diff options
Diffstat (limited to 'sci-libs/netcdf/files')
5 files changed, 312 insertions, 0 deletions
diff --git a/sci-libs/netcdf/files/netcdf-4.1.1-fortran.patch b/sci-libs/netcdf/files/netcdf-4.1.1-fortran.patch new file mode 100644 index 000000000000..825fd3b893a1 --- /dev/null +++ b/sci-libs/netcdf/files/netcdf-4.1.1-fortran.patch @@ -0,0 +1,15 @@ +Default to gfortran if cannot figure out F77 compiler + +https://bugs.gentoo.org/show_bug.cgi?id=348922 + +--- netcdf-4.1.1/configure.ac ++++ netcdf-4.1.1/configure.ac +@@ -973,7 +973,7 @@ + *) + # If it's a gnu compiler, guess f2c. + if test "x$ac_cv_fc_compiler_gnu" = xyes; then +- AC_DEFINE(f2cFortran, [1], [Turned on by netCDF configure.]) ++ AC_DEFINE(gFortran, [1], [Turned on by netCDF configure.]) + fi + ;; + esac diff --git a/sci-libs/netcdf/files/netcdf-4.1.1-implicits.patch b/sci-libs/netcdf/files/netcdf-4.1.1-implicits.patch new file mode 100644 index 000000000000..a30aafc91348 --- /dev/null +++ b/sci-libs/netcdf/files/netcdf-4.1.1-implicits.patch @@ -0,0 +1,80 @@ +Fix implicit function declarations + +--- libsrc/nc.c ++++ libsrc/nc.c +@@ -15,7 +15,7 @@ + # include <mpp/shmem.h> + # include <intrinsics.h> + #endif +-#ifdef HAVE_UNISTD ++#ifdef HAVE_UNISTD_H + #include <unistd.h> + #endif + +--- fortran/fort-nc4.c ++++ fortran/fort-nc4.c +@@ -30,6 +30,14 @@ + /* These are in libsrc4/nc4vars.c... */ + int nc_inq_var_chunking_ints(int ncid, int varid, int *contiguousp, int *chunksizesp); + int nc_def_var_chunking_ints(int ncid, int varid, int contiguous, int *chunksizes); ++int nc_set_var_chunk_cache_ints(int ncid, int varid, int size, int nelems, int preemption); ++int nc_get_var_chunk_cache_ints(int ncid, int varid, int *sizep, int *nelemsp, int *preemptionp); ++ ++/* These are in libsrc4/nc4file.c... */ ++int nc_set_chunk_cache_ints(int size, int nelems, int preemption); ++int nc_get_chunk_cache_ints(int *sizep, int *nelemsp, int *preemptionp); ++int nc_create_par_fortran(const char *path, int cmode, int comm, int info, int *ncidp); ++int nc_open_par_fortran(const char *path, int mode, int comm, int info, int *ncidp); + + FCALLSCFUN5(NF_INT, nc_create_par_fortran, NF_CREATE_PAR, nf_create_par, + STRING, FINT2CINT, FINT2CINT, FINT2CINT, PCINT2FINT) +--- libncdap3/oc/daplex.c ++++ libncdap3/oc/daplex.c +@@ -86,6 +86,8 @@ + SCAN_PROG + }; + ++int daperror(DAPparsestate* state, const char* msg); ++ + /**************************************************/ + + int +--- libncdap3/oc/ocinternal.c ++++ libncdap3/oc/ocinternal.c +@@ -37,6 +37,8 @@ + #endif + + extern OCnode* makeunlimiteddimension(void); ++int occurlopen(CURL** curlp); ++void occurlclose(CURL* curl); + + #ifdef WIN32 + #include <fcntl.h> +--- libncdap3/oc/dapparse.c ++++ libncdap3/oc/dapparse.c +@@ -11,6 +11,7 @@ + static OCtype octypefor(Object etype); + static char* scopeduplicates(OClist* list); + static int check_int32(char* val, long* value); ++void setwordchars(DAPlexstate* lexstate, int kind); + + /****************************************************/ + +--- libncdap3/ncdap3.c ++++ libncdap3/ncdap3.c +@@ -4,6 +4,7 @@ + * $Id$ + *********************************************************************/ + #include "config.h" ++#include "netcdf3.h" + #include "ncdap3.h" + #include "dispatch3.h" + #include "dapdispatch3.h" +--- libncdap3/oc/dapparselex.h ++++ libncdap3/oc/dapparselex.h +@@ -88,4 +88,5 @@ + extern void daplexinit(char* input, DAPlexstate** lexstatep); + extern void daplexcleanup(DAPlexstate** lexstatep); + ++void dassetup(DAPparsestate* state); + #endif /*DAPPARSELEX_H*/ diff --git a/sci-libs/netcdf/files/netcdf-4.1.1-mpi-fix.patch b/sci-libs/netcdf/files/netcdf-4.1.1-mpi-fix.patch new file mode 100644 index 000000000000..4656ef1e3cbc --- /dev/null +++ b/sci-libs/netcdf/files/netcdf-4.1.1-mpi-fix.patch @@ -0,0 +1,32 @@ +Ensure hdf5.h is included before netcdf.h to avoid build error with openmpi >= 1.4.1 + +--- libsrc4/nc4internal.h ++++ libsrc4/nc4internal.h +@@ -8,13 +8,13 @@ + + #include <config.h> + #include <stdio.h> ++#include <hdf5.h> + #include "error.h" + #include <stdlib.h> + #include <ctype.h> + #include <stdarg.h> + #include <string.h> + #include "netcdf3.h" +-#include <hdf5.h> + #include <netcdf.h> + + #ifdef USE_PARALLEL +--- libncdap4/ncdap4.h ++++ libncdap4/ncdap4.h +@@ -12,9 +12,9 @@ + #include <stdio.h> + + #include "config.h" ++#include "nc4internal.h" + #include "netcdf.h" + #include "nc.h" +-#include "nc4internal.h" + #include "ncdap.h" + #include "getvara.h" + #include "constraints3.h" diff --git a/sci-libs/netcdf/files/netcdf-4.1.1-parallel-build.patch b/sci-libs/netcdf/files/netcdf-4.1.1-parallel-build.patch new file mode 100644 index 000000000000..22708e2201e9 --- /dev/null +++ b/sci-libs/netcdf/files/netcdf-4.1.1-parallel-build.patch @@ -0,0 +1,40 @@ +Avoid building fortran modules twice, just install them instead. + +https://bugs.gentoo.org/296174 + +--- netcdf-4.1.1/f90/Makefile.am ++++ netcdf-4.1.1/f90/Makefile.am +@@ -101,17 +101,25 @@ + # Some fortran compilers change the file names of .mod files to all + # uppercase. Just to be special. + if UPPER_CASE_MOD +-nodist_include_HEADERS = TYPESIZES.mod NETCDF.mod +-TYPESIZES.mod: typeSizes.o +-NETCDF.mod: $(NETCDF_O) +-BUILT_SOURCES = TYPESIZES.mod ++NETCDF_MODULES = TYPESIZES.mod NETCDF.mod + else +-nodist_include_HEADERS = typesizes.mod netcdf.mod +-typesizes.mod: typeSizes.o +-netcdf.mod: $(NETCDF_O) +-BUILT_SOURCES = typesizes.mod ++NETCDF_MODULES = typesizes.mod netcdf.mod + endif + ++NETCDF_LO := $(NETCDF_O:.o=.lo) ++$(NETCDF_LO): typeSizes.o ++install-data-local: ++ test -z "$(includedir)" || $(MKDIR_P) "$(DESTDIR)$(includedir)" ++ @list='$(NETCDF_MODULES)'; test -n "$(includedir)" || list=; \ ++ for p in $$list; do \ ++ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ ++ echo "$$d$$p"; \ ++ done | $(am__base_list) | \ ++ while read files; do \ ++ echo " $(INSTALL_HEADER) $$files '$(DESTDIR)$(includedir)'"; \ ++ $(INSTALL_HEADER) $$files "$(DESTDIR)$(includedir)" || exit $$?; \ ++ done ++ + # This is what we are building: a convenience library of F90 functions. + noinst_LTLIBRARIES = libnetcdff90.la + diff --git a/sci-libs/netcdf/files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch b/sci-libs/netcdf/files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch new file mode 100644 index 000000000000..783a5b06e991 --- /dev/null +++ b/sci-libs/netcdf/files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch @@ -0,0 +1,145 @@ +From 435d8a03ed28bb5ad63aff12cbc6ab91531b6bc8 Mon Sep 17 00:00:00 2001 +From: Quincey Koziol <quincey@koziol.cc> +Date: Wed, 7 May 2014 08:45:15 -0500 +Subject: [PATCH] Account for the HDF5 library not having the MPI-POSIX VFD + configured in. + +--- + RELEASE_NOTES.md | 2 ++ + libsrc4/nc4file.c | 40 ++++++++++++++++++++++++++++++++++++++++ + nc_test4/tst_nc4perf.c | 5 +++++ + nc_test4/tst_parallel3.c | 5 +++++ + 4 files changed, 52 insertions(+) + +diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md +index 27f228c..1a69d17 100644 +--- a/RELEASE_NOTES.md ++++ b/RELEASE_NOTES.md +@@ -9,6 +9,8 @@ This file contains a high-level description of this package's evolution. Release + + ### 4.3.3-rc1 Released TBD + ++* When the NC_MPIPOSIX flag is given for parallel I/O access and the HDF5 library does not have the MPI-POSIX VFD configured in, the NC_MPIPOSIX flag is transparently aliased to the NC_MPIIO flag within the netCDF-4 library. ++ + ## 4.3.2 Released 2014-04-23 + + * As part of an ongoing project, the Doxygen-generated netcdf documentation has been reorganized. The goal is to make the documentation easier to parse, and to eliminate redundant material. This project is ongoing. +diff --git a/libsrc4/nc4file.c b/libsrc4/nc4file.c +index ec3bb0c..5c957be 100644 +--- a/libsrc4/nc4file.c ++++ b/libsrc4/nc4file.c +@@ -308,12 +308,21 @@ nc4_create_file(const char *path, int cmode, MPI_Comm comm, MPI_Info info, + if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0) + BAIL(NC_EPARINIT); + } ++#ifdef USE_PARALLEL_POSIX + else /* MPI/POSIX */ + { + LOG((4, "creating parallel file with MPI/posix")); + if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0) + BAIL(NC_EPARINIT); + } ++#else /* USE_PARALLEL_POSIX */ ++ /* Should not happen! Code in NC4_create/NC4_open should alias the ++ * NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not ++ * available in HDF5. -QAK ++ */ ++ else /* MPI/POSIX */ ++ BAIL(NC_EPARINIT); ++#endif /* USE_PARALLEL_POSIX */ + + /* Keep copies of the MPI Comm & Info objects */ + if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm)) +@@ -465,6 +474,17 @@ NC4_create(const char* path, int cmode, size_t initialsz, int basepe, + ) + return NC_EINVAL; + ++#ifndef USE_PARALLEL_POSIX ++/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias ++ * the NC_MPIPOSIX flag to NC_MPIIO. -QAK ++ */ ++ if(cmode & NC_MPIPOSIX) ++ { ++ cmode &= ~NC_MPIPOSIX; ++ cmode |= NC_MPIIO; ++ } ++#endif /* USE_PARALLEL_POSIX */ ++ + cmode |= NC_NETCDF4; + + /* Apply default create format. */ +@@ -2168,12 +2188,21 @@ nc4_open_file(const char *path, int mode, MPI_Comm comm, + if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0) + BAIL(NC_EPARINIT); + } ++#ifdef USE_PARALLEL_POSIX + else /* MPI/POSIX */ + { + LOG((4, "opening parallel file with MPI/posix")); + if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0) + BAIL(NC_EPARINIT); + } ++#else /* USE_PARALLEL_POSIX */ ++ /* Should not happen! Code in NC4_create/NC4_open should alias the ++ * NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not ++ * available in HDF5. -QAK ++ */ ++ else /* MPI/POSIX */ ++ BAIL(NC_EPARINIT); ++#endif /* USE_PARALLEL_POSIX */ + + /* Keep copies of the MPI Comm & Info objects */ + if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm)) +@@ -2640,6 +2669,17 @@ NC4_open(const char *path, int mode, int basepe, size_t *chunksizehintp, + (mode & NC_MPIIO && mode & NC_MPIPOSIX)) + return NC_EINVAL; + ++#ifndef USE_PARALLEL_POSIX ++/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias ++ * the NC_MPIPOSIX flag to NC_MPIIO. -QAK ++ */ ++ if(mode & NC_MPIPOSIX) ++ { ++ mode &= ~NC_MPIPOSIX; ++ mode |= NC_MPIIO; ++ } ++#endif /* USE_PARALLEL_POSIX */ ++ + + /* Depending on the type of file, open it. */ + +diff --git a/nc_test4/tst_nc4perf.c b/nc_test4/tst_nc4perf.c +index 47af70e..3528b82 100644 +--- a/nc_test4/tst_nc4perf.c ++++ b/nc_test4/tst_nc4perf.c +@@ -244,6 +244,11 @@ int test_pio_4d(size_t cache_size, int facc_type, int access_flag, MPI_Comm comm + return 0; + } + ++/* Note: When the MPI-POSIX VFD is not compiled in to HDF5, the NC_MPIPOSIX ++ * flag will be aliased to the NC_MPIIO flag within the library, and ++ * therefore this test will exercise the aliasing, with the MPI-IO VFD, ++ * under that configuration. -QAK ++ */ + #define NUM_MODES 2 + #define NUM_FACC 2 + #define NUM_CHUNK_COMBOS_2D 3 +diff --git a/nc_test4/tst_parallel3.c b/nc_test4/tst_parallel3.c +index 27f9c98..9fa534f 100644 +--- a/nc_test4/tst_parallel3.c ++++ b/nc_test4/tst_parallel3.c +@@ -129,6 +129,11 @@ int main(int argc, char **argv) + if (mpi_rank == 0) + SUMMARIZE_ERR; + ++/* Note: When the MPI-POSIX VFD is not compiled in to HDF5, the NC_MPIPOSIX ++ * flag will be aliased to the NC_MPIIO flag within the library, and ++ * therefore this test will exercise the aliasing, with the MPI-IO VFD, ++ * under that configuration. -QAK ++ */ + if (mpi_rank == 0) + printf("*** Testing parallel IO for raw-data with MPIPOSIX-IO (driver)..."); + facc_type = NC_NETCDF4|NC_MPIPOSIX; +-- +2.0.3 + |