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Accepting request 986553 from science:HPC

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OBS-URL: https://build.opensuse.org/request/show/986553
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/mvapich2?expand=0&rev=31
This commit is contained in:
Dominique Leuenberger 2022-07-05 10:08:57 +00:00 committed by Git OBS Bridge
commit d2a1ff7bdb
6 changed files with 170 additions and 7 deletions
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11
_constraints Normal file
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@ -0,0 +1,11 @@
<constraints>
<hardware>
<processors>8</processors>
<disk>
<size unit="G">10</size>
</disk>
<physicalmemory>
<size unit="G">16</size>
</physicalmemory>
</hardware>
</constraints>

3
mvapich2-2.3.6.tar.gz
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@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:b3a62f2a05407191b856485f99da05f5e769d6381cd63e2fcb83ee98fc46a249
size 21016727

BIN
mvapich2-2.3.7-1.tar.gz (Stored with Git LFS) Normal file
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46
mvapich2.changes
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@ -1,3 +1,49 @@
-------------------------------------------------------------------
Wed Jun 29 12:54:33 UTC 2022 - Klaus Kämpf <kkaempf@suse.com>
- add pass-correct-size-to-snprintf.patch to fix potential buffer
overflows (required to make 'sundials' testsuite pass)
- Update to mvapich2 2.3.7
* Features and Enhancements (since 2.3.6):
- Added support for systems with Rockport's switchless networks
* Added automatic architecture detection
* Optimized performance for point-to-point operations
- Added support for the Cray Slingshot 10 interconnect
- Enhanced support for blocking collective offload using
Mellanox SHARP
* Scatter and Scatterv
- Enhanced support for non-blocking collective offload using
Mellanox SHARP
* Iallreduce, Ibarrier, Ibcast, and Ireduce
* Bug Fixes (since 2.3.6):
- Removed several deprectated functions
- Thanks to Honggang Li @RedHat for the report
- Fixed a bug where tools like CMake FindMPI would not
detect MVAPICH when compiled without Hydra mpiexec
- Thanks to Chris Chambreau and Adam Moody @LLNL for the report
- Fixed compilation error when building with mpirun and without hydra
- Thanks to James Long @University of Illinois for the report
- Fixed issue with setting RoCE mode correctly without RDMA_CM.
- Thanks to Nicolas Gagnon @Rockport Networks for the report
- Fixed an issue on heterogeneous clusters where QP attributes were
set incorrectly
- Thanks to X-ScaleSolutions for the report and fix
- Fixed a memory leak in improbe on the PSM channel
- Thanks to Gregory Lee @LLNL Beichuan Yan @University of Colorado
for the report
- Added retry logic for PSM connection establishment
- Thanks to Gregory Lee @LLNL for the report and X-ScaleSolutions
for the patch
- Fixed an initialization error when using PSM and gcc's -pg option
- Thanks to Gregory Lee @LLNL for the report and X-ScaleSolutions for
the patch
- Fixed a potential integer overflow when transfering large arrays
- Thanks to Alexander Melnikov for the report and patch
- Fix Url: link
-------------------------------------------------------------------
Wed Feb 16 11:07:12 UTC 2022 - Nicolas Morey-Chaisemartin <nmoreychaisemartin@suse.com>

11
mvapich2.spec
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@ -19,8 +19,9 @@
%global flavor @BUILD_FLAVOR@%{nil}
%define pname mvapich2
%define vers 2.3.6
%define _vers 2_3_6
%define vers 2.3.7
%define _vers 2_3_7
%define rc_ver -1
%if "%{flavor}" == ""
ExclusiveArch: do_not_build
@ -241,7 +242,7 @@ License: BSD-3-Clause
Group: Development/Libraries/Parallel
Version: %{vers}
Release: 0
Source0: http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-%{version}.tar.gz
Source0: http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-%{version}%{?rc_ver}.tar.gz
Source1: mpivars.sh
Source2: mpivars.csh
Source3: macros.hpc-mvapich2
@ -252,13 +253,14 @@ Patch2: mvapich2-arm-support.patch
# It's been merged upstream, should be removed with the next release
Patch3: 0001-Drop-GCC-check.patch
Patch4: reproducible.patch
Patch5: pass-correct-size-to-snprintf.patch
## Armv7 specific patches
# PATCH-FIX-UPSTREAM 0001-Drop-real128.patch (https://github.com/pmodels/mpich/issues/4005)
Patch50: 0001-Drop-real128.patch
Patch51: 0001-Drop-Real-16.patch
URL: http://mvapich.cse.ohio-state.edu/overview/mvapich2/
URL: http://mvapich.cse.ohio-state.edu
BuildRoot: %{_tmppath}/%{name}-%{version}-build
%if %{without skip_hpc_build}
@ -389,6 +391,7 @@ is based on MPICH2 and MVICH. This package contains the static libraries
%patch2
%patch3
%patch4
%patch5 -p1
# Only apply these patches on Armv7
%ifarch armv7hl

103
pass-correct-size-to-snprintf.patch Normal file
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@ -0,0 +1,103 @@
diff -wruN -x '*~' -x '*.o' -x '*.a' -x '*.so' -x '*.so.[0-9]' -x autom4te.cache -x .deps -x .libs ../orig-mvapich2-2.3.7-1/src/mpid/ch3/channels/common/src/affinity/hwloc_bind.c ./src/mpid/ch3/channels/common/src/affinity/hwloc_bind.c
--- ../orig-mvapich2-2.3.7-1/src/mpid/ch3/channels/common/src/affinity/hwloc_bind.c 2022-05-16 18:58:22.000000000 +0200
+++ ./src/mpid/ch3/channels/common/src/affinity/hwloc_bind.c 2022-06-29 15:07:17.700058168 +0200
@@ -2107,7 +2107,7 @@
for (i = 0; i < g_smpi.num_local_nodes; ++i) {
hwloc_bitmap_clr(*free_sock_cpuset, local_core_ids[i]);
}
- hwloc_bitmap_snprintf(cpu_str, 128, *free_sock_cpuset);
+ hwloc_bitmap_snprintf(cpu_str, sizeof(cpu_str), *free_sock_cpuset);
PRINT_DEBUG(DEBUG_INIT_verbose, "Free sock_cpuset = %s\n", cpu_str);
}
@@ -3190,11 +3190,11 @@
for (i = 0; i < local_procs; i++) {
curr = count;
for (k = 0; k < num_app_threads; k++) {
- j += snprintf (mapping+j, _POSIX2_LINE_MAX, "%d,", mv2_core_map[curr]);
+ j += snprintf (mapping+j, sizeof(mapping)-j, "%d,", mv2_core_map[curr]);
curr = (curr + 1) % num_pu;
}
mapping [--j] = '\0';
- j += snprintf (mapping+j, _POSIX2_LINE_MAX, ":");
+ j += snprintf (mapping+j, sizeof(mapping)-j, ":");
count = (count + hw_threads_per_core) % num_pu;
}
} else if (mv2_hybrid_binding_policy == HYBRID_LINEAR) {
@@ -3203,14 +3203,14 @@
* resources */
for (i = 0; i < local_procs; i++) {
for (k = 0; k < num_app_threads; k++) {
- j += snprintf (mapping+j, _POSIX2_LINE_MAX, "%d,", mv2_core_map[curr]);
+ j += snprintf (mapping+j, sizeof(mapping)-j, "%d,", mv2_core_map[curr]);
curr = ((curr + hw_threads_per_core) >= num_pu) ?
((curr + hw_threads_per_core+ ++step) % num_pu) :
(curr + hw_threads_per_core) % num_pu;
}
mapping [--j] = '\0';
- j += snprintf (mapping+j, _POSIX2_LINE_MAX, ":");
+ j += snprintf (mapping+j, sizeof(mapping)-j, ":");
}
} else if (mv2_hybrid_binding_policy == HYBRID_SPREAD) {
#if defined(CHANNEL_MRAIL)
@@ -3232,12 +3232,12 @@
for (i = 0; i < local_procs; i++) {
for (k = curr; k < curr+chunk; k++) {
for (l = 0; l < hw_threads_per_core; l++) {
- j += snprintf (mapping+j, _POSIX2_LINE_MAX, "%d,",
+ j += snprintf (mapping+j, sizeof(mapping)-j, "%d,",
mv2_core_map[k * hw_threads_per_core + l]);
}
}
mapping [--j] = '\0';
- j += snprintf (mapping+j, _POSIX2_LINE_MAX, ":");
+ j += snprintf (mapping+j, sizeof(mapping)-j, ":");
curr = (curr + chunk) % size;
}
} else {
@@ -3252,11 +3252,11 @@
for (i = 0; i < num_sockets; i++) {
for (k = curr; k < curr+ranks_per_sock; k++) {
for (l = 0; l < hw_threads_per_core; l++) {
- j += snprintf (mapping+j, _POSIX2_LINE_MAX, "%d,",
+ j += snprintf (mapping+j, sizeof(mapping)-j, "%d,",
mv2_core_map[k * hw_threads_per_core + l]);
}
mapping [--j] = '\0';
- j += snprintf (mapping+j, _POSIX2_LINE_MAX, ":");
+ j += snprintf (mapping+j, sizeof(mapping)-j, ":");
}
curr = (curr + ((num_pu_per_socket/hw_threads_per_core) * chunk)) % size;
}
@@ -3265,7 +3265,7 @@
/* Bunch mapping: Bind each MPI rank to a single phyical core of first
* socket followed by second secket */
for (i = 0; i < local_procs; i++) {
- j += snprintf (mapping+j, _POSIX2_LINE_MAX, "%d:", mv2_core_map[k]);
+ j += snprintf (mapping+j, sizeof(mapping)-j, "%d:", mv2_core_map[k]);
k = (k + hw_threads_per_core) % size;
}
} else if (mv2_hybrid_binding_policy == HYBRID_SCATTER) {
@@ -3283,7 +3283,7 @@
return MPI_ERR_OTHER;
}
for (i = 0; i < local_procs; i++) {
- j += snprintf (mapping+j, _POSIX2_LINE_MAX, "%d:", mv2_core_map[k]);
+ j += snprintf (mapping+j, sizeof(mapping)-j, "%d:", mv2_core_map[k]);
k = (i % num_sockets == 0) ?
(k + num_pu_per_socket) % size :
(k + num_pu_per_socket + hw_threads_per_core) % size;
@@ -3315,10 +3315,10 @@
/* NUMA mapping: Bind consecutive MPI ranks to different NUMA domains in
* round-robin fashion. */
for (i = 0; i < local_procs; i++) {
- j += snprintf (mapping+j, _POSIX2_LINE_MAX, "%d,",
+ j += snprintf (mapping+j, sizeof(mapping)-j, "%d,",
mv2_core_map_per_numa[node_base_pu+node_offset]);
mapping [--j] = '\0';
- j += snprintf (mapping+j, _POSIX2_LINE_MAX, ":");
+ j += snprintf (mapping+j, sizeof(mapping)-j, ":");
node_base_pu = (node_base_pu + num_pu_per_numanode) % size;
node_offset = (node_base_pu == 0) ?
(node_offset + ((hw_threads_per_core > 0) ? hw_threads_per_core : 1)) :