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Sync from SUSE:ALP:Source:Standard:1.0 netcdf revision 4f2f1bb6e18d41c5750e6c1147343b62

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This commit is contained in:
Adrian Schröter 2024-01-05 09:38:40 +01:00
commit 0c0cc44571
12 changed files with 2596 additions and 0 deletions
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23
.gitattributes vendored Normal file
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## Default LFS
*.7z filter=lfs diff=lfs merge=lfs -text
*.bsp filter=lfs diff=lfs merge=lfs -text
*.bz2 filter=lfs diff=lfs merge=lfs -text
*.gem filter=lfs diff=lfs merge=lfs -text
*.gz filter=lfs diff=lfs merge=lfs -text
*.jar filter=lfs diff=lfs merge=lfs -text
*.lz filter=lfs diff=lfs merge=lfs -text
*.lzma filter=lfs diff=lfs merge=lfs -text
*.obscpio filter=lfs diff=lfs merge=lfs -text
*.oxt filter=lfs diff=lfs merge=lfs -text
*.pdf filter=lfs diff=lfs merge=lfs -text
*.png filter=lfs diff=lfs merge=lfs -text
*.rpm filter=lfs diff=lfs merge=lfs -text
*.tbz filter=lfs diff=lfs merge=lfs -text
*.tbz2 filter=lfs diff=lfs merge=lfs -text
*.tgz filter=lfs diff=lfs merge=lfs -text
*.ttf filter=lfs diff=lfs merge=lfs -text
*.txz filter=lfs diff=lfs merge=lfs -text
*.whl filter=lfs diff=lfs merge=lfs -text
*.xz filter=lfs diff=lfs merge=lfs -text
*.zip filter=lfs diff=lfs merge=lfs -text
*.zst filter=lfs diff=lfs merge=lfs -text

143
Fix-spurious-uninitialized-variable-warning.patch Normal file
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From: Egbert Eich <eich@suse.com>
Date: Sat Jul 10 15:05:08 2021 +0200
Subject: Fix spurious uninitialized variable warning
Patch-mainline: Not yet
Git-repo: https://github.com/Unidata/netcdf-c
Git-commit: 7b4bb9bd0f882e658e4a3e512dda73e90e6c8a18
References:
These variables are not really uninitialized when used, however gcc
isn't able to determine this.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
libdispatch/nctime.c | 6 +++---
libhdf5/hdf5internal.c | 2 +-
libnczarr/zinternal.c | 2 +-
libnczarr/zsync.c | 4 ++--
ncgen3/getfill.c | 10 +++++-----
ncgen3/load.c | 10 +++++-----
nczarr_test/ncdumpchunks.c | 2 +-
oc2/ocdump.c | 4 ++--
8 files changed, 20 insertions(+), 20 deletions(-)
Index: netcdf-c-4.9.2/libdispatch/nctime.c
===================================================================
--- netcdf-c-4.9.2.orig/libdispatch/nctime.c
+++ netcdf-c-4.9.2/libdispatch/nctime.c
@@ -789,8 +789,8 @@ cdComp2Rel(cdCalenType timetype, cdCompT
CdTime humantime;
CdTimeType old_timetype;
cdUnitTime unit;
- double base_etm, etm, delta;
- long ndel, hoursInYear;
+ double base_etm, etm, delta = 0.; /* GCC */
+ long ndel = 0, hoursInYear;
/* Parse the relunits */
if(cdParseRelunits(timetype, relunits, &unit, &base_comptime))
@@ -982,7 +982,7 @@ cdRel2Comp(cdCalenType timetype, char* r
cdCompTime base_comptime;
cdUnitTime unit, baseunits;
double base_etm, result_etm;
- double delta;
+ double delta = 0.; /* GCC */
long idelta;
/* Parse the relunits */
Index: netcdf-c-4.9.2/libhdf5/hdf5internal.c
===================================================================
--- netcdf-c-4.9.2.orig/libhdf5/hdf5internal.c
+++ netcdf-c-4.9.2/libhdf5/hdf5internal.c
@@ -882,7 +882,7 @@ nc4_hdf5_find_grp_var_att(int ncid, int
NC_FILE_INFO_T *my_h5;
NC_GRP_INFO_T *my_grp;
NC_VAR_INFO_T *my_var = NULL;
- NC_ATT_INFO_T *my_att;
+ NC_ATT_INFO_T *my_att = NULL; /* GCC */
char my_norm_name[NC_MAX_NAME + 1] = "";
NCindex *attlist = NULL;
int retval;
Index: netcdf-c-4.9.2/libnczarr/zinternal.c
===================================================================
--- netcdf-c-4.9.2.orig/libnczarr/zinternal.c
+++ netcdf-c-4.9.2/libnczarr/zinternal.c
@@ -571,7 +571,7 @@ ncz_find_grp_var_att(int ncid, int varid
NC_FILE_INFO_T *my_h5;
NC_GRP_INFO_T *my_grp;
NC_VAR_INFO_T *my_var = NULL;
- NC_ATT_INFO_T *my_att;
+ NC_ATT_INFO_T *my_att = NULL; /* GCC */
char my_norm_name[NC_MAX_NAME + 1] = "";
NCindex *attlist = NULL;
int retval;
Index: netcdf-c-4.9.2/ncgen3/getfill.c
===================================================================
--- netcdf-c-4.9.2.orig/ncgen3/getfill.c
+++ netcdf-c-4.9.2/ncgen3/getfill.c
@@ -51,11 +51,11 @@ nc_fill(
void *datp, /* where to start filling */
union generic fill_val) /* value to use */
{
- char *char_valp; /* pointers used to accumulate data values */
- short *short_valp;
- int *long_valp;
- float *float_valp;
- double *double_valp;
+ char *char_valp = NULL; /* GCC *//* pointers used to accumulate data values */
+ short *short_valp = NULL; /* GCC */
+ int *long_valp = NULL; /* GCC */
+ float *float_valp = NULL; /* GCC */
+ double *double_valp = NULL; /* GCC */
switch (type) {
case NC_CHAR:
Index: netcdf-c-4.9.2/ncgen3/load.c
===================================================================
--- netcdf-c-4.9.2.orig/ncgen3/load.c
+++ netcdf-c-4.9.2/ncgen3/load.c
@@ -504,11 +504,11 @@ load_netcdf(
int stat = NC_NOERR;
size_t start[NC_MAX_VAR_DIMS];
size_t count[NC_MAX_VAR_DIMS];
- char *charvalp;
- short *shortvalp;
- int *intvalp;
- float *floatvalp;
- double *doublevalp;
+ char *charvalp = NULL; /* GCC */
+ short *shortvalp = NULL; /* GCC */
+ int *intvalp = NULL; /* GCC */
+ float *floatvalp = NULL; /* GCC */
+ double *doublevalp = NULL; /* GCC */
/* load values into variable */
Index: netcdf-c-4.9.2/nczarr_test/ncdumpchunks.c
===================================================================
--- netcdf-c-4.9.2.orig/nczarr_test/ncdumpchunks.c
+++ netcdf-c-4.9.2/nczarr_test/ncdumpchunks.c
@@ -303,7 +303,7 @@ dump(Format* format)
char sindices[64];
#ifdef H5
int i;
- hid_t fileid, grpid, datasetid;
+ hid_t fileid = H5P_DEFAULT, grpid = H5P_DEFAULT, datasetid = H5P_DEFAULT; /* GCC */
hid_t dxpl_id = H5P_DEFAULT; /*data transfer property list */
unsigned int filter_mask = 0;
hsize_t hoffset[NC_MAX_VAR_DIMS];
Index: netcdf-c-4.9.2/oc2/ocdump.c
===================================================================
--- netcdf-c-4.9.2.orig/oc2/ocdump.c
+++ netcdf-c-4.9.2/oc2/ocdump.c
@@ -464,8 +464,8 @@ ocreadfile(FILE* file, off_t datastart,
void
ocdd(OCstate* state, OCnode* root, int xdrencoded, int level)
{
- char* mem;
- size_t len;
+ char* mem = NULL; /* GCC */
+ size_t len = 0; /* GCC */
if(root->tree->data.file != NULL) {
if(!ocreadfile(root->tree->data.file,
root->tree->data.bod,

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NCD4_dumpbytes-Add-missing-initialization-of-float-types.patch Normal file
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From: Egbert Eich <eich@suse.com>
Date: Mon Jul 12 08:24:58 2021 +0200
Subject: NCD4_dumpbytes(): Add missing initialization of float types
Patch-mainline: Not yet
Git-repo: https://github.com/Unidata/netcdf-c
Git-commit: 429efb0b136d35c54f9db23f3c6affa1087514d2
References:
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
libdap4/d4dump.c | 2 ++
1 file changed, 2 insertions(+)
diff --git a/libdap4/d4dump.c b/libdap4/d4dump.c
index b2e18931..442227ec 100644
--- a/libdap4/d4dump.c
+++ b/libdap4/d4dump.c
@@ -45,6 +45,8 @@ NCD4_dumpbytes(size_t size, const void* data0, int swap)
v.i32[0] = *((int*)pos);
v.u64[0] = *((unsigned long long*)pos);
v.i64[0] = *((long long*)pos);
+ v.f32[0] = *((float*)pos);
+ v.f64[0] = *((double*)pos);
if(swap) {
swapinline16(v.u16);
swapinline32(v.u32);

29
NCZ_def_var_chunking-make-sure-cs-is-set-before-used.patch Normal file
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From: Egbert Eich <eich@suse.com>
Date: Mon Jul 12 11:57:24 2021 +0200
Subject: NCZ_def_var_chunking(): make sure 'cs' is set before used
Patch-mainline: Not yet
Git-repo: https://github.com/Unidata/netcdf-c
Git-commit: 47584171d90e03b9ddad94cbc7edf1ab20f9d468
References:
'cs' was only set when 'var->ndim' != 0. Thus cs could have been
uninitialized when ncz_dev_var_extra() was called.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
libnczarr/zvar.c | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/libnczarr/zvar.c b/libnczarr/zvar.c
index 28ab00fb..d9e6af5b 100644
--- a/libnczarr/zvar.c
+++ b/libnczarr/zvar.c
@@ -865,7 +865,7 @@ int
ncz_def_var_chunking_ints(int ncid, int varid, int contiguous, int *chunksizesp)
{
NC_VAR_INFO_T *var;
- size_t *cs;
+ size_t *cs = NULL;
int i, retval;
/* Get pointer to the var. */

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_multibuild Normal file
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@ -0,0 +1,8 @@
<multibuild>
<package>serial</package>
<package>openmpi4</package>
<package>gnu-hpc</package>
<package>gnu-openmpi4-hpc</package>
<package>gnu-mvapich2-hpc</package>
<package>gnu-mpich-hpc</package>
</multibuild>

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BIN
netcdf-c-4.9.2.tar.gz (Stored with Git LFS) Normal file
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1505
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netcdf.spec Normal file
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@ -0,0 +1,760 @@
#
# spec file
#
# Copyright (c) 2023 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
# upon. The license for this file, and modifications and additions to the
# file, is the same license as for the pristine package itself (unless the
# license for the pristine package is not an Open Source License, in which
# case the license is the MIT License). An "Open Source License" is a
# license that conforms to the Open Source Definition (Version 1.9)
# published by the Open Source Initiative.
# Please submit bugfixes or comments via https://bugs.opensuse.org/
#
%global flavor @BUILD_FLAVOR@%{nil}
%define _do_check 1
%define ver 4.9.2
%define _ver 4_9_2
%define pname netcdf
%define sonum 19
%if 0%{?sle_version} >= 150200
%define DisOMPI1 ExclusiveArch: do_not_build
%endif
%if !0%{?is_opensuse} && 0%{?sle_version:1}
%if 0%{?sle_version} < 150200
%define DisOMPI3 ExclusiveArch: do_not_build
%endif
%if 0%{?sle_version} < 150300
%define DisOMPI4 ExclusiveArch: do_not_build
%endif
%endif
%bcond_with valgrind_checks
# Keep disabled until properly set up on HDF5 library side
%bcond_with plugins
%if "%flavor" == ""
%define package_name %{pname}
ExclusiveArch: do_not_build
%endif
ExcludeArch: s390
%if "%{flavor}" == "serial"
%bcond_with hpc
%endif
%if "%{flavor}" == "gnu-hpc"
%global compiler_family gnu
%undefine c_f_ver
%undefine mpi_flavor
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu-openmpi4-hpc"
%{?DisOMPI4}
%global compiler_family gnu
%undefine c_f_ver
%define mpi_flavor openmpi
%define mpi_ver 4
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu-openmpi5-hpc"
%{?DisOMPI5}
%global compiler_family gnu
%undefine c_f_ver
%define mpi_flavor openmpi
%define mpi_ver 5
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu-mvapich2-hpc"
%global compiler_family gnu
%undefine c_f_ver
%define mpi_flavor mvapich2
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu-mpich-hpc"
%global compiler_family gnu
%undefine c_f_ver
%define mpi_flavor mpich
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu7-hpc"
%global compiler_family gnu
%define c_f_ver 7
%undefine mpi_flavor
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu7-openmpi4-hpc"
%{?DisOMPI4}
%global compiler_family gnu
%define c_f_ver 7
%define mpi_flavor openmpi
%define mpi_ver 4
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu7-openmpi5-hpc"
%{?DisOMPI5}
%global compiler_family gnu
%define c_f_ver 7
%define mpi_flavor openmpi
%define mpi_ver 5
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu7-mvapich2-hpc"
%global compiler_family gnu
%define c_f_ver 7
%define mpi_flavor mvapich2
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu7-mpich-hpc"
%global compiler_family gnu
%define c_f_ver 7
%define mpi_flavor mpich
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu8-hpc"
%global compiler_family gnu
%define c_f_ver 8
%undefine mpi_flavor
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu8-openmpi4-hpc"
%{?DisOMPI4}
%global compiler_family gnu
%define c_f_ver 8
%define mpi_flavor openmpi
%define mpi_ver 4
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu8-openmpi5-hpc"
%{?DisOMPI5}
%global compiler_family gnu
%define c_f_ver 8
%define mpi_flavor openmpi
%define mpi_ver 5
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu8-mvapich2-hpc"
%global compiler_family gnu
%define c_f_ver 8
%define mpi_flavor mvapich2
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu8-mpich-hpc"
%global compiler_family gnu
%define c_f_ver 8
%define mpi_flavor mpich
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu9-hpc"
%global compiler_family gnu
%define c_f_ver 9
%undefine mpi_flavor
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu9-openmpi4-hpc"
%{?DisOMPI4}
%global compiler_family gnu
%define c_f_ver 9
%define mpi_flavor openmpi
%define mpi_ver 4
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu9-openmpi5-hpc"
%{?DisOMPI5}
%global compiler_family gnu
%define c_f_ver 9
%define mpi_flavor openmpi
%define mpi_ver 5
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu9-mvapich2-hpc"
%global compiler_family gnu
%define c_f_ver 9
%define mpi_flavor mvapich2
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu9-mpich-hpc"
%global compiler_family gnu
%define c_f_ver 9
%define mpi_flavor mpich
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu10-hpc"
%global compiler_family gnu
%define c_f_ver 10
%undefine mpi_flavor
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu10-openmpi4-hpc"
%{?DisOMPI4}
%global compiler_family gnu
%define c_f_ver 10
%define mpi_flavor openmpi
%define mpi_ver 4
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu10-openmpi5-hpc"
%{?DisOMPI5}
%global compiler_family gnu
%define c_f_ver 10
%define mpi_flavor openmpi
%define mpi_ver 5
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu10-mvapich2-hpc"
%global compiler_family gnu
%define c_f_ver 10
%define mpi_flavor mvapich2
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu10-mpich-hpc"
%global compiler_family gnu
%define c_f_ver 10
%define mpi_flavor mpich
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu11-openmpi4-hpc"
%{?DisOMPI4}
%global compiler_family gnu
%define c_f_ver 11
%define mpi_flavor openmpi
%define mpi_ver 4
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu11-openmpi5-hpc"
%{?DisOMPI5}
%global compiler_family gnu
%define c_f_ver 11
%define mpi_flavor openmpi
%define mpi_ver 5
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu11-mvapich2-hpc"
%global compiler_family gnu
%define c_f_ver 11
%define mpi_flavor mvapich2
%bcond_without hpc
%endif
%if "%{flavor}" == "gnu11-mpich-hpc"
%global compiler_family gnu
%define c_f_ver 11
%define mpi_flavor mpich
%bcond_without hpc
%endif
%if "%{flavor}" == "mvapich2"
%define mpi_flavor mvapich2
%bcond_with hpc
%endif
%if "%{flavor}" == "openmpi4"
%{?DisOMPI4}
%define mpi_flavor openmpi
%define mpi_ver 4
%bcond_with hpc
%endif
%if "%{flavor}" == "openmpi5"
%{?DisOMPI5}
%define mpi_flavor openmpi
%define mpi_ver 5
%bcond_with hpc
%endif
%{?mpi_flavor:%{bcond_without mpi}}%{!?mpi_flavor:%{bcond_with mpi}}
%{?with_hpc:%{!?compiler_family:%global compiler_family gnu}}
%{?with_mpi:%{!?mpi_flavor:error "No MPI family specified!"}}
# openmpi 1 was called just "openmpi" in Leap 15.x/SLE15
%if 0%{?suse_version} >= 1550 || "%{mpi_flavor}" != "openmpi" || "%{mpi_ver}" != "1"
%define mpi_ext %{?mpi_ver}
%endif
%if %{with hpc}
ExcludeArch: %ix86
%{hpc_init -c %compiler_family %{?c_f_ver:-v %{c_f_ver}} %{?with_mpi:-m {%mpi_flavor}} %{?mpi_ver:-V %{mpi_ver}} %{?ext:-e %{ext}}}
%define package_name %{hpc_package_name %_ver}
%define libname(s:) lib%{pname}%{hpc_package_name_tail %_ver}
%define p_prefix %hpc_prefix
%define p_bindir %hpc_bindir
%define p_libdir %hpc_libdir
%define p_mandir %hpc_mandir
%define p_includedir %hpc_includedir
%else
%define package_name %{pname}%{p_suffix}
%define libname(s:) lib%{pname}%{-s*}%{?p_suffix}
%if %{without mpi}
%define p_prefix %_prefix
%define p_bindir %_bindir
%define p_libdir %_libdir
%define p_mandir %_mandir
%define p_includedir %_includedir
%else
%define p_prefix /usr/%{_lib}/mpi/gcc/%{mpi_flavor}%{?mpi_ext}
%define p_bindir %{p_prefix}/bin
%define p_libdir %{p_prefix}/%{_lib}
%define p_mandir %{p_prefix}/share/man
%define p_includedir %{p_prefix}/include
%endif
%endif
%define p_suffix %{?with_mpi:-%{mpi_flavor}%{?mpi_ext}}
%define hdf5_module_file %{?with_mpi:p}hdf5
%define purpose_compiler %{?nil:%{!?with_hpc:.}
%{?with_hpc:built for the %{compiler_family} compiler%{?c_f_ver: version %c_f_ver}.}
}
%define purpose() This package contains %{?with_mpi:the %{mpi_flavor}%{?mpi_ver} version of }%{**}%{purpose_compiler}
%if %{with valgrind_checks}
%ifnarch %ix86 x86_64 ppc ppc64 s390x armv7l aarch64
%{error: Vagrind not support on this platform!}
%else
%define valgrind_checks 1
%endif
%endif
Name: %{package_name}
Summary: Command-line programs for the NetCDF scientific data format
License: NetCDF
Group: Productivity/Scientific/Other
Version: %ver
Release: 0
URL: https://www.unidata.ucar.edu/software/netcdf/
Source: https://downloads.unidata.ucar.edu/netcdf-c/%{version}/%{pname}-c-%{version}.tar.gz
Source1: nc-config.1.gz
Patch6: parseServers-Fix-uninitialized-variable-simplify-error-path.patch
Patch8: val_NC_check_voff-Fix-uninitialized-variable-warning.patch
Patch9: pr_att-Fix-uninitialized-variable.patch
Patch10: NCD4_dumpbytes-Add-missing-initialization-of-float-types.patch
Patch11: NCZ_def_var_chunking-make-sure-cs-is-set-before-used.patch
Patch12: Fix-spurious-uninitialized-variable-warning.patch
BuildRequires: autoconf
BuildRequires: automake
BuildRequires: gawk
BuildRequires: libcurl-devel >= 7.18.0
BuildRequires: libtool
BuildRequires: pkg-config
BuildRequires: unzip
BuildRequires: zlib-devel >= 1.2.5
BuildRequires: pkgconfig(libxml-2.0)
BuildRequires: pkgconfig(libzstd)
%if 0%{?valgrind_checks}
BuildRequires: valgrind
%endif
%if %{without hpc}
BuildRequires: gcc-c++
BuildRequires: gcc-fortran
BuildRequires: hdf5%{p_suffix}-devel
BuildRequires: libhdf5_hl%{p_suffix}
%if %{with mpi}
BuildRequires: %{mpi_flavor}%{?mpi_ext}-devel
%endif
%else
BuildRequires: %{compiler_family}%{?c_f_ver}-compilers-hpc-macros-devel
BuildRequires: hdf5-%{compiler_family}%{?c_f_ver}%{?with_mpi:-%{mpi_flavor}%{?mpi_ver}}-hpc-devel
# Install libhdf5*-<compiler_family>-hpc explicitly for %%requires_eq:
BuildRequires: libhdf5-%{compiler_family}%{?c_f_ver}%{?with_mpi:-%{mpi_flavor}%{?mpi_ver}}-hpc
BuildRequires: libhdf5_hl-%{compiler_family}%{?c_f_ver}%{?with_mpi:-%{mpi_flavor}%{?mpi_ver}}-hpc
BuildRequires: lua-lmod
BuildRequires: suse-hpc
%if %{with mpi}
BuildRequires: %{mpi_flavor}%{?mpi_ver}-%{compiler_family}%{?c_f_ver}-hpc-macros-devel
%endif
%endif
Requires: %{libname -s %{sonum}} = %{version}
%description
NetCDF is a set of software libraries and self-describing,
machine-independent data formats that support the creation, access,
and sharing of array-oriented scientific data.
%{purpose utility functions for working with NetCDF files}
%{?with_hpc:%{hpc_master_package}}
%package -n %{libname -s %{sonum}}
Summary: Shared libraries for the NetCDF scientific data format
Group: Productivity/Scientific/Other
%if %{without hpc}
# To avoid unresolvable errors due to multiple providers of the library
%{requires_eq \--whatprovides libhdf5%{p_suffix}}
%{requires_eq \--whatprovides libhdf5_hl%{p_suffix}}
%else
%{hpc_requires}
%{requires_eq libhdf5%{hpc_package_name_tail}}
%{requires_eq libhdf5_hl%{hpc_package_name_tail}}
%endif
%description -n %{libname -s %{sonum}}
NetCDF is a set of software libraries and self-describing,
machine-independent data formats that support the creation, access,
and sharing of array-oriented scientific data.
NetCDF (network Common Data Form) is an interface for array-oriented
data access and a collection of software libraries
for C, Fortran, C++, and Perl that provides an implementation of the
interface. The NetCDF library also defines a machine-independent
format for representing scientific data. Together, the interface,
library, and format support the creation, access, and sharing of
scientific data.
NetCDF data is:
- Self-Describing: A NetCDF file includes information about the
data it contains.
- Network-transparent: A NetCDF file is represented in a form that
can be accessed by computers with different ways of storing
integers, characters, and floating-point numbers.
- Direct-access: A small subset of a large dataset may be accessed
efficiently, without first reading through all the preceding
data.
- Appendable: Data can be appended to a NetCDF dataset along one
dimension without copying the dataset or redefining its
structure. The structure of a NetCDF dataset can be changed,
though this sometimes causes the dataset to be copied.
- Sharable: One writer and multiple readers may simultaneously
access the same NetCDF file.
%{purpose the NetCDF runtime libraries}
%{?with_hpc:%{hpc_master_package -L -l}}
%package devel-data
Summary: Development data files for %{name}
Group: Development/Libraries/C and C++
Provides: %{pname}-rpm-macros = %version
Conflicts: otherproviders(%{pname}-rpm-macros)
%description devel-data
NetCDF is a set of software libraries and self-describing,
machine-independent data formats that support the creation, access,
and sharing of array-oriented scientific data.
This package contains generic files needed to create projects that use
any version of NetCDF.
%package devel
Summary: Development files for %{name}
Group: Development/Libraries/C and C++
Requires: %{libname -s %{sonum}} = %{version}
%{!?with_hpc:Requires: %{pname}-devel-data = %{version}}
Requires: libcurl-devel >= 7.18.0
Requires: pkgconfig
Requires: zlib-devel >= 1.2.5
%if %{without hpc}
%{requires_eq hdf5%{p_suffix}-devel}
%{?with_mpi:Requires: %{mpi_flavor}%{?mpi_ext}-devel}
%else
%{hpc_requires_devel}
%{requires_eq hdf5%{hpc_package_name_tail}-devel}
%endif
%description devel
NetCDF is a set of software libraries and self-describing,
machine-independent data formats that support the creation, access,
and sharing of array-oriented scientific data.
%{purpose all files needed to create projects that use NetCDF}
%{?with_hpc:%{hpc_master_package devel}}
%package devel-static
Summary: Static development files for %{name}
Group: Development/Libraries/C and C++
%if %{without hpc}
%{requires_eq hdf5%{p_suffix}-devel}
%else
Requires: %{name}-devel = %{version}
%endif
Requires: libcurl-devel >= 7.18.0
Requires: zlib-devel >= 1.2.5
%description devel-static
NetCDF is a set of software libraries and self-describing,
machine-independent data formats that support the creation, access,
and sharing of array-oriented scientific data.
%{purpose the static libraries for NetCDF}
%prep
%{?with_hpc:%hpc_debug}
%setup -q -n %{pname}-c-%{version}
%autopatch -p1
# Create baselib.conf dynamically (non-HPC build only).
%if %{without hpc}
cat > %{_sourcedir}/baselibs.conf <<EOF
%{libname -s %{sonum}}
EOF
%endif
# Fix spurious-executable-perm RPMLINT warning
chmod a-x RELEASE_NOTES.md
%build
%global _lto_cflags %{_lto_cflags} -ffat-lto-objects
%{?with_hpc:%{hpc_setup}}
%{?with_hpc:module load %{hdf5_module_file}}
%if %{without mpi}
export CC=gcc CXX=g++ FC=gfortran
%else
export CC=%{!?with_hpc:/usr/%_lib/mpi/gcc/%{mpi_flavor}%{?mpi_ext}/bin/}mpicc
export FC=%{!?with_hpc:/usr/%_lib/mpi/gcc/%{mpi_flavor}%{?mpi_ext}/bin/}mpif90
export CXX=%{!?with_hpc:/usr/%_lib/mpi/gcc/%{mpi_flavor}%{?mpi_ext}/bin/}mpic++
%endif
autoreconf -fv
export CFLAGS="%{optflags} %{?with_hpc:-L$HDF5_LIB -I$HDF5_INC}"
export CXXFLAGS="%{optflags} %{?with_hpc:-L$HDF5_LIB -I$HDF5_INC}"
export FCFLAGS="%{optflags} %{?with_hpc:-L$HDF5_LIB -I$HDF5_INC}"
%{?with_hpc:export LDFLAGS="-L$HDF5_LIB"}
%if %{without hpc}
%configure \
--prefix=%{p_prefix} \
--bindir=%{p_bindir} \
--libdir=%{p_libdir} \
--includedir=%{p_includedir} \
--mandir=%{p_mandir} \
%else
%hpc_configure \
%endif
--enable-shared \
--enable-netcdf-4 \
--enable-dap \
--enable-extra-example-tests \
--disable-dap-remote-tests \
--with-pic \
--disable-doxygen \
--enable-static \
%if %{with plugins}
--enable-plugins \
--with-plugin-dir=%{p_libdir}/hdf5/plugin/
%else
--disable-plugins \
%endif
# --enable-logging \
%make_build
# Build tests without executing
%make_build check TESTS=""
%install
%{?with_hpc:%{hpc_setup}}
%{?with_hpc:module load %{hdf5_module_file}}
%{?with_hpc:export CFLAGS="-L$HDF5_LIB -I$HDF5_INC"}
make install DESTDIR="%{buildroot}"
mkdir -p %{buildroot}%{_mandir}/man1
install -m644 %{S:1} %{buildroot}%{p_mandir}/man1
rm -f %{buildroot}%{p_libdir}/*.la
# install netcdf_par.h which is skipped when mpicc in not detected
install -m644 include/netcdf_par.h %{buildroot}%{p_includedir}/netcdf_par.h
%if %{without mpi} && %{without hpc}
# rpm macro for version checking
mkdir -p %{buildroot}%{_rpmmacrodir}
cat > %{buildroot}%{_rpmmacrodir}/macros.netcdf <<EOF
#
# RPM macros for hdf5 packaging
#
%_netcdf_sonum %{sonum}
%_netcdf_version %{version}
EOF
%endif
%if %{without hpc}
%if %{with mpi}
# Module files
mkdir -p %{buildroot}%{_datadir}/modules/%{pname}-%{mpi_flavor}%{?mpi_ext}
cat << EOF > %{buildroot}%{_datadir}/modules/%{pname}-%{mpi_flavor}%{?mpi_ext}/%version
#%%Module
proc ModulesHelp { } {
global dotversion
puts stderr "\tLoads the %{pname}-%{mpi_flavor} %version Environment"
}
module-whatis "Loads the %{pname}-%{mpi_flavor} %version Environment."
prepend-path PATH %{p_bindir}
prepend-path MANPATH %{p_mandir}
prepend-path LD_LIBRARY_PATH %{p_libdir}
prepend-path LIBRARY_PATH %{p_libdir}
prepend-path CPATH %{p_includedir}
prepend-path C_INCLUDE_PATH %{p_includedir}
prepend-path CPLUS_INCLUDE_PATH %{p_includedir}
EOF
%endif
%else
%hpc_write_modules_files
#%%Module1.0#####################################################################
proc ModulesHelp { } {
puts stderr " "
puts stderr "This module loads the NetCDF C API built with the %{compiler_family} compiler"
puts stderr "toolchain and the %{mpi_flavor}%{?mpi_ver} MPI stack."
puts stderr " "
puts stderr "Note that this build of NetCDF leverages the HDF I/O library and requires linkage"
puts stderr "against hdf5. Consequently, the phdf5 package is loaded automatically with this module."
puts stderr "A typical compilation step for C applications requiring NetCDF is as follows:"
puts stderr " "
puts stderr "\\\$CC -I\\\$NETCDF_INC app.c -L\\\$NETCDF_LIB -lnetcdf -L\\\$HDF5_LIB -lhdf5"
puts stderr "\nVersion %{version}\n"
}
module-whatis "Name: %{hpc_upcase %pname} built with %{compiler_family} toolchain"
module-whatis "Version: %{version}"
module-whatis "Category: runtime library"
module-whatis "Description: %{SUMMARY:0}"
module-whatis "%{url}"
set version %{version}
# Require phdf5
if [ expr [ module-info mode load ] || [module-info mode display ] ] {
if { ![is-loaded %{hdf5_module_file}] } {
module load %{hdf5_module_file}
}
}
prepend-path PATH %{hpc_bindir}
prepend-path MANPATH %{hpc_mandir}
prepend-path LD_LIBRARY_PATH %{hpc_libdir}
setenv %{hpc_upcase %pname}_DIR %{hpc_prefix}
setenv %{hpc_upcase %pname}_BIN %{hpc_bindir}
if {[file isdirectory %{hpc_includedir}]} {
prepend-path LIBRARY_PATH %{hpc_libdir}
prepend-path CPATH %{hpc_includedir}
prepend-path C_INCLUDE_PATH %{hpc_includedir}
prepend-path CPLUS_INCLUDE_PATH %{hpc_includedir}
prepend-path INCLUDE %{hpc_includedir}
%hpc_modulefile_add_pkgconfig_path
setenv %{hpc_upcase %pname}_LIB %{hpc_libdir}
setenv %{hpc_upcase %pname}_INC %{hpc_includedir}
}
EOF
%endif
%if 0%{?_do_check}
%check
%if %{with hpc}
%{hpc_setup}
module load %{hdf5_module_file}
%else
%if %{with mpi}
. /usr/%_lib/mpi/gcc/%{mpi_flavor}%{?mpi_ext}/bin/mpivars.sh
%endif
%endif
%ifarch ppc64 s390x %ix86
# tst_netcdf4_4 fails on ix86 - https://github.com/Unidata/netcdf-c/issues/2433
make check || { echo -e "WARNING: ignore check error for ppc64/s390x/ix86"; }
%else
make check
%endif
%if 0%{?valgrind_checks}
make check-valgrind
%endif
%endif
%if %{with hpc} || %{with mpi}
%define ldconfig_args -N %p_libdir
%endif
%post -n %{libname -s %{sonum}}
/sbin/ldconfig %{?ldconfig_args}
%postun -n %{libname -s %{sonum}}
/sbin/ldconfig %{?ldconfig_args}
%{?with_hpc:%hpc_module_delete_if_default}
%files
%license COPYRIGHT
%doc README.md RELEASE_NOTES.md
%{?with_hpc:%dir %hpc_datadir}
%{?with_hpc:%dir %p_mandir}
%{p_bindir}%{!?with_hpc:/*}
%exclude %{p_bindir}/nc-config
%if "%{flavor}" != "serial"
%dir %{p_mandir}/man1
%endif
%{p_mandir}/man1/*
%files -n %{libname -s %{sonum}}
%if %{with hpc}
%hpc_dirs
%hpc_modules_files
%else
%if %{with mpi}
%dir %{_datadir}/modules
%{_datadir}/modules/%{pname}-%{mpi_flavor}%{?mpi_ext}
%endif
%endif
%{p_libdir}/libnetcdf.so.%{sonum}*
%if %{without mpi} && %{without hpc}
%files devel-data
%{_rpmmacrodir}/macros.netcdf
%endif
%files devel
%{p_bindir}/nc-config
%{p_includedir}%{!?with_hpc:/*}
%{p_libdir}/*.so
%{?with_hpc:%hpc_pkgconfig_file}
%{p_libdir}/pkgconfig/netcdf.pc
%if "%{flavor}" != "serial"
%dir %{p_mandir}/man3
%endif
%{p_mandir}/man3/*
%{p_libdir}/libnetcdf.settings
%files devel-static
%{p_libdir}/libnetcdf.a
%changelog

40
parseServers-Fix-uninitialized-variable-simplify-error-path.patch Normal file
View File

@ -0,0 +1,40 @@
From: Egbert Eich <eich@suse.com>
Date: Sat Jul 10 09:41:22 2021 +0200
Subject: parseServers(): Fix uninitialized variable simplify error path
Patch-mainline: Not yet
Git-repo: https://github.com/Unidata/netcdf-c
Git-commit: 06fbbbc78023abca48ae3a69aa409f7f0a4cf3a3
References:
When rtslen == 0 code jumped to 'done' where it checked for rts being
!= NULL. At this point, rts was not yet set.
Fixed code paths eliminating unneeded tests and jumps.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
include/nctestserver.h | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/include/nctestserver.h b/include/nctestserver.h
index 978210c8..e7b63b80 100644
--- a/include/nctestserver.h
+++ b/include/nctestserver.h
@@ -47,7 +47,7 @@ parseServers(const char* remotetestservers)
size_t rtslen = strlen(remotetestservers);
/* Keep LGTM quiet */
- if(rtslen > MAXREMOTETESTSERVERS) goto done;
+ if(rtslen > MAXREMOTETESTSERVERS) return NULL;
list = (char**)malloc(sizeof(char*) * (int)(rtslen/2));
if(list == NULL) return NULL;
rts = strdup(remotetestservers);
@@ -65,8 +65,8 @@ parseServers(const char* remotetestservers)
*l = NULL;
servers = list;
list = NULL;
+ free(rts);
done:
- if(rts) free(rts);
if(list) free(list);
return servers;
}

27
pr_att-Fix-uninitialized-variable.patch Normal file
View File

@ -0,0 +1,27 @@
From: Egbert Eich <eich@suse.com>
Date: Sat Jul 10 14:57:29 2021 +0200
Subject: pr_att(): Fix uninitialized variable
Patch-mainline: Not yet
Git-repo: https://github.com/Unidata/netcdf-c
Git-commit: 66eade948d044832b0ca5feff824e1aca3c7fe68
References:
Fix uninitialized variable in error path.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
ncdump/ncdump.c | 1 +
1 file changed, 1 insertion(+)
diff --git a/ncdump/ncdump.c b/ncdump/ncdump.c
index d333cc37..41f44683 100644
--- a/ncdump/ncdump.c
+++ b/ncdump/ncdump.c
@@ -896,6 +896,7 @@ pr_att(
value = *((uint64_t *)data + i);
break;
default:
+ value = 0; /* GCC */
error("enum must have an integer base type: %d", base_nc_type);
}
NC_CHECK( nc_inq_enum_ident(ncid, att.type, value,

29
val_NC_check_voff-Fix-uninitialized-variable-warning.patch Normal file
View File

@ -0,0 +1,29 @@
From: Egbert Eich <eich@suse.com>
Date: Sat Jul 10 10:43:10 2021 +0200
Subject: val_NC_check_voff(): Fix uninitialized variable warning
Patch-mainline: Not yet
Git-repo: https://github.com/Unidata/netcdf-c
Git-commit: 8b6a94698ff2a862b0188c8c74c9832c967e76f1
References:
Make variables used in error message match the condition that triggered
the message.
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
ncdump/ncvalidator.c | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/ncdump/ncvalidator.c b/ncdump/ncvalidator.c
index 3cb6353f..37d7de06 100644
--- a/ncdump/ncvalidator.c
+++ b/ncdump/ncvalidator.c
@@ -2075,7 +2075,7 @@ val_NC_check_voff(NC *ncp)
if (ncp->begin_rec < prev_off) {
if (verbose) printf("Error:\n");
- if (verbose) printf("\tRecord variable section begin offset (%lld) is less than fixed-size variable section end offset (%lld)\n", varp->begin, prev_off);
+ if (verbose) printf("\tRecord variable section begin offset (%lld) is less than fixed-size variable section end offset (%lld)\n", ncp->begin_rec, prev_off);
nerrs++;
DEBUG_ASSIGN_ERROR(status, NC_ENOTNC)
}