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Accepting request 873286 from science:HPC

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OBS-URL: https://build.opensuse.org/request/show/873286
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/mvapich2?expand=0&rev=25
This commit is contained in:
Dominique Leuenberger 2021-02-18 19:41:10 +00:00 committed by Git OBS Bridge
commit b51d1efda8
4 changed files with 89 additions and 8 deletions
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26
mvapich2-fix-double-free.patch Normal file
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@ -0,0 +1,26 @@
commit 29cf7e8f54363de3ad614b3480517f02b84ade5e
Author: Nicolas Morey-Chaisemartin <nmoreychaisemartin@suse.com>
Date: Thu May 2 09:56:40 2019 +0200
mvapich2 fix double free
Fix double free that causes a SEGV when mvapich2 fails to open
a rdma device
Signed-off-by: Nicolas Morey-Chaisemartin <nmoreychaisemartin@suse.com>
diff --git src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_priv.c src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_priv.c
index 89f666c8988b..48454297223c 100644
--- src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_priv.c
+++ src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_priv.c
@@ -790,10 +790,6 @@ int rdma_open_hca(struct mv2_MPIDI_CH3I_RDMA_Process_t *proc)
}
if (!ib_dev) {
- /* Clean up before exit */
- if (dev_list) {
- ibv_free_device_list(dev_list);
- }
MPIR_ERR_SETFATALANDJUMP1(mpi_errno, MPI_ERR_OTHER, "**fail",
"**fail %s", "No IB device found");
}

37
mvapich2-remove-deprecated-sys_siglist.patch Normal file
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@ -0,0 +1,37 @@
commit d8dc7133c2c8255f194e1fa5e550ef1bd4796bf6
Author: Nicolas Morey-Chaisemartin <nmoreychaisemartin@suse.com>
Date: Thu Oct 15 10:12:24 2020 +0200
mvapich2 remove deprecated sys_siglist
sys_siglist has been deprecated and even removed from newer glibc version.
Use strsignal as a replacement
Signed-off-by: Nicolas Morey-Chaisemartin <nmoreychaisemartin@suse.com>
diff --git src/mpid/ch3/channels/common/src/util/error_handling.c src/mpid/ch3/channels/common/src/util/error_handling.c
index b6c67c41c056..27f7e63a64ac 100644
--- src/mpid/ch3/channels/common/src/util/error_handling.c
+++ src/mpid/ch3/channels/common/src/util/error_handling.c
@@ -69,7 +69,7 @@ int show_backtrace = 0;
// Signal handler for errors
void error_sighandler(int sig, siginfo_t *info, void *secret) {
// Always print error
- PRINT_ERROR( "Caught error: %s (signal %d)\n", sys_siglist[sig], sig );
+ PRINT_ERROR( "Caught error: %s (signal %d)\n", strsignal(sig), sig );
// Show backtrace if required
if (show_backtrace) print_backtrace();
// Raise the signal again with default handler
diff --git src/pm/mpirun/mpispawn.c src/pm/mpirun/mpispawn.c
index dd0c6f06f1c5..bcb562ea7552 100644
--- src/pm/mpirun/mpispawn.c
+++ src/pm/mpirun/mpispawn.c
@@ -800,7 +800,7 @@ void child_handler(int signal)
gethostname(my_host_name, MAX_HOST_LEN);
rank = mt_id;
- PRINT_DEBUG(DEBUG_Fork_verbose, "mpispawn child_handler: got signal %d: %s\n", signal, sys_siglist[signal]);
+ PRINT_DEBUG(DEBUG_Fork_verbose, "mpispawn child_handler: got signal %d: %s\n", signal, strsignal(signal));
while (1) {
do {
pid = waitpid(-1, &status, WNOHANG);

13
mvapich2.changes
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@ -1,3 +1,16 @@
-------------------------------------------------------------------
Thu Feb 18 04:46:04 UTC 2021 - Nicolas Morey-Chaisemartin <nmoreychaisemartin@suse.com>
- Re-add mvapich2-fix-double-free.patch as the bug was
somehow be reintroduced (bsc#1144000)
- Add mvapich2-remove-deprecated-sys_siglist.patch to
fix compilation errors with newer glibc
-------------------------------------------------------------------
Sun Nov 29 13:44:44 UTC 2020 - Egbert Eich <eich@suse.com>
- HPC: Fix environment module settings for MANPATH.
-------------------------------------------------------------------
Sat Jul 25 07:03:57 UTC 2020 - Egbert Eich <eich@suse.com>

21
mvapich2.spec
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@ -1,7 +1,7 @@
#
# spec file for package mvapich2
# spec file for package %{package_name}
#
# Copyright (c) 2020 SUSE LLC
# Copyright (c) 2021 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@ -254,6 +254,9 @@ Patch3: 0001-Drop-GCC-check.patch
Patch4: reproducible.patch
Patch5: fix-missing-return-code.patch
Patch6: wrapper-revert-ldflag-order-change.patch
Patch7: mvapich2-fix-double-free.patch
Patch8: mvapich2-remove-deprecated-sys_siglist.patch
## Armv7 specific patches
# PATCH-FIX-UPSTREAM 0001-Drop-real128.patch (https://github.com/pmodels/mpich/issues/4005)
Patch50: 0001-Drop-real128.patch
@ -393,6 +396,8 @@ is based on MPICH2 and MVICH. This package contains the static libraries
%patch4 -p1
%patch5
%patch6
%patch7
%patch8
# Only apply these patches on Armv7
%ifarch armv7hl
@ -461,7 +466,7 @@ rm -f %{buildroot}%{p_libdir}/libfmpich.la \
%{buildroot}%{p_libdir}/libopa.la \
%{buildroot}%{p_libdir}/libmpi.la \
%{buildroot}%{p_libdir}/libmpicxx.la \
%{buildroot}%{p_libdir}/libmpifort.la
%{buildroot}%{p_libdir}/libmpifort.la
install -m 0755 -d %{buildroot}%{_datadir}/doc/%{name}
install -m 0644 COPYRIGHT* %{buildroot}%{_datadir}/doc/%{name}
install -m 0644 CHANGE* %{buildroot}%{_datadir}/doc/%{name}
@ -519,9 +524,9 @@ module-whatis "URL: %{url}"
set version %{version}
prepend-path PATH %{hpc_prefix}/bin
prepend-path MANPATH %{hpc_prefix}/man
prepend-path LD_LIBRARY_PATH %{hpc_prefix}/%_lib
prepend-path PATH %{hpc_bindir}
prepend-path MANPATH %{hpc_mandir}
prepend-path LD_LIBRARY_PATH %{hpc_libdir}
prepend-path MODULEPATH %{hpc_modulepath}
prepend-path MPI_DIR %{hpc_prefix}
%{hpc_modulefile_add_pkgconfig_path}
@ -577,7 +582,7 @@ fi
%hpc_mpi_dirs
%hpc_modules_files
%endif
%doc %{_datadir}/doc/%{name}/COPYRIGHT*
%doc %{_datadir}/doc/%{name}/COPYRIGHT*
%doc %{_datadir}/doc/%{name}/CHANGE*
%dir %{p_prefix}
%dir %{p_bindir}
@ -596,7 +601,7 @@ fi
%files doc
%defattr(-, root, root)
%doc %{_datadir}/doc/%{name}
%exclude /%{_datadir}/doc/%{name}/COPYRIGHT*
%exclude /%{_datadir}/doc/%{name}/COPYRIGHT*
%exclude /%{_datadir}/doc/%{name}/CHANGE*
%files devel