* [gentoo-commits] repo/gentoo:master commit in: sci-libs/netcdf/files/
@ 2023-03-17 10:40 Andrew Ammerlaan
0 siblings, 0 replies; 3+ messages in thread
From: Andrew Ammerlaan @ 2023-03-17 10:40 UTC (permalink / raw
To: gentoo-commits
commit: 79af0a321004056c8d47ee8d17f63f8b288bd332
Author: Michael Mair-Keimberger <mmk <AT> levelnine <DOT> at>
AuthorDate: Thu Mar 16 17:16:45 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Mar 17 10:40:31 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=79af0a32
sci-libs/netcdf: remove unused patch
Signed-off-by: Michael Mair-Keimberger <mmk <AT> levelnine.at>
Closes: https://github.com/gentoo/gentoo/pull/30157
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
.../files/netcdf-4.9.0-fix-musl-execinfo_h.patch | 46 ----------------------
1 file changed, 46 deletions(-)
diff --git a/sci-libs/netcdf/files/netcdf-4.9.0-fix-musl-execinfo_h.patch b/sci-libs/netcdf/files/netcdf-4.9.0-fix-musl-execinfo_h.patch
deleted file mode 100644
index 7b711327512a..000000000000
--- a/sci-libs/netcdf/files/netcdf-4.9.0-fix-musl-execinfo_h.patch
+++ /dev/null
@@ -1,46 +0,0 @@
-# Conditionally include execinfo as it's not available on all libc
-# systems. There is a PR upstream for a similiar issue but the actual
-# issus is not reproducable on Gentoo [math library not found] [1], so
-# for now this is a temporary fix and can be removed once the PR [1]
-# is merged upstream.
-# [1]: https://github.com/Unidata/netcdf-c/pull/1701
-#
-# Closes: https://bugs.gentoo.org/828677
---- a/libhdf5/hdf5debug.c
-+++ b/libhdf5/hdf5debug.c
-@@ -5,7 +5,7 @@
- #include "config.h"
- #include <stdarg.h>
- #include <stdio.h>
--#if !defined _WIN32 && !defined __CYGWIN__
-+#ifdef HAVE_EXECINFO_H
- #include <execinfo.h>
- #endif
-
-@@ -15,15 +15,18 @@
-
- #define STSIZE 1000
-
-+#ifdef HAVE_EXECINFO_H
- #ifdef H5BACKTRACE
- # if !defined _WIN32 && !defined __CYGWIN__
- static void* stacktrace[STSIZE];
- # endif
- #endif
-+#endif
-
- int
- nch5breakpoint(int err)
- {
-+#ifdef HAVE_EXECINFO_H
- #ifdef H5BACKTRACE
- # if !defined _WIN32 && !defined __CYGWIN__
- int count = 0;
-@@ -39,6 +42,7 @@ nch5breakpoint(int err)
- if(trace != NULL) free(trace);
- # endif
- # endif
-+#endif
- #endif
- return err;
- }
^ permalink raw reply related [flat|nested] 3+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-libs/netcdf/files/
@ 2021-02-27 15:38 Conrad Kostecki
0 siblings, 0 replies; 3+ messages in thread
From: Conrad Kostecki @ 2021-02-27 15:38 UTC (permalink / raw
To: gentoo-commits
commit: 6552a105bd9efbcd159a05f851a8417ee69a8646
Author: Michael Mair-Keimberger <mmk <AT> levelnine <DOT> at>
AuthorDate: Fri Feb 26 16:52:32 2021 +0000
Commit: Conrad Kostecki <conikost <AT> gentoo <DOT> org>
CommitDate: Sat Feb 27 15:36:18 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6552a105
sci-libs/netcdf: remove unused patch
Closes: https://github.com/gentoo/gentoo/pull/19672
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Michael Mair-Keimberger <mmk <AT> levelnine.at>
Signed-off-by: Conrad Kostecki <conikost <AT> gentoo.org>
.../files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch | 145 ---------------------
1 file changed, 145 deletions(-)
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
deleted file mode 100644
index 783a5b06e99..00000000000
--- a/sci-libs/netcdf/files/netcdf-4.3.2-HDF5-1.8.13+-compat.patch
+++ /dev/null
@@ -1,145 +0,0 @@
-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
-
^ permalink raw reply related [flat|nested] 3+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-libs/netcdf/files/
@ 2017-01-29 20:10 David Seifert
0 siblings, 0 replies; 3+ messages in thread
From: David Seifert @ 2017-01-29 20:10 UTC (permalink / raw
To: gentoo-commits
commit: 3cecce2cc54b02e18fc5c282a78f544829619945
Author: Michael Mair-Keimberger (asterix) <m.mairkeimberger <AT> gmail <DOT> com>
AuthorDate: Sun Jan 29 09:12:24 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jan 29 20:09:38 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3cecce2c
sci-libs/netcdf: remove unused patches
Closes: https://github.com/gentoo/gentoo/pull/3709
sci-libs/netcdf/files/netcdf-4.1.1-fortran.patch | 15 ----
sci-libs/netcdf/files/netcdf-4.1.1-implicits.patch | 80 ----------------------
sci-libs/netcdf/files/netcdf-4.1.1-mpi-fix.patch | 32 ---------
.../netcdf/files/netcdf-4.1.1-parallel-build.patch | 40 -----------
4 files changed, 167 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
deleted file mode 100644
index 825fd3b..00000000
--- a/sci-libs/netcdf/files/netcdf-4.1.1-fortran.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-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
deleted file mode 100644
index a30aafc..00000000
--- a/sci-libs/netcdf/files/netcdf-4.1.1-implicits.patch
+++ /dev/null
@@ -1,80 +0,0 @@
-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
deleted file mode 100644
index 4656ef1..00000000
--- a/sci-libs/netcdf/files/netcdf-4.1.1-mpi-fix.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-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
deleted file mode 100644
index 22708e2..00000000
--- a/sci-libs/netcdf/files/netcdf-4.1.1-parallel-build.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-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
-
^ permalink raw reply related [flat|nested] 3+ messages in thread
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