff --git a/sys-cluster/AXL/metadata.xml b/sys-cluster/AXL/metadata.xml deleted file mode 100644 index 654a26366..000000000 --- a/sys-cluster/AXL/metadata.xml +++ /dev/null @@ -1,13 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <upstream> - <remote-id type="github">ECP-VeloC/AXL</remote-id> - </upstream> - <longdescription lang="en">AXL defines a common interface for transferring files between layers in a storage hierarchy. It abstracts vendor-specific APIs and provides synchronous and asynchronous methods using POSIX. One creates a transfer object, defining the transfer type, and then one adds files to the transfer. Once all files have been added, one initiates the transfer and can then later test or wait for its completion. The library optionally records the state of ongoing transfers, so that they can be identified or terminated even if the process that initiated the transfer has been restarted. - </longdescription> -</pkgmetadata> diff --git a/sys-cluster/Graph500/Graph500-1.2.ebuild b/sys-cluster/Graph500/Graph500-1.2.ebuild deleted file mode 100644 index 36601d979..000000000 --- a/sys-cluster/Graph500/Graph500-1.2.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit cmake - -MYPN="${PN,,}" -MYP="${MYPN}-${PV}" - -DESCRIPTION="Graph500 reference implementations" -HOMEPAGE="https://github.com/Graph500/graph500" -SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/${MYP}.tar.gz" -S="${WORKDIR}/${MYPN}-${MYP}" - -KEYWORDS="~amd64" -LICENSE="MIT Boost-1.0" -SLOT="0" -IUSE="mpi openmp" - -RDEPEND=" - sys-libs/binutils-libs - mpi? ( virtual/mpi ) -" -DEPEND="${RDEPEND}" -BDEPEND="app-admin/chrpath" - -PATCHES=( - "${FILESDIR}/${P}-MPI_Type_create_struct.patch" - "${FILESDIR}/${P}-static-inline.patch" -) - -src_prepare() { - cp "${FILESDIR}/${P}-CMakeLists.txt" CMakeLists.txt || die - cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DBUILD_MPI=$(usex mpi) - -DBUILD_OPENMP=$(usex openmp) - ) - cmake_src_configure -} - -src_install() { - cmake_src_install - dosym ./libgenerator-seq.so "/usr/$(get_libdir)/libGraphGenlib.so" - dodoc README Graph500.org - insinto "/usr/share/doc/${PF}/html" - doins *.html - insinto "/usr/share/octave/site/m/${PN}" - doins -r octave/* - - if use mpi ; then - chrpath -d "${ED}/usr/bin/graph500_mpi_one_sided" || die - chrpath -d "${ED}/usr/bin/graph500_mpi_simple" || die - chrpath -d "${ED}/usr/bin/generator_test_mpi" || die - fi -} diff --git a/sys-cluster/Graph500/Manifest b/sys-cluster/Graph500/Manifest deleted file mode 100644 index 70c9f8dbf..000000000 --- a/sys-cluster/Graph500/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST graph500-1.2.tar.gz 368889 BLAKE2B f0afe4b89edab710b4c0149d5e726ba5758d2cc1852a8837ee7ffbc87dae23ce212b39b27e2301908f652c5dc7ea07525125decdb559e6585df4a80e68ff0686 SHA512 f62d5f4c1144234baf619a7e3f05eed5bfc2c6b7c9b8bd317cceb9652fbdba057976cb83d06e58d8290fe8caf79b113d5ab8ba9122d79f71c12e04af410b3afc diff --git a/sys-cluster/Graph500/files/Graph500-1.2-CMakeLists.txt b/sys-cluster/Graph500/files/Graph500-1.2-CMakeLists.txt deleted file mode 100644 index f9ed40739..000000000 --- a/sys-cluster/Graph500/files/Graph500-1.2-CMakeLists.txt +++ /dev/null @@ -1,135 +0,0 @@ -cmake_minimum_required(VERSION 3.15) -project(graph500 LANGUAGES C) -set(CMAKE_POSITION_INDEPENDENT_CODE ON) -include(GNUInstallDirs) - -SET(GRAPH500_SOURCES - "${CMAKE_CURRENT_SOURCE_DIR}/options.c" - "${CMAKE_CURRENT_SOURCE_DIR}/rmat.c" - "${CMAKE_CURRENT_SOURCE_DIR}/kronecker.c" - "${CMAKE_CURRENT_SOURCE_DIR}/verify.c" - "${CMAKE_CURRENT_SOURCE_DIR}/prng.c" - "${CMAKE_CURRENT_SOURCE_DIR}/xalloc.c" - "${CMAKE_CURRENT_SOURCE_DIR}/timer.c" -) -ADD_LIBRARY(GRAPH500_OBJECTS OBJECT ${GRAPH500_SOURCES}) -target_include_directories(GRAPH500_OBJECTS PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}") - -SET(GENERATOR_SRC - "${CMAKE_CURRENT_SOURCE_DIR}/generator/btrd_binomial_distribution.c" - "${CMAKE_CURRENT_SOURCE_DIR}/generator/splittable_mrg.c" - "${CMAKE_CURRENT_SOURCE_DIR}/generator/mrg_transitions.c" - "${CMAKE_CURRENT_SOURCE_DIR}/generator/graph_generator.c" - "${CMAKE_CURRENT_SOURCE_DIR}/generator/permutation_gen.c" - "${CMAKE_CURRENT_SOURCE_DIR}/generator/make_graph.c" - "${CMAKE_CURRENT_SOURCE_DIR}/generator/utils.c" - "${CMAKE_CURRENT_SOURCE_DIR}/generator/scramble_edges.c" -) - -ADD_LIBRARY(generator-seq SHARED ${GENERATOR_SRC} $<TARGET_OBJECTS:GRAPH500_OBJECTS>) -target_compile_definitions(generator-seq PUBLIC GRAPH_GENERATOR_SEQ) -target_include_directories(generator-seq PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/generator") -target_link_libraries(generator-seq PUBLIC -liberty) -install(TARGETS generator-seq LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}") - -if(BUILD_OPENMP) - find_package(OpenMP REQUIRED) - - ADD_LIBRARY(generator-omp SHARED ${GENERATOR_SRC} $<TARGET_OBJECTS:GRAPH500_OBJECTS>) - set_target_properties(generator-omp PROPERTIES COMPILE_FLAGS "-fopenmp") - target_compile_definitions(generator-omp PUBLIC GRAPH_GENERATOR_OMP) - target_include_directories(generator-omp PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/generator") - target_link_libraries(generator-omp PUBLIC OpenMP::OpenMP_C -liberty) - install(TARGETS generator-omp LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}") - - ADD_EXECUTABLE(omp-csr - "${CMAKE_CURRENT_SOURCE_DIR}/omp-csr/omp-csr.c" - "${CMAKE_CURRENT_SOURCE_DIR}/graph500.c" - ) - target_link_libraries(omp-csr generator-omp -lm) - install(TARGETS omp-csr RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}") - - ADD_EXECUTABLE(generator_test_omp "${CMAKE_CURRENT_SOURCE_DIR}/generator/generator_test_omp.c") - target_link_libraries(generator_test_omp generator-omp -lm) - install(TARGETS generator_test_omp RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}") -endif() - -ADD_EXECUTABLE(seq-list - "${CMAKE_CURRENT_SOURCE_DIR}/seq-list/seq-list.c" - "${CMAKE_CURRENT_SOURCE_DIR}/graph500.c" -) -target_link_libraries(seq-list generator-seq -lm) -install(TARGETS seq-list RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}") - -ADD_EXECUTABLE(seq-csr - "${CMAKE_CURRENT_SOURCE_DIR}/seq-csr/seq-csr.c" - "${CMAKE_CURRENT_SOURCE_DIR}/graph500.c" -) -target_link_libraries(seq-csr generator-seq -lm) -install(TARGETS seq-csr RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}") - -ADD_EXECUTABLE(generator_test_seq "${CMAKE_CURRENT_SOURCE_DIR}/generator/generator_test_seq.c") -target_link_libraries(generator_test_seq generator-seq -lm) -install(TARGETS generator_test_seq RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}") - -if(BUILD_MPI) - find_package(MPI REQUIRED) - - ADD_LIBRARY(graph_generator_mpi SHARED - "${CMAKE_CURRENT_SOURCE_DIR}/generator/apply_permutation_mpi.c" - ${GENERATOR_SRC} - ) - target_compile_definitions(graph_generator_mpi PUBLIC restrict=__restrict__ GRAPH_GENERATOR_MPI GRAPHGEN_DISTRIBUTED_MEMORY) - target_include_directories(graph_generator_mpi - PUBLIC - "${CMAKE_CURRENT_SOURCE_DIR}/generator" - PRIVATE - ${MPI_INCLUDE_PATH} - ) - target_link_libraries(graph_generator_mpi PUBLIC ${MPI_LIBRARIES} ${MPI_LINK_FLAGS} -liberty) - install(TARGETS graph_generator_mpi LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}") - - ADD_EXECUTABLE(generator_test_mpi "${CMAKE_CURRENT_SOURCE_DIR}/generator/generator_test_mpi.c") - target_compile_definitions(graph_generator_mpi PUBLIC restrict=__restrict__ GRAPH_GENERATOR_MPI GRAPHGEN_DISTRIBUTED_MEMORY) - target_include_directories(generator_test_mpi - PUBLIC - "${CMAKE_CURRENT_SOURCE_DIR}/generator" - PRIVATE - ${MPI_INCLUDE_PATH} - ) - target_link_libraries(generator_test_mpi graph_generator_mpi ${MPI_LIBRARIES} ${MPI_LINK_FLAGS} -lm) - install(TARGETS generator_test_mpi RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}") - - SET(graph500_mpi_src - "${CMAKE_CURRENT_SOURCE_DIR}/mpi/convert_to_csr.c" - "${CMAKE_CURRENT_SOURCE_DIR}/mpi/find_roots.c" - "${CMAKE_CURRENT_SOURCE_DIR}/mpi/utils.c" - "${CMAKE_CURRENT_SOURCE_DIR}/mpi/validate.c" - ) - ADD_LIBRARY(graph500_mpi_obj OBJECT ${graph500_mpi_src}) - target_include_directories(graph500_mpi_obj PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/mpi") - target_compile_definitions(graph500_mpi_obj PUBLIC restrict=__restrict__ GRAPH_GENERATOR_MPI GRAPHGEN_DISTRIBUTED_MEMORY) - ADD_LIBRARY(graph500_mpi SHARED $<TARGET_OBJECTS:graph500_mpi_obj>) - install(TARGETS graph500_mpi LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}") - - ADD_EXECUTABLE(graph500_mpi_simple - "${CMAKE_CURRENT_SOURCE_DIR}/mpi/main.c" - "${CMAKE_CURRENT_SOURCE_DIR}/mpi/bfs_simple.c" - ) - target_compile_definitions(graph500_mpi_simple PUBLIC restrict=__restrict__ GRAPH_GENERATOR_MPI GRAPHGEN_DISTRIBUTED_MEMORY) - target_link_libraries(graph500_mpi_simple graph500_mpi graph_generator_mpi -lm) - install(TARGETS graph500_mpi_simple RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}") - - ADD_EXECUTABLE(graph500_mpi_one_sided - "${CMAKE_CURRENT_SOURCE_DIR}/mpi/main.c" - "${CMAKE_CURRENT_SOURCE_DIR}/mpi/bfs_one_sided.c" - ) - target_compile_definitions(graph500_mpi_simple PUBLIC restrict=__restrict__ GRAPH_GENERATOR_MPI GRAPHGEN_DISTRIBUTED_MEMORY) - target_link_libraries(graph500_mpi_one_sided graph500_mpi graph_generator_mpi -lm) - install(TARGETS graph500_mpi_one_sided RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}") -endif() - - -install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/" DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/graph500" FILES_MATCHING PATTERN "*.h") -install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/mpi/" DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/graph500/mpi" FILES_MATCHING PATTERN "*.h") -install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/generator/" DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/graph500/generator" FILES_MATCHING PATTERN "*.h") diff --git a/sys-cluster/Graph500/files/Graph500-1.2-MPI_Type_create_struct.patch b/sys-cluster/Graph500/files/Graph500-1.2-MPI_Type_create_struct.patch deleted file mode 100644 index 00719ae08..000000000 --- a/sys-cluster/Graph500/files/Graph500-1.2-MPI_Type_create_struct.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/generator/permutation_gen.c -+++ b/generator/permutation_gen.c -@@ -251,7 +251,7 @@ - indices[0] -= temp_base; - indices[1] -= temp_base; - MPI_Datatype old_types[] = {INT64_T_MPI_TYPE, INT64_T_MPI_TYPE}; -- MPI_Type_struct(2, blocklens, indices, old_types, &slot_data_type); -+ MPI_Type_create_struct(2, blocklens, indices, old_types, &slot_data_type); - MPI_Type_commit(&slot_data_type); - } - diff --git a/sys-cluster/Graph500/files/Graph500-1.2-static-inline.patch b/sys-cluster/Graph500/files/Graph500-1.2-static-inline.patch deleted file mode 100644 index 0b1f63a28..000000000 --- a/sys-cluster/Graph500/files/Graph500-1.2-static-inline.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/generator/generator_test_seq.c -+++ b/generator/generator_test_seq.c -@@ -20,7 +20,7 @@ - - #include "make_graph.h" - --inline double get_time() { -+static inline double get_time() { - struct timeval tv; - gettimeofday(&tv, NULL); - return tv.tv_sec + tv.tv_usec * 1.e-6; diff --git a/sys-cluster/Graph500/metadata.xml b/sys-cluster/Graph500/metadata.xml deleted file mode 100644 index c8887a6ef..000000000 --- a/sys-cluster/Graph500/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <upstream> - <bugs-to>https://github.com/Graph500/graph500/issues</bugs-to> - <remote-id type="github">Graph500/graph500</remote-id> - </upstream> -</pkgmetadata> diff --git a/sys-cluster/SIONfwd/Manifest b/sys-cluster/SIONfwd/Manifest deleted file mode 100644 index ca547bc19..000000000 --- a/sys-cluster/SIONfwd/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST SIONfwd-v1.0.1.tar.bz2 9531 BLAKE2B fd998f9785e2d5de7c9431121109ca1a02ab3de648672db2fa2f45957788407850c8ffb75f93d283e4bd39c53f6627c8c93c637428812eaa86602c855cbd2fdd SHA512 3e71d0fbab76ae89b1a21be38a95986f1e5e913ea7bb5b17f3c21a905f5bda04634889264bdd101de833db8f069bc473093b805e5f6f453ac40290059fa2c51e diff --git a/sys-cluster/SIONfwd/SIONfwd-1.0.1.ebuild b/sys-cluster/SIONfwd/SIONfwd-1.0.1.ebuild deleted file mode 100644 index 84a979319..000000000 --- a/sys-cluster/SIONfwd/SIONfwd-1.0.1.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI="7" - -MYP="${PN}-v${PV}" - -inherit cmake - -DESCRIPTION="A minimalistic I/O forwarding server and client library for SIONlib" -HOMEPAGE="https://gitlab.jsc.fz-juelich.de/cstao-public/SIONlib/SIONfwd" -SRC_URI="https://gitlab.jsc.fz-juelich.de/cstao-public/SIONlib/SIONfwd/-/archive/v${PV}/${MYP}.tar.bz2" -S="${WORKDIR}/${MYP}" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="test" - -RDEPEND="virtual/mpi" -DEPEND="${RDEPEND}" - -#RESTRICT="!test? ( test )" -RESTRICT="test" #test failures related to MPI - -src_configure() { - mycmakeargs=( - -DBUILD_SHARED_LIBS=ON - -DCMAKE_BUILD_TYPE=Release - -DSIONfwd_BUILD_TESTING=$(usex test) - ) - cmake_src_configure -} - -src_test() { - ./test.sh || die -} diff --git a/sys-cluster/SIONfwd/metadata.xml b/sys-cluster/SIONfwd/metadata.xml deleted file mode 100644 index a2607a709..000000000 --- a/sys-cluster/SIONfwd/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <longdescription lang="en"> -SIONfwd uses MPI's port mechanism to establish dynamic connections between server and client which are then used to transmit remote procedure calls (RPCs). -Both client and server have to be launched trough an MPI process startup mechanism (e.g. the mpiexec program), but using different MPI_COMM_WORLD, i.e. separate invocations of the startup mechanism. -The server prints the information that the client needs to connect to its stdout. -The client expects to find this information in certain environment variables. -A shell function that reads the information from the server and exports the environment variables required by the client is provided by the server (sionfwd-server bash-defs). -See the file test.sh for details. - </longdescription> - <upstream> - <bugs-to>https://gitlab.jsc.fz-juelich.de/cstao-public/SIONlib/SIONfwd/-/issues</bugs-to> - </upstream> -</pkgmetadata> diff --git a/sys-cluster/adios2/Manifest b/sys-cluster/adios2/Manifest deleted file mode 100644 index 4dc9a3d55..000000000 --- a/sys-cluster/adios2/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST adios2-2.8.1.gh.tar.gz 5747375 BLAKE2B 1c2b2845db90be83fc911f53724ab8a72aca93562720a03c05084f61611e3247525160a00810c9f492cd9743e70ac7ad3db601771905a4ab53d089b943971416 SHA512 50001f73318a4deb63a487a817f0b151904f39bd3d9d3d0a04fe77e4323f639b625472fb82b32702fdfc990bf765aff65793ca6817f2798a5cf4b6c72f9a38d7 diff --git a/sys-cluster/adios2/adios2-2.8.1-r1.ebuild b/sys-cluster/adios2/adios2-2.8.1-r1.ebuild deleted file mode 100644 index 2775b3dbb..000000000 --- a/sys-cluster/adios2/adios2-2.8.1-r1.ebuild +++ /dev/null @@ -1,127 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -FORTRAN_NEEDED="fortran" -MYPN="${PN^^}" -PYTHON_COMPAT=( python3_10 ) - -inherit cmake python-single-r1 fortran-2 - -DESCRIPTION="Next generation of ADIOS developed in the Exascale Computing Program" -HOMEPAGE=" - https://csmd.ornl.gov/software/adios2 - https://github.com/ornladios/adios2 -" -SRC_URI="https://github.com/ornladios/${MYPN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" -S="${WORKDIR}/${MYPN}-${PV}" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64" -IUSE="blosc bzip2 endian-reverse examples fortran hdf5 mpi png profile python sodium sst szip test zeromq zfp" - -RDEPEND=" - dev-cpp/nlohmann_json - dev-cpp/yaml-cpp:= - dev-libs/atl - dev-libs/dill - >dev-libs/ffs-1.6.0 - dev-libs/kwsys:= - dev-libs/perfstubs:=[timers] - dev-libs/pugixml - net-libs/enet - >net-libs/evpath-4.5.0 - - blosc? ( dev-libs/c-blosc:= ) - bzip2? ( app-arch/bzip2 ) - hdf5? ( sci-libs/hdf5:=[mpi=] ) - mpi? ( virtual/mpi[cxx] ) - png? ( media-libs/libpng:= ) - python? ( - ${PYTHON_DEPS} - $(python_gen_cond_dep ' - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pybind11[${PYTHON_USEDEP}] - ') - mpi? ( $(python_gen_cond_dep 'dev-python/mpi4py[${PYTHON_USEDEP}]') ) - ) - sodium? ( dev-libs/libsodium:= ) - sst? ( sys-block/libfabric:= ) - szip? ( virtual/szip ) - zeromq? ( net-libs/zeromq:= ) - zfp? ( dev-libs/zfp ) -" -DEPEND=" - ${RDEPEND} - test? ( dev-cpp/gtest ) -" -BDEPEND="virtual/pkgconfig" - -PATCHES=( - "${FILESDIR}/${P}-system-libs.patch" - "${FILESDIR}/${P}-sandbox.patch" -) -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" -RESTRICT="!test? ( test )" - -pkg_setup() { - use fortran && fortran-2_pkg_setup - use python && python-single-r1_pkg_setup -} - -src_configure() { - local mycmakeargs=( - -DBUILD_SHARED_LIBS=ON - -DADIOS2_USE_BP5=OFF - -DADIOS2_USE_CUDA=OFF - -DADIOS2_USE_DataMan=OFF - -DADIOS2_USE_DataSpaces=OFF - -DADIOS2_USE_EXTERNAL_ATL=ON - -DADIOS2_USE_EXTERNAL_DEPENDENCIES=ON - -DADIOS2_USE_EXTERNAL_DILL=ON - -DADIOS2_USE_EXTERNAL_ENET=ON - -DADIOS2_USE_EXTERNAL_FFS=ON - -DADIOS2_USE_EXTERNAL_EVPATH=ON - -DADIOS2_USE_EXTERNAL_GTEST=ON - -DADIOS2_USE_EXTERNAL_NLOHMANN_JSON=ON - -DADIOS2_USE_EXTERNAL_PUGIXML=ON - -DADIOS2_USE_EXTERNAL_PYBIND11=ON - -DADIOS2_USE_EXTERNAL_YAMLCPP=ON - -DADIOS2_USE_IME=OFF - -DADIOS2_USE_LIBPRESSIO=OFF - -DADIOS2_USE_MGARD=OFF - - -DADIOS2_BUILD_EXAMPLES="$(usex examples)" - -DADIOS2_BUILD_EXAMPLES_EXPERIMENTAL="$(usex examples)" - -DADIOS2_USE_Blosc="$(usex blosc)" - -DADIOS2_USE_BZip2="$(usex bzip2)" - -DADIOS2_USE_Endian_Reverse="$(usex endian-reverse)" - -DADIOS2_USE_Fortran="$(usex fortran)" - -DADIOS2_USE_HDF5="$(usex hdf5)" - -DADIOS2_USE_MPI="$(usex mpi)" - -DADIOS2_USE_PNG="$(usex png)" - -DADIOS2_USE_Profiling="$(usex profile)" - -DADIOS2_USE_Python="$(usex python)" - -DADIOS2_USE_Sodium="$(usex sodium)" - -DADIOS2_USE_SST="$(usex sst)" - -DADIOS2_USE_SZ="$(usex szip)" - -DADIOS2_USE_ZeroMQ="$(usex zeromq)" - -DADIOS2_USE_ZFP="$(usex zfp)" - -DBUILD_TESTING="$(usex python)" - ) - cmake_src_configure -} - -src_prepare() { - rm -r thirdparty/{atl,dill,enet,EVPath,ffs,GTest,KWSys,mingw-w64,pugixml,pybind11,yaml-cpp} || die - rm -r thirdparty/nlohmann_json/nlohmann_json_wrapper/single_include || die - rm -r thirdparty/perfstubs/perfstubs || die - cmake_src_prepare -} - -src_install() { - cmake_src_install - dodoc ReadMe.md -} diff --git a/sys-cluster/adios2/files/adios2-2.8.1-sandbox.patch b/sys-cluster/adios2/files/adios2-2.8.1-sandbox.patch deleted file mode 100644 index d1d3db92a..000000000 --- a/sys-cluster/adios2/files/adios2-2.8.1-sandbox.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- a/cmake/install/pre/CMakeLists.txt -+++ b/cmake/install/pre/CMakeLists.txt -@@ -1,9 +1,3 @@ --install(CODE " -- message(\"Pre-installation cleanup of CMake files\") -- file(REMOVE_RECURSE \"${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_CMAKEDIR}\") --" -- COMPONENT adios2_core-development --) - file(GLOB ADIOS2_MODULE_FILES - "${ADIOS2_SOURCE_DIR}/cmake/Find*.cmake" - "${ADIOS2_SOURCE_DIR}/cmake/CMake*.cmake" diff --git a/sys-cluster/adios2/files/adios2-2.8.1-system-libs.patch b/sys-cluster/adios2/files/adios2-2.8.1-system-libs.patch deleted file mode 100644 index 86f2c8958..000000000 --- a/sys-cluster/adios2/files/adios2-2.8.1-system-libs.patch +++ /dev/null @@ -1,307 +0,0 @@ ---- a/source/adios2/CMakeLists.txt -+++ b/source/adios2/CMakeLists.txt -@@ -127,7 +127,7 @@ - $<BUILD_INTERFACE:${ADIOS2_SOURCE_DIR}/source> - $<BUILD_INTERFACE:${ADIOS2_BINARY_DIR}/source> - ) --target_link_libraries(adios2_core PRIVATE adios2sys_interface adios2::thirdparty::pugixml -+target_link_libraries(adios2_core PRIVATE -lkwsys adios2::thirdparty::pugixml - adios2::thirdparty::yaml-cpp adios2::thirdparty::nlohmann_json adios2::thirdparty::perfstubs-interface) - target_link_libraries(adios2_core PUBLIC ${CMAKE_THREAD_LIBS_INIT}) - target_compile_features(adios2_core PUBLIC "$<BUILD_INTERFACE:${ADIOS2_CXX11_FEATURES}>") -@@ -151,7 +151,7 @@ - toolkit/format/bp5/BP5Serializer.cpp - toolkit/format/bp5/BP5Deserializer.cpp toolkit/format/bp5/BP5Deserializer.tcc - ) -- target_link_libraries(adios2_core PRIVATE ffs::ffs) -+ target_link_libraries(adios2_core PRIVATE ffs) - endif() - - if(ADIOS2_HAVE_DAOS) ---- a/source/adios2/core/ADIOS.cpp -+++ b/source/adios2/core/ADIOS.cpp -@@ -19,7 +19,7 @@ - #include "adios2/helper/adiosCommDummy.h" - #include "adios2/helper/adiosFunctions.h" //InquireKey, BroadcastFile - #include "adios2/operator/OperatorFactory.h" --#include <adios2sys/SystemTools.hxx> -+#include <kwsys/SystemTools.hxx> - - #include <adios2-perfstubs-interface.h> - -@@ -53,7 +53,7 @@ - #endif - if (!configFile.empty()) - { -- if (!adios2sys::SystemTools::FileExists(configFile)) -+ if (!kwsys::SystemTools::FileExists(configFile)) - { - helper::Throw<std::logic_error>("Core", "ADIOS", "ADIOS", - "config file " + configFile + ---- a/source/adios2/core/IO.cpp -+++ b/source/adios2/core/IO.cpp -@@ -39,7 +39,7 @@ - #include "adios2/helper/adiosComm.h" - #include "adios2/helper/adiosFunctions.h" //BuildParametersMap - #include "adios2/helper/adiosString.h" --#include <adios2sys/SystemTools.hxx> // FileIsDirectory() -+#include <kwsys/SystemTools.hxx> // FileIsDirectory() - - #ifdef ADIOS2_HAVE_DATAMAN // external dependencies - #include "adios2/engine/dataman/DataManReader.h" -@@ -559,13 +559,13 @@ - else if ((mode_to_use == Mode::Read) || - (mode_to_use == Mode::ReadRandomAccess)) - { -- if (adios2sys::SystemTools::FileIsDirectory(name)) -+ if (kwsys::SystemTools::FileIsDirectory(name)) - { - char v = helper::BPVersion(name, comm, m_TransportsParameters); - engineTypeLC = "bp"; - engineTypeLC.push_back(v); - } -- else if (adios2sys::SystemTools::FileIsDirectory(name + ".tier0")) -+ else if (kwsys::SystemTools::FileIsDirectory(name + ".tier0")) - { - engineTypeLC = "mhs"; - } ---- a/source/adios2/helper/adiosDynamicBinder.cpp -+++ b/source/adios2/helper/adiosDynamicBinder.cpp -@@ -18,8 +18,8 @@ - #include <stdexcept> // for runtime_error - #include <vector> // for vector - --#include <adios2sys/DynamicLoader.hxx> --#include <adios2sys/SystemTools.hxx> -+#include <kwsys/DynamicLoader.hxx> -+#include <kwsys/SystemTools.hxx> - - namespace adios2 - { -@@ -28,7 +28,7 @@ - - struct DynamicBinder::Impl - { -- adios2sys::DynamicLoader::LibraryHandle m_LibraryHandle; -+ kwsys::DynamicLoader::LibraryHandle m_LibraryHandle; - }; - - DynamicBinder::DynamicBinder(std::string libName) : DynamicBinder(libName, "") -@@ -76,14 +76,14 @@ - // ConvertToOutputPath() will change slashes if we're running on - // a Windows system - fileName = -- adios2sys::SystemTools::ConvertToOutputPath(fileName); -+ kwsys::SystemTools::ConvertToOutputPath(fileName); - } - else - { - fileName = prefix + libName + suffix; - } - m_Impl->m_LibraryHandle = -- adios2sys::DynamicLoader::OpenLibrary(fileName); -+ kwsys::DynamicLoader::OpenLibrary(fileName); - searchedLibs.push_back(fileName); - if (m_Impl->m_LibraryHandle) - { -@@ -110,13 +110,13 @@ - - DynamicBinder::~DynamicBinder() - { -- adios2sys::DynamicLoader::CloseLibrary(m_Impl->m_LibraryHandle); -+ kwsys::DynamicLoader::CloseLibrary(m_Impl->m_LibraryHandle); - } - - DynamicBinder::VoidSymbolPointer - DynamicBinder::GetSymbol(std::string symbolName) - { -- return adios2sys::DynamicLoader::GetSymbolAddress(m_Impl->m_LibraryHandle, -+ return kwsys::DynamicLoader::GetSymbolAddress(m_Impl->m_LibraryHandle, - symbolName); - } - ---- a/source/adios2/helper/adiosPluginManager.cpp -+++ b/source/adios2/helper/adiosPluginManager.cpp -@@ -17,7 +17,7 @@ - #include "adios2/helper/adiosLog.h" - #include "adios2/helper/adiosString.h" - --#include <adios2sys/SystemTools.hxx> -+#include <kwsys/SystemTools.hxx> - - #include <memory> - #include <stdexcept> -@@ -110,13 +110,13 @@ - } - - std::string allPluginPaths; -- adios2sys::SystemTools::GetEnv(pluginEnvVarName, allPluginPaths); -+ kwsys::SystemTools::GetEnv(pluginEnvVarName, allPluginPaths); - if (allPluginPaths.empty()) - { - return OpenPlugin(pluginName, pluginLibrary, ""); - } - auto pathsSplit = -- adios2sys::SystemTools::SplitString(allPluginPaths, ':', false); -+ kwsys::SystemTools::SplitString(allPluginPaths, ':', false); - - bool loaded = false; - auto pathIt = pathsSplit.begin(); ---- a/source/adios2/helper/adiosSystem.cpp -+++ b/source/adios2/helper/adiosSystem.cpp -@@ -13,7 +13,7 @@ - #include <stdexcept> // std::runtime_error, std::exception - #include <system_error> - --#include <adios2sys/SystemTools.hxx> -+#include <kwsys/SystemTools.hxx> - - #include "adios2/common/ADIOSTypes.h" - #include "adios2/helper/adiosComm.h" -@@ -37,7 +37,7 @@ - - bool CreateDirectory(const std::string &fullPath) noexcept - { -- return static_cast<bool>(adios2sys::SystemTools::MakeDirectory(fullPath)); -+ return static_cast<bool>(kwsys::SystemTools::MakeDirectory(fullPath)); - } - - bool IsLittleEndian() noexcept -@@ -168,7 +168,7 @@ - if (!comm.Rank()) - { - std::string mmdFileName = name + PathSeparator + "mmd.0"; -- if (adios2sys::SystemTools::PathExists(mmdFileName)) -+ if (kwsys::SystemTools::PathExists(mmdFileName)) - { - version = '5'; - } ---- a/source/adios2/operator/plugin/PluginOperator.cpp -+++ b/source/adios2/operator/plugin/PluginOperator.cpp -@@ -21,7 +21,7 @@ - #include "adios2/helper/adiosPluginManager.h" - #include "adios2/helper/adiosString.h" - --#include <adios2sys/SystemTools.hxx> -+#include <kwsys/SystemTools.hxx> - - namespace adios2 - { ---- a/source/utils/bpls/bpls.cpp -+++ b/source/utils/bpls/bpls.cpp -@@ -57,8 +57,8 @@ - - #include "adios2/helper/adiosString.h" // EndsWith - #include "adios2/helper/adiosSystem.h" //isHDF5File --#include <adios2sys/CommandLineArguments.hxx> --#include <adios2sys/SystemTools.hxx> -+#include <kwsys/CommandLineArguments.hxx> -+#include <kwsys/SystemTools.hxx> - #include <pugixml.hpp> - - namespace adios2 -@@ -202,8 +202,8 @@ - bool option_help_was_called = false; - int optioncb_help(const char *argument, const char *value, void *call_data) - { -- // adios2sys::CommandLineArguments *arg = -- // static_cast<adios2sys::CommandLineArguments *>(call_data); -+ // kwsys::CommandLineArguments *arg = -+ // static_cast<kwsys::CommandLineArguments *>(call_data); - // printf("%s\n", arg->GetHelp()); - display_help(); - option_help_was_called = true; -@@ -431,7 +431,7 @@ - - void introspect_file(const char *filename) noexcept - { -- if (adios2sys::SystemTools::FileIsDirectory(filename)) -+ if (kwsys::SystemTools::FileIsDirectory(filename)) - { - if (!introspectAsBPDir(filename)) - { -@@ -460,7 +460,7 @@ - } - } - --int process_unused_args(adios2sys::CommandLineArguments &arg) -+int process_unused_args(kwsys::CommandLineArguments &arg) - { - int nuargs; - char **uargs; -@@ -541,9 +541,9 @@ - - init_globals(); - -- adios2sys::CommandLineArguments arg; -+ kwsys::CommandLineArguments arg; - arg.Initialize(argc, argv); -- typedef adios2sys::CommandLineArguments argT; -+ typedef kwsys::CommandLineArguments argT; - arg.StoreUnusedArguments(true); - arg.AddCallback("-v", argT::NO_ARGUMENT, optioncb_verbose, nullptr, ""); - arg.AddCallback("--verbose", argT::NO_ARGUMENT, optioncb_verbose, nullptr, -@@ -1521,7 +1521,7 @@ - if (verbose > 1) - printf("\nADIOS Open: read header info from %s\n", path); - -- if (!adios2sys::SystemTools::FileExists(path)) -+ if (!kwsys::SystemTools::FileExists(path)) - { - fprintf(stderr, "\nError: input path %s does not exist\n", path); - return 4; ---- a/source/utils/CMakeLists.txt -+++ b/source/utils/CMakeLists.txt -@@ -11,7 +11,7 @@ - - # BPLS - add_executable(bpls ./bpls/bpls.cpp) --target_link_libraries(bpls adios2_core adios2sys adios2::thirdparty::pugixml) -+target_link_libraries(bpls adios2_core -lkwsys adios2::thirdparty::pugixml) - target_include_directories(bpls PRIVATE ${PROJECT_BINARY_DIR}) - set_property(TARGET bpls PROPERTY OUTPUT_NAME bpls${ADIOS2_EXECUTABLE_SUFFIX}) - install(TARGETS bpls EXPORT adios2 -@@ -30,7 +30,7 @@ - - # BPSPLIT - #add_executable(bpsplit ./bpsplit/bpsplit.cpp) --#target_link_libraries(bpsplit adios2::cxx11 adios2sys_interface adios2::thirdparty::pugixml) -+#target_link_libraries(bpsplit adios2::cxx11 -lkwsys adios2::thirdparty::pugixml) - #install(TARGETS bpsplit EXPORT adios2 - # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - #) ---- a/thirdparty/CMakeLists.txt -+++ b/thirdparty/CMakeLists.txt -@@ -33,8 +33,6 @@ - option(ADIOS2_USE_EXTERNAL_YAMLCPP - "Use an externally supplied yaml-cpp library" "${ADIOS2_USE_EXTERNAL_DEPENDENCIES}") - --add_subdirectory(KWSys) -- - add_subdirectory(perfstubs) - adios2_add_thirdparty_target(perfstubs-interface perfstubs-interface) - ---- a/thirdparty/perfstubs/CMakeLists.txt -+++ b/thirdparty/perfstubs/CMakeLists.txt -@@ -1,12 +1,3 @@ --message_start_thirdparty() -- --if (NOT WIN32 AND BUILD_SHARED_LIBS AND ADIOS2_HAVE_Profiling) -- set(PERFSTUBS_USE_TIMERS ON CACHE INTERNAL "") -- add_subdirectory(perfstubs) --else() -- set(PERFSTUBS_USE_TIMERS OFF CACHE INTERNAL "") --endif() -- - add_library(perfstubs-interface INTERFACE) - - configure_file( -@@ -19,7 +10,6 @@ - ) - - if (PERFSTUBS_USE_TIMERS) -+ find_package(perfstubs REQUIRED) - target_link_libraries(perfstubs-interface INTERFACE perfstubs) - endif() -- --message_end_thirdparty() diff --git a/sys-cluster/adios2/metadata.xml b/sys-cluster/adios2/metadata.xml deleted file mode 100644 index e9e547384..000000000 --- a/sys-cluster/adios2/metadata.xml +++ /dev/null @@ -1,46 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <upstream> - <bugs-to>https://github.com/ornladios/ADIOS2/issues</bugs-to> - <remote-id type="github">ornladios/ADIOS2</remote-id> - </upstream> - <longdescription lang="en"> -This is ADIOS2: The Adaptable Input/Output (I/O) System. - -ADIOS2 is developed as part of the United States Department of Energy's Exascale Computing Project. It is a framework for scientific data I/O to publish and subscribe to data when and where required. - -ADIOS2 transports data as groups of self-describing variables and attributes across different media types (such as files, wide-area-networks, and remote direct memory access) using a common application programming interface for all transport modes. ADIOS2 can be used on supercomputers, cloud systems, and personal computers. - -ADIOS2 focuses on: - - Performance I/O scalability in high performance computing (HPC) applications. - Adaptability unified interfaces to allow for several modes of transport (files, memory-to-memory) - Ease of Use two-level application programming interface (APIs) - - Full APIs for HPC applications: C++11, Fortran 90, C 99, Python 2 and 3 - Simplified High-Level APIs for data analysis: Python 2 and 3, C++11, Matlab - -In addition, ADIOS2 APIs are based on: - - MPI Although ADIOS2 is MPI-based, it can also be used in non-MPI serial code. - - Data Groups ADIOS2 favors a deferred/prefetch/grouped variables transport mode by default to maximize data-per-request ratios. Sync mode, one variable at a time, is treated as the special case. - - Data Steps ADIOS2 follows the actual production/consumption of data using an I/O “steps” abstraction removing the need to manage extra indexing information. - - Data Engines ADIOS2 Engine abstraction allows for reusing the APIs for different transport modes removing the need for drastic code changes. - </longdescription> - <use> - <flag name="blosc">Enable support for Blosc transforms</flag> - <flag name="endian-reverse">Enable support for Little/Big Endian Interoperability</flag> - <flag name="sodium">Enable support for Sodium for encryption</flag> - <flag name="sst">Enable support for SST</flag> - <flag name="zeromq">Enable support for ZeroMQ</flag> - <flag name="zfp">Enable support for ZFP transforms</flag> - </use> -</pkgmetadata> diff --git a/sys-cluster/dimemas/Manifest b/sys-cluster/dimemas/Manifest deleted file mode 100644 index bdcf56b47..000000000 --- a/sys-cluster/dimemas/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST dimemas-5.4.2_p20220601.gh.tar.gz 802490 BLAKE2B d43829ba082c914fe37d0a5388578c5f77d102e1b5b412194b5b34ac9c830290f342ace3334bc97468c16ff58a89d1aef44956d703d68ca87d55e8abe7ec92c7 SHA512 54e6a8325ae7397fd2fae3f47e7b6cae9d9ea1aeaf6340b07e1ea04c26e8420c2a575498a6f33cf4a9c0ab3614756a23631316c5968fea2656166f40de5d7218 diff --git a/sys-cluster/dimemas/dimemas-5.4.2_p20220601.ebuild b/sys-cluster/dimemas/dimemas-5.4.2_p20220601.ebuild deleted file mode 100644 index 608dcbe54..000000000 --- a/sys-cluster/dimemas/dimemas-5.4.2_p20220601.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 2019-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -COMMIT="0dc28fafb8a917cee8d6ffd4a037cdc1f8755101" -PYTHON_COMPAT=( pypy3 python3_{10..11} ) - -inherit autotools java-pkg-opt-2 python-any-r1 - -DESCRIPTION="High-abstracted network simulator for message-passing programs" -HOMEPAGE="https://github.com/bsc-performance-tools/dimemas" -SRC_URI="https://github.com/bsc-performance-tools/dimemas/archive/${COMMIT}.tar.gz -> ${PF}.gh.tar.gz" -S="${WORKDIR}/${PN}-${COMMIT}" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="~amd64" - -IUSE="idle-accounting irecv-startup original-links wait-logical-recv" - -CDEPEND=" - dev-libs/boost:= - sys-libs/zlib - java? ( dev-java/commons-io:1 ) -" -DEPEND=" - ${CDEPEND} - ${PYTHON_DEPS} - java? ( virtual/jdk:1.8 ) -" -RDEPEND=" - ${CDEPEND} - java? ( virtual/jre:1.8 ) -" - -PATCHES=( "${FILESDIR}/${PN}-5.4.2-gui.patch" ) - -src_prepare() { - default - java-pkg_clean - if use java; then - pushd ./GUI/lib || die - java-pkg_jar-from commons-io-1 commons-io.jar commons-io-2.4.jar - popd || die - fi - eautoreconf -} - -src_configure() { - local myconf=( - --with-boost="${EPREFIX}/usr" - --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" - - $(use_enable idle-accounting) - $(use_enable irecv-startup) - $(use_enable original-links) - $(use_enable wait-logical-recv) - ) - econf "${myconf[@]}" -} - -src_install() { - default - dodoc README.md ChangeLog - mkdir -p "${ED}/usr/share/doc/${PF}/examples" || die - mv "${ED}/usr/share/lib_extern_model_example" "${ED}/usr/share/doc/${PF}/examples/" || die - docompress -x "${ED}/usr/share/doc/${PF}/examples" - mkdir -p "${ED}/usr/share/${PN}" || die - mv "${ED}/usr/share/cfgs" "${ED}/usr/share/${PN}/" || die - if use java; then - java-pkg_newjar "${ED}/usr/$(get_libdir)/GUI/dimemas-gui-5.4.2.jar" "dimemas-gui.jar" - rm -r "${ED}/usr/$(get_libdir)/GUI" || die - fi - find "${ED}" -name '*.la' -delete || die -} diff --git a/sys-cluster/dimemas/files/dimemas-5.4.2-gui.patch b/sys-cluster/dimemas/files/dimemas-5.4.2-gui.patch deleted file mode 100644 index 4cd05cd95..000000000 --- a/sys-cluster/dimemas/files/dimemas-5.4.2-gui.patch +++ /dev/null @@ -1,35 +0,0 @@ ---- a/GUI/src/DimemasGUI.in -+++ b/GUI/src/DimemasGUI.in -@@ -1,29 +1,9 @@ - #!/bin/sh - --DIMEMAS_HOME=$(dirname $(readlink -f $0))/.. --if [ -d "$DIMEMAS_HOME/lib" ]; then -- LIBDIR="/lib" --elif [ -d "$DIMEMAS_HOME/lib64" ]; then -- LIBDIR="/lib64" --else -- echo "$DIMEMAS_HOME/{lib|lib64} not found" -- exit 1 --fi -+DIMEMAS_HOME=/usr - --DIMEMAS_GUI_JAR=$DIMEMAS_HOME/$LIBDIR/GUI/@@JARFILE@@ -+DIMEMAS_GUI_JAR="${DIMEMAS_HOME}/share/dimemas/lib/dimemas-gui.jar" - --if ! [ -e $DIMEMAS_GUI_JAR ]; then -- echo "Dimemas GUI 'jar' file (@@JARFILE@@) not found" -- echo "Check your Dimemas instalation." -- exit 1 --fi -- --if which java >/dev/null 2>&1 ; then -- JAVA_BIN=`which java` --else -- echo "No Java Runtime found on your path." -- echo "Please check the JRE installation" -- exit 1 --fi -+JAVA_BIN=`java-config -J` - - $JAVA_BIN @@JVMFLAGS@@ -DDIMEMAS_HOME=$DIMEMAS_HOME -jar $DIMEMAS_GUI_JAR $@ diff --git a/sys-cluster/dimemas/metadata.xml b/sys-cluster/dimemas/metadata.xml deleted file mode 100644 index a5d25678b..000000000 --- a/sys-cluster/dimemas/metadata.xml +++ /dev/null @@ -1,24 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <longdescription lang="en"> -This package contains the source code of Dimemas simulator, its graphical -user interface and the Paraver to Dimemas trace translator, 'prv2dim'. -You can find the old Dimemas trace format (.trf) to new format (.dim) translator -'trf2dim' until Dimemas package version 5.3.0 - </longdescription> - <upstream> - <bugs-to>https://github.com/bsc-performance-tools/dimemas/issues</bugs-to> - <remote-id type="github">bsc-performance-tools/dimemas</remote-id> - </upstream> - <use> - <flag name="idle-accounting">if enabled, idle CPU regions are computed as CPU consumption in the accouting stats</flag> - <flag name="irecv-startup">if enabled defined Dimemas considers initial startups on MPI_Irecv functions</flag> - <flag name="original-links">if enabled Dimemas uses the original protocol to manage links</flag> - <flag name="wait-logical-recv">if enabled Dimemas puts logical receive time when MPI_Wait is called (not on MPI_Irecv)</flag> - </use> -</pkgmetadata> diff --git a/sys-cluster/dtcmp/Manifest b/sys-cluster/dtcmp/Manifest deleted file mode 100644 index 0fbe49a61..000000000 --- a/sys-cluster/dtcmp/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST dtcmp-1.1.2.tar.gz 76820 BLAKE2B bd67112567515fefff171e1b9e0da5d93e2b5bec88246de33e3b382bcc6029f1fc18a658ce185634615c37f1a10b5759eb04f2039f334ea5deaa680a005c6d5f SHA512 c8094ca5009ba10d40be3da55498b97837865d87b3deaa813b31de2083c38aa30b55c91ead053e2ef0454c53948aafa233f9251295ca29a0233f28a169cbd5c2 -DIST dtcmp-1.1.4.tar.gz 77123 BLAKE2B 45e6ae9b7726ea3185350fb3850c81a7e212625d2a9f0b60e3e21e1d72038af0094a68303064fbd261209b968c2df3d72f6ccda4a0c78b1557b54d5bdfcca391 SHA512 2686e44aeaab37ff065ecb7f898dfa57a4e7d1c99c8785544c10c8d14a736ae9da4623d938f7380b487cadc61ced6c050118a16e5c238e57b47a926e0cfca44b diff --git a/sys-cluster/dtcmp/dtcmp-1.1.2.ebuild b/sys-cluster/dtcmp/dtcmp-1.1.2.ebuild deleted file mode 100644 index b0f3c17bd..000000000 --- a/sys-cluster/dtcmp/dtcmp-1.1.2.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 2019-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit autotools - -DESCRIPTION="Datatype Compare Library for sorting and ranking distributed data using MPI" -HOMEPAGE="https://github.com/LLNL/dtcmp" -SRC_URI="https://github.com/LLNL/dtcmp/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - sys-cluster/lwgrp - virtual/mpi -" -DEPEND="${RDEPEND}" - -src_prepare() { - default - eautoreconf -} - -src_configure() { - local myconf=( - --with-lwgrp="${EPREFIX}/usr" - ) - econf "${myconf[@]}" -} - -src_install() { - default - rm -r "${ED}/usr/share/${PN}" || die - find "${ED}" -name '*.la' -delete || die - find "${ED}" -name '*.a' -delete || die -} diff --git a/sys-cluster/dtcmp/dtcmp-1.1.4.ebuild b/sys-cluster/dtcmp/dtcmp-1.1.4.ebuild deleted file mode 100644 index 92f0d11d5..000000000 --- a/sys-cluster/dtcmp/dtcmp-1.1.4.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 2019-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit autotools - -DESCRIPTION="Datatype Compare Library for sorting and ranking distributed data using MPI" -HOMEPAGE="https://github.com/LLNL/dtcmp" -SRC_URI="https://github.com/LLNL/dtcmp/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - sys-cluster/lwgrp - virtual/mpi -" -DEPEND="${RDEPEND}" - -src_prepare() { - default - eautoreconf -} - -src_configure() { - local myconf=( - --with-lwgrp="${EPREFIX}/usr" - ) - econf "${myconf[@]}" -} - -src_install() { - default - rm -r "${ED}/usr/share/${PN}" || die - find "${ED}" -name '*.la' -delete || die - find "${ED}" -name '*.a' -delete || die -} diff --git a/sys-cluster/dtcmp/metadata.xml b/sys-cluster/dtcmp/metadata.xml deleted file mode 100644 index 3b785e312..000000000 --- a/sys-cluster/dtcmp/metadata.xml +++ /dev/null @@ -1,56 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <longdescription lang="en"> -The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined comparison operations to compare the values of two items which can be arbitrary MPI datatypes. Using these comparison operations, the library provides various routines for manipulating data, which may be distributed over the processes of an MPI communicator including: - -search - search for a target value in an ordered list of values -merge - combine multiple ordered lists into a single ordered list -partition - divide a list of items into lower and higher values around a specified pivot value -select - identify the kth largest value -sort - sort data items into an ordered list -rank - assign group ids and ranks to a list of items -scan - execute a segmented scan on an ordered list of values -The DTCMP library is designed to provide a high-level interface to the above functionality. These high-level routines will invoke various algorithm implementations to achieve the desired output. The goal of DTCMP is to be efficient given the input and the data distribution among processes. It is also intended to be portable to different platforms and to allow for easy addition of new algorithms over time. - -While performance is important, the goal is not to provide the fastest routines. The generality provided by the DTCMP API that makes portability possible also tends to reduce performance in some respects, e.g., forcing memory copies, abstracting some details about datatype, etc. Most likely a hand-tuned algorithm for the precise problem at hand will always be faster than DTCMP. However, DTCMP should be fast, efficient, and portable, so it will generally be a good option except for those cases where the application bottleneck demands absolute performance. - -Currently, the following pre-defined comparison operations are provided. More will be added with time. All pre-defined operations have the following naming convention: - -DTCMP_OP_TYPE_DIRECTION -where TYPE may be one of: - -SHORT - C short -INT - C int -LONG - C long -LONGLONG - C long long -UNSIGNEDSHORT - C unsigned short -UNSIGNEDINT - C unsigned int -UNSIGNEDLONG - C unsigned long -UNSIGNEDLONGLONG - C unsigned long long -INT8T - C int8_t -INT16T - C int16_t -INT32T - C int32_t -INT64T - C int64_t -UINT8T - C uint8_t -UINT16T - C uint16_t -UINT32T - C uint32_t -UINT64T - C uint64_t -FLOAT - C float -DOUBLE - C double -LONGDOUBLE - C long double -and DIRECTION may be one of: - -ASCEND - order values from smallest to largest -DESCEND - order values from largest to smallest -Often when sorting data, each item contains a "key" that determines its position within the global order and a "value", called "satellite data", which travels with the key value but has no affect on its order. DTCMP assumes that satellite data is relatively small and is attached to the key in the same input buffer. In many DTCMP routines, one must specify the datatype for the key and another datatype for the key with its satellite data. The first is often named "key" and the second "keysat". The key datatype is used to infer the type and size of the key when comparing key values. This can be exploited to select optimized comparison routines, e.g., radix sort on integers, and it enables the library to siphon off and only process the key component if needed. The keysat type is needed to copy full items in memory or transfer items between processes. - </longdescription> - <upstream> - <bugs-to>https://github.com/LLNL/dtcmp/issues</bugs-to> - <remote-id type="github">LLNL/dtcmp</remote-id> - </upstream> -</pkgmetadata> diff --git a/sys-cluster/fti/Manifest b/sys-cluster/fti/Manifest deleted file mode 100644 index ecb4bf5d4..000000000 --- a/sys-cluster/fti/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST fti-1.6.tar.gz 1752536 BLAKE2B 5e4757700a4911cd82cbd0a7426e39ef081c38809e39d4564a8aeea24e370ed9a87654c664ee14afaa95a394275db817271cf393d3b7febce9f578d5874e520e SHA512 068e43d6c433c57c88acd8b39a0f05a012e87084fa8e0a912216f8e9725310bfab46ba8a23b02560287e7408ccb1ed62ead61768deb9135d9eb1b3fd19bed290 diff --git a/sys-cluster/fti/files/fti-add-spinx-ext-autodoc.patch b/sys-cluster/fti/files/fti-add-spinx-ext-autodoc.patch deleted file mode 100644 index cc34e3719..000000000 --- a/sys-cluster/fti/files/fti-add-spinx-ext-autodoc.patch +++ /dev/null @@ -1,20 +0,0 @@ -From 65f203e50cd08489d2c49ec8a645d82f104c6b29 Mon Sep 17 00:00:00 2001 -From: Alessandro Barbieri <lssndrbarbieri@gmail.com> -Date: Sat, 31 Jul 2021 08:11:00 +0200 -Subject: [PATCH] add sphinx.ext.autodoc to doc extensions - ---- - docs/source/conf.py | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - ---- a/docs/source/conf.py -+++ b/docs/source/conf.py -@@ -31,7 +31,7 @@ - # Add any Sphinx extension module names here, as strings. They can be - # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom - # ones. --extensions = ['breathe', 'sphinx.ext.autosectionlabel'] -+extensions = ['breathe', 'sphinx.ext.autosectionlabel', 'sphinx.ext.autodoc'] - - # Add any paths that contain templates here, relative to this directory. - templates_path = ['_templates'] diff --git a/sys-cluster/fti/files/fti-sionlib-includedir.patch b/sys-cluster/fti/files/fti-sionlib-includedir.patch deleted file mode 100644 index dab1df493..000000000 --- a/sys-cluster/fti/files/fti-sionlib-includedir.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -126,7 +126,7 @@ - # Library: SIONLib (Optional) - if(ENABLE_SIONLIB) - set(SIONLIBBASE "" CACHE FILEPATH "base path to SIONlib installation") -- set(SIONLIB_INCLUDE_DIR "${SIONLIBBASE}/include/") -+ set(SIONLIB_INCLUDE_DIR "/usr/include/sionlib") - - list(APPEND INC_PRIV ${SIONLIB_INCLUDE_DIR}) - find_library(SIONLIB_MPI NAMES "sionmpi_64" diff --git a/sys-cluster/fti/fti-1.6-r1.ebuild b/sys-cluster/fti/fti-1.6-r1.ebuild deleted file mode 100644 index e02bce235..000000000 --- a/sys-cluster/fti/fti-1.6-r1.ebuild +++ /dev/null @@ -1,85 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI="7" - -DOCS_BUILDER="sphinx" -DOCS_DEPEND=" - dev-python/breathe - dev-python/sphinx-rtd-theme -" -DOCS_DIR="${S}/docs/source" -FORTRAN_NEEDED="fortran" -PYTHON_COMPAT=( python3_10 pypy3 ) - -inherit cmake python-any-r1 docs fortran-2 - -DESCRIPTION="Fault Tolerance Interface" -HOMEPAGE="https://github.com/leobago/fti" -SRC_URI="https://github.com/leobago/fti/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc examples fi-io hdf5 fortran openssl sionlib test tutorial" - -#TODO: unbundle jerasure bpp iniparser -RDEPEND=" - sys-libs/zlib - virtual/mpi - - hdf5? ( sci-libs/hdf5[mpi] ) - openssl? ( dev-libs/openssl ) - sionlib? ( sys-cluster/sionlib ) -" -DEPEND="${RDEPEND}" -BDEPEND="doc? ( app-text/doxygen )" - -PATCHES=( - "${FILESDIR}/${PN}-sionlib-includedir.patch" - "${FILESDIR}/${PN}-add-spinx-ext-autodoc.patch" -) -#RESTRICT="!test? ( test )" -RESTRICT="test" - -pkg_setup() { - fortran-2_pkg_setup -} - -src_configure() { - local mycmakeargs=( - -DSIONLIBBASE="${EPREFIX}/usr/$(get_libdir)" - -DENABLE_COVERAGE=OFF - -DENABLE_IME_NATIVE=OFF - - -DENABLE_DOCU=$(usex doc) - -DENABLE_EXAMPLES=$(usex examples) - -DENABLE_FI_IO=$(usex fi-io) - -DENABLE_FORTRAN=$(usex fortran) - -DENABLE_HDF5=$(usex hdf5) - -DENABLE_OPENSSL=$(usex openssl) - -DENABLE_SIONLIB=$(usex sionlib) - -DENABLE_TESTS=$(usex test) - -DENABLE_TUTORIAL=$(usex tutorial) - ) - cmake_src_configure -} - -src_compile() { - cmake_src_compile - docs_compile -} - -src_install() { - cmake_src_install - einstalldocs - if use examples; then - mkdir -p "${ED}/usr/libexec/${PN}" || die - mv "${ED}/usr/bin/examples" "${ED}/usr/libexec/${PN}/examples" || die - fi - if use tutorial; then - mkdir -p "${ED}/usr/libexec/${PN}" || die - mv "${ED}/usr/bin/tutorial" "${ED}/usr/libexec/${PN}/tutorial" || die - fi - find "${ED}" -name '*.a' -delete || die -} diff --git a/sys-cluster/fti/metadata.xml b/sys-cluster/fti/metadata.xml deleted file mode 100644 index 43b9729c5..000000000 --- a/sys-cluster/fti/metadata.xml +++ /dev/null @@ -1,24 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <upstream> - <bugs-to>https://github.com/leobago/fti/issues</bugs-to> - <remote-id type="github">leobago/fti</remote-id> - </upstream> - <longdescription lang="en"> -FTI stands for Fault Tolerance Interface and is a library that aims to give computational scientists the means to perform fast and efficient multilevel checkpointing in large scale supercomputers. FTI leverages local storage plus data replication and erasure codes to provide several levels of reliability and performance. FTI is application-level checkpointing and allows users to select which datasets needs to be protected, in order to improve efficiency and avoid wasting space, time and energy. In addition, it offers a direct data interface so that users do not need to deal with files and/or directory names. All metadata is managed by FTI in a transparent fashion for the user. If desired, users can dedicate one process per node to overlap fault tolerance workload and scientific computation, so that post-checkpoint tasks are executed asynchronously. - </longdescription> - <use> - <flag name="openssl">To use the <pkg>dev-libs/openssl</pkg> MD5 rather than the built-in</flag> - <flag name="fortran">Enables the build of a Fortran wrapper</flag> - <flag name="sionlib">Enables the parallel I/O <pkg>sys-cluster/sionlib</pkg> for FTI</flag> - <flag name="hdf5">Enables the HDF5 checkpoints for FTI</flag> - <flag name="tutorial">Enables the generation of tutorial files</flag> - <flag name="fi-io">Enables the I/O failure injection mechanism</flag> - <flag name="test">Enables the generation of tests</flag> - </use> -</pkgmetadata> diff --git a/sys-cluster/launchmon/Manifest b/sys-cluster/launchmon/Manifest deleted file mode 100644 index 71d291fb1..000000000 --- a/sys-cluster/launchmon/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST launchmon-1.0.2_p20210430.tar.gz 303361 BLAKE2B e1aaed16fee557a33492bd7df2fa95fc9c42e76a2b246ae37522ca7ac36b244acb63ca74c67f91b33c542dbe9628cc67f163294b47595ab4aee4156aad22d55c SHA512 11e158d0a49b369355275117673f9810a65b79aa75d481c6103ca5e49a3b674e2d8cb3b04ec0ffa956cb9f08a6148a31ba859c5f0f8eb38a813ae0cdacdde347 diff --git a/sys-cluster/launchmon/files/launchmon-1.0.2_p20210430-fix-bashism.patch b/sys-cluster/launchmon/files/launchmon-1.0.2_p20210430-fix-bashism.patch deleted file mode 100644 index 5088c99e3..000000000 --- a/sys-cluster/launchmon/files/launchmon-1.0.2_p20210430-fix-bashism.patch +++ /dev/null @@ -1,80 +0,0 @@ -From 1a651a0bb19ad8c0752b497eed125a901d7f83da Mon Sep 17 00:00:00 2001 -From: Alessandro Barbieri <lssndrbarbieri@gmail.com> -Date: Wed, 25 Aug 2021 09:13:37 +0200 -Subject: [PATCH] fix == bashism - ---- - config/x_ac_handshake.m4 | 20 ++++++++++---------- - 1 file changed, 10 insertions(+), 10 deletions(-) - ---- a/config/x_ac_handshake.m4 -+++ b/config/x_ac_handshake.m4 -@@ -50,7 +50,7 @@ AC_DEFUN([X_AC_HANDSHAKE],[ - - #Check for munge availability - PKG_CHECK_MODULES(MUNGE, munge, , [AC_MSG_NOTICE([pkg-config could not find munge])]) -- if test "x$MUNGE_LIBS" == "x"; then -+ if test "x$MUNGE_LIBS" = "x"; then - MUNGE_LIBS=-lmunge - fi - CFLAGS="$CFLAGS $MUNGE_CFLAGS" -@@ -66,26 +66,26 @@ AC_DEFUN([X_AC_HANDSHAKE],[ - - #If the user did not specify security options, then make some choices based on what we have - if test "x$EXPLICIT_SEC" != "xtrue"; then -- if test "x$HAVE_MUNGE" == "xtrue"; then -+ if test "x$HAVE_MUNGE" = "xtrue"; then - MUNGE="true" - else - ENABLE_NULL_ENCRYPTION="true" - fi - fi - -- if test "x$WANT_MUNGE" == "xtrue"; then -- if test "x$HAVE_MUNGE" == "xtrue"; then -+ if test "x$WANT_MUNGE" = "xtrue"; then -+ if test "x$HAVE_MUNGE" = "xtrue"; then - MUNGE="true" - else - AC_MSG_ERROR([Could not find munge]) - fi - fi - -- if test "x$WANT_KEYFILE" == "xtrue"; then -+ if test "x$WANT_KEYFILE" = "xtrue"; then - KEYFILE="true" - fi - -- if test "x$WANT_NOSEC" == "xtrue"; then -+ if test "x$WANT_NOSEC" = "xtrue"; then - ENABLE_NULL_ENCRYPTION="true" - fi - -@@ -100,7 +100,7 @@ AC_DEFUN([X_AC_HANDSHAKE],[ - #if test "x$KEYFILE" != "x"; then - # AC_MSG_ERROR([Keyfile security is not supported at this time]) - #fi -- #if test "x$ENABLE_NULL_ENCRYPTION x$MUNGE" == "xtrue xtrue"; then -+ #if test "x$ENABLE_NULL_ENCRYPTION x$MUNGE" = "xtrue xtrue"; then - # AC_MSG_ERROR([Cannot support multiple security models at this time]) - #fi - #Remove above when expanding to more than munge -@@ -108,15 +108,15 @@ AC_DEFUN([X_AC_HANDSHAKE],[ - AC_DEFINE_UNQUOTED([SEC_KEYDIR], "[$SEC_KEYDIR]",[Directory to store key files in]) - AC_SUBST(MUNGE_CFLAGS) - AC_SUBST(MUNGE_LIBS) -- if test "x$MUNGE" == "xtrue"; then -+ if test "x$MUNGE" = "xtrue"; then - AC_MSG_NOTICE([Enabling munge for security authentication]) - AC_DEFINE([MUNGE], [1], [Use munge for authentication]) - fi -- if test "x$KEYFILE" == "xtrue"; then -+ if test "x$KEYFILE" = "xtrue"; then - AC_MSG_NOTICE([Enabling keyfile for security authentication]) - AC_DEFINE([KEYFILE], [1], [Use keyfile for authentication]) - fi -- if test "x$ENABLE_NULL_ENCRYPTION" == "xtrue"; then -+ if test "x$ENABLE_NULL_ENCRYPTION" = "xtrue"; then - AC_MSG_NOTICE([WARNING: No secure handshake will be used for the COBO layer!!!]); - AC_DEFINE([ENABLE_NULL_ENCRYPTION], [1], [Allow NULL encryption]) - fi]) diff --git a/sys-cluster/launchmon/launchmon-1.0.2_p20210430-r2.ebuild b/sys-cluster/launchmon/launchmon-1.0.2_p20210430-r2.ebuild deleted file mode 100644 index 0d55c8226..000000000 --- a/sys-cluster/launchmon/launchmon-1.0.2_p20210430-r2.ebuild +++ /dev/null @@ -1,59 +0,0 @@ -# Copyright 2019-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -COMMIT="98ab769c53563f47c4319ce3c98ac394b4870bac" -MYPV="$(ver_cut 1-3)" - -inherit autotools flag-o-matic - -DESCRIPTION="Enables HPC run-time tools to co-locate tool daemons with a parallel job" -HOMEPAGE="https://github.com/LLNL/LaunchMON" -SRC_URI="https://github.com/LLNL/LaunchMON/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/LaunchMON-${COMMIT}" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="~amd64" -IUSE="+munge test tracing-cost" - -RDEPEND=" - dev-libs/boost:= - dev-libs/libgcrypt - dev-libs/libgpg-error - virtual/libelf - virtual/mpi - - munge? ( sys-auth/munge ) -" -DEPEND="${RDEPEND}" - -PATCHES=( "${FILESDIR}/${P}-fix-bashism.patch" ) -RESTRICT="!test? ( test )" - -src_prepare() { - default - sed -e "s|m4_esyscmd.*|${MYPV})|g" -i configure.ac || die - eautoreconf -} - -src_configure() { - append-cxxflags "-std=c++14" - local sec="none" - use munge && sec="munge" - local myconf=( - --enable-shared - --enable-sec-${sec} - $(use_enable tracing-cost) - ) - - econf "${myconf[@]}" -} - -src_install() { - default - mv "${ED}/usr/etc" "${ED}" || die - find "${ED}" -name '*.la' -delete || die - find "${ED}" -name '*.a' -delete || die -} diff --git a/sys-cluster/launchmon/metadata.xml b/sys-cluster/launchmon/metadata.xml deleted file mode 100644 index 1299b2c51..000000000 --- a/sys-cluster/launchmon/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <longdescription lang="en"> -LaunchMON is a software infrastructure that enables HPC run-time tools to co-locate tool daemons with a parallel job. Its API allows a tool to identify all the remote processes of a job and to scalably launch daemons into the relevant nodes. - </longdescription> - <use> - <flag name="munge">enable munge for connection authentication</flag> - <flag name="tracing-cost">enable tracing cost measuring codes</flag> - </use> - <upstream> - <bugs-to>https://github.com/LLNL/LaunchMON/issues</bugs-to> - <remote-id type="github">LLNL/LaunchMON</remote-id> - </upstream> -</pkgmetadata> diff --git a/sys-cluster/libbsctools/Manifest b/sys-cluster/libbsctools/Manifest deleted file mode 100644 index a065a4cc5..000000000 --- a/sys-cluster/libbsctools/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST libbsctools-1.0.6.tar.gz 45485 BLAKE2B f3b4e0bf3f583d101c34915a4cd656a7a57f2118d0580bed6e444c0c2436c40a0c7ce0d2dbaf519b3c62cf4de235f421f7cdb67eae81cb459a35807430762367 SHA512 508af8d8328bdf3b3828012a1b630fe6b88f0a3f0058651bacda3d306e610297196f8ce4bcbcd43e05ef55d851b7582b21416df3394aae205253c2b7ba1fc44d diff --git a/sys-cluster/libbsctools/libbsctools-1.0.6-r2.ebuild b/sys-cluster/libbsctools/libbsctools-1.0.6-r2.ebuild deleted file mode 100644 index c232707b0..000000000 --- a/sys-cluster/libbsctools/libbsctools-1.0.6-r2.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 2019-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="libbsctools" -HOMEPAGE="https://github.com/bsc-performance-tools/libbsctools" -SRC_URI="https://github.com/bsc-performance-tools/libbsctools/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND="dev-libs/boost:=" -DEPEND="${RDEPEND}" - -src_prepare() { - default - ./bootstrap || die -} - -src_install() { - MAKEOPTS="-j1" emake DESTDIR="${D}" install - dodoc NEWS README AUTHORS - mv "${ED}/usr/share/example" "${ED}/usr/share/doc/${PF}/examples" || die - docompress -x "/usr/share/doc/${PF}/examples" - find "${D}" -name '*.la' -delete || die - find "${D}" -name '*.a' -delete || die -} diff --git a/sys-cluster/libbsctools/metadata.xml b/sys-cluster/libbsctools/metadata.xml deleted file mode 100644 index ca767f76e..000000000 --- a/sys-cluster/libbsctools/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <upstream> - <bugs-to>https://github.com/bsc-performance-tools/libbsctools/issues</bugs-to> - <remote-id type="github">bsc-performance-tools/libbsctools</remote-id> - </upstream> -</pkgmetadata> diff --git a/sys-cluster/lwgrp/Manifest b/sys-cluster/lwgrp/Manifest deleted file mode 100644 index 5ae7fa9e4..000000000 --- a/sys-cluster/lwgrp/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST lwgrp-1.0.3.tar.gz 39217 BLAKE2B 2e17fce02989832670a7bcd73f80e3aabe185b5d1120777f3d3d2e0bd630e62b6ae64638b724ca3edd9d9c7d7177e505433c16382b5e1fdbc79e8a1b1de1a622 SHA512 b8acdd5fcec8de01f80acfe0f6df33fe3281bd6465a33ad739af06189782f116ac32caacbd458d2e04ba2eaedfbebf67f42cc343f7bee43f8d708e2b8b3c1565 -DIST lwgrp-1.0.5.tar.gz 41509 BLAKE2B a07a2d16b9f578fc1ee5843e85a295fec85bc86b4e291cfb1b559e12063173026d98bd556deef7d05f36d12c1d6c9ae1f168c690fd7f68f3583dc68ca9391e03 SHA512 8f960bc45f9c028d79b4a6d149ba2fada9451b8ad480fa6e0d0da81762ca459e9bd991df25643603eb9c69c2f83a97caeb0b8a39bd89c55584265c38862087de diff --git a/sys-cluster/lwgrp/lwgrp-1.0.3.ebuild b/sys-cluster/lwgrp/lwgrp-1.0.3.ebuild deleted file mode 100644 index d74dc038e..000000000 --- a/sys-cluster/lwgrp/lwgrp-1.0.3.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 2019-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit autotools - -DESCRIPTION="Light-weight Group Library" -HOMEPAGE="https://github.com/LLNL/lwgrp" -SRC_URI="https://github.com/LLNL/lwgrp/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" -IUSE="mpianysource" - -RDEPEND="virtual/mpi" -DEPEND="${RDEPEND}" - -src_prepare() { - default - eautoreconf -} - -src_configure() { - local myconf=( - $(use_enable mpianysource) - ) - econf "${myconf[@]}" -} - -src_install() { - default - rm -r "${ED}/usr/share/${PN}" || die - find "${ED}" -name '*.la' -delete || die - find "${ED}" -name '*.a' -delete || die -} diff --git a/sys-cluster/lwgrp/lwgrp-1.0.5.ebuild b/sys-cluster/lwgrp/lwgrp-1.0.5.ebuild deleted file mode 100644 index 67de1624e..000000000 --- a/sys-cluster/lwgrp/lwgrp-1.0.5.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 2019-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit autotools - -DESCRIPTION="Light-weight Group Library" -HOMEPAGE="https://github.com/LLNL/lwgrp" -SRC_URI="https://github.com/LLNL/lwgrp/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" -IUSE="mpianysource" - -RDEPEND="virtual/mpi" -DEPEND="${RDEPEND}" - -src_prepare() { - default - eautoreconf -} - -src_configure() { - local myconf=( - $(use_enable mpianysource) - ) - econf "${myconf[@]}" -} - -src_install() { - default - rm -r "${ED}/usr/share/${PN}" || die - find "${ED}" -name '*.la' -delete || die - find "${ED}" -name '*.a' -delete || die -} diff --git a/sys-cluster/lwgrp/metadata.xml b/sys-cluster/lwgrp/metadata.xml deleted file mode 100644 index ec46fd094..000000000 --- a/sys-cluster/lwgrp/metadata.xml +++ /dev/null @@ -1,58 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <longdescription lang="en"> -The light-weight group library defines data structures and collective -operations to group MPI processes as an ordered set. Such groups are -useful as substitutes for MPI communicators when the overhead of -communicator creation is too costly. For example, certain sorting -algorithms recursively divide processes into subgroups as the sort -algorithm progresses. These groups may be different with each -invocation, so that it is inefficient to create and destroy -communicators during the sort routine. - -Data structures: -chain - each member records addresses of left and right members first and last rank set boundary to MPI_PROC_NULL -ring - like the chain, except first and last rank wrap around -logchain - each member records addresses of each member 2^d hops to left and right d=0..log(N)-1 (MPI_PROC_NULL at ends) -logring - each member records addresses of each member 2^d hops to left and right with wrap at ends - -We represent groups of processes using a doubly-linked list called -a "chain". This is a very simple struct that records the number -of processes in the group, the rank of the local process within the -group, the address of the local process, and the addresses of the -processes having ranks one less (left) and one more (right) than the -local process. We implement the LWGRP library on top of MPI, so for -addresses we record a parent communicator and ranks within that -communicator. To be light-weight, the reference to the communicator -is a literal copy of the handle value, not a full dup. - -Since each member only stores the addresses for a few other group -members, it is the responsibility of higher level software to exchange -address information for more general point-to-point communication. -Additionally, the caller is responsible for choosing tag values as a -group context. - -There is also a "ring", which is like a chain, but it wraps around -at the ends. - -There are two structures, called a logchain and logring, used to cache -adddresses of more group members. These structures must be used in -conjunction with either a chain or ring, respectively. They cache -addresses for processes that are 2^d hops to the left and right sides -where d ranges from 0 to log(N)-1 inclusive. This pattern enables -one to construct trees, and so it's useful to cache this information -for use in collective operations. - </longdescription> - <use> - <flag name="mpianysource">Specify whether to use MPI_ANY_SOURCE</flag> - </use> - <upstream> - <bugs-to>https://github.com/LLNL/lwgrp/issues</bugs-to> - <remote-id type="github">LLNL/lwgrp</remote-id> - </upstream> -</pkgmetadata> diff --git a/sys-cluster/mpi-benchmarks/Manifest b/sys-cluster/mpi-benchmarks/Manifest deleted file mode 100644 index 87015f994..000000000 --- a/sys-cluster/mpi-benchmarks/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST IMB-v2021.3.tar.gz 221038 BLAKE2B d776e482a6632d9a538af0f8b89928322860ca6782f7c96bb47af0f9c6387eddc487bffbf3fde3e5c0477b7c9e9cbe7856857110890389f5ee42865051ef185b SHA512 fdb1a2426b5999c58c5d15228c64a80f28f4051d438e86a132f0fc42c3cda88f0e1bbcb792316617864d0f4d07d89143a96f3824bd4806fc8cde3c2dcb1d4094 diff --git a/sys-cluster/mpi-benchmarks/files/mpi-benchmarks-2021.3-makefile.patch b/sys-cluster/mpi-benchmarks/files/mpi-benchmarks-2021.3-makefile.patch deleted file mode 100644 index fbf00de64..000000000 --- a/sys-cluster/mpi-benchmarks/files/mpi-benchmarks-2021.3-makefile.patch +++ /dev/null @@ -1,142 +0,0 @@ ---- a/src_c/Makefile -+++ b/src_c/Makefile -@@ -106,10 +106,10 @@ - -mkdir -p $@ - - $(BINARY): $(OBJ) -- $(CC) $(LDFLAGS) $^ -o $@ -+ $(CC) $(CFLAGS) -fPIE $(LDFLAGS) $^ -o $@ - - $(BUILDDIR)/%.o: %.c -- $(CC) $(CFLAGS) -D$(TARGET) -DIMB2018 -c $< -o $@ -+ $(CC) $(CFLAGS) -fPIC -D$(TARGET) -DIMB2018 -c $< -o $@ - - clean: - rm -rf $(BUILDDIR) $(OBJ) $(BINARY) ---- a/src_c/P2P/Makefile -+++ b/src_c/P2P/Makefile -@@ -50,11 +50,11 @@ - TARGET=P2P - BINARY:=IMB-P2P - --override CFLAGS += -O3 -Wall -Wextra -pedantic -Wno-long-long -+override CFLAGS += -Wall -Wextra -pedantic -Wno-long-long - override LDFLAGS += -lm - - ifeq ($(origin CC),default) --CC=mpiicc -+CC=mpicc - endif - - all: $(BINARY) -@@ -72,10 +72,10 @@ - IMB_OBJ = $(IMB_SRC:.c=.o) - - $(BINARY): $(IMB_OBJ) -- $(CC) $(CFLAGS) -o $@ $^ $(LDFLAGS) -+ $(CC) $(CFLAGS) -fPIE -o $@ $^ $(LDFLAGS) - - %.o: %.c -- $(CC) $(CFLAGS) -c -o $@ $< -+ $(CC) $(CFLAGS) -fPIC -c -o $@ $< - - clean: - rm -f $(IMB_OBJ) $(BINARY) ---- a/src_cpp/Makefile -+++ b/src_cpp/Makefile -@@ -49,11 +49,7 @@ - - all: announce - --ifdef WITH_YAML_CPP --all: libyaml-cpp.a --else - all: --endif - - ifndef TARGET - TARGET=example -@@ -71,14 +67,14 @@ - endif - - ifeq ($(origin CC),default) --CC=mpiicc -+CC ?= mpicc - endif - ifeq ($(origin CXX),default) --CXX=mpiicpc -+CXX ?= mpicxx - endif - override CPPFLAGS += -I. --override CFLAGS += -g -O0 -Wall -Wno-long-long --override CXXFLAGS += -g -O0 -Wall -Wextra -pedantic -Wno-long-long -+override CFLAGS += -g -Wall -Wno-long-long -+override CXXFLAGS += -g -Wall -Wextra -pedantic -Wno-long-long - ifdef WITH_OPENMP - override CFLAGS += -fopenmp - override CXXFLAGS += -fopenmp -@@ -103,7 +99,7 @@ - all: $(BINARY) - - ifdef WITH_YAML_CPP --override CPPFLAGS += -Iyamlcpp/include -Iyamlcpp/test -+override CPPFLAGS += -I/usr/include/yaml-cpp - YAMLCPP_SRC = yamlcpp/src/aliasmanager.cpp \ - yamlcpp/src/binary.cpp \ - yamlcpp/src/conversion.cpp \ -@@ -140,8 +136,6 @@ - yamlcpp/test/old-api/parsertests.cpp \ - yamlcpp/test/old-api/spectests.cpp - --YAMLCPP_OBJ = $(YAMLCPP_SRC:.cpp=.o) --YAMLCPP_TEST_OBJ = $(YAMLCPP_TEST_SRC:.cpp=.o) - endif - - IMB_SRC = imb.cpp args_parser.cpp args_parser_utests.cpp scope.cpp -@@ -160,14 +154,7 @@ - scope.h - - ifdef WITH_YAML_CPP --libyaml-cpp.a: $(YAMLCPP_OBJ) -- ar qc $@ $^ -- ranlib $@ -- --yamltest: $(YAMLCPP_TEST_OBJ) libyaml-cpp.a -- $(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $^ -- --YAML_CPP_LIB = libyaml-cpp.a -+YAML_CPP_LIB = -lyaml-cpp - YAML_TEST = yamltest - override CPPFLAGS += -DWITH_YAML_CPP - endif -@@ -176,25 +163,21 @@ - @if test "$(ANNOUNCE)" -eq "1"; then echo "NOTE: Building target: $(TARGET), binary name: $(BINARY)"; fi - @if test "$(ANNOUNCE)" -eq "1"; then echo "NOTE: Use make TARGET=<DIR_NAME> to select a target suite"; fi - --$(BINARY): $(IMB_OBJ) $(BECHMARK_SUITE_OBJ) $(ADDITIONAL_OBJ) $(YAML_CPP_LIB) -- $(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $^ $(LDFLAGS) -+$(BINARY): $(IMB_OBJ) $(BECHMARK_SUITE_OBJ) $(ADDITIONAL_OBJ) -+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIE -o $@ $^ $(LDFLAGS) $(YAML_CPP_LIB) - - %.o: %.cpp -- $(CXX) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $< -+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -c -o $@ $< - - %.o: %.c -- $(CC) $(CPPFLAGS) $(CFLAGS) -c -o $@ $< -+ $(CC) $(CPPFLAGS) $(CFLAGS) -fPIC -c -o $@ $< - - clean: announce -- rm -f $(IMB_OBJ) $(YAMLCPP_OBJ) $(BECHMARK_SUITE_OBJ) $(ADDITIONAL_OBJ) $(BINARY) $(YAML_CPP_LIB) $(YAML_TEST) -+ rm -f $(IMB_OBJ) $(YAMLCPP_OBJ) $(BECHMARK_SUITE_OBJ) $(ADDITIONAL_OBJ) $(BINARY) - - - $(BECHMARK_SUITE_OBJ): $(HEADERS) Makefile - $(IMB_OBJ): $(HEADERS) Makefile - --ifdef WITH_YAML_CPP --$(YAMLCPP_OBJ): Makefile --endif -- - .PHONY: announce clean all - diff --git a/sys-cluster/mpi-benchmarks/metadata.xml b/sys-cluster/mpi-benchmarks/metadata.xml deleted file mode 100644 index 65e83dc05..000000000 --- a/sys-cluster/mpi-benchmarks/metadata.xml +++ /dev/null @@ -1,13 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <longdescription lang="en">Intel(R) MPI Benchmarks provides a set of elementary benchmarks that conform to MPI-1, MPI-2, and MPI-3 standard. You can run all of the supported benchmarks, or a subset specified in the command line using one executable file. Use command-line parameters to specify various settings, such as time measurement, message lengths, and selection of communicators.</longdescription> - <upstream> - <remote-id type="github">intel/mpi-benchmarks</remote-id> - <bugs-to>https://github.com/intel/mpi-benchmarks/issues</bugs-to> - </upstream> -</pkgmetadata> diff --git a/sys-cluster/mpi-benchmarks/mpi-benchmarks-2021.3.ebuild b/sys-cluster/mpi-benchmarks/mpi-benchmarks-2021.3.ebuild deleted file mode 100644 index 3a98c36bc..000000000 --- a/sys-cluster/mpi-benchmarks/mpi-benchmarks-2021.3.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 2019-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -MYP="IMB-v${PV}" - -DESCRIPTION="Intel MPI Benchmarks" -HOMEPAGE=" - https://www.intel.com/content/www/us/en/developer/articles/technical/intel-mpi-benchmarks.html - https://github.com/intel/mpi-benchmarks -" -SRC_URI="https://github.com/intel/${PN}/archive/refs/tags/${MYP}.tar.gz" -S="${WORKDIR}/${PN}-${MYP}" - -LICENSE="BSD CPL-1.0" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND="virtual/mpi[cxx]" -DEPEND="${RDEPEND}" - -PATCHES=( "${FILESDIR}/${P}-makefile.patch" ) - -src_configure() { - export CC=mpicc - export CXX=mpicxx - default -} - -src_install() { - dodoc ReadMe_IMB.txt README.md - dobin IMB-* -} diff --git a/sys-cluster/muster/Manifest b/sys-cluster/muster/Manifest deleted file mode 100644 index f570446a4..000000000 --- a/sys-cluster/muster/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST muster-1.0.1.tar.gz 117835 BLAKE2B e20e80acc7d3b8ba407d8949d5b5d1cc4562d4db13c4fa24de264446eb79de6cc3a669d61740b12fd1a8198e44453acede4cf0eaa46a38b9b92ff7506d5c234f SHA512 71a07bd9771e8cbeff9f288ec5f6b77bc2ce97a2227f52de202b0b3d9ff709a716cd32f55bfc5b2567cca929057b083138494532986f8cd97c6e3336732d3640 diff --git a/sys-cluster/muster/metadata.xml b/sys-cluster/muster/metadata.xml deleted file mode 100644 index 205bfc450..000000000 --- a/sys-cluster/muster/metadata.xml +++ /dev/null @@ -1,32 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <upstream> - <remote-id type="github">LLNL/muster</remote-id> - </upstream> - <longdescription lang="en"> -The Muster library provides implementations of serial and parallel K-Medoids -clustering algorithms. It is intended as a general framework for parallel -cluster analysis, particularly for performance data analysis on systems with -very large numbers of processes. - -The parallel implementations in the Muster are designed to perform well even -in environments where the data to be clustered is entirely distributed. For -example, many performance tools need to analyze one data element from each -process in a system. To analyze this data efficiently, clustering algorithms -that move as little data as possible are required. In Muster, we exploit -sampled clustering algorithms to realize this efficiency. - -The parallel algorithms in Muster are implemented using the Message Passing -Interface (MPI), making them suitable for use on many of the world's largest -supercomputers. They should, however, also run efficiently on your laptop. - </longdescription> - <use> - <flag name="pmpi">Build with PMPI bindings</flag> - <flag name="tests">Build and install test programs</flag> - </use> -</pkgmetadata> diff --git a/sys-cluster/muster/muster-1.0.1.ebuild b/sys-cluster/muster/muster-1.0.1.ebuild deleted file mode 100644 index 49032d21f..000000000 --- a/sys-cluster/muster/muster-1.0.1.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI="7" - -DOCS_BUILDER="doxygen" -DOCS_DIR="${S}" - -inherit cmake docs - -DESCRIPTION="Massively Scalable Clustering" -HOMEPAGE="https://github.com/LLNL/muster" -SRC_URI="https://github.com/LLNL/muster/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc pmpi tests" - -RDEPEND=" - dev-libs/boost:= - virtual/mpi -" -DEPEND="${RDEPEND}" - -src_prepare() { - sed -e "s|DESTINATION lib|DESTINATION $(get_libdir)|g" -i src/CMakeLists.txt || die - cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DINSTALL_TESTS=$(usex tests) - -DMUSTER_USE_PMPI=$(usex pmpi) - ) - cmake_src_configure -} - -src_compile() { - cmake_src_compile - docs_compile -} - -src_install() { - cmake_src_install - einstalldocs - if use tests; then - mkdir -p "${ED}/usr/libexec/${PN}/" || die - mv "${ED}"/usr/bin/*-test "${ED}/usr/libexec/${PN}/" || die - fi -} diff --git a/sys-cluster/opari2/Manifest b/sys-cluster/opari2/Manifest deleted file mode 100644 index 663a51e4f..000000000 --- a/sys-cluster/opari2/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST opari2-2.0.6.tar.gz 1355638 BLAKE2B 343f747de622fd6bf03c8aa7c250c6293868427e9e5f6e077a72b618afd683b6f4e30d8ff8e1c2f01b28bbb401e1522df9803006bd109c859b688b6cbf383a0e SHA512 253dd353c3dbda148a5ca22124163362528db76343ec668d1fa6f45556befb6ef44c1b6cf2d8977ba712866c5f95db5d1461b943b14c2418cb45c3627882b573 diff --git a/sys-cluster/opari2/metadata.xml b/sys-cluster/opari2/metadata.xml deleted file mode 100644 index 5434af068..000000000 --- a/sys-cluster/opari2/metadata.xml +++ /dev/null @@ -1,13 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <longdescription lang="en"> -OPARI2 is a tool to automatically instrument C, C++ and Fortran source code files in which pragmas (C/C++) or directives (Fortran) are used. Currently OpenMP and POMP user instrumentation are supported. Function calls to the pomp2_lib.h and pomp2_user_lib.h are inserted around or as replacement for supported directives. By implementing the respective APIs, detailed measurements regarding the runtime behavior of an applications can be made. A conforming implementation needs to implement all functions associated with the supported programming model. The original OPARI was developed to perform source-to-source instrumentation of OpenMP programs. Therefore the main focus of this document still lies on support for OpenMP. -OpenMP 3.0 introduced tasking to OpenMP. To support this feature the POMP2 adapter needs to do some bookkeeping in regard to specific task IDs. The pomp2_lib.c provided with this package includes the necessary code so it is strongly advised to use it as a basis for writing an adapter to your own tool. -A detailed description of the first OPARI version has been published by Mohr et al. in "Design and prototype of a performance tool interface for OpenMP" (Journal of supercomputing, 23, 2002). - </longdescription> -</pkgmetadata> diff --git a/sys-cluster/opari2/opari2-2.0.6.ebuild b/sys-cluster/opari2/opari2-2.0.6.ebuild deleted file mode 100644 index c5a7fcf78..000000000 --- a/sys-cluster/opari2/opari2-2.0.6.ebuild +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright 2019-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit autotools toolchain-funcs - -DESCRIPTION="OpenMP Pragma And Region Instrumentor" -HOMEPAGE="https://www.vi-hps.org/projects/score-p" -SRC_URI="https://perftools.pages.jsc.fz-juelich.de/cicd/${PN}/tags/${P}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND="${RDEPEND}" - -src_prepare() { - tc-export CC CXX AR F77 FC CPP - export CXXCPP="${CPP}" - export CC_FOR_BUILD="${CC}" - export CXX_FOR_BUILD="${CXX}" - export FC_FOR_BUILD="${FC}" - export F77_FOR_BUILD="${F77}" - export CFLAGS_FOR_BUILD="${CFLAGS}" - export CXXFLAGS_FOR_BUILD="${CXXFLAGS}" - export FFLAGS_FOR_BUILD="${FFLAGS}" - export FCFLAGS_FOR_BUILD="${FCFLAGS}" - export LDFLAGS_FOR_BUILD="${LDFLAGS}" - export CPPFLAGS_FOR_BUILD="${CPPFLAGS}" - - default - eautoreconf -} - -src_install() { - default - dodoc OPEN_ISSUES README - find "${ED}" -name '*.la' -delete || die - find "${ED}" -name '*.a' -delete || die -} diff --git a/sys-cluster/otf2/Manifest b/sys-cluster/otf2/Manifest deleted file mode 100644 index 1bb17c409..000000000 --- a/sys-cluster/otf2/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST otf2-2.3.tar.gz 5321226 BLAKE2B a217ac2bcc0fa777dccc99a0f90a143b3cfea66ff717cfe66f68d2d59407023b1f0e419d9c4275d27f201fa3df0c5a89d4730052039144b02a2136e390e85fbb SHA512 c27c768f178e512c46683667d70bc2ad3871b17b8978356b13917d3fc12b49b4ee5d5767e9e10a247bbc7f2e911aaae7455bfec8f36704236d55c16454fa0a4c -DIST otf2-3.0.tar.gz 5260678 BLAKE2B cb783c8466e2be424452284ac03df13306f1bad1163adcf113b4bcf93fe2be4e7fb05053ccf09d825db3e3f21b40667d4c03365be96ab240b4e1376ba6943703 SHA512 63cef15091d4071860211a5f52c375be089a3c8dc5ce28df0078197f2a2b7c45c2ecd9e677cb7ecf02339716bd0b2b692d1cb17c1ad1114978ffaa29cd28ff43 diff --git a/sys-cluster/otf2/files/otf2-2.3-respect-flags.patch b/sys-cluster/otf2/files/otf2-2.3-respect-flags.patch deleted file mode 100644 index 091e6f80b..000000000 --- a/sys-cluster/otf2/files/otf2-2.3-respect-flags.patch +++ /dev/null @@ -1,95 +0,0 @@ ---- a/doc/examples/Makefile -+++ b/doc/examples/Makefile -@@ -37,78 +37,78 @@ - pthread: $(ALL_PTHREAD) - - otf2_reader_example.o: otf2_reader_example.c -- gcc -std=c99 `otf2-config --cflags` \ -+ $(CC) -fPIC -std=c99 `otf2-config --cflags` \ - -c otf2_reader_example.c \ - -o otf2_reader_example.o - - otf2_reader_example: otf2_reader_example.o -- gcc otf2_reader_example.o \ -+ $(CC) -fPIE otf2_reader_example.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_reader_example - - otf2_writer_example.o: otf2_writer_example.c -- gcc -std=c99 `otf2-config --cflags` \ -+ $(CC) -fPIC -std=c99 `otf2-config --cflags` \ - -c otf2_writer_example.c \ - -o otf2_writer_example.o - - otf2_writer_example: otf2_writer_example.o -- gcc otf2_writer_example.o \ -+ $(CC) -fPIE otf2_writer_example.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_writer_example - - otf2_mpi_reader_example.o: otf2_mpi_reader_example.c -- mpicc -std=c99 `otf2-config --cflags` \ -+ $(MPICC) -fPIC -std=c99 `otf2-config --cflags` \ - -c otf2_mpi_reader_example.c \ - -o otf2_mpi_reader_example.o - - otf2_mpi_reader_example: otf2_mpi_reader_example.o -- mpicc otf2_mpi_reader_example.o \ -+ $(MPICC) -fPIE otf2_mpi_reader_example.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_mpi_reader_example - - otf2_mpi_reader_example_cc.o: otf2_mpi_reader_example.cc -- mpic++ `otf2-config --cflags` \ -+ $(MPICXX) -fPIC `otf2-config --cflags` \ - -c otf2_mpi_reader_example.cc \ - -o otf2_mpi_reader_example_cc.o - - otf2_mpi_reader_example_cc: otf2_mpi_reader_example_cc.o -- mpic++ otf2_mpi_reader_example_cc.o \ -+ $(MPICXX) -fPIE otf2_mpi_reader_example_cc.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_mpi_reader_example_cc - - otf2_mpi_writer_example.o: otf2_mpi_writer_example.c -- mpicc -std=c99 `otf2-config --cflags` \ -+ $(MPICC) -fPIC -std=c99 `otf2-config --cflags` \ - -c otf2_mpi_writer_example.c \ - -o otf2_mpi_writer_example.o - - otf2_mpi_writer_example: otf2_mpi_writer_example.o -- mpicc otf2_mpi_writer_example.o \ -+ $(MPICC) -fPIE otf2_mpi_writer_example.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_mpi_writer_example - - otf2_openmp_writer_example.o: otf2_openmp_writer_example.c -- gcc -std=c99 -fopenmp `otf2-config --cflags` \ -+ $(CC) -fPIC -std=c99 -fopenmp `otf2-config --cflags` \ - -c otf2_openmp_writer_example.c \ - -o otf2_openmp_writer_example.o - - otf2_openmp_writer_example: otf2_openmp_writer_example.o -- gcc -fopenmp otf2_openmp_writer_example.o \ -+ $(CC) -fPIE -fopenmp otf2_openmp_writer_example.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_openmp_writer_example - - otf2_pthread_writer_example.o: otf2_pthread_writer_example.c -- gcc -std=c99 -pthread `otf2-config --cflags` \ -+ $(CC) -fPIC -std=c99 -pthread `otf2-config --cflags` \ - -c otf2_pthread_writer_example.c \ - -o otf2_pthread_writer_example.o - - otf2_pthread_writer_example: otf2_pthread_writer_example.o -- gcc -pthread otf2_pthread_writer_example.o \ -+ $(CC) -fPIE -pthread otf2_pthread_writer_example.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_pthread_writer_example diff --git a/sys-cluster/otf2/files/otf2-3.0-respect-flags.patch b/sys-cluster/otf2/files/otf2-3.0-respect-flags.patch deleted file mode 100644 index 6fd8c6ca5..000000000 --- a/sys-cluster/otf2/files/otf2-3.0-respect-flags.patch +++ /dev/null @@ -1,95 +0,0 @@ ---- a/doc/examples/Makefile -+++ b/doc/examples/Makefile -@@ -37,78 +37,78 @@ - pthread: $(ALL_PTHREAD) - - otf2_reader_example.o: otf2_reader_example.c -- gcc -std=c99 `otf2-config --cflags` \ -+ $(CC) $(CFLAGS) -fPIC -std=c99 `otf2-config --cflags` \ - -c otf2_reader_example.c \ - -o otf2_reader_example.o - - otf2_reader_example: otf2_reader_example.o -- gcc otf2_reader_example.o \ -+ $(CC) $(CFLAGS) $(LDFLAGS) -fPIE otf2_reader_example.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_reader_example - - otf2_writer_example.o: otf2_writer_example.c -- gcc -std=c99 `otf2-config --cflags` \ -+ $(CC) $(CFLAGS) -fPIC -std=c99 `otf2-config --cflags` \ - -c otf2_writer_example.c \ - -o otf2_writer_example.o - - otf2_writer_example: otf2_writer_example.o -- gcc otf2_writer_example.o \ -+ $(CC) $(CFLAGS) $(LDFLAGS) -fPIE otf2_writer_example.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_writer_example - - otf2_mpi_reader_example.o: otf2_mpi_reader_example.c -- mpicc -std=c99 `otf2-config --cflags` \ -+ $(MPICC) $(CFLAGS) -fPIC -std=c99 `otf2-config --cflags` \ - -c otf2_mpi_reader_example.c \ - -o otf2_mpi_reader_example.o - - otf2_mpi_reader_example: otf2_mpi_reader_example.o -- mpicc otf2_mpi_reader_example.o \ -+ $(MPICC) $(CFLAGS) $(LDFLAGS) -fPIE otf2_mpi_reader_example.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_mpi_reader_example - - otf2_mpi_reader_example_cc.o: otf2_mpi_reader_example.cc -- mpic++ `otf2-config --cflags` \ -+ $(MPICXX) $(CXXFLAGS) -fPIC \ - -c otf2_mpi_reader_example.cc \ - -o otf2_mpi_reader_example_cc.o - - otf2_mpi_reader_example_cc: otf2_mpi_reader_example_cc.o -- mpic++ otf2_mpi_reader_example_cc.o \ -+ $(MPICXX) $(CXXFLAGS) $(LDFLAGS) -fPIE otf2_mpi_reader_example_cc.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_mpi_reader_example_cc - - otf2_mpi_writer_example.o: otf2_mpi_writer_example.c -- mpicc -std=c99 `otf2-config --cflags` \ -+ $(MPICC) $(CFLAGS) -fPIC -std=c99 `otf2-config --cflags` \ - -c otf2_mpi_writer_example.c \ - -o otf2_mpi_writer_example.o - - otf2_mpi_writer_example: otf2_mpi_writer_example.o -- mpicc otf2_mpi_writer_example.o \ -+ $(MPICC) $(CFLAGS) $(LDFLAGS) -fPIE otf2_mpi_writer_example.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_mpi_writer_example - - otf2_openmp_writer_example.o: otf2_openmp_writer_example.c -- gcc -std=c99 -fopenmp `otf2-config --cflags` \ -+ $(CC) $(CFLAGS) -fPIC -std=c99 -fopenmp `otf2-config --cflags` \ - -c otf2_openmp_writer_example.c \ - -o otf2_openmp_writer_example.o - - otf2_openmp_writer_example: otf2_openmp_writer_example.o -- gcc -fopenmp otf2_openmp_writer_example.o \ -+ $(CC) $(CFLAGS) $(LDFLAGS) -fPIE -fopenmp otf2_openmp_writer_example.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_openmp_writer_example - - otf2_pthread_writer_example.o: otf2_pthread_writer_example.c -- gcc -std=c99 -pthread `otf2-config --cflags` \ -+ $(CC) $(CFLAGS) -fPIC -std=c99 -pthread `otf2-config --cflags` \ - -c otf2_pthread_writer_example.c \ - -o otf2_pthread_writer_example.o - - otf2_pthread_writer_example: otf2_pthread_writer_example.o -- gcc -pthread otf2_pthread_writer_example.o \ -+ $(CC) $(CFLAGS) $(LDFLAGS) -fPIE -pthread otf2_pthread_writer_example.o \ - `otf2-config --ldflags` \ - `otf2-config --libs` \ - -o otf2_pthread_writer_example diff --git a/sys-cluster/otf2/metadata.xml b/sys-cluster/otf2/metadata.xml deleted file mode 100644 index df214d380..000000000 --- a/sys-cluster/otf2/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <use> - <flag name="sionlib">Enable <pkg>sys-cluster/sionlibl</pkg> support</flag> - </use> -</pkgmetadata> diff --git a/sys-cluster/otf2/otf2-2.3-r3.ebuild b/sys-cluster/otf2/otf2-2.3-r3.ebuild deleted file mode 100644 index e817ea850..000000000 --- a/sys-cluster/otf2/otf2-2.3-r3.ebuild +++ /dev/null @@ -1,95 +0,0 @@ -# Copyright 2019-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( pypy3 python3_{10..11} ) - -inherit python-single-r1 toolchain-funcs - -DESCRIPTION="highly scalable, memory efficient event trace data format" -HOMEPAGE="https://www.vi-hps.org/projects/score-p" -SRC_URI="https://perftools.pages.jsc.fz-juelich.de/cicd/otf2/tags/${P}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0/2.3" -KEYWORDS="~amd64" -IUSE="debug sionlib test" - -RDEPEND=" - ${PYTHON_DEPS} - $(python_gen_cond_dep 'dev-python/six[${PYTHON_USEDEP}]') - - sionlib? ( sys-cluster/sionlibl:= ) -" -DEPEND="${RDEPEND}" - -#RESTRICT="!test? ( test )" -RESTRICT="test" #tests are failing -REQUIRED_USE="${PYTHON_REQUIRED_USE}" -PATCHES=( "${FILESDIR}/${P}-respect-flags.patch" ) - -src_configure() { - tc-export CC CXX FC F77 CPP - rm build-config/common/platforms/platform-* || die - - cat > build-config/common/platforms/platform-backend-user-provided <<-EOF || die - CC=${CC} - CXX=${CXX} - FC=${FC} - F77=${F77} - CPP=${CPP} - CXXCPP=${CPP} - EOF - - cat > build-config/common/platforms/platform-frontend-user-provided <<-EOF || die - CC_FOR_BUILD=${CC} - F77_FOR_BUILD=${F77} - FC_FOR_BUILD=${FC} - CXX_FOR_BUILD=${CXX} - LDFLAGS_FOR_BUILD=${LDFLAGS} - CFLAGS_FOR_BUILD=${CFLAGS} - CXXFLAGS_FOR_BUILD=${CXXFLAGS} - CPPFLAGS_FOR_BUILD=${CPPFLAGS} - FCFLAGS_FOR_BUILD=${FCFLAGS} - FFLAGS_FOR_BUILD=${FFLAGS} - EOF - - cat > build-config/common/platforms/platform-mpi-user-provided <<-EOF || die - MPICC=mpicc - MPICXX=mpicxx - MPIF77=mpif77 - MPIFC=mpif90 - MPI_CPPFLAGS=${CPPFLAGS} - MPI_CFLAGS=${CFLAGS} - MPI_CXXFLAGS=${CXXFLAGS} - MPI_FFLAGS=${FFLAGS} - MPI_FCFLAGS=${FCFLAGS} - MPI_LDFLAGS=${LDFLAGS} - EOF - - local myconf=( - --disable-platform-mic - --disable-static - --enable-shared - --with-custom-compilers - - $(use_enable test backend-test-runs) - $(use_enable debug) - ) - - if use sionlib; then - myconf+=( "--with-sionlib=${EPREFIX}/usr" ) - myconf+=( "--with-sionlib-headers=${EPREFIX}/usr/include/sionlibl" ) - else - myconf+=( "--without-sionlib" ) - fi - - econf "${myconf[@]}" -} - -src_install() { - default - - find "${ED}" -name '*.la' -delete || die -} diff --git a/sys-cluster/otf2/otf2-3.0.ebuild b/sys-cluster/otf2/otf2-3.0.ebuild deleted file mode 100644 index cb426c181..000000000 --- a/sys-cluster/otf2/otf2-3.0.ebuild +++ /dev/null @@ -1,95 +0,0 @@ -# Copyright 2019-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( pypy3 python3_{10..11} ) - -inherit python-single-r1 toolchain-funcs - -DESCRIPTION="highly scalable, memory efficient event trace data format" -HOMEPAGE="https://www.vi-hps.org/projects/score-p" -SRC_URI="https://perftools.pages.jsc.fz-juelich.de/cicd/otf2/tags/${P}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0/3.0" -KEYWORDS="~amd64" -IUSE="debug sionlib test" - -RDEPEND=" - ${PYTHON_DEPS} - $(python_gen_cond_dep 'dev-python/six[${PYTHON_USEDEP}]') - - sionlib? ( sys-cluster/sionlibl:= ) -" -DEPEND="${RDEPEND}" - -#RESTRICT="!test? ( test )" -RESTRICT="test" #tests are failing -REQUIRED_USE="${PYTHON_REQUIRED_USE}" -PATCHES=( "${FILESDIR}/${P}-respect-flags.patch" ) - -src_configure() { - tc-export CC CXX FC F77 CPP - rm build-config/common/platforms/platform-* || die - - cat > build-config/common/platforms/platform-backend-user-provided <<-EOF || die - CC=${CC} - CXX=${CXX} - FC=${FC} - F77=${F77} - CPP=${CPP} - CXXCPP=${CPP} - EOF - - cat > build-config/common/platforms/platform-frontend-user-provided <<-EOF || die - CC_FOR_BUILD=${CC} - F77_FOR_BUILD=${F77} - FC_FOR_BUILD=${FC} - CXX_FOR_BUILD=${CXX} - LDFLAGS_FOR_BUILD=${LDFLAGS} - CFLAGS_FOR_BUILD=${CFLAGS} - CXXFLAGS_FOR_BUILD=${CXXFLAGS} - CPPFLAGS_FOR_BUILD=${CPPFLAGS} - FCFLAGS_FOR_BUILD=${FCFLAGS} - FFLAGS_FOR_BUILD=${FFLAGS} - EOF - - cat > build-config/common/platforms/platform-mpi-user-provided <<-EOF || die - MPICC=mpicc - MPICXX=mpicxx - MPIF77=mpif77 - MPIFC=mpif90 - MPI_CPPFLAGS=${CPPFLAGS} - MPI_CFLAGS=${CFLAGS} - MPI_CXXFLAGS=${CXXFLAGS} - MPI_FFLAGS=${FFLAGS} - MPI_FCFLAGS=${FCFLAGS} - MPI_LDFLAGS=${LDFLAGS} - EOF - - local myconf=( - --disable-platform-mic - --disable-static - --enable-shared - --with-custom-compilers - - $(use_enable test backend-test-runs) - $(use_enable debug) - ) - - if use sionlib; then - myconf+=( "--with-sionlib=${EPREFIX}/usr" ) - myconf+=( "--with-sionlib-headers=${EPREFIX}/usr/include/sionlibl" ) - else - myconf+=( "--without-sionlib" ) - fi - - econf "${myconf[@]}" -} - -src_install() { - default - - find "${ED}" -name '*.la' -delete || die -} diff --git a/sys-cluster/parallel-netcdf/Manifest b/sys-cluster/parallel-netcdf/Manifest deleted file mode 100644 index eba2d268b..000000000 --- a/sys-cluster/parallel-netcdf/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pnetcdf-1.12.2.tar.gz 2355892 BLAKE2B ea94d63caa8d42b727084be0580c43e0ac03325acafb046a057092b41880a875a1ca04d1b0183062aed3d7182103217c02165c0f65e722b50129931fb7c93e82 SHA512 b482eadb4955a312fab885aa89c08817c010ed6ff69dff3cfa9c530f1b645b788973029909a8f6fd428170103cfa0784e1bfe085a48d9bcd2446dbd0d40ed67d diff --git a/sys-cluster/parallel-netcdf/files/parallel-netcdf-1.12.2-no-DESTDIR-for-info-clarity.patch b/sys-cluster/parallel-netcdf/files/parallel-netcdf-1.12.2-no-DESTDIR-for-info-clarity.patch deleted file mode 100644 index 4a3393b2c..000000000 --- a/sys-cluster/parallel-netcdf/files/parallel-netcdf-1.12.2-no-DESTDIR-for-info-clarity.patch +++ /dev/null @@ -1,55 +0,0 @@ ---- a/Makefile.am -+++ b/Makefile.am -@@ -65,40 +65,40 @@ - @echo '+----------------------------------------------------------------------------+' - @echo '|' - @echo '| PnetCDF has been successfully installed under' -- @echo '| $(DESTDIR)$(prefix)' -+ @echo '| $(prefix)' - @echo '|' - @echo '| * PnetCDF header files have been installed in' -- @echo '| $(DESTDIR)$(prefix)/include' -+ @echo '| $(prefix)/include' - @echo '| * PnetCDF library files have been installed in' -- @echo '| $(DESTDIR)$(exec_prefix)/lib' -+ @echo '| $(exec_prefix)/lib' - @echo '| * PnetCDF utility programs have been installed in' -- @echo '| $(DESTDIR)$(exec_prefix)/bin' -+ @echo '| $(exec_prefix)/bin' - @echo '| * PnetCDF man pages have been installed in' -- @echo '| $(DESTDIR)$(prefix)/share/man' -+ @echo '| $(prefix)/share/man' - @echo '|' - @echo '| To compile your PnetCDF programs, please add the following to the command' - @echo '| line, so the compiler can find the PnetCDF header files:' -- @echo '| -I$(DESTDIR)$(prefix)/include' -+ @echo '| -I$(prefix)/include' - @echo '|' - @if test "x$(has_fortran)" = xyes -a 'x$(FC_MODINC)' != 'x-I' ; then \ - echo '| Add the following line to compile your Fortran programs' ; \ -- echo '| $(FC_MODINC)$(DESTDIR)$(prefix)/include' ; \ -+ echo '| $(FC_MODINC)$(prefix)/include' ; \ - echo '|' ; \ - fi - @echo '| Add the following line to link your program to PnetCDF library:' -- @echo '| -L$(DESTDIR)$(exec_prefix)/lib -lpnetcdf' -+ @echo '| -L$(exec_prefix)/lib -lpnetcdf' - @echo '|' - @if test "x$(enable_shared)" = xyes ; then \ - echo '| Add the following to your run-time environment variable LD_LIBRARY_PATH,' ; \ - echo '| when linking your executable with the PnetCDF shared libraries.' ; \ - if test "x$(enable_netcdf4)" = xyes -a "x$(enable_adios)" = xyes ; then \ -- echo '| $(DESTDIR)$(exec_prefix)/lib:$(netcdf4_libdir):$(adios_libdir)' ; \ -+ echo '| $(exec_prefix)/lib:$(netcdf4_libdir):$(adios_libdir)' ; \ - elif test "x$(enable_netcdf4)" = xyes ; then \ -- echo '| $(DESTDIR)$(exec_prefix)/lib:$(netcdf4_libdir)' ; \ -+ echo '| $(exec_prefix)/lib:$(netcdf4_libdir)' ; \ - elif test "x$(enable_adios)" = xyes ; then \ -- echo '| $(DESTDIR)$(exec_prefix)/lib:$(adios_libdir)' ; \ -+ echo '| $(exec_prefix)/lib:$(adios_libdir)' ; \ - else \ -- echo '| $(DESTDIR)$(exec_prefix)/lib' ; \ -+ echo '| $(exec_prefix)/lib' ; \ - fi ; \ - echo '|' ; \ - fi diff --git a/sys-cluster/parallel-netcdf/files/parallel-netcdf-1.12.2-respect-flags.patch b/sys-cluster/parallel-netcdf/files/parallel-netcdf-1.12.2-respect-flags.patch deleted file mode 100644 index 0d345c6a3..000000000 --- a/sys-cluster/parallel-netcdf/files/parallel-netcdf-1.12.2-respect-flags.patch +++ /dev/null @@ -1,44 +0,0 @@ ---- a/src/utils/ncmpidiff/Makefile.am -+++ b/src/utils/ncmpidiff/Makefile.am -@@ -18,7 +18,7 @@ - cdfdiff_SOURCES = cdfdiff.c - - cdfdiff$(EXEEXT): cdfdiff.c Makefile -- $(SEQ_CC) -I$(top_srcdir)/src/utils/ncvalidator -o $@ $< -+ $(SEQ_CC) $(CFLAGS) $(LDFLAGS) -fPIE -I$(top_srcdir)/src/utils/ncvalidator -o $@ $< - - $(top_builddir)/src/libs/libpnetcdf.la: - set -e; cd $(top_builddir)/src/libs && $(MAKE) $(MFLAGS) ---- a/src/utils/ncoffsets/Makefile.am -+++ b/src/utils/ncoffsets/Makefile.am -@@ -10,7 +10,7 @@ - EXTRA_DIST = ncoffsets.c - - ncoffsets$(EXEEXT): ncoffsets.c -- $(SEQ_CC) -o $@ $< -+ $(SEQ_CC) $(CFLAGS) $(LDFLAGS) -fPIE -o $@ $< - - dist_man_MANS = ncoffsets.1 - ---- a/src/utils/ncvalidator/Makefile.am -+++ b/src/utils/ncvalidator/Makefile.am -@@ -76,7 +76,7 @@ - TST_HDF5_FILES = pad_superblock.h5 - - ncvalidator$(EXEEXT): ncvalidator.c Makefile -- $(SEQ_CC) -o $@ $< -+ $(SEQ_CC) $(CFLAGS) $(LDFLAGS) -fPIE -o $@ $< - - # autimake 1.11.3 has not yet implemented AM_TESTS_ENVIRONMENT - # For newer versions, we can use AM_TESTS_ENVIRONMENT instead ---- a/src/utils/pnetcdf_version/Makefile.am -+++ b/src/utils/pnetcdf_version/Makefile.am -@@ -22,7 +22,7 @@ - endif - - pnetcdf_version$(EXEEXT): pnetcdf_version.c -- $(SEQ_CC) $(XDEFS) -o $@ $< -+ $(SEQ_CC) $(CFLAGS) $(LDFLAGS) -fPIE $(XDEFS) -o $@ $< - - dist_man_MANS = pnetcdf_version.1 - diff --git a/sys-cluster/parallel-netcdf/metadata.xml b/sys-cluster/parallel-netcdf/metadata.xml deleted file mode 100644 index f58af5d80..000000000 --- a/sys-cluster/parallel-netcdf/metadata.xml +++ /dev/null @@ -1,25 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <description>comaintainers welcome</description> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <upstream> - <bugs-to>https://github.com/Parallel-NetCDF/PnetCDF/issues</bugs-to> - <remote-id type="github">Parallel-NetCDF/PnetCDF</remote-id> - </upstream> - <use> - <flag name="burst-buffering">Enable burst buffer driver support</flag> - <flag name="cxx">Turn on support for the C++ interface</flag> - <flag name="erange-fill">Disable use of fill value when out-of-range type conversion causes NC_ERANGE error</flag> - <flag name="fortran">Turn on support for the Fortran interface</flag> - <flag name="file-sync"> Disable MPI file sync if you know your file system can provide data consistency</flag> - <flag name="netcdf">Enable NetCDF-4 feature</flag> - <flag name="null-byte-header-padding">Enable check for null-byte header padding when reading files in classic formats</flag> - <flag name="relax-coord-bound">Use stricter rule for error NC_EINVALCOORDS to disallow coordinate start argument equal to dimension size when argument count is zero</flag> - <flag name="subfiling">Enable subfiling support</flag> - <flag name="threadsafe">Enable thread-safe capability</flag> - </use> -</pkgmetadata> diff --git a/sys-cluster/parallel-netcdf/parallel-netcdf-1.12.2.ebuild b/sys-cluster/parallel-netcdf/parallel-netcdf-1.12.2.ebuild deleted file mode 100644 index 7ddf1f2c4..000000000 --- a/sys-cluster/parallel-netcdf/parallel-netcdf-1.12.2.ebuild +++ /dev/null @@ -1,95 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -FORTRAN_NEEDED=fortran -MYP="pnetcdf-${PV}" - -inherit autotools fortran-2 - -DESCRIPTION="Parallel extension to netCDF" -HOMEPAGE=" - https://parallel-netcdf.github.io - https://trac.mcs.anl.gov/projects/parallel-netcdf -" -SRC_URI="https://parallel-netcdf.github.io/Release/${MYP}.tar.gz" -S="${WORKDIR}/${MYP}" - -LICENSE="UCAR-Unidata" -SLOT="0" -KEYWORDS="~amd64" -IUSE="burst-buffering +cxx debug doc +erange-fill +file-sync +fortran netcdf -null-byte-header-padding +relax-coord-bound subfiling threadsafe" - -RDEPEND=" - netcdf? ( sci-libs/netcdf[mpi] ) - virtual/mpi -" -# adios? ( sys-cluster/adios ) -DEPEND="${RDEPEND}" -BDEPEND=" - doc? ( - app-text/doxygen - dev-texlive/texlive-latex - ) -" - -RESTRICT="test" # tests require MPI set up -PATCHES=( - "${FILESDIR}/${P}-no-DESTDIR-for-info-clarity.patch" - "${FILESDIR}/${P}-respect-flags.patch" -) - -pkg_setup() { - fortran-2_pkg_setup -} - -src_prepare() { - default - eautoreconf -} - -src_configure() { - export MPIF77=/usr/bin/mpif77 - export MPIF90=/usr/bin/mpif90 - export VARTEXFONTS="${T}/fonts" - - local myconf=( - --enable-shared - --with-mpi="${EPREFIX}/usr" - - $(use_enable burst-buffering) - $(use_enable cxx) - $(use_enable debug) - $(use_enable doc doxygen) - $(use_enable erange-fill) - $(use_enable file-sync) - $(use_enable fortran) - $(use_enable netcdf netcdf4) - $(use_enable null-byte-header-padding) - $(use_enable relax-coord-bound) - $(use_enable subfiling) - $(use_enable threadsafe thread-safe) - ) -# $(use_enable adios) -# if use adios; then -# myconf+=( "--with-adios=${EPREFIX}/usr" ) -# else -# myconf+=( "--without-adios" ) -# fi - if use netcdf; then - myconf+=( "--with-netcdf4=${EPREFIX}/usr" ) - else - myconf+=( "--without-netcdf4" ) - fi - - econf "${myconf[@]}" -} - -src_install() { - default - dodoc doc/README.{ADIOS.md,NetCDF4.md,burst_buffering,consistency,large_files} doc/pbs.script - use doc && dodoc doc/pnetcdf-api/pnetcdf-api.pdf - find "${ED}" -name '*.la' -delete || die -} diff --git a/sys-cluster/psort/Manifest b/sys-cluster/psort/Manifest deleted file mode 100644 index d17e2b517..000000000 --- a/sys-cluster/psort/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST psort-1.0.tar.gz 644944 BLAKE2B 55419576e3cbe3268f3a313f3a651a244825a147cef3f2a2ffb822494e63f6fd166d22b588f7e6753f85d8d0a241e603dfb2242b8f30cc21f2aa9b9a98b6251c SHA512 3d53f4d7002e12e0a7660d3e9a87cedead013a056537d6a472e87ef9043ec174cb55b43b767c7acefdce70a761db2ad004c2ef9776436a55638d1658c7b662e1 diff --git a/sys-cluster/psort/files/psort-1.0-make_pair.patch b/sys-cluster/psort/files/psort-1.0-make_pair.patch deleted file mode 100644 index cfc96c7bf..000000000 --- a/sys-cluster/psort/files/psort-1.0-make_pair.patch +++ /dev/null @@ -1,77 +0,0 @@ ---- a/src/funnel.h -+++ b/src/funnel.h -@@ -204,7 +204,7 @@ - }; - - inline void add_stream(RanIt begin, RanIt end) -- { *last_stream++ = std::make_pair(begin,end); } -+ { *last_stream++ = std::pair(begin,end); } - inline stream_iterator begin() - { return stream_iterator(input_streams); } - inline stream_iterator end() ---- a/src/psort_splitters.h -+++ b/src/psort_splitters.h -@@ -87,8 +87,8 @@ - // keep a list of ranges, trying to "activate" them at each branch - vector< pair<_RandomAccessIter, _RandomAccessIter> > d_ranges(nproc - 1); - vector< pair<_Distance *, _Distance *> > t_ranges(nproc - 1); -- d_ranges[0] = make_pair(first, last); -- t_ranges[0] = make_pair(targets, targets + (nproc - 1)); -+ d_ranges[0] = pair(first, last); -+ t_ranges[0] = pair(targets, targets + (nproc - 1)); - - // invariant: subdist[i][rank] == d_ranges[i].second - d_ranges[i].first - // amount of data each proc still has in the search -@@ -181,7 +181,7 @@ - // sum to get the global range of indices - vector<pair<_Distance, _Distance> > ind_global(n_act); - for (int k = 0; k < n_act; ++k) { -- ind_global[k] = make_pair(0, 0); -+ ind_global[k] = pair(0, 0); - for (int i = 0; i < nproc; ++i) { - ind_global[k].first += ind_all[2 * (i * n_act + k)]; - ind_global[k].second += ind_all[2 * (i * n_act + k) + 1]; -@@ -223,9 +223,9 @@ - } - - if ((split_low - t_ranges[k].first) > 0) { -- t_ranges_x[n_act_x] = make_pair (t_ranges[k].first, split_low); -+ t_ranges_x[n_act_x] = pair (t_ranges[k].first, split_low); - // lop off local_ind_low..end -- d_ranges_x[n_act_x] = make_pair (d_ranges[k].first, -+ d_ranges_x[n_act_x] = pair (d_ranges[k].first, - first + ind_local[2 * k]); - for (int i = 0; i < nproc; ++i) { - subdist_x[n_act_x][i] = ind_all[2 * (i * n_act + k)] - outleft[k][i]; -@@ -235,9 +235,9 @@ - } - - if ((t_ranges[k].second - split_high) > 0) { -- t_ranges_x[n_act_x] = make_pair (split_high, t_ranges[k].second); -+ t_ranges_x[n_act_x] = pair (split_high, t_ranges[k].second); - // lop off begin..local_ind_high -- d_ranges_x[n_act_x] = make_pair (first + ind_local[2 * k + 1], -+ d_ranges_x[n_act_x] = pair (first + ind_local[2 * k + 1], - d_ranges[k].second); - for (int i = 0; i < nproc; ++i) { - subdist_x[n_act_x][i] = outleft[k][i] ---- a/src/sort.timpl.h -+++ b/src/sort.timpl.h -@@ -194,7 +194,7 @@ - return *this; - } - std::pair<RanIt,RanIt> operator*() -- { return make_pair(begin,end); } -+ { return pair(begin,end); } - bool operator==(const iterator& rhs) - { return begin == rhs.begin; } - private: -@@ -251,7 +251,7 @@ - begin_cache = end_cache = malloc.allocate(rec_calls); - for( Diff d=run_size; d>static_cast<Diff>(Splitter::switch_to_cache_aware()); d=run_size_<Splitter>(d), ++end_cache ) - new(end_cache) Merger(Splitter::prefered_order_output(d), talloc); -- return make_pair(begin_cache,end_cache); -+ return pair(begin_cache,end_cache); - } - - template<class Merger, class Splitter, class It, class OutIt, class Alloc> diff --git a/sys-cluster/psort/files/psort-1.0-makefile.patch b/sys-cluster/psort/files/psort-1.0-makefile.patch deleted file mode 100644 index 6446f62ae..000000000 --- a/sys-cluster/psort/files/psort-1.0-makefile.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- a/driver/Makefile -+++ b/driver/Makefile -@@ -1,8 +1,7 @@ - include ./Make.inc - - psort: psort_driver.cc -- $(CXX) $(CXXFLAGS) -I../src psort_driver.cc -o psort $(LIBS) -- strip psort -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) -fPIE -I../src psort_driver.cc -o psort $(LIBS) - - clean: - rm -f *.o psort results ---- a/driver/Make.inc -+++ b/driver/Make.inc -@@ -1,4 +1,4 @@ - CXX=mpic++ --CXXFLAGS=-O2 -DUSE_FUNNEL -Wall -+CXXFLAGS+=-DUSE_FUNNEL -Wall - LIBS=-lm - diff --git a/sys-cluster/psort/metadata.xml b/sys-cluster/psort/metadata.xml deleted file mode 100644 index 951d690fd..000000000 --- a/sys-cluster/psort/metadata.xml +++ /dev/null @@ -1,10 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <longdescription lang="en">PSORT is a parallel sorting code for distributed and shared memory architectures. It uses MPI for communication, and is designed to minimize the volume of communication. It has been tested on terabyte datasets with up to 256 processors. It does not use sampling to locate splitters, and hence no prior knowledge of the probability distribution is required. It provides several options for splitting, sequential sorting and merging. A parallel sample sort is also included. - </longdescription> -</pkgmetadata> diff --git a/sys-cluster/psort/psort-1.0.ebuild b/sys-cluster/psort/psort-1.0.ebuild deleted file mode 100644 index 2c8c9dcc7..000000000 --- a/sys-cluster/psort/psort-1.0.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 2019-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DESCRIPTION="Parallel sorting code for distributed and shared memory architectures" -HOMEPAGE="https://web.archive.org/web/20181126115900/http://gauss.cs.ucsb.edu/code/index.shtml" -SRC_URI="https://web.archive.org/web/20181126115900/http://gauss.cs.ucsb.edu/code/${PN}/${P}.tar.gz" - -LICENSE="MIT GPL-2+" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND="virtual/mpi" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}/${P}-make_pair.patch" - "${FILESDIR}/${P}-makefile.patch" -) - -src_compile() { - pushd driver || die - emake - popd || die -} - -src_install() { - dodoc README doc/psort.pdf - insinto "/usr/include/psort" - doins src/*.h driver/*.h - dobin driver/psort -} diff --git a/sys-cluster/rankstr/Manifest b/sys-cluster/rankstr/Manifest deleted file mode 100644 index 9af504183..000000000 --- a/sys-cluster/rankstr/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST rankstr-0.1.0.tar.gz 14909 BLAKE2B 488386e2588e71db43d59b02ba277cc409df21615ae6c8e2fa822a0aee2ebf4d0ac4f09c262759b7c4066cf118420404d297c9dfcf2fe80bdd19977a2e120174 SHA512 be36c6316fe2286015f704dbf8733ae2b682f32f5c180cfa5e1adf91ebec2dcba24af1fda8a9f83612edb20327d21aaaf869bb41fcdfb7873b0f1aab7bf6c36a -DIST rankstr-0.2.0.tar.gz 14805 BLAKE2B cb448147dec904fd306069e452039f3cb219961748d73de313bc559dded1e77c12771a1330b3e73960dbc59b5d3255f3bc9221d813ac82fd6eabab3d562f244b SHA512 af9ac1ae3272626c39d0e5628bd12b9bb14db70fe8e752961919f2cda1e69da3637c84c32584d7f4c89d58cfebdf71efa1b2fb7903059ce2792c64596a06475a diff --git a/sys-cluster/rankstr/files/rankstr-0.1.0-no-static.patch b/sys-cluster/rankstr/files/rankstr-0.1.0-no-static.patch deleted file mode 100644 index 642334890..000000000 --- a/sys-cluster/rankstr/files/rankstr-0.1.0-no-static.patch +++ /dev/null @@ -1,16 +0,0 @@ ---- a/src/CMakeLists.txt -+++ b/src/CMakeLists.txt -@@ -24,13 +24,3 @@ - SET_TARGET_PROPERTIES(rankstr PROPERTIES OUTPUT_NAME rankstr CLEAN_DIRECT_OUTPUT 1) - INSTALL(TARGETS rankstr DESTINATION ${CMAKE_INSTALL_LIBDIR}) - ENDIF() -- --ADD_LIBRARY(rankstr-static STATIC $<TARGET_OBJECTS:rankstr_o>) --IF(RANKSTR_LINK_STATIC) -- SET_TARGET_PROPERTIES(rankstr-static PROPERTIES LINK_SEARCH_START_STATIC 1) -- SET_TARGET_PROPERTIES(rankstr-static PROPERTIES LINK_SEARCH_END_STATIC 1) --ENDIF(RANKSTR_LINK_STATIC) --TARGET_LINK_LIBRARIES(rankstr-static ${RANKSTR_EXTERNAL_LIBS}) -- --SET_TARGET_PROPERTIES(rankstr-static PROPERTIES OUTPUT_NAME rankstr CLEAN_DIRECT_OUTPUT 1) --INSTALL(TARGETS rankstr-static DESTINATION ${CMAKE_INSTALL_LIBDIR}) diff --git a/sys-cluster/rankstr/files/rankstr-no-static.patch b/sys-cluster/rankstr/files/rankstr-no-static.patch deleted file mode 100644 index c3072eaa8..000000000 --- a/sys-cluster/rankstr/files/rankstr-no-static.patch +++ /dev/null @@ -1,16 +0,0 @@ ---- a/src/CMakeLists.txt -+++ b/src/CMakeLists.txt -@@ -22,13 +22,3 @@ - TARGET_LINK_LIBRARIES(rankstr ${RANKSTR_EXTERNAL_LIBS}) - SET_TARGET_PROPERTIES(rankstr PROPERTIES OUTPUT_NAME rankstr CLEAN_DIRECT_OUTPUT 1) - INSTALL(TARGETS rankstr DESTINATION ${CMAKE_INSTALL_LIBDIR}) -- --ADD_LIBRARY(rankstr-static STATIC $<TARGET_OBJECTS:rankstr_o>) --IF(RANKSTR_LINK_STATIC) -- SET_TARGET_PROPERTIES(rankstr-static PROPERTIES LINK_SEARCH_START_STATIC 1) -- SET_TARGET_PROPERTIES(rankstr-static PROPERTIES LINK_SEARCH_END_STATIC 1) --ENDIF(RANKSTR_LINK_STATIC) --TARGET_LINK_LIBRARIES(rankstr-static ${RANKSTR_EXTERNAL_LIBS}) -- --SET_TARGET_PROPERTIES(rankstr-static PROPERTIES OUTPUT_NAME rankstr CLEAN_DIRECT_OUTPUT 1) --INSTALL(TARGETS rankstr-static DESTINATION ${CMAKE_INSTALL_LIBDIR}) diff --git a/sys-cluster/rankstr/metadata.xml b/sys-cluster/rankstr/metadata.xml deleted file mode 100644 index 695db8fb1..000000000 --- a/sys-cluster/rankstr/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <upstream> - <remote-id type="github">ECP-VeloC/rankstr</remote-id> - </upstream> - <longdescription lang="en">The rankstr (rank string) library provides functions that identify unique strings across an MPI communicator. - -A key use case is to split a communicator into subcommunicators such that all processes in a resulting subcommunicator consist of those processes that provided an identical input string. rankstr_mpi_comm_split is a function like MPI_Comm_split, but it takes a variable-length string as the color argument insead of an integer value. - -The rankstr_mpi function does not output a communicator, but instead returns a unique integer for each unique string. - -For scalability, the implementation uses a distributed, bitonic sort via point-to-point messages over the input communicator to compare string values. The caller must provide two distinct tag values that are safe for the function to use for its point-to-point messages. - </longdescription> -</pkgmetadata> diff --git a/sys-cluster/rankstr/rankstr-0.1.0.ebuild b/sys-cluster/rankstr/rankstr-0.1.0.ebuild deleted file mode 100644 index 2daa65413..000000000 --- a/sys-cluster/rankstr/rankstr-0.1.0.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit cmake - -DESCRIPTION="Split an MPI communicator into subcomms based on string values" -HOMEPAGE="https://github.com/ECP-VeloC/rankstr" -SRC_URI="https://github.com/ECP-VeloC/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="test" - -RDEPEND="virtual/mpi" -DEPEND="${RDEPEND}" - -PATCHES=( "${FILESDIR}/${P}-no-static.patch" ) -RESTRICT="!test? ( test )" - -src_configure() { - local mycmakeargs=( - -DBUILD_SHARED_LIBS=ON - -DENABLE_TESTS=$(usex test) - -DRANKSTR_LINK_STATIC=OFF - ) - cmake_src_configure -} diff --git a/sys-cluster/rankstr/rankstr-0.2.0.ebuild b/sys-cluster/rankstr/rankstr-0.2.0.ebuild deleted file mode 100644 index 373a03796..000000000 --- a/sys-cluster/rankstr/rankstr-0.2.0.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit cmake - -DESCRIPTION="Split an MPI communicator into subcomms based on string values" -HOMEPAGE="https://github.com/ECP-VeloC/rankstr" -SRC_URI="https://github.com/ECP-VeloC/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="test" - -RDEPEND="virtual/mpi" -DEPEND="${RDEPEND}" - -PATCHES=( "${FILESDIR}/${PN}-0.1.0-no-static.patch" ) -RESTRICT="test" # tests require an MPI setup - -src_configure() { - local mycmakeargs=( - -DBUILD_SHARED_LIBS=ON - -DENABLE_TESTS=$(usex test) - -DRANKSTR_LINK_STATIC=OFF - ) - cmake_src_configure -} diff --git a/sys-cluster/sionlib/Manifest b/sys-cluster/sionlib/Manifest deleted file mode 100644 index 292998421..000000000 --- a/sys-cluster/sionlib/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST sionlib-1.7.7.tar.gz 489080 BLAKE2B 1ffd06d1b245034b28700af1249135347cdd731a7af23ad96a27b5b5a11d64d9a67249fcd1c44cea43face1066e7ae1d59681e84cef2041e18f02e0c3e8f70ee SHA512 f270467e09893adf1af6103557365acbc9a3e73fe08716a21de6f59b25be9b187ee1c1ec1d878a9599e735f98da470b5e2e184774c27ed0ff0c330c5bf0a5677 diff --git a/sys-cluster/sionlib/files/sionlib-build-shared-libraries.patch b/sys-cluster/sionlib/files/sionlib-build-shared-libraries.patch deleted file mode 100644 index 178707fc4..000000000 --- a/sys-cluster/sionlib/files/sionlib-build-shared-libraries.patch +++ /dev/null @@ -1,385 +0,0 @@ ---- a/src/cppinterface/Makefile -+++ b/src/cppinterface/Makefile -@@ -30,7 +30,7 @@ - ifeq ($(CXXENABLE),1) - - USER_HDRS = sion_cxx_base.hpp sion_cxx_serial.hpp sion_cxx_common.hpp sion_cxx_mpi.hpp sion_cxx_ompi.hpp sion_cxx_omp.hpp --USER_LIBS = lib$(SION_LIBNAME_CXX_SER).a lib$(SION_LIBNAME_CXX_MPI).a -+USER_LIBS = lib$(SION_LIBNAME_CXX_SER).so lib$(SION_LIBNAME_CXX_MPI).so - else - USER_HDRS = - USER_LIBS = -@@ -57,13 +57,15 @@ - - all: $(USER_LIBS) - -+../lib/lib$(SION_LIBNAME_SER).so : -+ make -C ../lib lib$(SION_LIBNAME_SER).so - --lib$(SION_LIBNAME_CXX_SER).a : $(SION_OBJS_SER) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_SER) -+lib$(SION_LIBNAME_CXX_SER).so : $(SION_OBJS_SER) ../lib/lib$(SION_LIBNAME_SER).so -+ $(CXX) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_CXX_SER).so -shared -o $@ $(SION_OBJS_SER) -L../lib -l$(SION_LIBNAME_SER) - @echo "*** $@ built" - --lib$(SION_LIBNAME_CXX_MPI).a : $(SION_OBJS_MPI) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_MPI) -+lib$(SION_LIBNAME_CXX_MPI).so : $(SION_OBJS_MPI) -+ $(MPICXX) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_CXX_MPI).so -shared -o $@ $(SION_OBJS_MPI) - @echo "*** $@ built" - - sion_cxx_base.o : -@@ -118,7 +120,7 @@ - done - - clean: -- rm -f *.o lib*.a -+ rm -f *.o lib*.so - - #------------------------------------------------------------------------------ - # Dependencies ---- a/src/fortraninterface/Makefile -+++ b/src/fortraninterface/Makefile -@@ -39,7 +39,7 @@ - - USER_HDRS = sion_f77.H sion_f77.h - USER_MODS = sion_f90.mod --USER_LIBS = lib$(SION_LIBNAME_F77_SER).a lib$(SION_LIBNAME_F77_MPI).a lib$(SION_LIBNAME_F90_SER).a lib$(SION_LIBNAME_F90_MPI).a -+USER_LIBS = lib$(SION_LIBNAME_F77_SER).so lib$(SION_LIBNAME_F77_MPI).so lib$(SION_LIBNAME_F90_SER).so lib$(SION_LIBNAME_F90_MPI).so - else - USER_HDRS = - USER_MODS = -@@ -56,39 +56,47 @@ - SION_OBJS_F77_SER += sion_f77_omp.o sion_fortran_omp.o - SION_OBJS_F90_SER += sion_f90_omp.o sion_fortran_omp.o - USER_MODS += sion_f90_omp.mod -+ F77_SER_LIBS = $(OMPFLAG) -L../parlib -l$(SION_LIBNAME_OMP) -L../lib -l$(SION_LIBNAME_GEN) -+ F90_SER_LIBS = $(OMPFLAG) -L../parlib -l$(SION_LIBNAME_OMP) -L../lib -l$(SION_LIBNAME_GEN) - endif - - ifeq ($(MPIENABLE),1) - SION_OBJS_F77_MPI += sion_f77_mpi.o sion_fortran_mpi.o sion_fortran_writeread_mpi_f77.o - SION_OBJS_F90_MPI += sion_f90_mpi.o sion_fortran_mpi.o sion_fortran_writeread_mpi_f90.o - USER_MODS += sion_f90_mpi.mod -+ F77_MPI_LIBS = -L../parlib -l$(SION_LIBNAME_MPI) -+ F90_MPI_LIBS = -L../parlib -l$(SION_LIBNAME_MPI) - endif - - ifeq ($(HYBENABLE),1) - SION_OBJS_F77_MPI += sion_f77_ompi.o sion_fortran_ompi.o - SION_OBJS_F90_MPI += sion_f90_ompi.o sion_fortran_ompi.o - USER_MODS += sion_f90_ompi.mod -+ F77_MPI_LIBS = $(HYBFLAG) -L../parlib -l$(SION_LIBNAME_OMPI) -+ F90_MPI_LIBS = $(HYBFLAG) -L../parlib -l$(SION_LIBNAME_OMPI) - endif - - SION_DEPEND_OBJS=sion_fortran.o sion_fortran_omp.o sion_fortran_mpi.o sion_fortran_ompi.o sion_fortran_writeread_f77.o sion_fortran_writeread_f90.o sion_fortran_writeread_mpi_f77.o sion_fortran_writeread_mpi_f90.o - - all: $(USER_LIBS) $(USER_MODS) - -+../lib/lib$(SION_LIBNAME_SER).so : -+ make -C ../lib lib$(SION_LIBNAME_SER).so - --lib$(SION_LIBNAME_F77_SER).a : $(SION_OBJS_F77_SER) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_F77_SER) -+lib$(SION_LIBNAME_F77_SER).so : $(SION_OBJS_F77_SER) ../lib/lib$(SION_LIBNAME_SER).so -+ $(F77) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_F77_SER).so -shared -o $@ $(SION_OBJS_F77_SER) $(F77_SER_LIBS) - @echo "*** $@ built" - --lib$(SION_LIBNAME_F77_MPI).a : $(SION_OBJS_F77_MPI) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_F77_MPI) -+lib$(SION_LIBNAME_F77_MPI).so : $(SION_OBJS_F77_MPI) -+ $(MPIF77) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_F77_MPI).so -shared -o $@ $(SION_OBJS_F77_MPI) $(F77_MPI_LIBS) - @echo "*** $@ built" - --lib$(SION_LIBNAME_F90_SER).a : $(SION_OBJS_F90_SER) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_F90_SER) -+lib$(SION_LIBNAME_F90_SER).so : $(SION_OBJS_F90_SER) ../lib/lib$(SION_LIBNAME_SER).so -+ $(F90) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_F90_SER).so -shared -o $@ $(SION_OBJS_F90_SER) $(F90_SER_LIBS) - @echo "*** $@ built" - --lib$(SION_LIBNAME_F90_MPI).a : $(SION_OBJS_F90_MPI) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_F90_MPI) -+lib$(SION_LIBNAME_F90_MPI).so : $(SION_OBJS_F90_MPI) -+ $(MPIF90) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_F90_MPI).so -shared -o $@ $(SION_OBJS_F90_MPI) $(F90_MPI_LIBS) - @echo "*** $@ built" - - # F77 interface -@@ -206,7 +214,7 @@ - done - - clean: -- rm -f *.o lib*.a *.mod -+ rm -f *.o lib*.so *.mod - - #------------------------------------------------------------------------------ - # Dependencies ---- a/src/lib/Makefile -+++ b/src/lib/Makefile -@@ -66,26 +66,31 @@ - SION_CXX_HDR = sion_cxx.h - endif - --USER_HDRS = sion.h sion_common.h sion_serial.h sion_const.h sion_datatypes.h sion_platform.h sion_debug.h $(SION_CXX_HDR) --USER_LIBS = lib$(SION_LIBNAME_SER).a lib$(SION_LIBNAME_COM).a lib$(SION_LIBNAME_COM_LOCK_PTHREADS).a lib$(SION_LIBNAME_COM_LOCK_NONE).a -+ifneq ($(PTHREADSUPPORT),"no") -+LOCKLIB = $(SION_LIBNAME_COM_LOCK_PTHREADS) -+else -+LOCKLIB = $(SION_LIBNAME_COM_LOCK_NONE) -+endif - -+USER_HDRS = sion.h sion_common.h sion_serial.h sion_const.h sion_datatypes.h sion_platform.h sion_debug.h $(SION_CXX_HDR) -+USER_LIBS = lib$(SION_LIBNAME_SER).so lib$(SION_LIBNAME_COM).so lib$(SION_LIBNAME_COM_LOCK_PTHREADS).so lib$(SION_LIBNAME_COM_LOCK_NONE).so - --all: lib$(SION_LIBNAME_COM).a lib$(SION_LIBNAME_SER).a lib$(SION_LIBNAME_COM_LOCK_PTHREADS).a lib$(SION_LIBNAME_COM_LOCK_NONE).a -+all: lib$(SION_LIBNAME_COM).so lib$(SION_LIBNAME_SER).so lib$(SION_LIBNAME_COM_LOCK_PTHREADS).so lib$(SION_LIBNAME_COM_LOCK_NONE).so - --lib$(SION_LIBNAME_COM).a : $(SION_COMMON_OBJS) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_COMMON_OBJS) -+lib$(SION_LIBNAME_COM).so : $(SION_COMMON_OBJS) lib$(LOCKLIB).so -+ $(CC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_COM).so -shared -o $@ $(SION_COMMON_OBJS) $(SIONFWD_LIBS) -L. -l$(LOCKLIB) - @echo "*** $@ built" - --lib$(SION_LIBNAME_COM_LOCK_PTHREADS).a : $(SION_COMMON_LOCK_PTHREADS_OBJS) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_COMMON_LOCK_PTHREADS_OBJS) -+lib$(SION_LIBNAME_COM_LOCK_PTHREADS).so : $(SION_COMMON_LOCK_PTHREADS_OBJS) -+ $(CC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_COM_LOCK_PTHREADS).so -shared -o $@ $(SION_COMMON_LOCK_PTHREADS_OBJS) - @echo "*** $@ built" - --lib$(SION_LIBNAME_COM_LOCK_NONE).a : $(SION_COMMON_LOCK_NONE_OBJS) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_COMMON_LOCK_NONE_OBJS) -+lib$(SION_LIBNAME_COM_LOCK_NONE).so : $(SION_COMMON_LOCK_NONE_OBJS) -+ $(CC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_COM_LOCK_NONE).so -shared -o $@ $(SION_COMMON_LOCK_NONE_OBJS) - @echo "*** $@ built" - --lib$(SION_LIBNAME_SER).a : $(SION_SER_OBJS) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_SER_OBJS) -+lib$(SION_LIBNAME_SER).so : $(SION_SER_OBJS) lib$(SION_LIBNAME_COM).so -+ $(CC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_SER).so -shared -o $@ $(SION_SER_OBJS) -L. -l$(SION_LIBNAME_COM) - @echo "*** $@ built" - - sion_lock_pthreads.o: sion_lock.c -@@ -178,7 +183,7 @@ - done - - clean: -- rm -f *.o lib*.a -+ rm -f *.o lib*.so - - #------------------------------------------------------------------------------ - # Dependencies ---- a/src/parlib/Makefile -+++ b/src/parlib/Makefile -@@ -29,7 +29,7 @@ - .SUFFIXES: .cpp .c .f - - USER_HDRS = sion_datatypes_mpi.h sion_mpi.h sion_ompi.h sion_omp.h sion_generic.h --USER_LIBS = lib$(SION_LIBNAME_GEN).a -+USER_LIBS = lib$(SION_LIBNAME_GEN).so - - SION_OBJS_GEN = sion_generic.o \ - sion_generic_internal.o \ -@@ -46,7 +46,7 @@ - sion_omp_cb_gen.o \ - sion_omp_internal_gen.o - USER_HDRS += sion_omp.h -- USER_LIBS += lib$(SION_LIBNAME_OMP).a -+ USER_LIBS += lib$(SION_LIBNAME_OMP).so - endif - - ifeq ($(MPIENABLE),1) -@@ -58,7 +58,7 @@ - sion_mpi_util.o \ - sion_mpi_file_check.o - USER_HDRS += sion_datatypes_mpi.h sion_mpi.h -- USER_LIBS += lib$(SION_LIBNAME_MPI).a -+ USER_LIBS += lib$(SION_LIBNAME_MPI).so - endif - ifeq ($(HYBENABLE),1) - SION_OBJS_HYB = sion_ompi_gen.o \ -@@ -67,16 +67,18 @@ - sion_ompi_util.o \ - sion_ompi_internal_gen.o - USER_HDRS += sion_datatypes_mpi.h sion_ompi.h -- USER_LIBS += lib$(SION_LIBNAME_OMPI).a -+ USER_LIBS += lib$(SION_LIBNAME_OMPI).so - endif - - ifeq ($(HYBENABLE),1) - LOCKCC =$(HYBCC) - LOCKCFLAGS=$(CHYBFLAGS) -+ LOCKLINK=$(HYBFLAG) - else - ifeq ($(OMPENABLE),1) - LOCKCC =$(OMPCC) - LOCKCFLAGS=$(COMPFLAGS) -+ LOCKLINK=$(OMPFLAG) - else - LOCKCC =$(CC) - LOCKCFLAGS=$(CFLAGS) -@@ -87,20 +89,23 @@ - - all: $(USER_LIBS) - --lib$(SION_LIBNAME_GEN).a : $(SION_OBJS_GEN) $(SION_OBJS_INTERNAL) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_GEN) $(SION_OBJS_INTERNAL) -+../lib/lib$(SION_LIBNAME_COM).so : -+ make -C ../lib lib$(SION_LIBNAME_COM).so -+ -+lib$(SION_LIBNAME_GEN).so : $(SION_OBJS_GEN) $(SION_OBJS_INTERNAL) ../lib/lib$(SION_LIBNAME_COM).so -+ $(CC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_GEN).so -shared -o $@ $(SION_OBJS_GEN) $(SION_OBJS_INTERNAL) $(LOCKLINK) -L../lib -l$(SION_LIBNAME_COM) - @echo "*** $@ built" - --lib$(SION_LIBNAME_OMP).a : $(SION_OBJS_OMP) $(SION_OBJS_INTERNAL) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_OMP) $(SION_OBJS_INTERNAL) -+lib$(SION_LIBNAME_OMP).so : $(SION_OBJS_OMP) $(SION_OBJS_INTERNAL) ../lib/lib$(SION_LIBNAME_COM).so lib$(SION_LIBNAME_GEN).so -+ $(CC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_OMP).so -shared -o $@ $(SION_OBJS_OMP) $(SION_OBJS_INTERNAL) $(LOCKLINK) -L../lib -l$(SION_LIBNAME_COM) -L. -l$(SION_LIBNAME_GEN) $(OMPFLAG) - @echo "*** $@ built" - --lib$(SION_LIBNAME_MPI).a : $(SION_OBJS_MPI) $(SION_OBJS_INTERNAL) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_MPI) $(SION_OBJS_INTERNAL) -+lib$(SION_LIBNAME_MPI).so : $(SION_OBJS_MPI) $(SION_OBJS_INTERNAL) ../lib/lib$(SION_LIBNAME_COM).so lib$(SION_LIBNAME_GEN).so -+ $(MPICC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_MPI).so -shared -o $@ $(SION_OBJS_MPI) $(SION_OBJS_INTERNAL) $(LOCKLINK) -L../lib -l$(SION_LIBNAME_COM) -L. -l$(SION_LIBNAME_GEN) - @echo "*** $@ built" - --lib$(SION_LIBNAME_OMPI).a : $(SION_OBJS_HYB) $(SION_OBJS_INTERNAL) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_HYB) $(SION_OBJS_INTERNAL) -+lib$(SION_LIBNAME_OMPI).so : $(SION_OBJS_HYB) $(SION_OBJS_INTERNAL) ../lib/lib$(SION_LIBNAME_COM).so lib$(SION_LIBNAME_GEN).so -+ $(HYBCC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_OMPI).so -shared -o $@ $(SION_OBJS_HYB) $(SION_OBJS_INTERNAL) $(LOCKLINK) -L../lib -l$(SION_LIBNAME_COM) -L. -l$(SION_LIBNAME_GEN) $(HYBFLAG) - @echo "*** $@ built" - - sion_generic.o : sion_generic.c -@@ -224,7 +229,7 @@ - done - - clean: -- rm -f *.o lib*.a opari* -+ rm -f *.o lib*.so opari* - - #------------------------------------------------------------------------------ - # Dependencies ---- a/src/parutils/Makefile -+++ b/src/parutils/Makefile -@@ -30,12 +30,18 @@ - COMPFLAGS = $(OMPMFLAG) $(OMPFLAG) - CHYBFLAGS = $(HYBMFLAG) $(HYBFLAG) - --CMPILDFLAGS = $(LDFLAGS) -L../parlib -l$(SION_LIBNAME_MPI) -L../lib -l$(SION_LIBNAME_GEN) -L../lib -l$(SION_LIBNAME_COM) -l$(SION_LIBNAME_COM_LOCK_PTHREADS) $(HINTSLIB) $(CACHELIB) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) -+ifneq ($(PTHREADSUPPORT),"no") -+LOCKLIB = $(SION_LIBNAME_COM_LOCK_PTHREADS) -+else -+LOCKLIB = $(SION_LIBNAME_COM_LOCK_NONE) -+endif -+ -+CMPILDFLAGS = $(LDFLAGS) -L../lib -l$(LOCKLIB) -L../lib -l$(SION_LIBNAME_COM) -L../parlib -l$(SION_LIBNAME_GEN) -L../parlib -l$(SION_LIBNAME_MPI) $(HINTSLIB) $(CACHELIB) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) - --COMPLDFLAGS = $(LDFLAGS) -L../parlib -l$(SION_LIBNAME_OMP) -L../lib -l$(SION_LIBNAME_COM) -l$(SION_LIBNAME_COM_LOCK_PTHREADS) $(HINTSLIB) $(CACHELIB) $(OMPFLAG) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) --CHYBLDFLAGS = $(LDFLAGS) -L../parlib -l$(SION_LIBNAME_OMPI) -L../lib -l$(SION_LIBNAME_GEN) -L../lib -l$(SION_LIBNAME_COM) -l$(SION_LIBNAME_COM_LOCK_PTHREADS) $(HINTSLIB) $(CACHELIB) $(OMPFLAG) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) -+COMPLDFLAGS = $(LDFLAGS) -L../lib -l$(LOCKLIB) -L../lib -l$(SION_LIBNAME_COM) -L../parlib -l$(SION_LIBNAME_OMP) $(HINTSLIB) $(CACHELIB) $(OMPFLAG) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) -+CHYBLDFLAGS = $(LDFLAGS) -L../lib -l$(LOCKLIB) -L../lib -l$(SION_LIBNAME_COM) -L../parlib -l$(SION_LIBNAME_GEN) -L../parlib -l$(SION_LIBNAME_OMPI) $(HINTSLIB) $(CACHELIB) $(OMPFLAG) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) - --FMPILDFLAGS = $(LDFLAGS) -L../parlib -l$(SION_LIBNAME_MPI) -L../lib -l$(SION_LIBNAME_GEN) -L../lib -l$(SION_LIBNAME_SER) -l$(SION_LIBNAME_COM) -l$(SION_LIBNAME_COM_LOCK_PTHREADS) $(HINTSLIB) $(CACHELIB) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) -+FMPILDFLAGS = $(LDFLAGS) -L../lib -l$(LOCKLIB) -L../lib -l$(SION_LIBNAME_COM) -L../lib -l$(SION_LIBNAME_SER) -L../parlib -l$(SION_LIBNAME_GEN) -L../parlib -l$(SION_LIBNAME_MPI) $(HINTSLIB) $(CACHELIB) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) - FOMPLDFLAGS = $(COMPLDFLAGS) $(OMPFLAG) - FHYBLDFLAGS = $(COMPILDFLAGS) $(OMPFLAG) - -@@ -55,6 +61,13 @@ - ifeq ($(FORTRANENABLE),1) - ifeq ($(MPIENABLE),1) - USER_UTILS += fpartest -+ F77_MPI_LIBS = -L../parlib -l$(SION_LIBNAME_MPI) -+ endif -+ ifeq ($(OMPENABLE),1) -+ F77_SER_LIBS = $(OMPFLAG) -L../parlib -l$(SION_LIBNAME_OMP) -+ endif -+ ifeq ($(HYBENABLE),1) -+ F77_MPI_LIBS = $(HYBFLAG) -L../parlib -l$(SION_LIBNAME_OMPI) - endif - endif - -@@ -75,10 +88,10 @@ - - all: $(USER_UTILS) - --partest: $(PARTEST_OBJS) ../parlib/lib$(SION_LIBNAME_MPI).a ../parlib/lib$(SION_LIBNAME_GEN).a ../lib/lib$(SION_LIBNAME_SER).a -+partest: $(PARTEST_OBJS) ../parlib/lib$(SION_LIBNAME_MPI).so ../parlib/lib$(SION_LIBNAME_GEN).so ../lib/lib$(SION_LIBNAME_SER).so - $(MPICC) -o $@ $(PARTEST_OBJS) -L../lib -l$(SION_LIBNAME_SER) $(CMPILDFLAGS) $(MPILIB) - --ompi_partest: $(PARTEST_OMPI_OBJS) ../parlib/lib$(SION_LIBNAME_OMPI).a ../parlib/lib$(SION_LIBNAME_OMP).a ../lib/lib$(SION_LIBNAME_SER).a -+ompi_partest: $(PARTEST_OMPI_OBJS) ../parlib/lib$(SION_LIBNAME_OMPI).so ../parlib/lib$(SION_LIBNAME_OMP).so ../lib/lib$(SION_LIBNAME_SER).so - $(HYBCC) -o $@ $(PARTEST_OMPI_OBJS) $(CHYBLDFLAGS) -L../parlib -l$(SION_LIBNAME_OMP) -L../lib -l$(SION_LIBNAME_SER) $(MPILIB) - - ompi_partest.o : ompi_partest.c -@@ -114,8 +127,8 @@ - fpartest.o : fpartest.F90 - $(MPIF90) $(FFLAGS) -c fpartest.F90 - --fpartest: fpartest.o ../parlib/lib$(SION_LIBNAME_MPI).a ../parlib/lib$(SION_LIBNAME_GEN).a ../lib/lib$(SION_LIBNAME_SER).a ../fortraninterface/lib$(SION_LIBNAME_F77_MPI).a ../fortraninterface/lib$(SION_LIBNAME_F77_SER).a -- $(MPIF90) -o $@ fpartest.o -L../fortraninterface -l$(SION_LIBNAME_F77_MPI) -l$(SION_LIBNAME_F77_SER) $(FMPILDFLAGS) $(MPILIB) -+fpartest: fpartest.o ../parlib/lib$(SION_LIBNAME_MPI).so ../parlib/lib$(SION_LIBNAME_GEN).so ../lib/lib$(SION_LIBNAME_SER).so ../fortraninterface/lib$(SION_LIBNAME_F77_MPI).so ../fortraninterface/lib$(SION_LIBNAME_F77_SER).so -+ $(MPIF90) -o $@ fpartest.o -L../fortraninterface -l$(SION_LIBNAME_F77_MPI) -l$(SION_LIBNAME_F77_SER) $(FMPILDFLAGS) $(MPILIB) $(F77_MPI_LIBS) $(F77_SER_LIBS) - - - install: all -@@ -161,7 +174,7 @@ - @rm -f header.tmp - - clean: -- rm -f *.o lib*.a $(USER_UTILS) -+ rm -f *.o lib*.so $(USER_UTILS) - - #------------------------------------------------------------------------------ - # Dependencies ---- a/src/utils/Makefile -+++ b/src/utils/Makefile -@@ -45,32 +45,32 @@ - siondump.o : siondump.c - $(CC) $(CFLAGS) -c siondump.c - --siondefrag.o : siondefrag.c ../lib/lib$(SION_LIBNAME_SER).a -+siondefrag.o : siondefrag.c ../lib/lib$(SION_LIBNAME_SER).so - $(CC) $(CFLAGS) -c siondefrag.c - --sionsplit.o : sionsplit.c ../lib/lib$(SION_LIBNAME_SER).a -+sionsplit.o : sionsplit.c ../lib/lib$(SION_LIBNAME_SER).so - $(CC) $(CFLAGS) -c sionsplit.c - --sioncat.o : sioncat.c ../lib/lib$(SION_LIBNAME_SER).a -+sioncat.o : sioncat.c ../lib/lib$(SION_LIBNAME_SER).so - $(CC) $(CFLAGS) -c sioncat.c - --sionversion.o : sionversion.c ../lib/lib$(SION_LIBNAME_SER).a -+sionversion.o : sionversion.c ../lib/lib$(SION_LIBNAME_SER).so - $(CC) $(CFLAGS) -c sionversion.c - --siondump: siondump.o ../lib/lib$(SION_LIBNAME_SER).a ../lib/lib$(SION_LIBNAME_COM).a ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).a -+siondump: siondump.o ../lib/lib$(SION_LIBNAME_SER).so ../lib/lib$(SION_LIBNAME_COM).so ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).so - $(CC) -o $@ siondump.o $(LDFLAGS) - cp siondump $(TOPDIR)/.. - --siondefrag: siondefrag.o ../lib/lib$(SION_LIBNAME_SER).a ../lib/lib$(SION_LIBNAME_COM).a ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).a -+siondefrag: siondefrag.o ../lib/lib$(SION_LIBNAME_SER).so ../lib/lib$(SION_LIBNAME_COM).so ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).so - $(CC) -o $@ siondefrag.o $(LDFLAGS) - --sionsplit: sionsplit.o ../lib/lib$(SION_LIBNAME_SER).a ../lib/lib$(SION_LIBNAME_COM).a ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).a -+sionsplit: sionsplit.o ../lib/lib$(SION_LIBNAME_SER).so ../lib/lib$(SION_LIBNAME_COM).so ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).so - $(CC) -o $@ sionsplit.o $(LDFLAGS) - --sioncat: sioncat.o ../lib/lib$(SION_LIBNAME_SER).a ../lib/lib$(SION_LIBNAME_COM).a ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).a -+sioncat: sioncat.o ../lib/lib$(SION_LIBNAME_SER).so ../lib/lib$(SION_LIBNAME_COM).so ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).so - $(CC) -o $@ sioncat.o $(LDFLAGS) - --sionversion: sionversion.o ../lib/lib$(SION_LIBNAME_SER).a ../lib/lib$(SION_LIBNAME_COM).a ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).a -+sionversion: sionversion.o ../lib/lib$(SION_LIBNAME_SER).so ../lib/lib$(SION_LIBNAME_COM).so ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).so - $(CC) -o $@ sionversion.o $(LDFLAGS) - - -@@ -136,7 +136,7 @@ - @rm -f header.tmp - - clean: -- rm -f *.o lib*.a $(USER_UTILS) -+ rm -f *.o lib*.so $(USER_UTILS) - - #------------------------------------------------------------------------------ - # Dependencies diff --git a/sys-cluster/sionlib/files/sionlib-respect-flags-v3.patch b/sys-cluster/sionlib/files/sionlib-respect-flags-v3.patch deleted file mode 100644 index e71d7d46d..000000000 --- a/sys-cluster/sionlib/files/sionlib-respect-flags-v3.patch +++ /dev/null @@ -1,185 +0,0 @@ ---- a/config/determine-cc.sh -+++ b/config/determine-cc.sh -@@ -1,7 +1,6 @@ - #!/bin/sh - # determine what compiler is behind "cc" (and presumably "CC" and "ftn") wrapper - --CC=`which cc 2>/dev/null` - COMP= - if [ -z "$CC" ]; then - echo "No 'cc' located!" ---- a/config/determine-compiler-version.sh -+++ b/config/determine-compiler-version.sh -@@ -24,8 +24,8 @@ - | cut -d\ -f 1` - COMPVER="${CVER}/${FVER}" - ;; -- gnu) COMPVER=`gcc -dumpfullversion -dumpversion` -- #COMPVER=`gcc -v 2>&1 | grep -i 'Version [0-9]' \ -+ gnu) COMPVER=`${CC} -dumpfullversion -dumpversion` -+ #COMPVER=`${CC} -v 2>&1 | grep -i 'Version [0-9]' \ - # | sed -e 's/^.*ersion \(.\..\..\).*$/\1/'` - ;; - *) ErrorAndExit "Unknown compiler '${COMP}'" ---- a/config/select-compiler.sh -+++ b/config/select-compiler.sh -@@ -9,7 +9,7 @@ - CPS="" - COMP="" - --GNU=`which gcc 2> /dev/null` -+GNU="${CC}" - if [ -n "${GNU}" ] - then - NCPS=`expr ${NCPS} + 1` ---- a/config/select-mpi.sh -+++ b/config/select-mpi.sh -@@ -76,7 +76,6 @@ - if [ -z "${MPIS}" ]; then MPIS="${MPI}"; else MPIS="${MPIS}|${MPI}"; fi - fi - --MPICC=`which mpicc 2> /dev/null` - if [ -n "${MPICC}" ] - then - FMPI="" -@@ -86,7 +85,7 @@ - MPIROOTDIR1=`dirname ${MBINDIR}` - - echo "#include <mpi.h>" > conftest.c -- mpicc -E conftest.c | grep '/mpi.h"' | head -1 > mpiconf.txt -+ "${MPICC}" -E conftest.c | grep '/mpi.h"' | head -1 > mpiconf.txt - MINCDIR=`cat mpiconf.txt | sed -e 's#^.* "##' -e 's#/mpi.h".*##'` - if [ -n "${MINCDIR}" ] - then ---- a/mf/Makefile.defs.linux-gomp -+++ b/mf/Makefile.defs.linux-gomp -@@ -23,24 +23,19 @@ - #------------------------------------------------------------------------------ - # SIONlib General Settings - #------------------------------------------------------------------------------ --OPTFLAGS = -g -O0 -Wall -+CFLAGS += -std=c99 $(PFLAG) $(OPTFLAGS) -fPIC - --CC = gcc --CFLAGS = -std=c99 $(PFLAG) $(OPTFLAGS) -fPIC -+CXXFLAGS += $(PFLAG) $(OPTFLAGS) -fPIC - --CXX = g++ --CXXFLAGS = $(PFLAG) $(OPTFLAGS) -O3 -- --F77 = gfortran --FFLAGS = $(PFLAG) $(OPTFLAGS) -+FFLAGS += $(PFLAG) $(OPTFLAGS) -fPIC - - F90 = $(F77) --F90FLAGS = $(PFLAG) $(OPTFLAGS) -ffree-form -+F90FLAGS += $(PFLAG) $(OPTFLAGS) -ffree-form -fPIC $(FCFLAGS) - - FPP = - FDOPT = -D - --LDFLAGS = $(PFLAG) $(OPTFLAGS) $(HINTSLIB) -+LDFLAGS += $(PFLAG) $(OPTFLAGS) $(HINTSLIB) - UTILLIB = - FOBASE = pomp_fwrapper_base.o - -@@ -101,10 +96,6 @@ - #------------------------------------------------------------------------------ - - MPIENABLE = 1 --MPICC = mpicc --MPICXX = mpicxx --MPIF77 = mpif77 --MPIF90 = mpif90 - MPILIB = -lmpich - PMPILIB = -lpmpich - #PMPILIB = # MPICH2 -@@ -139,8 +130,7 @@ - #------------------------------------------------------------------------------ - - SZLIB = szlib --SZLIB_OPTFLAGS = -O3 --SZLIB_CFLAGS = -I$(TOPDIR)/utils/szlib -DELG_COMPRESSED -DCUBE_COMPRESSED -+SZLIB_CFLAGS = -I$(TOPDIR)/utils/szlib -DELG_COMPRESSED -DCUBE_COMPRESSED $(CFLAGS) - SZLIB_LIBPATH = -L$(TOPDIR)/utils/szlib - SZLIB_LIB = -lsc.z - ---- a/mf/Makefile.defs.linux-gomp10 -+++ b/mf/Makefile.defs.linux-gomp10 -@@ -23,24 +23,19 @@ - #------------------------------------------------------------------------------ - # SIONlib General Settings - #------------------------------------------------------------------------------ --OPTFLAGS = -g -O0 -Wall -+CFLAGS += -std=c99 $(PFLAG) -fPIC - --CC = gcc --CFLAGS = -std=c99 $(PFLAG) $(OPTFLAGS) -fPIC -+CXXFLAGS += $(PFLAG) -fPIC - --CXX = g++ --CXXFLAGS = $(PFLAG) $(OPTFLAGS) -O3 -- --F77 = gfortran --FFLAGS = $(PFLAG) $(OPTFLAGS) -fallow-argument-mismatch -+FFLAGS += $(PFLAG) -fallow-argument-mismatch -fPIC - - F90 = $(F77) --F90FLAGS = $(PFLAG) $(OPTFLAGS) -ffree-form -fallow-argument-mismatch -+F90FLAGS += $(PFLAG) -ffree-form -fallow-argument-mismatch -fPIC $(FCFLAGS) - - FPP = - FDOPT = -D - --LDFLAGS = $(PFLAG) $(OPTFLAGS) $(HINTSLIB) -+LDFLAGS += $(PFLAG) $(HINTSLIB) - UTILLIB = - FOBASE = pomp_fwrapper_base.o - -@@ -101,10 +96,6 @@ - #------------------------------------------------------------------------------ - - MPIENABLE = 1 --MPICC = mpicc --MPICXX = mpicxx --MPIF77 = mpif77 --MPIF90 = mpif90 - MPILIB = -lmpich - PMPILIB = -lpmpich - #PMPILIB = # MPICH2 -@@ -139,7 +130,7 @@ - #------------------------------------------------------------------------------ - - SZLIB = szlib --SZLIB_OPTFLAGS = -O3 -+SZLIB_OPTFLAGS = $(CFLAGS) - SZLIB_CFLAGS = -I$(TOPDIR)/utils/szlib -DELG_COMPRESSED -DCUBE_COMPRESSED - SZLIB_LIBPATH = -L$(TOPDIR)/utils/szlib - SZLIB_LIB = -lsc.z ---- a/src/fortraninterface/Makefile -+++ b/src/fortraninterface/Makefile -@@ -121,21 +121,21 @@ - $(CPP) $(F90FLAGS) $(F90FLAGS_CPP) $(F90MPIFLAGS) -P -E -I ../lib sion_f90_mpi.F90 > sion_f90_mpi.f90 - sion_f90_mpi.mod : sion_f90_mpi.o - sion_f90_mpi.o : sion_f90_mpi.f90 sion_f90.mod $(SION_HDRS) -- $(MPIF90) $(F90FLAGS) -c sion_f90_mpi.f90 -+ $(MPIF90) $(F90FLAGS) $(F90MPIFLAGS) -c sion_f90_mpi.f90 - - # F90 Interface (OMP) - sion_f90_omp.f90: sion_f90_omp.F90 - $(CPP) $(F90OMPFLAGS) $(F90FLAGS) $(F90FLAGS_CPP) -P -E -I ../lib sion_f90_omp.F90 > sion_f90_omp.f90 - sion_f90_omp.mod : sion_f90_omp.o - sion_f90_omp.o : sion_f90_omp.f90 sion_f90.mod $(SION_HDRS) -- $(OMPF90) $(F90FLAGS) -c sion_f90_omp.f90 -+ $(OMPF90) $(F90FLAGS) $(F90OMPFLAGS) -c sion_f90_omp.f90 - - # F90 Interface (OMPI) - sion_f90_ompi.f90: sion_f90_ompi.F90 $(SION_HDRS) - $(CPP) $(F90MPIFLAGS) $(F90OMPFLAGS) $(F90FLAGS) $(F90FLAGS_CPP) -P -E -I ../lib sion_f90_ompi.F90 > sion_f90_ompi.f90 - sion_f90_ompi.mod : sion_f90_ompi.o - sion_f90_ompi.o : sion_f90_ompi.f90 $(SION_HDRS) -- $(MPIF90) $(F90FLAGS) -c sion_f90_ompi.f90 -+ $(MPIF90) $(F90FLAGS) $(F90MPIFLAGS) -c sion_f90_ompi.f90 - - - diff --git a/sys-cluster/sionlib/metadata.xml b/sys-cluster/sionlib/metadata.xml deleted file mode 100644 index 52da79403..000000000 --- a/sys-cluster/sionlib/metadata.xml +++ /dev/null @@ -1,39 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <longdescription lang="en"> -SIONlib is a library for writing and reading data from several thousands of parallel tasks into/from one or a small number of physical files. Only the open and close functions are collective while file access can be performed independently. - -SIONlib can be used as a replacement for standard I/O APIs (e.g. POSIX) that are used to access distinct files from every parallel process. SIONlib will bundle the data into one or few files in a coordinated fashion in order to sidestep sequentialising mechanism in the file system. At the same time, the task-per-file picture is maintained for the application, every process has access to its logical file only. File access is performed using SIONlib equivalents to standard C-I/O functionality (fwrite becomes sion_write, fseek becomes sion_seek, etc.) which have similar semantics as their C counterparts. - -Internally, the physical files are sub-divided into sequences of blocks, which themselves contain one chunk of data belonging to every logical file. In case the amount to be written to a file is known up front, it can optionally be specified when opening the file and the sequence of blocks collapses into a single block with one chunk per task containing all of its data. If a chunk size cannot be specified ahead of time, a sensible default is chosen and reads and writes that cross chunk boundaries are handled transparently by SIONlib. - -SIONlib also uses information about the block size of the underlying file system, because access to the same block from different tasks often leads to contention. - -Both, the estimated chunk size and file system block size are used to align individual chunks with file system blocks. Ensuring contention-free access to file system blocks enables efficient parallel writing and reading. - -SIONlib provides two different interfaces: one for parallel access (with implementations for different parallel programming technologies such as MPI, OpenMP and hybrid MPI+OpenMP) and one for sequential access which is also used internally by the SIONlib utilities. - </longdescription> - <upstream> - <bugs-to>https://gitlab.jsc.fz-juelich.de/cstao-public/SIONlib/SIONlib/-/issues</bugs-to> - </upstream> - <use> - <!--<flag name="cuda">enable CUDA aware interface</flag>--> - <flag name="cxx">Enable C++ support</flag> - <flag name="debug">enable SIONlib debug</flag> - <flag name="deep-est-sdv">deep-est-sdv collector selection plug-in for MSA-aware collective I/O</flag> - <flag name="fortran">Enable Fortran support</flag> - <flag name="hostname-regex">hostname-regex collector selection plug-in for MSA-aware collective I/O</flag> - <flag name="mpi">enable mpi</flag> - <flag name="python">enable python support</flag> - <flag name="ompi">enable hybrid openmp mpi</flag> - <flag name="openmp">enable openmp</flag> - <flag name="parutils">Enable compilation of parutils (used for benchmarking)</flag> - <flag name="pthreads">configure SIONlib to use pthreads for locking</flag> - <flag name="sionfwd">enable I/O forwarding with <pkg>sys-cluster/SIONfwd</pkg></flag> - </use> -</pkgmetadata> diff --git a/sys-cluster/sionlib/sionlib-1.7.7-r4.ebuild b/sys-cluster/sionlib/sionlib-1.7.7-r4.ebuild deleted file mode 100644 index 73fa9c89d..000000000 --- a/sys-cluster/sionlib/sionlib-1.7.7-r4.ebuild +++ /dev/null @@ -1,150 +0,0 @@ -# Copyright 2019-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DOCS_BUILDER="doxygen" -DOCS_CONFIG_NAME="doxy" -FORTRAN_NEEDED="fortran" -PYTHON_COMPAT=( pypy3 python3_{10..11} ) - -inherit docs edo flag-o-matic fortran-2 python-any-r1 toolchain-funcs - -DESCRIPTION="Scalable I/O library for parallel access to task-local files" -HOMEPAGE="https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html" -SRC_URI="http://apps.fz-juelich.de/jsc/sionlib/download.php?version=${PV} -> ${P}.tar.gz" -S="${WORKDIR}/${PN}" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" -IUSE="+cxx debug deep-est-sdv doc examples +fortran hostname-regex +mpi +ompi +openmp +parutils +pthreads python sionfwd" #cuda - -RDEPEND=" - mpi? ( virtual/mpi ) - openmp? ( || ( sys-devel/gcc:*[openmp] sys-libs/libomp ) ) - sionfwd? ( sys-cluster/SIONfwd ) -" -DEPEND=" - ${RDEPEND} - ${PYTHON_DEPS} -" - -REQUIRED_USE=" - ompi? ( mpi openmp ) - ?? ( hostname-regex deep-est-sdv ) -" -PATCHES=( - "${FILESDIR}/${PN}-respect-flags-v3.patch" - "${FILESDIR}/${PN}-build-shared-libraries.patch" -) - -pkg_setup() { - FORTRAN_NEED_OPENMP=0 - use openmp && FORTRAN_NEED_OPENMP=1 - - fortran-2_pkg_setup -} - -src_configure() { - tc-export AR CC CXX F77 FC - export MPICC=/usr/bin/mpicc - export MPICXX=/usr/bin/mpicxx - export MPIF77=/usr/bin/mpif77 - export MPIF90=/usr/bin/mpif90 - export F90=$(tc-getFC) - export OMPF77=$(tc-getF77) - export OMPF90=$(tc-getFC) - - append-fflags -fallow-argument-mismatch - - local msa="none" - use deep-est-sdv && msa="deep-est-sdv" - use hostname-regex && msa="hostname-regex" - - local myconf=( - --disable-gcovr - --disable-kcov - --disable-mic - --msa="${msa}" - --prefix="${T}/prefix/usr" - $(use_enable debug) - $(use_enable pthreads) - ) - - #custom configure? - use cxx || myconf+=( "--disable-cxx" ) - use fortran || myconf+=( "--disable-fortran" ) - if use mpi; then - myconf+=( "--mpi=$(detect_mpi_implementation || die)" ) - else - myconf+=( "--disable-mpi" ) - fi - use ompi || myconf+=( "--disable-ompi" ) - use openmp || myconf+=( "--disable-omp" ) - use parutils || myconf+=( "--disable-parutils" ) - - use python && myconf+=( "--enable-python=3" ) - use sionfwd && myconf+=( "--enable-sionfwd=${EPREFIX}/usr" ) - - ./configure "${myconf[@]}" || die -} - -src_compile() { - export VARTEXFONTS="${T}/fonts" - emake C_AR=$(tc-getAR) F90=$(tc-getFC) - docs_compile -} - -src_install() { - mkdir -p "${T}/prefix/usr/share/doc/${PF}" || die - default - - if use examples ; then - mv "${T}/prefix/usr/examples" "${T}/prefix/usr/share/doc/${PF}/" || die - else - rm -r "${T}/prefix/usr/examples" || die - fi - - insinto "/usr/include/sionlib" - doins -r "${T}"/prefix/usr/include/* - rm -r "${T}/prefix/usr/include" || die - - exeinto "/usr/libexec/${PN}" - doexe "${T}"/prefix/usr/bin/*partest - rm "${T}"/prefix/usr/bin/*partest || die - - # move 64 bit libraries to lib64 - libs64=( "${T}"/prefix/usr/lib/*64* ) - if [[ ${#libs64[@]} -gt 0 ]]; then - mkdir "${T}/prefix/usr/lib64" || die - for l in "${libs64[@]}" ; do - mv "${l}" "${T}/prefix/usr/lib64/" || die - done - fi - - rsync -ravXHA "${T}/prefix/usr" "${ED}/" || die - docompress -x "/usr/share/doc/${PF}/examples" - - find "${ED}" -name '*.la' -delete || die -} - -detect_mpi_implementation() { - cat > testmpi.c <<- EOF -#include "mpi.h" -#include "stdio.h" - -int main(){ - #ifdef OPEN_MPI - printf("%s","openmpi"); - #endif - - #ifdef MPICH - printf("%s%i","mpich",MPICH_NAME); - #endif - return 0; -} -EOF - edo ${CC} testmpi.c -o testmpi - ./testmpi || die -} diff --git a/sys-cluster/sionlibl/Manifest b/sys-cluster/sionlibl/Manifest deleted file mode 100644 index a16495014..000000000 --- a/sys-cluster/sionlibl/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST sionlibll-1.7.7.tar.gz 490515 BLAKE2B 76971dd6d80222144b40da345d58311911aab09c6a5250b85d4a2731d2f93cdbd39d87dd6bbafdeaba88f06603105076267f6956417916f118ec45e07fa59269 SHA512 6ef46a0905552c558595bf6b72225a290d73dc87fa33c9862de5e4bd4d683792437646f7b4ab8a463b4a50d1b4a79aec96a66e577e815de3f23e9274be2681af diff --git a/sys-cluster/sionlibl/files/sionlibl-build-shared-libraries.patch b/sys-cluster/sionlibl/files/sionlibl-build-shared-libraries.patch deleted file mode 100644 index d40276d6e..000000000 --- a/sys-cluster/sionlibl/files/sionlibl-build-shared-libraries.patch +++ /dev/null @@ -1,385 +0,0 @@ ---- a/src/cppinterface/Makefile -+++ b/src/cppinterface/Makefile -@@ -30,7 +30,7 @@ - ifeq ($(CXXENABLE),1) - - USER_HDRS = sion_cxx_base.hpp sion_cxx_serial.hpp sion_cxx_common.hpp sion_cxx_mpi.hpp sion_cxx_ompi.hpp sion_cxx_omp.hpp --USER_LIBS = lib$(SION_LIBNAME_CXX_SER).a lib$(SION_LIBNAME_CXX_MPI).a -+USER_LIBS = lib$(SION_LIBNAME_CXX_SER).so lib$(SION_LIBNAME_CXX_MPI).so - else - USER_HDRS = - USER_LIBS = -@@ -57,13 +57,15 @@ - - all: $(USER_LIBS) - -+../lib/lib$(SION_LIBNAME_SER).so : -+ make -C ../lib lib$(SION_LIBNAME_SER).so - --lib$(SION_LIBNAME_CXX_SER).a : $(SION_OBJS_SER) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_SER) -+lib$(SION_LIBNAME_CXX_SER).so : $(SION_OBJS_SER) ../lib/lib$(SION_LIBNAME_SER).so -+ $(CXX) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_CXX_SER).so -shared -o $@ $(SION_OBJS_SER) -L../lib -l$(SION_LIBNAME_SER) - @echo "*** $@ built" - --lib$(SION_LIBNAME_CXX_MPI).a : $(SION_OBJS_MPI) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_MPI) -+lib$(SION_LIBNAME_CXX_MPI).so : $(SION_OBJS_MPI) -+ $(MPICXX) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_CXX_MPI).so -shared -o $@ $(SION_OBJS_MPI) - @echo "*** $@ built" - - sion_cxx_base.o : -@@ -118,7 +120,7 @@ - done - - clean: -- rm -f *.o lib*.a -+ rm -f *.o lib*.so - - #------------------------------------------------------------------------------ - # Dependencies ---- a/src/fortraninterface/Makefile -+++ b/src/fortraninterface/Makefile -@@ -39,7 +39,7 @@ - - USER_HDRS = sion_f77.H sion_f77.h - USER_MODS = sion_f90.mod --USER_LIBS = lib$(SION_LIBNAME_F77_SER).a lib$(SION_LIBNAME_F77_MPI).a lib$(SION_LIBNAME_F90_SER).a lib$(SION_LIBNAME_F90_MPI).a -+USER_LIBS = lib$(SION_LIBNAME_F77_SER).so lib$(SION_LIBNAME_F77_MPI).so lib$(SION_LIBNAME_F90_SER).so lib$(SION_LIBNAME_F90_MPI).so - else - USER_HDRS = - USER_MODS = -@@ -56,39 +56,47 @@ - SION_OBJS_F77_SER += sion_f77_omp.o sion_fortran_omp.o - SION_OBJS_F90_SER += sion_f90_omp.o sion_fortran_omp.o - USER_MODS += sion_f90_omp.mod -+ F77_SER_LIBS = $(OMPFLAG) -L../parlib -l$(SION_LIBNAME_OMP) -L../lib -l$(SION_LIBNAME_GEN) -+ F90_SER_LIBS = $(OMPFLAG) -L../parlib -l$(SION_LIBNAME_OMP) -L../lib -l$(SION_LIBNAME_GEN) - endif - - ifeq ($(MPIENABLE),1) - SION_OBJS_F77_MPI += sion_f77_mpi.o sion_fortran_mpi.o sion_fortran_writeread_mpi_f77.o - SION_OBJS_F90_MPI += sion_f90_mpi.o sion_fortran_mpi.o sion_fortran_writeread_mpi_f90.o - USER_MODS += sion_f90_mpi.mod -+ F77_MPI_LIBS = -L../parlib -l$(SION_LIBNAME_MPI) -+ F90_MPI_LIBS = -L../parlib -l$(SION_LIBNAME_MPI) - endif - - ifeq ($(HYBENABLE),1) - SION_OBJS_F77_MPI += sion_f77_ompi.o sion_fortran_ompi.o - SION_OBJS_F90_MPI += sion_f90_ompi.o sion_fortran_ompi.o - USER_MODS += sion_f90_ompi.mod -+ F77_MPI_LIBS = $(HYBFLAG) -L../parlib -l$(SION_LIBNAME_OMPI) -+ F90_MPI_LIBS = $(HYBFLAG) -L../parlib -l$(SION_LIBNAME_OMPI) - endif - - SION_DEPEND_OBJS=sion_fortran.o sion_fortran_omp.o sion_fortran_mpi.o sion_fortran_ompi.o sion_fortran_writeread_f77.o sion_fortran_writeread_f90.o sion_fortran_writeread_mpi_f77.o sion_fortran_writeread_mpi_f90.o - - all: $(USER_LIBS) $(USER_MODS) - -+../lib/lib$(SION_LIBNAME_SER).so : -+ make -C ../lib lib$(SION_LIBNAME_SER).so - --lib$(SION_LIBNAME_F77_SER).a : $(SION_OBJS_F77_SER) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_F77_SER) -+lib$(SION_LIBNAME_F77_SER).so : $(SION_OBJS_F77_SER) ../lib/lib$(SION_LIBNAME_SER).so -+ $(F77) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_F77_SER).so -shared -o $@ $(SION_OBJS_F77_SER) $(F77_SER_LIBS) - @echo "*** $@ built" - --lib$(SION_LIBNAME_F77_MPI).a : $(SION_OBJS_F77_MPI) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_F77_MPI) -+lib$(SION_LIBNAME_F77_MPI).so : $(SION_OBJS_F77_MPI) -+ $(MPIF77) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_F77_MPI).so -shared -o $@ $(SION_OBJS_F77_MPI) $(F77_MPI_LIBS) - @echo "*** $@ built" - --lib$(SION_LIBNAME_F90_SER).a : $(SION_OBJS_F90_SER) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_F90_SER) -+lib$(SION_LIBNAME_F90_SER).so : $(SION_OBJS_F90_SER) ../lib/lib$(SION_LIBNAME_SER).so -+ $(F90) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_F90_SER).so -shared -o $@ $(SION_OBJS_F90_SER) $(F90_SER_LIBS) - @echo "*** $@ built" - --lib$(SION_LIBNAME_F90_MPI).a : $(SION_OBJS_F90_MPI) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_F90_MPI) -+lib$(SION_LIBNAME_F90_MPI).so : $(SION_OBJS_F90_MPI) -+ $(MPIF90) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_F90_MPI).so -shared -o $@ $(SION_OBJS_F90_MPI) $(F90_MPI_LIBS) - @echo "*** $@ built" - - # F77 interface -@@ -206,7 +214,7 @@ - done - - clean: -- rm -f *.o lib*.a *.mod -+ rm -f *.o lib*.so *.mod - - #------------------------------------------------------------------------------ - # Dependencies ---- a/src/lib/Makefile -+++ b/src/lib/Makefile -@@ -66,26 +66,31 @@ - SION_CXX_HDR = sion_cxx.h - endif - --USER_HDRS = sion.h sion_libversion_rep.h sion_common.h sion_serial.h sion_const.h sion_datatypes.h sion_platform.h sion_debug.h $(SION_CXX_HDR) --USER_LIBS = lib$(SION_LIBNAME_SER).a lib$(SION_LIBNAME_COM).a lib$(SION_LIBNAME_COM_LOCK_PTHREADS).a lib$(SION_LIBNAME_COM_LOCK_NONE).a -+ifneq ($(PTHREADSUPPORT),"no") -+LOCKLIB = $(SION_LIBNAME_COM_LOCK_PTHREADS) -+else -+LOCKLIB = $(SION_LIBNAME_COM_LOCK_NONE) -+endif - -+USER_HDRS = sion.h sion_libversion_rep.h sion_common.h sion_serial.h sion_const.h sion_datatypes.h sion_platform.h sion_debug.h $(SION_CXX_HDR) -+USER_LIBS = lib$(SION_LIBNAME_SER).so lib$(SION_LIBNAME_COM).so lib$(SION_LIBNAME_COM_LOCK_PTHREADS).so lib$(SION_LIBNAME_COM_LOCK_NONE).so - --all: lib$(SION_LIBNAME_COM).a lib$(SION_LIBNAME_SER).a lib$(SION_LIBNAME_COM_LOCK_PTHREADS).a lib$(SION_LIBNAME_COM_LOCK_NONE).a -+all: lib$(SION_LIBNAME_COM).so lib$(SION_LIBNAME_SER).so lib$(SION_LIBNAME_COM_LOCK_PTHREADS).so lib$(SION_LIBNAME_COM_LOCK_NONE).so - --lib$(SION_LIBNAME_COM).a : $(SION_COMMON_OBJS) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_COMMON_OBJS) -+lib$(SION_LIBNAME_COM).so : $(SION_COMMON_OBJS) lib$(LOCKLIB).so -+ $(CC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_COM).so -shared -o $@ $(SION_COMMON_OBJS) $(SIONFWD_LIBS) -L. -l$(LOCKLIB) - @echo "*** $@ built" - --lib$(SION_LIBNAME_COM_LOCK_PTHREADS).a : $(SION_COMMON_LOCK_PTHREADS_OBJS) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_COMMON_LOCK_PTHREADS_OBJS) -+lib$(SION_LIBNAME_COM_LOCK_PTHREADS).so : $(SION_COMMON_LOCK_PTHREADS_OBJS) -+ $(CC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_COM_LOCK_PTHREADS).so -shared -o $@ $(SION_COMMON_LOCK_PTHREADS_OBJS) - @echo "*** $@ built" - --lib$(SION_LIBNAME_COM_LOCK_NONE).a : $(SION_COMMON_LOCK_NONE_OBJS) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_COMMON_LOCK_NONE_OBJS) -+lib$(SION_LIBNAME_COM_LOCK_NONE).so : $(SION_COMMON_LOCK_NONE_OBJS) -+ $(CC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_COM_LOCK_NONE).so -shared -o $@ $(SION_COMMON_LOCK_NONE_OBJS) - @echo "*** $@ built" - --lib$(SION_LIBNAME_SER).a : $(SION_SER_OBJS) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_SER_OBJS) -+lib$(SION_LIBNAME_SER).so : $(SION_SER_OBJS) lib$(SION_LIBNAME_COM).so -+ $(CC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_SER).so -shared -o $@ $(SION_SER_OBJS) -L. -l$(SION_LIBNAME_COM) - @echo "*** $@ built" - - sion_lock_pthreads.o: sion_lock.c -@@ -178,7 +183,7 @@ - done - - clean: -- rm -f *.o lib*.a -+ rm -f *.o lib*.so - - #------------------------------------------------------------------------------ - # Dependencies ---- a/src/parlib/Makefile -+++ b/src/parlib/Makefile -@@ -29,7 +29,7 @@ - .SUFFIXES: .cpp .c .f - - USER_HDRS = sion_datatypes_mpi.h sion_mpi.h sion_ompi.h sion_omp.h sion_generic.h --USER_LIBS = lib$(SION_LIBNAME_GEN).a -+USER_LIBS = lib$(SION_LIBNAME_GEN).so - - SION_OBJS_GEN = sion_generic.o \ - sion_generic_internal.o \ -@@ -46,7 +46,7 @@ - sion_omp_cb_gen.o \ - sion_omp_internal_gen.o - USER_HDRS += sion_omp.h -- USER_LIBS += lib$(SION_LIBNAME_OMP).a -+ USER_LIBS += lib$(SION_LIBNAME_OMP).so - endif - - ifeq ($(MPIENABLE),1) -@@ -58,7 +58,7 @@ - sion_mpi_util.o \ - sion_mpi_file_check.o - USER_HDRS += sion_datatypes_mpi.h sion_mpi.h -- USER_LIBS += lib$(SION_LIBNAME_MPI).a -+ USER_LIBS += lib$(SION_LIBNAME_MPI).so - endif - ifeq ($(HYBENABLE),1) - SION_OBJS_HYB = sion_ompi_gen.o \ -@@ -67,16 +67,18 @@ - sion_ompi_util.o \ - sion_ompi_internal_gen.o - USER_HDRS += sion_datatypes_mpi.h sion_ompi.h -- USER_LIBS += lib$(SION_LIBNAME_OMPI).a -+ USER_LIBS += lib$(SION_LIBNAME_OMPI).so - endif - - ifeq ($(HYBENABLE),1) - LOCKCC =$(HYBCC) - LOCKCFLAGS=$(CHYBFLAGS) -+ LOCKLINK=$(HYBFLAG) - else - ifeq ($(OMPENABLE),1) - LOCKCC =$(OMPCC) - LOCKCFLAGS=$(COMPFLAGS) -+ LOCKLINK=$(OMPFLAG) - else - LOCKCC =$(CC) - LOCKCFLAGS=$(CFLAGS) -@@ -87,20 +89,23 @@ - - all: $(USER_LIBS) - --lib$(SION_LIBNAME_GEN).a : $(SION_OBJS_GEN) $(SION_OBJS_INTERNAL) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_GEN) $(SION_OBJS_INTERNAL) -+../lib/lib$(SION_LIBNAME_COM).so : -+ make -C ../lib lib$(SION_LIBNAME_COM).so -+ -+lib$(SION_LIBNAME_GEN).so : $(SION_OBJS_GEN) $(SION_OBJS_INTERNAL) ../lib/lib$(SION_LIBNAME_COM).so -+ $(CC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_GEN).so -shared -o $@ $(SION_OBJS_GEN) $(SION_OBJS_INTERNAL) $(LOCKLINK) -L../lib -l$(SION_LIBNAME_COM) - @echo "*** $@ built" - --lib$(SION_LIBNAME_OMP).a : $(SION_OBJS_OMP) $(SION_OBJS_INTERNAL) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_OMP) $(SION_OBJS_INTERNAL) -+lib$(SION_LIBNAME_OMP).so : $(SION_OBJS_OMP) $(SION_OBJS_INTERNAL) ../lib/lib$(SION_LIBNAME_COM).so lib$(SION_LIBNAME_GEN).so -+ $(CC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_OMP).so -shared -o $@ $(SION_OBJS_OMP) $(SION_OBJS_INTERNAL) $(LOCKLINK) -L../lib -l$(SION_LIBNAME_COM) -L. -l$(SION_LIBNAME_GEN) $(OMPFLAG) - @echo "*** $@ built" - --lib$(SION_LIBNAME_MPI).a : $(SION_OBJS_MPI) $(SION_OBJS_INTERNAL) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_MPI) $(SION_OBJS_INTERNAL) -+lib$(SION_LIBNAME_MPI).so : $(SION_OBJS_MPI) $(SION_OBJS_INTERNAL) ../lib/lib$(SION_LIBNAME_COM).so lib$(SION_LIBNAME_GEN).so -+ $(MPICC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_MPI).so -shared -o $@ $(SION_OBJS_MPI) $(SION_OBJS_INTERNAL) $(LOCKLINK) -L../lib -l$(SION_LIBNAME_COM) -L. -l$(SION_LIBNAME_GEN) - @echo "*** $@ built" - --lib$(SION_LIBNAME_OMPI).a : $(SION_OBJS_HYB) $(SION_OBJS_INTERNAL) -- $(C_AR) $(AFLAG) -rcs $@ $(SION_OBJS_HYB) $(SION_OBJS_INTERNAL) -+lib$(SION_LIBNAME_OMPI).so : $(SION_OBJS_HYB) $(SION_OBJS_INTERNAL) ../lib/lib$(SION_LIBNAME_COM).so lib$(SION_LIBNAME_GEN).so -+ $(HYBCC) $(LDFLAGS) -Wl,-soname,lib$(SION_LIBNAME_OMPI).so -shared -o $@ $(SION_OBJS_HYB) $(SION_OBJS_INTERNAL) $(LOCKLINK) -L../lib -l$(SION_LIBNAME_COM) -L. -l$(SION_LIBNAME_GEN) $(HYBFLAG) - @echo "*** $@ built" - - sion_generic.o : sion_generic.c -@@ -224,7 +229,7 @@ - done - - clean: -- rm -f *.o lib*.a opari* -+ rm -f *.o lib*.so opari* - - #------------------------------------------------------------------------------ - # Dependencies ---- a/src/parutils/Makefile -+++ b/src/parutils/Makefile -@@ -30,12 +30,18 @@ - COMPFLAGS = $(OMPMFLAG) $(OMPFLAG) - CHYBFLAGS = $(HYBMFLAG) $(HYBFLAG) - --CMPILDFLAGS = $(LDFLAGS) -L../parlib -l$(SION_LIBNAME_MPI) -L../lib -l$(SION_LIBNAME_GEN) -L../lib -l$(SION_LIBNAME_COM) -l$(SION_LIBNAME_COM_LOCK_PTHREADS) $(HINTSLIB) $(CACHELIB) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) -+ifneq ($(PTHREADSUPPORT),"no") -+LOCKLIB = $(SION_LIBNAME_COM_LOCK_PTHREADS) -+else -+LOCKLIB = $(SION_LIBNAME_COM_LOCK_NONE) -+endif -+ -+CMPILDFLAGS = $(LDFLAGS) -L../lib -l$(LOCKLIB) -L../lib -l$(SION_LIBNAME_COM) -L../parlib -l$(SION_LIBNAME_GEN) -L../parlib -l$(SION_LIBNAME_MPI) $(HINTSLIB) $(CACHELIB) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) - --COMPLDFLAGS = $(LDFLAGS) -L../parlib -l$(SION_LIBNAME_OMP) -L../lib -l$(SION_LIBNAME_COM) -l$(SION_LIBNAME_COM_LOCK_PTHREADS) $(HINTSLIB) $(CACHELIB) $(OMPFLAG) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) --CHYBLDFLAGS = $(LDFLAGS) -L../parlib -l$(SION_LIBNAME_OMPI) -L../lib -l$(SION_LIBNAME_GEN) -L../lib -l$(SION_LIBNAME_COM) -l$(SION_LIBNAME_COM_LOCK_PTHREADS) $(HINTSLIB) $(CACHELIB) $(OMPFLAG) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) -+COMPLDFLAGS = $(LDFLAGS) -L../lib -l$(LOCKLIB) -L../lib -l$(SION_LIBNAME_COM) -L../parlib -l$(SION_LIBNAME_OMP) $(HINTSLIB) $(CACHELIB) $(OMPFLAG) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) -+CHYBLDFLAGS = $(LDFLAGS) -L../lib -l$(LOCKLIB) -L../lib -l$(SION_LIBNAME_COM) -L../parlib -l$(SION_LIBNAME_GEN) -L../parlib -l$(SION_LIBNAME_OMPI) $(HINTSLIB) $(CACHELIB) $(OMPFLAG) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) - --FMPILDFLAGS = $(LDFLAGS) -L../parlib -l$(SION_LIBNAME_MPI) -L../lib -l$(SION_LIBNAME_GEN) -L../lib -l$(SION_LIBNAME_SER) -l$(SION_LIBNAME_COM) -l$(SION_LIBNAME_COM_LOCK_PTHREADS) $(HINTSLIB) $(CACHELIB) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) -+FMPILDFLAGS = $(LDFLAGS) -L../lib -l$(LOCKLIB) -L../lib -l$(SION_LIBNAME_COM) -L../lib -l$(SION_LIBNAME_SER) -L../parlib -l$(SION_LIBNAME_GEN) -L../parlib -l$(SION_LIBNAME_MPI) $(HINTSLIB) $(CACHELIB) $(CUDA_LIBRARY_PATHS) $(CUDA_LIBRARIES) $(SIONFWD_LIBS) $(IMELIB_LIBPATH) $(IMELIB_LIB) - FOMPLDFLAGS = $(COMPLDFLAGS) $(OMPFLAG) - FHYBLDFLAGS = $(COMPILDFLAGS) $(OMPFLAG) - -@@ -55,6 +61,13 @@ - ifeq ($(FORTRANENABLE),1) - ifeq ($(MPIENABLE),1) - USER_UTILS += fpartest -+ F77_MPI_LIBS = -L../parlib -l$(SION_LIBNAME_MPI) -+ endif -+ ifeq ($(OMPENABLE),1) -+ F77_SER_LIBS = $(OMPFLAG) -L../parlib -l$(SION_LIBNAME_OMP) -+ endif -+ ifeq ($(HYBENABLE),1) -+ F77_MPI_LIBS = $(HYBFLAG) -L../parlib -l$(SION_LIBNAME_OMPI) - endif - endif - -@@ -75,10 +88,10 @@ - - all: $(USER_UTILS) - --partest: $(PARTEST_OBJS) ../parlib/lib$(SION_LIBNAME_MPI).a ../parlib/lib$(SION_LIBNAME_GEN).a ../lib/lib$(SION_LIBNAME_SER).a -+partest: $(PARTEST_OBJS) ../parlib/lib$(SION_LIBNAME_MPI).so ../parlib/lib$(SION_LIBNAME_GEN).so ../lib/lib$(SION_LIBNAME_SER).so - $(MPICC) -o $@ $(PARTEST_OBJS) -L../lib -l$(SION_LIBNAME_SER) $(CMPILDFLAGS) $(MPILIB) - --ompi_partest: $(PARTEST_OMPI_OBJS) ../parlib/lib$(SION_LIBNAME_OMPI).a ../parlib/lib$(SION_LIBNAME_OMP).a ../lib/lib$(SION_LIBNAME_SER).a -+ompi_partest: $(PARTEST_OMPI_OBJS) ../parlib/lib$(SION_LIBNAME_OMPI).so ../parlib/lib$(SION_LIBNAME_OMP).so ../lib/lib$(SION_LIBNAME_SER).so - $(HYBCC) -o $@ $(PARTEST_OMPI_OBJS) $(CHYBLDFLAGS) -L../parlib -l$(SION_LIBNAME_OMP) -L../lib -l$(SION_LIBNAME_SER) $(MPILIB) - - ompi_partest.o : ompi_partest.c -@@ -114,8 +127,8 @@ - fpartest.o : fpartest.F90 - $(MPIF90) $(FFLAGS) -c fpartest.F90 - --fpartest: fpartest.o ../parlib/lib$(SION_LIBNAME_MPI).a ../parlib/lib$(SION_LIBNAME_GEN).a ../lib/lib$(SION_LIBNAME_SER).a ../fortraninterface/lib$(SION_LIBNAME_F77_MPI).a ../fortraninterface/lib$(SION_LIBNAME_F77_SER).a -- $(MPIF90) -o $@ fpartest.o -L../fortraninterface -l$(SION_LIBNAME_F77_MPI) -l$(SION_LIBNAME_F77_SER) $(FMPILDFLAGS) $(MPILIB) -+fpartest: fpartest.o ../parlib/lib$(SION_LIBNAME_MPI).so ../parlib/lib$(SION_LIBNAME_GEN).so ../lib/lib$(SION_LIBNAME_SER).so ../fortraninterface/lib$(SION_LIBNAME_F77_MPI).so ../fortraninterface/lib$(SION_LIBNAME_F77_SER).so -+ $(MPIF90) -o $@ fpartest.o -L../fortraninterface -l$(SION_LIBNAME_F77_MPI) -l$(SION_LIBNAME_F77_SER) $(FMPILDFLAGS) $(MPILIB) $(F77_MPI_LIBS) $(F77_SER_LIBS) - - - install: all -@@ -161,7 +174,7 @@ - @rm -f header.tmp - - clean: -- rm -f *.o lib*.a $(USER_UTILS) -+ rm -f *.o lib*.so $(USER_UTILS) - - #------------------------------------------------------------------------------ - # Dependencies ---- a/src/utils/Makefile -+++ b/src/utils/Makefile -@@ -45,32 +45,32 @@ - siondump.o : siondump.c - $(CC) $(CFLAGS) -c siondump.c - --siondefrag.o : siondefrag.c ../lib/lib$(SION_LIBNAME_SER).a -+siondefrag.o : siondefrag.c ../lib/lib$(SION_LIBNAME_SER).so - $(CC) $(CFLAGS) -c siondefrag.c - --sionsplit.o : sionsplit.c ../lib/lib$(SION_LIBNAME_SER).a -+sionsplit.o : sionsplit.c ../lib/lib$(SION_LIBNAME_SER).so - $(CC) $(CFLAGS) -c sionsplit.c - --sioncat.o : sioncat.c ../lib/lib$(SION_LIBNAME_SER).a -+sioncat.o : sioncat.c ../lib/lib$(SION_LIBNAME_SER).so - $(CC) $(CFLAGS) -c sioncat.c - --sionversion.o : sionversion.c ../lib/lib$(SION_LIBNAME_SER).a -+sionversion.o : sionversion.c ../lib/lib$(SION_LIBNAME_SER).so - $(CC) $(CFLAGS) -c sionversion.c - --siondump: siondump.o ../lib/lib$(SION_LIBNAME_SER).a ../lib/lib$(SION_LIBNAME_COM).a ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).a -+siondump: siondump.o ../lib/lib$(SION_LIBNAME_SER).so ../lib/lib$(SION_LIBNAME_COM).so ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).so - $(CC) -o $@ siondump.o $(LDFLAGS) - cp siondump $(TOPDIR)/.. - --siondefrag: siondefrag.o ../lib/lib$(SION_LIBNAME_SER).a ../lib/lib$(SION_LIBNAME_COM).a ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).a -+siondefrag: siondefrag.o ../lib/lib$(SION_LIBNAME_SER).so ../lib/lib$(SION_LIBNAME_COM).so ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).so - $(CC) -o $@ siondefrag.o $(LDFLAGS) - --sionsplit: sionsplit.o ../lib/lib$(SION_LIBNAME_SER).a ../lib/lib$(SION_LIBNAME_COM).a ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).a -+sionsplit: sionsplit.o ../lib/lib$(SION_LIBNAME_SER).so ../lib/lib$(SION_LIBNAME_COM).so ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).so - $(CC) -o $@ sionsplit.o $(LDFLAGS) - --sioncat: sioncat.o ../lib/lib$(SION_LIBNAME_SER).a ../lib/lib$(SION_LIBNAME_COM).a ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).a -+sioncat: sioncat.o ../lib/lib$(SION_LIBNAME_SER).so ../lib/lib$(SION_LIBNAME_COM).so ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).so - $(CC) -o $@ sioncat.o $(LDFLAGS) - --sionversion: sionversion.o ../lib/lib$(SION_LIBNAME_SER).a ../lib/lib$(SION_LIBNAME_COM).a ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).a -+sionversion: sionversion.o ../lib/lib$(SION_LIBNAME_SER).so ../lib/lib$(SION_LIBNAME_COM).so ../lib/lib$(SION_LIBNAME_COM_LOCK_NONE).so - $(CC) -o $@ sionversion.o $(LDFLAGS) - - -@@ -136,7 +136,7 @@ - @rm -f header.tmp - - clean: -- rm -f *.o lib*.a $(USER_UTILS) -+ rm -f *.o lib*.so $(USER_UTILS) - - #------------------------------------------------------------------------------ - # Dependencies diff --git a/sys-cluster/sionlibl/files/sionlibl-respect-flags-v3.patch b/sys-cluster/sionlibl/files/sionlibl-respect-flags-v3.patch deleted file mode 100644 index e71d7d46d..000000000 --- a/sys-cluster/sionlibl/files/sionlibl-respect-flags-v3.patch +++ /dev/null @@ -1,185 +0,0 @@ ---- a/config/determine-cc.sh -+++ b/config/determine-cc.sh -@@ -1,7 +1,6 @@ - #!/bin/sh - # determine what compiler is behind "cc" (and presumably "CC" and "ftn") wrapper - --CC=`which cc 2>/dev/null` - COMP= - if [ -z "$CC" ]; then - echo "No 'cc' located!" ---- a/config/determine-compiler-version.sh -+++ b/config/determine-compiler-version.sh -@@ -24,8 +24,8 @@ - | cut -d\ -f 1` - COMPVER="${CVER}/${FVER}" - ;; -- gnu) COMPVER=`gcc -dumpfullversion -dumpversion` -- #COMPVER=`gcc -v 2>&1 | grep -i 'Version [0-9]' \ -+ gnu) COMPVER=`${CC} -dumpfullversion -dumpversion` -+ #COMPVER=`${CC} -v 2>&1 | grep -i 'Version [0-9]' \ - # | sed -e 's/^.*ersion \(.\..\..\).*$/\1/'` - ;; - *) ErrorAndExit "Unknown compiler '${COMP}'" ---- a/config/select-compiler.sh -+++ b/config/select-compiler.sh -@@ -9,7 +9,7 @@ - CPS="" - COMP="" - --GNU=`which gcc 2> /dev/null` -+GNU="${CC}" - if [ -n "${GNU}" ] - then - NCPS=`expr ${NCPS} + 1` ---- a/config/select-mpi.sh -+++ b/config/select-mpi.sh -@@ -76,7 +76,6 @@ - if [ -z "${MPIS}" ]; then MPIS="${MPI}"; else MPIS="${MPIS}|${MPI}"; fi - fi - --MPICC=`which mpicc 2> /dev/null` - if [ -n "${MPICC}" ] - then - FMPI="" -@@ -86,7 +85,7 @@ - MPIROOTDIR1=`dirname ${MBINDIR}` - - echo "#include <mpi.h>" > conftest.c -- mpicc -E conftest.c | grep '/mpi.h"' | head -1 > mpiconf.txt -+ "${MPICC}" -E conftest.c | grep '/mpi.h"' | head -1 > mpiconf.txt - MINCDIR=`cat mpiconf.txt | sed -e 's#^.* "##' -e 's#/mpi.h".*##'` - if [ -n "${MINCDIR}" ] - then ---- a/mf/Makefile.defs.linux-gomp -+++ b/mf/Makefile.defs.linux-gomp -@@ -23,24 +23,19 @@ - #------------------------------------------------------------------------------ - # SIONlib General Settings - #------------------------------------------------------------------------------ --OPTFLAGS = -g -O0 -Wall -+CFLAGS += -std=c99 $(PFLAG) $(OPTFLAGS) -fPIC - --CC = gcc --CFLAGS = -std=c99 $(PFLAG) $(OPTFLAGS) -fPIC -+CXXFLAGS += $(PFLAG) $(OPTFLAGS) -fPIC - --CXX = g++ --CXXFLAGS = $(PFLAG) $(OPTFLAGS) -O3 -- --F77 = gfortran --FFLAGS = $(PFLAG) $(OPTFLAGS) -+FFLAGS += $(PFLAG) $(OPTFLAGS) -fPIC - - F90 = $(F77) --F90FLAGS = $(PFLAG) $(OPTFLAGS) -ffree-form -+F90FLAGS += $(PFLAG) $(OPTFLAGS) -ffree-form -fPIC $(FCFLAGS) - - FPP = - FDOPT = -D - --LDFLAGS = $(PFLAG) $(OPTFLAGS) $(HINTSLIB) -+LDFLAGS += $(PFLAG) $(OPTFLAGS) $(HINTSLIB) - UTILLIB = - FOBASE = pomp_fwrapper_base.o - -@@ -101,10 +96,6 @@ - #------------------------------------------------------------------------------ - - MPIENABLE = 1 --MPICC = mpicc --MPICXX = mpicxx --MPIF77 = mpif77 --MPIF90 = mpif90 - MPILIB = -lmpich - PMPILIB = -lpmpich - #PMPILIB = # MPICH2 -@@ -139,8 +130,7 @@ - #------------------------------------------------------------------------------ - - SZLIB = szlib --SZLIB_OPTFLAGS = -O3 --SZLIB_CFLAGS = -I$(TOPDIR)/utils/szlib -DELG_COMPRESSED -DCUBE_COMPRESSED -+SZLIB_CFLAGS = -I$(TOPDIR)/utils/szlib -DELG_COMPRESSED -DCUBE_COMPRESSED $(CFLAGS) - SZLIB_LIBPATH = -L$(TOPDIR)/utils/szlib - SZLIB_LIB = -lsc.z - ---- a/mf/Makefile.defs.linux-gomp10 -+++ b/mf/Makefile.defs.linux-gomp10 -@@ -23,24 +23,19 @@ - #------------------------------------------------------------------------------ - # SIONlib General Settings - #------------------------------------------------------------------------------ --OPTFLAGS = -g -O0 -Wall -+CFLAGS += -std=c99 $(PFLAG) -fPIC - --CC = gcc --CFLAGS = -std=c99 $(PFLAG) $(OPTFLAGS) -fPIC -+CXXFLAGS += $(PFLAG) -fPIC - --CXX = g++ --CXXFLAGS = $(PFLAG) $(OPTFLAGS) -O3 -- --F77 = gfortran --FFLAGS = $(PFLAG) $(OPTFLAGS) -fallow-argument-mismatch -+FFLAGS += $(PFLAG) -fallow-argument-mismatch -fPIC - - F90 = $(F77) --F90FLAGS = $(PFLAG) $(OPTFLAGS) -ffree-form -fallow-argument-mismatch -+F90FLAGS += $(PFLAG) -ffree-form -fallow-argument-mismatch -fPIC $(FCFLAGS) - - FPP = - FDOPT = -D - --LDFLAGS = $(PFLAG) $(OPTFLAGS) $(HINTSLIB) -+LDFLAGS += $(PFLAG) $(HINTSLIB) - UTILLIB = - FOBASE = pomp_fwrapper_base.o - -@@ -101,10 +96,6 @@ - #------------------------------------------------------------------------------ - - MPIENABLE = 1 --MPICC = mpicc --MPICXX = mpicxx --MPIF77 = mpif77 --MPIF90 = mpif90 - MPILIB = -lmpich - PMPILIB = -lpmpich - #PMPILIB = # MPICH2 -@@ -139,7 +130,7 @@ - #------------------------------------------------------------------------------ - - SZLIB = szlib --SZLIB_OPTFLAGS = -O3 -+SZLIB_OPTFLAGS = $(CFLAGS) - SZLIB_CFLAGS = -I$(TOPDIR)/utils/szlib -DELG_COMPRESSED -DCUBE_COMPRESSED - SZLIB_LIBPATH = -L$(TOPDIR)/utils/szlib - SZLIB_LIB = -lsc.z ---- a/src/fortraninterface/Makefile -+++ b/src/fortraninterface/Makefile -@@ -121,21 +121,21 @@ - $(CPP) $(F90FLAGS) $(F90FLAGS_CPP) $(F90MPIFLAGS) -P -E -I ../lib sion_f90_mpi.F90 > sion_f90_mpi.f90 - sion_f90_mpi.mod : sion_f90_mpi.o - sion_f90_mpi.o : sion_f90_mpi.f90 sion_f90.mod $(SION_HDRS) -- $(MPIF90) $(F90FLAGS) -c sion_f90_mpi.f90 -+ $(MPIF90) $(F90FLAGS) $(F90MPIFLAGS) -c sion_f90_mpi.f90 - - # F90 Interface (OMP) - sion_f90_omp.f90: sion_f90_omp.F90 - $(CPP) $(F90OMPFLAGS) $(F90FLAGS) $(F90FLAGS_CPP) -P -E -I ../lib sion_f90_omp.F90 > sion_f90_omp.f90 - sion_f90_omp.mod : sion_f90_omp.o - sion_f90_omp.o : sion_f90_omp.f90 sion_f90.mod $(SION_HDRS) -- $(OMPF90) $(F90FLAGS) -c sion_f90_omp.f90 -+ $(OMPF90) $(F90FLAGS) $(F90OMPFLAGS) -c sion_f90_omp.f90 - - # F90 Interface (OMPI) - sion_f90_ompi.f90: sion_f90_ompi.F90 $(SION_HDRS) - $(CPP) $(F90MPIFLAGS) $(F90OMPFLAGS) $(F90FLAGS) $(F90FLAGS_CPP) -P -E -I ../lib sion_f90_ompi.F90 > sion_f90_ompi.f90 - sion_f90_ompi.mod : sion_f90_ompi.o - sion_f90_ompi.o : sion_f90_ompi.f90 $(SION_HDRS) -- $(MPIF90) $(F90FLAGS) -c sion_f90_ompi.f90 -+ $(MPIF90) $(F90FLAGS) $(F90MPIFLAGS) -c sion_f90_ompi.f90 - - - diff --git a/sys-cluster/sionlibl/metadata.xml b/sys-cluster/sionlibl/metadata.xml deleted file mode 100644 index 52da79403..000000000 --- a/sys-cluster/sionlibl/metadata.xml +++ /dev/null @@ -1,39 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>lssndrbarbieri@gmail.com</email> - <name>Alessandro Barbieri</name> - </maintainer> - <longdescription lang="en"> -SIONlib is a library for writing and reading data from several thousands of parallel tasks into/from one or a small number of physical files. Only the open and close functions are collective while file access can be performed independently. - -SIONlib can be used as a replacement for standard I/O APIs (e.g. POSIX) that are used to access distinct files from every parallel process. SIONlib will bundle the data into one or few files in a coordinated fashion in order to sidestep sequentialising mechanism in the file system. At the same time, the task-per-file picture is maintained for the application, every process has access to its logical file only. File access is performed using SIONlib equivalents to standard C-I/O functionality (fwrite becomes sion_write, fseek becomes sion_seek, etc.) which have similar semantics as their C counterparts. - -Internally, the physical files are sub-divided into sequences of blocks, which themselves contain one chunk of data belonging to every logical file. In case the amount to be written to a file is known up front, it can optionally be specified when opening the file and the sequence of blocks collapses into a single block with one chunk per task containing all of its data. If a chunk size cannot be specified ahead of time, a sensible default is chosen and reads and writes that cross chunk boundaries are handled transparently by SIONlib. - -SIONlib also uses information about the block size of the underlying file system, because access to the same block from different tasks often leads to contention. - -Both, the estimated chunk size and file system block size are used to align individual chunks with file system blocks. Ensuring contention-free access to file system blocks enables efficient parallel writing and reading. - -SIONlib provides two different interfaces: one for parallel access (with implementations for different parallel programming technologies such as MPI, OpenMP and hybrid MPI+OpenMP) and one for sequential access which is also used internally by the SIONlib utilities. - </longdescription> - <upstream> - <bugs-to>https://gitlab.jsc.fz-juelich.de/cstao-public/SIONlib/SIONlib/-/issues</bugs-to> - </upstream> - <use> - <!--<flag name="cuda">enable CUDA aware interface</flag>--> - <flag name="cxx">Enable C++ support</flag> - <flag name="debug">enable SIONlib debug</flag> - <flag name="deep-est-sdv">deep-est-sdv collector selection plug-in for MSA-aware collective I/O</flag> - <flag name="fortran">Enable Fortran support</flag> - <flag name="hostname-regex">hostname-regex collector selection plug-in for MSA-aware collective I/O</flag> - <flag name="mpi">enable mpi</flag> - <flag name="python">enable python support</flag> - <flag name="ompi">enable hybrid openmp mpi</flag> - <flag name="openmp">enable openmp</flag> - <flag name="parutils">Enable compilation of parutils (used for benchmarking)</flag> - <flag name="pthreads">configure SIONlib to use pthreads for locking</flag> - <flag name="sionfwd">enable I/O forwarding with <pkg>sys-cluster/SIONfwd</pkg></flag> - </use> -</pkgmetadata> diff --git a/sys-cluster/sionlibl/sionlibl-1.7.7-r3.ebuild b/sys-cluster/sionlibl/sionlibl-1.7.7-r3.ebuild deleted file mode 100644 index d4f889cdb..000000000 --- a/sys-cluster/sionlibl/sionlibl-1.7.7-r3.ebuild +++ /dev/null @@ -1,158 +0,0 @@ -# Copyright 2019-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DOCS_BUILDER="doxygen" -DOCS_CONFIG_NAME="doxy" -FORTRAN_NEEDED="fortran" -PYTHON_COMPAT=( pypy3 python3_{10..11} ) - -inherit docs edo flag-o-matic fortran-2 python-any-r1 toolchain-funcs - -DESCRIPTION="Scalable I/O library for parallel access to task-local files" -HOMEPAGE="https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html" -SRC_URI="http://apps.fz-juelich.de/jsc/sionlib/download.php?version=${PV}l -> ${PN}l-${PV}.tar.gz" -S="${WORKDIR}/sionlib" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" -IUSE="+cxx debug deep-est-sdv doc examples +fortran hostname-regex +mpi +ompi +openmp +parutils +pthreads python sionfwd" #cuda - -RDEPEND=" - mpi? ( virtual/mpi ) - openmp? ( || ( sys-devel/gcc:*[openmp] sys-libs/libomp ) ) - sionfwd? ( sys-cluster/SIONfwd ) -" -DEPEND=" - ${RDEPEND} - ${PYTHON_DEPS} -" - -REQUIRED_USE=" - ompi? ( mpi openmp ) - ?? ( hostname-regex deep-est-sdv ) -" -PATCHES=( - "${FILESDIR}/${PN}-respect-flags-v3.patch" - "${FILESDIR}/${PN}-build-shared-libraries.patch" -) - -pkg_setup() { - FORTRAN_NEED_OPENMP=0 - use openmp && FORTRAN_NEED_OPENMP=1 - - fortran-2_pkg_setup -} - -src_configure() { - tc-export AR CC CXX F77 FC - export MPICC=/usr/bin/mpicc - export MPICXX=/usr/bin/mpicxx - export MPIF77=/usr/bin/mpif77 - export MPIF90=/usr/bin/mpif90 - export F90=$(tc-getFC) - export OMPF77=$(tc-getF77) - export OMPF90=$(tc-getFC) - - append-fflags -fallow-argument-mismatch - - local msa="none" - use deep-est-sdv && msa="deep-est-sdv" - use hostname-regex && msa="hostname-regex" - - local myconf=( - --disable-gcovr - --disable-kcov - --disable-mic - --msa="${msa}" - --prefix="${T}/prefix/usr" - $(use_enable debug) - $(use_enable pthreads) - ) - - #custom configure? - use cxx || myconf+=( "--disable-cxx" ) - use fortran || myconf+=( "--disable-fortran" ) - if use mpi; then - myconf+=( "--mpi=$(detect_mpi_implementation || die)" ) - else - myconf+=( "--disable-mpi" ) - fi - use ompi || myconf+=( "--disable-ompi" ) - use openmp || myconf+=( "--disable-omp" ) - use parutils || myconf+=( "--disable-parutils" ) - - use python && myconf+=( "--enable-python=3" ) - use sionfwd && myconf+=( "--enable-sionfwd=${EPREFIX}/usr" ) - - edo ./configure "${myconf[@]}" -} - -src_compile() { - export VARTEXFONTS="${T}/fonts" - emake C_AR=$(tc-getAR) F90=$(tc-getFC) - docs_compile -} - -src_install() { - mkdir -p "${T}/prefix/usr/share/doc/${PF}" || die - default - - if use examples ; then - mv "${T}/prefix/usr/examples" "${T}/prefix/usr/share/doc/${PF}/" || die - else - rm -r "${T}/prefix/usr/examples" || die - fi - - insinto "/usr/include/sionlibl" - doins -r "${T}"/prefix/usr/include/* - rm -r "${T}/prefix/usr/include" || die - - exeinto "/usr/libexec/${PN}" - doexe "${T}"/prefix/usr/bin/*partest - rm "${T}"/prefix/usr/bin/*partest || die - - for b in "${T}"/prefix/usr/bin/sion* ; do - n=$(basename "${b}") - newbin "${T}/prefix/usr/bin/${n}" "l${n}" - rm "${b}" || die - done - - # move 64 bit libraries to lib64 - libs64=( "${T}"/prefix/usr/lib/*64* ) - if [[ ${#libs64[@]} -gt 0 ]]; then - mkdir "${T}/prefix/usr/lib64" || die - for l in "${libs64[@]}" ; do - mv "${l}" "${T}/prefix/usr/lib64/" || die - done - fi - - rsync -ravXHA "${T}/prefix/usr" "${ED}/" || die - docompress -x "/usr/share/doc/${PF}/examples" - - #TODO: build shared libs - #find "${ED}" -name '*.a' -delete || die - find "${ED}" -name '*.la' -delete || die -} - -detect_mpi_implementation() { - cat > testmpi.c <<- EOF -#include "mpi.h" -#include "stdio.h" - -int main(){ - #ifdef OPEN_MPI - printf("%s","openmpi"); - #endif - - #ifdef MPICH - printf("%s%i","mpich",MPICH_NAME); - #endif - return 0; -} -EOF - edo ${CC} testmpi.c -o testmpi - ./testmpi || die -} diff --git a/sys-cluster/usort/Manifest b/sys-cluster/usort/Manifest deleted file mode 100644 index 7b691dce4..000000000 --- a/sys-cluster/usort/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST usort-0_pre20211230-r1.tar.gz 36255 BLAKE2B 1137c96141c3bdd26cdddb650224ae276e88eac2f8190210ba9673030f7867f110411040ba4415821fef9b85f1af737f3e880ab15ded164fe3cd8135fcf9d725 SHA512 82474b33e0c74d6ce78a4e34bbbbb0e666646a708bbd56b298e3ae054c0c9682bfe6ea126f4f88c7047ad34eb1bc8aec6936f5cfb867dd5b3254052361b397ea diff --git a/sys-cluster/usort/files/usort-0_pre20211230-cmake.patch b/sys-cluster/usort/files/usort-0_pre20211230-cmake.patch deleted file mode 100644 index 616e15fd7..000000000 --- a/sys-cluster/usort/files/usort-0_pre20211230-cmake.patch +++ /dev/null @@ -1,34 +0,0 @@ ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -26,15 +26,25 @@ - - include_directories(include) - --add_executable(usort src/main.cpp src/parUtils.cpp src/binUtils.cpp src/sort_profiler.cpp) --target_link_libraries(usort ${MPI_LIBRARIES} m) -+add_library(Usortlib src/parUtils.cpp src/binUtils.cpp) -+target_include_directories(Usortlib PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/include") -+target_link_libraries(Usortlib ${MPI_LIBRARIES} m) -+ -+add_executable(usort src/main.cpp src/sort_profiler.cpp) -+target_include_directories(usort PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/include") -+target_link_libraries(usort ${MPI_LIBRARIES} m Usortlib) - - if(MPI_COMPILE_FLAGS) -- set_target_properties(usort PROPERTIES -- COMPILE_FLAGS "${MPI_COMPILE_FLAGS}") -+ set_target_properties(Usortlib PROPERTIES COMPILE_FLAGS "${MPI_COMPILE_FLAGS}") -+ set_target_properties(usort PROPERTIES COMPILE_FLAGS "${MPI_COMPILE_FLAGS}") - endif() - - if(MPI_LINK_FLAGS) -- set_target_properties(usort PROPERTIES -- LINK_FLAGS "${MPI_LINK_FLAGS}") -+ set_target_properties(Usortlib PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}") -+ set_target_properties(usort PROPERTIES LINK_FLAGS "${MPI_LINK_FLAGS}") - endif() -+ -+include(GNUInstallDirs) -+install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/include/" DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/usort") -+install(TARGETS Usortlib LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}") -+install(TARGETS usort LIBRARY DESTINATION "${CMAKE_INSTALL_BINDIR}") diff --git a/sys-cluster/usort/files/usort-0_pre20211230-fix-fpermissive.patch b/sys-cluster/usort/files/usort-0_pre20211230-fix-fpermissive.patch deleted file mode 100644 index d99d4117e..000000000 --- a/sys-cluster/usort/files/usort-0_pre20211230-fix-fpermissive.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/include/ompUtils.tcc -+++ b/include/ompUtils.tcc -@@ -4,6 +4,7 @@ - #include <vector> - #include <algorithm> - // #include <seqUtils.h> -+#include <cstring> - - - diff --git a/sys-cluster/usort/files/usort-0_pre20211230-rename-THRESHOLD.patch b/sys-cluster/usort/files/usort-0_pre20211230-rename-THRESHOLD.patch deleted file mode 100644 index 6a0c5f901..000000000 --- a/sys-cluster/usort/files/usort-0_pre20211230-rename-THRESHOLD.patch +++ /dev/null @@ -1,31 +0,0 @@ ---- a/include/seqUtils.h -+++ b/include/seqUtils.h -@@ -30,7 +30,7 @@ - * The routine runs fastest with a uniform distribution of elements. - * The vector l is declare dynamically using the calloc function. - * The variable ctr counts the number of times that flashsort is called. -- * THRESHOLD is a very important constant. It is the minimum number of -+ * USORT_THRESHOLD is a very important constant. It is the minimum number of - * elements required in a subclass before recursion is used. - * - * Templated version of flashsort based on original C code by ---- a/include/seqUtils.tcc -+++ b/include/seqUtils.tcc -@@ -121,7 +121,7 @@ - template <typename T> - void flashsort(T* a, int n, int m, int *ctr) - { -- const int THRESHOLD = 75; -+ const int USORT_THRESHOLD = 75; - const int CLASS_SIZE = 75; /* minimum value for m */ - - /* declare variables */ -@@ -192,7 +192,7 @@ - /**** Choice of RECURSION or STRAIGHT INSERTION *****/ - - for (k=0;k<(m-1);k++) -- if ( (nx = l[k+1]-l[k]) > THRESHOLD ) /* then use recursion */ -+ if ( (nx = l[k+1]-l[k]) > USORT_THRESHOLD ) /* then use recursion */ - { - flashsort(&a[l[k]+1],nx,CLASS_SIZE,ctr); - (*ctr)++; diff --git a/sys-cluster/usort/metadata.xml b/sys-cluster/usort/metadata.xml deleted file mode 100644 index ccdceeefb..000000000 --- a/sys-cluster/usort/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <name>Alessandro Barbieri</name> - <email>lssndrbarbieri@gmail.com</email> - </maintainer> - <upstream> - <bugs-to>https://github.com/hsundar/usort/issues</bugs-to> - <remote-id type="github">hsundar/usort</remote-id> - </upstream> -</pkgmetadata> diff --git a/sys-cluster/usort/usort-0_pre20211230-r1.ebuild b/sys-cluster/usort/usort-0_pre20211230-r1.ebuild deleted file mode 100644 index 4b1ef7037..000000000 --- a/sys-cluster/usort/usort-0_pre20211230-r1.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -COMMIT="902f5e3cbba66833bbf2d219c183d4705b3582c7" - -inherit cmake edos2unix - -DESCRIPTION='Fast distributed sorting routines using MPI and OpenMP' -HOMEPAGE="https://github.com/hsundar/usort" -SRC_URI="https://github.com/hsundar/${PN}/archive/${COMMIT}.tar.gz -> ${PF}.tar.gz" -S="${WORKDIR}/${PN}-${COMMIT}" - -KEYWORDS="~amd64" -LICENSE='MIT' -SLOT="0/${PV}" - -DEPEND="virtual/mpi" -RDEPEND="${DEPEND}" - -PATCHES=( - "${FILESDIR}/${P}-cmake.patch" - "${FILESDIR}/${P}-rename-THRESHOLD.patch" - "${FILESDIR}/${P}-fix-fpermissive.patch" -) - -src_prepare() { - edos2unix CMakeLists.txt include/{seqUtils.h,seqUtils.tcc,ompUtils.tcc} - cmake_src_prepare -} - -src_install() { - cmake_src_install - dodoc README.md -} |