From 15a9cd7613ccf97e9a9647f51ffb450e6ae92ec4 Mon Sep 17 00:00:00 2001 From: CentOS Sources Date: Tue, 30 Mar 2021 11:39:25 -0400 Subject: [PATCH] import mvapich2-2.3.5-1.el8 --- .gitignore | 2 +- .mvapich2.metadata | 2 +- ...nit-calculation-for-non-NUMA-machine.patch | 40 ------------ ...001-mvapich23-unbundle-contrib-hwloc.patch | 45 +++++++------ ...02-mvapich23-unbundle-osu_benchmarks.patch | 29 ++++----- SPECS/mvapich2.spec | 63 ++++--------------- 6 files changed, 56 insertions(+), 125 deletions(-) delete mode 100644 SOURCES/0001-Fix-Processing-Unit-calculation-for-non-NUMA-machine.patch diff --git a/.gitignore b/.gitignore index 00f399a..9b3b2d7 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1 @@ -SOURCES/mvapich2-2.3.3.tar.gz +SOURCES/mvapich2-2.3.5.tar.gz diff --git a/.mvapich2.metadata b/.mvapich2.metadata index e1f91d7..02ffe42 100644 --- a/.mvapich2.metadata +++ b/.mvapich2.metadata @@ -1 +1 @@ -c53074dd0836a250e7fd5a76bf1cc1ba9320f841 SOURCES/mvapich2-2.3.3.tar.gz +4158180718b1703afa76bcea3819eb86b5b355d1 SOURCES/mvapich2-2.3.5.tar.gz diff --git a/SOURCES/0001-Fix-Processing-Unit-calculation-for-non-NUMA-machine.patch b/SOURCES/0001-Fix-Processing-Unit-calculation-for-non-NUMA-machine.patch deleted file mode 100644 index 2d60988..0000000 --- a/SOURCES/0001-Fix-Processing-Unit-calculation-for-non-NUMA-machine.patch +++ /dev/null @@ -1,40 +0,0 @@ -From 3ba35a3261e2222326b3d81f273d3e8261cad942 Mon Sep 17 00:00:00 2001 -From: Honggang Li -Date: Thu, 2 Apr 2020 18:29:43 +0800 -Subject: [PATCH] Fix Processing Unit calculation for non-NUMA machine - -For hwloc without commit ba7d4976d38f, function - -hwloc_get_nbobjs_by_type(topology, HWLOC_OBJ_NUMANODE) - -return zero instead of one when no NUMA node exists. - -This patch fixes a floating point exception issue for non-NUMA -machine. - -Signed-off-by: Honggang Li ---- - src/mpid/ch3/channels/common/src/affinity/hwloc_bind.c | 7 ++++++- - 1 file changed, 6 insertions(+), 1 deletion(-) - -diff --git a/src/mpid/ch3/channels/common/src/affinity/hwloc_bind.c b/src/mpid/ch3/channels/common/src/affinity/hwloc_bind.c -index 7afb9f74248d..f1a1f1fefb97 100644 ---- a/src/mpid/ch3/channels/common/src/affinity/hwloc_bind.c -+++ b/src/mpid/ch3/channels/common/src/affinity/hwloc_bind.c -@@ -2748,7 +2748,12 @@ static int mv2_generate_implicit_cpu_mapping (int local_procs, int num_app_threa - - num_physical_cores_per_socket = num_physical_cores / num_sockets; - num_pu_per_socket = num_pu / num_sockets; -- num_pu_per_numanode = num_pu / num_numanodes; -+ -+ /* non-NUMA */ -+ if (num_numanodes == 0) -+ num_pu_per_numanode = num_pu; -+ else -+ num_pu_per_numanode = num_pu / num_numanodes; - - topodepth = hwloc_get_type_depth (topology, HWLOC_OBJ_CORE); - obj = hwloc_get_obj_by_depth (topology, topodepth, 0); /* check on core 0*/ --- -2.25.2 - diff --git a/SOURCES/0001-mvapich23-unbundle-contrib-hwloc.patch b/SOURCES/0001-mvapich23-unbundle-contrib-hwloc.patch index 374d0fd..a10afb1 100644 --- a/SOURCES/0001-mvapich23-unbundle-contrib-hwloc.patch +++ b/SOURCES/0001-mvapich23-unbundle-contrib-hwloc.patch @@ -1,30 +1,37 @@ -From c152d5a633876ff01ae69bd69d25c9ec08d0bbcb Mon Sep 17 00:00:00 2001 -From: Michal Schmidt -Date: Fri, 3 Nov 2017 11:49:50 +0100 +From 88e61b66e821f0f4bda5fed002065093146b352c Mon Sep 17 00:00:00 2001 +From: Honggang Li +Date: Tue, 1 Dec 2020 12:41:55 +0800 Subject: [PATCH 1/2] mvapich23: unbundle contrib/hwloc +Signed-off-by: Honggang Li --- - Makefile.in | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) + Makefile.in | 12 ++++++------ + 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Makefile.in b/Makefile.in -index 0d9ec512f5..ff3af667a4 100644 +index 140d9d8ecd6c..6bbf5f857bad 100644 --- a/Makefile.in +++ b/Makefile.in -@@ -3029,10 +3029,10 @@ bin_PROGRAMS = $(am__EXEEXT_1) src/env/mpichversion$(EXEEXT) \ - @BUILD_F77_BINDING_TRUE@@BUILD_PROFILING_LIB_TRUE@am__append_175 = -DMPICH_MPI_FROM_PMPI -DUSE_ONLY_MPI_NAMES - @BUILD_F77_BINDING_TRUE@@BUILD_FC_BINDING_TRUE@am__append_176 = $(mpi_fc_sources) - @BUILD_CXX_BINDING_TRUE@am__append_177 = lib/lib@MPICXXLIBNAME@.la --@BUILD_OSU_MVAPICH_TRUE@am__append_178 = contrib/hwloc -+@BUILD_OSU_MVAPICH_TRUE@am__append_178 = - @BUILD_OSU_MVAPICH_TRUE@am__append_179 = src/env/mpiname src/util/mv2_ckpt_rebuild osu_benchmarks --@BUILD_OSU_MVAPICH_TRUE@am__append_180 = -Icontrib/hwloc/include/ -I$(top_srcdir)/contrib/hwloc/include --@BUILD_OSU_MVAPICH_TRUE@am__append_181 = contrib/hwloc/src/libhwloc_embedded.la -+@BUILD_OSU_MVAPICH_TRUE@am__append_180 = -+@BUILD_OSU_MVAPICH_TRUE@am__append_181 = -lhwloc - @BUILD_COVERAGE_TRUE@am__append_182 = coverage-clean +@@ -3049,13 +3049,13 @@ bin_PROGRAMS = $(am__EXEEXT_1) src/env/mpichversion$(EXEEXT) \ + @BUILD_F77_BINDING_TRUE@@BUILD_PROFILING_LIB_TRUE@am__append_183 = -DMPICH_MPI_FROM_PMPI -DUSE_ONLY_MPI_NAMES + @BUILD_F77_BINDING_TRUE@@BUILD_FC_BINDING_TRUE@am__append_184 = $(mpi_fc_sources) + @BUILD_CXX_BINDING_TRUE@am__append_185 = lib/lib@MPICXXLIBNAME@.la +-@BUILD_HWLOC_v1_TRUE@@BUILD_OSU_MVAPICH_TRUE@am__append_186 = contrib/hwloc_v1 +-@BUILD_HWLOC_v1_FALSE@@BUILD_OSU_MVAPICH_TRUE@am__append_187 = contrib/hwloc_v2 ++@BUILD_HWLOC_v1_TRUE@@BUILD_OSU_MVAPICH_TRUE@am__append_186 = ++@BUILD_HWLOC_v1_FALSE@@BUILD_OSU_MVAPICH_TRUE@am__append_187 = + @BUILD_OSU_MVAPICH_TRUE@am__append_188 = src/env/mpiname src/util/mv2_ckpt_rebuild osu_benchmarks +-@BUILD_HWLOC_v1_TRUE@@BUILD_OSU_MVAPICH_TRUE@am__append_189 = -Icontrib/hwloc_v1/include/ -I$(top_srcdir)/contrib/hwloc_v1/include +-@BUILD_HWLOC_v1_TRUE@@BUILD_OSU_MVAPICH_TRUE@am__append_190 = contrib/hwloc_v1/src/libhwloc_embedded.la +-@BUILD_HWLOC_v1_FALSE@@BUILD_OSU_MVAPICH_TRUE@am__append_191 = -Icontrib/hwloc_v2/include/ -I$(top_srcdir)/contrib/hwloc_v2/include +-@BUILD_HWLOC_v1_FALSE@@BUILD_OSU_MVAPICH_TRUE@am__append_192 = contrib/hwloc_v2/hwloc/libhwloc_embedded.la ++@BUILD_HWLOC_v1_TRUE@@BUILD_OSU_MVAPICH_TRUE@am__append_189 = ++@BUILD_HWLOC_v1_TRUE@@BUILD_OSU_MVAPICH_TRUE@am__append_190 = -lhwloc ++@BUILD_HWLOC_v1_FALSE@@BUILD_OSU_MVAPICH_TRUE@am__append_191 = ++@BUILD_HWLOC_v1_FALSE@@BUILD_OSU_MVAPICH_TRUE@am__append_192 = -lhwloc + @BUILD_COVERAGE_TRUE@am__append_193 = coverage-clean subdir = . ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 -- -2.13.6 +2.25.4 diff --git a/SOURCES/0002-mvapich23-unbundle-osu_benchmarks.patch b/SOURCES/0002-mvapich23-unbundle-osu_benchmarks.patch index 8c63b4b..1cf8ca4 100644 --- a/SOURCES/0002-mvapich23-unbundle-osu_benchmarks.patch +++ b/SOURCES/0002-mvapich23-unbundle-osu_benchmarks.patch @@ -1,25 +1,26 @@ -From 3aad06949ee9edbb6376092c6891efa9a37b8f51 Mon Sep 17 00:00:00 2001 -From: Michal Schmidt -Date: Fri, 3 Nov 2017 11:51:33 +0100 +From 03bc868ca5580f2266d93b2805c79ce97b117767 Mon Sep 17 00:00:00 2001 +From: Honggang Li +Date: Tue, 1 Dec 2020 12:44:12 +0800 Subject: [PATCH 2/2] mvapich23: unbundle osu_benchmarks +Signed-off-by: Honggang Li --- Makefile.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile.in b/Makefile.in -index ff3af667a4..21e2754b56 100644 +index 6bbf5f857bad..500df0988a2f 100644 --- a/Makefile.in +++ b/Makefile.in -@@ -3030,7 +3030,7 @@ bin_PROGRAMS = $(am__EXEEXT_1) src/env/mpichversion$(EXEEXT) \ - @BUILD_F77_BINDING_TRUE@@BUILD_FC_BINDING_TRUE@am__append_176 = $(mpi_fc_sources) - @BUILD_CXX_BINDING_TRUE@am__append_177 = lib/lib@MPICXXLIBNAME@.la - @BUILD_OSU_MVAPICH_TRUE@am__append_178 = --@BUILD_OSU_MVAPICH_TRUE@am__append_179 = src/env/mpiname src/util/mv2_ckpt_rebuild osu_benchmarks -+@BUILD_OSU_MVAPICH_TRUE@am__append_179 = src/env/mpiname src/util/mv2_ckpt_rebuild - @BUILD_OSU_MVAPICH_TRUE@am__append_180 = - @BUILD_OSU_MVAPICH_TRUE@am__append_181 = -lhwloc - @BUILD_COVERAGE_TRUE@am__append_182 = coverage-clean +@@ -3051,7 +3051,7 @@ bin_PROGRAMS = $(am__EXEEXT_1) src/env/mpichversion$(EXEEXT) \ + @BUILD_CXX_BINDING_TRUE@am__append_185 = lib/lib@MPICXXLIBNAME@.la + @BUILD_HWLOC_v1_TRUE@@BUILD_OSU_MVAPICH_TRUE@am__append_186 = + @BUILD_HWLOC_v1_FALSE@@BUILD_OSU_MVAPICH_TRUE@am__append_187 = +-@BUILD_OSU_MVAPICH_TRUE@am__append_188 = src/env/mpiname src/util/mv2_ckpt_rebuild osu_benchmarks ++@BUILD_OSU_MVAPICH_TRUE@am__append_188 = src/env/mpiname src/util/mv2_ckpt_rebuild + @BUILD_HWLOC_v1_TRUE@@BUILD_OSU_MVAPICH_TRUE@am__append_189 = + @BUILD_HWLOC_v1_TRUE@@BUILD_OSU_MVAPICH_TRUE@am__append_190 = -lhwloc + @BUILD_HWLOC_v1_FALSE@@BUILD_OSU_MVAPICH_TRUE@am__append_191 = -- -2.13.6 +2.25.4 diff --git a/SPECS/mvapich2.spec b/SPECS/mvapich2.spec index c22a54a..06735eb 100644 --- a/SPECS/mvapich2.spec +++ b/SPECS/mvapich2.spec @@ -1,35 +1,7 @@ -# We only compile with gcc, but other people may want other compilers. -# Set the compiler here. -%define opt_cc gcc -# Optional CFLAGS to use with the specific compiler...gcc doesn't need any, -# so uncomment and define to use -#define opt_cflags -%define opt_cxx g++ -#define opt_cxxflags -%define opt_f77 gfortran -#define opt_fflags -%define opt_fc gfortran -#define opt_fcflags - %{!?python3_sitearch: %global python3_sitearch %(%{__python3} -c "from distutils.sysconfig import get_python_lib; print get_python_lib(1)")} -%define opt_cflags -O3 -fno-strict-aliasing -%define opt_cxxflags -O3 -%ifarch i386 -%define opt_cflags -m32 -O3 -fno-strict-aliasing -%define opt_cxxflags -m32 -O3 -%define opt_fflags -m32 -%define opt_fcflags -m32 -%endif -%ifarch x86_64 -%define opt_cflags -m64 -O3 -fno-strict-aliasing -%define opt_cxxflags -m64 -O3 -%define opt_fflags -m64 -%define opt_fcflags -m64 -%endif - Name: mvapich2 -Version: 2.3.3 +Version: 2.3.5 Release: 1%{?dist} Summary: OSU MVAPICH2 MPI package Group: Development/Libraries @@ -53,7 +25,6 @@ Source2: mvapich2.macros.in # the configure scripts and Makefiles accordingly. Patch1: 0001-mvapich23-unbundle-contrib-hwloc.patch Patch2: 0002-mvapich23-unbundle-osu_benchmarks.patch -Patch3: 0001-Fix-Processing-Unit-calculation-for-non-NUMA-machine.patch BuildRequires: gcc-gfortran BuildRequires: libibumad-devel, libibverbs-devel >= 1.1.3, librdmacm-devel @@ -123,7 +94,6 @@ Contains development headers and libraries for %{name}-psm2. %setup -q %patch1 -p1 %patch2 -p1 -%patch3 -p1 # bundled hwloc, knem kernel module rm -r contrib/ # limic kernel module @@ -175,16 +145,8 @@ cd psm2 --enable-cxx \ --disable-silent-rules \ --disable-wrapper-rpath \ - --with-hwloc-prefix=system \ - --with-device=ch3:psm \ - --with-ftb=no \ - --with-blcr=no \ - --with-fuse=no \ - CC=%{opt_cc} CFLAGS="%{?opt_cflags} %{build_cflags} $XFLAGS" \ - CXX=%{opt_cxx} CXXFLAGS="%{?opt_cxxflags} %{build_cflags} $XFLAGS" \ - FC=%{opt_fc} FCFLAGS="%{?opt_fcflags} %{build_cflags} $XFLAGS" \ - F77=%{opt_f77} FFLAGS="%{?opt_fflags} %{build_cflags} $XFLAGS" \ - LDFLAGS="%{build_ldflags}" + --with-hwloc=v2 \ + --with-device=ch3:psm # Remove rpath, part 2 find . -name libtool -exec \ @@ -220,15 +182,7 @@ cd default --enable-cxx \ --disable-silent-rules \ --disable-wrapper-rpath \ - --with-hwloc-prefix=system \ - --with-ftb=no \ - --with-blcr=no \ - --with-fuse=no \ - CC=%{opt_cc} CFLAGS="%{?opt_cflags} %{build_cflags} $XFLAGS" \ - CXX=%{opt_cxx} CXXFLAGS="%{?opt_cxxflags} %{build_cflags} $XFLAGS" \ - FC=%{opt_fc} FCFLAGS="%{?opt_fcflags} %{build_cflags} $XFLAGS" \ - F77=%{opt_f77} FFLAGS="%{?opt_fflags} %{build_cflags} $XFLAGS" \ - LDFLAGS="%{build_ldflags}" + --with-hwloc=v2 # Remove rpath, part 2 find . -name libtool -exec \ @@ -392,6 +346,15 @@ cd .. %changelog +* Tue Dec 01 2020 Honggang Li - 2.3.5-1 +- Update to upstream stable point release v2.3.5 +- Resolves: rhbz#1904914 + +* Wed Oct 14 2020 Honggang Li - 2.3.4-1 +- Update to upstream stable point release v2.3.4 +- Build against hwloc-2.2.0 +- Resolves: rhbz#1850084 + * Wed Apr 15 2020 Honggang Li - 2.3.3-1 - Update to upstream stable point release v2.3.3 - Fix floating point exception for non-NUMA machine