CVS commit: pkgsrc/parallel/openmpi

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/parallel/openmpi
From: "Adam Ciarcinski" <adam%netbsd.org@localhost>
Date: Wed, 17 Apr 2024 14:50:01 +0000

Module Name:    pkgsrc
Committed By:   adam
Date:           Wed Apr 17 14:50:01 UTC 2024

Modified Files:
        pkgsrc/parallel/openmpi: Makefile PLIST distinfo
Added Files:
        pkgsrc/parallel/openmpi: PLIST.Darwin PLIST.Linux

Log Message:
openmpi: updated to 4.1.6

Changes to v4.1.6 compared to v4.1.5:

- Fix configure issue with XCode 15.
- Update embedded PMIx to 3.2.5.  PMIx 3.2.5 addresses CVE-2023-41915.
  Note that prior versions of Open MPI (and their associated PMIx
  implementations) are not impacted by this CVE, because Open MPI
  never uses escalated privileges on behalf of an unprivileged user.
  We are backporting this change both because it is low risk and to
  avoid alarms from CVE scanners.
- Fix issue with buffered sends and MTL-based interfaces (Libfabric,
  PSM, Portals).
- Add missing MPI_F_STATUS_SIZE to mpi.h.  Thanks to @jprotze for
  reporting the issue.
- Update Fortran mpi module configure check to be more correct.
  Thanks to Sergey Kosukhin for identifying the issue and supplying
  the fix.
- Update to properly handle PMIx v>=4.2.3.  Thanks to Bruno Chareyre,
  Github user @sukanka, and Christof Koehler for raising the
  compatibility issues and helping test the fixes.
- Fix minor issues and add some minor performance optimizations with
  OFI support.
- Support the "striping_factor" and "striping_unit" MPI_Info names
  recomended by the MPI standard for parallel IO.
- Fixed some minor issues with UCX support.
- Minor optimization for 0-byte MPI_Alltoallw (i.e., make it a no-op).

Changes to v4.1.5 compared to v4.1.4:

- Fix crash in one-sided applications for certain process layouts.
- Update embedded OpenPMIx to version 3.2.4
- Fix issue building with ifort on MacOS.
- Backport patches to Libevent for CVE-2016-10195, CVE-2016-10196, and
  CVE-2016-10197.  Note that Open MPI's internal libevent does not
  use the impacted portions of the Libevent code base.
- SHMEM improvements:
  - Fix initializer bugs in SHMEM interface.
  - Fix unsigned type comparisons generating warnings.
  - Fix use after clear issue in shmem_ds_reset.
- UCX improvements
  - Fix memory registration bug that could occur when UCX was built
    but not selected.
  - Reduce overhead of add_procs with intercommunicators.
  - Enable multi_send_nb by default.
  - Call opal_progress while waiting for a UCX fence to complete.
- Fix data corruption bug in osc/rdma component.
- Fix overflow bug in alltoall collective
- Fix crash when displaying topology.
- Add some MPI_F_XXX constants that were missing from mpi.h.
- coll/ucc bug fixes.


To generate a diff of this commit:
cvs rdiff -u -r1.52 -r1.53 pkgsrc/parallel/openmpi/Makefile
cvs rdiff -u -r1.20 -r1.21 pkgsrc/parallel/openmpi/PLIST
cvs rdiff -u -r0 -r1.1 pkgsrc/parallel/openmpi/PLIST.Darwin
cvs rdiff -u -r0 -r1.3 pkgsrc/parallel/openmpi/PLIST.Linux
cvs rdiff -u -r1.23 -r1.24 pkgsrc/parallel/openmpi/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/parallel/openmpi/Makefile
diff -u pkgsrc/parallel/openmpi/Makefile:1.52 pkgsrc/parallel/openmpi/Makefile:1.53
--- pkgsrc/parallel/openmpi/Makefile:1.52       Thu Jan 12 11:34:10 2023
+++ pkgsrc/parallel/openmpi/Makefile    Wed Apr 17 14:50:01 2024
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile,v 1.52 2023/01/12 11:34:10 markd Exp $
+# $NetBSD: Makefile,v 1.53 2024/04/17 14:50:01 adam Exp $
 
-DISTNAME=      openmpi-4.1.4
+DISTNAME=      openmpi-4.1.6
 CATEGORIES=    parallel
-MASTER_SITES=  https://download.open-mpi.org/release/open-mpi/v4.1/
+MASTER_SITES=  https://download.open-mpi.org/release/open-mpi/v${PKGVERSION_NOREV:R}/
 EXTRACT_SUFX=  .tar.bz2
 
 MAINTAINER=    thor%NetBSD.org@localhost
@@ -17,7 +17,7 @@ USE_LIBTOOL=          yes
 USE_TOOLS+=            perl:run bash:run
 GNU_CONFIGURE=         yes
 CONFIG_SHELL=          bash
-CONFIGURE_ARGS+=       --sysconfdir=${PKG_SYSCONFDIR:Q}
+CONFIGURE_ARGS+=       --sysconfdir=${PKG_SYSCONFDIR}
 CONFIGURE_ARGS+=       --enable-contrib-no-build=vt # in separate package
 CONFIGURE_ARGS+=       --with-libltdl=${BUILDLINK_PREFIX.libltdl}
 # See below about external hwloc.
@@ -36,30 +36,23 @@ SHLIBTOOL_OVERRIDE= config/libtool.m4
 
 TEST_TARGET=   check
 
-# Unsurprisingly, files that are only produced on GNU/Linux systems.
-PLIST_VARS+=   linux
+# CPU with AVX support.
+PLIST_VARS+=   avx
 # \todo Explain.  Apparently built if !Linux.
 PLIST_VARS+=   pstattest
 # \todo Explain.
 PLIST_VARS+=   ignoretkr
-PLIST_VARS+=   noignoretkr
 
-
-.if ${OPSYS} == "Linux"
-PLIST.linux=           yes
+.if ${MACHINE_ARCH} == "x86_64"
+PLIST.avx=             yes
 .endif
 
 .if ${OPSYS} != "Linux"
 PLIST.pstattest=       yes
 .endif
 
-.if ${OPSYS} == "Linux" || ${OPSYS} == "NetBSD"
+.if ${OPSYS} == "Darwin" || ${OPSYS} == "Linux" || ${OPSYS} == "NetBSD"
 PLIST.ignoretkr=       yes
-.else
-# \todo Explain why on Darwin we don't set one of them.
-.  if ${OPSYS} != "Darwin"
-PLIST.noignoretkr=     yes
-.  endif
 .endif
 
 REPLACE_PERL=  ompi/tools/wrappers/mpijavac.pl.in

Index: pkgsrc/parallel/openmpi/PLIST
diff -u pkgsrc/parallel/openmpi/PLIST:1.20 pkgsrc/parallel/openmpi/PLIST:1.21
--- pkgsrc/parallel/openmpi/PLIST:1.20  Thu Aug 25 22:09:14 2022
+++ pkgsrc/parallel/openmpi/PLIST       Wed Apr 17 14:50:01 2024
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.20 2022/08/25 22:09:14 thor Exp $
+@comment $NetBSD: PLIST,v 1.21 2024/04/17 14:50:01 adam Exp $
 bin/aggregate_profile.pl
 bin/mpiCC
 bin/mpic++
@@ -49,7 +49,6 @@ lib/libmca_common_sm.la
 lib/libmpi.la
 ${PLIST.java}lib/libmpi_java.la
 ${PLIST.f90}lib/libmpi_mpifh.la
-${PLIST.f90}${PLIST.noignoretkr}lib/libmpi_usempi.la
 ${PLIST.f90}${PLIST.ignoretkr}lib/libmpi_usempi_ignore_tkr.la
 ${PLIST.f08}lib/libmpi_usempif08.la
 lib/libompitrace.la
@@ -113,7 +112,7 @@ lib/openmpi/mca_mpool_hugepage.la
 lib/openmpi/mca_odls_default.la
 lib/openmpi/mca_odls_pspawn.la
 lib/openmpi/mca_oob_tcp.la
-lib/openmpi/mca_op_avx.la
+${PLIST.avx}lib/openmpi/mca_op_avx.la
 lib/openmpi/mca_osc_monitoring.la
 lib/openmpi/mca_osc_pt2pt.la
 lib/openmpi/mca_osc_rdma.la
@@ -127,12 +126,10 @@ lib/openmpi/mca_pmix_pmix3x.la
 lib/openmpi/mca_pml_cm.la
 lib/openmpi/mca_pml_monitoring.la
 lib/openmpi/mca_pml_ob1.la
-${PLIST.linux}lib/openmpi/mca_pstat_linux.la
 ${PLIST.pstattest}lib/openmpi/mca_pstat_test.la
 ${PLIST.sge}lib/openmpi/mca_ras_gridengine.la
 lib/openmpi/mca_ras_simulator.la
 lib/openmpi/mca_rcache_grdma.la
-${PLIST.linux}lib/openmpi/mca_reachable_netlink.la
 lib/openmpi/mca_reachable_weighted.la
 lib/openmpi/mca_regx_fwd.la
 lib/openmpi/mca_regx_naive.la
@@ -179,7 +176,6 @@ lib/pmix/mca_bfrops_v20.la
 lib/pmix/mca_bfrops_v21.la
 lib/pmix/mca_bfrops_v3.la
 lib/pmix/mca_gds_ds12.la
-${PLIST.linux}lib/pmix/mca_gds_ds21.la
 lib/pmix/mca_gds_hash.la
 lib/pmix/mca_pcompress_zlib.la
 lib/pmix/mca_plog_default.la
@@ -696,7 +692,6 @@ share/openmpi/help-opal-runtime.txt
 share/openmpi/help-opal-shmem-mmap.txt
 share/openmpi/help-opal-shmem-posix.txt
 share/openmpi/help-opal-shmem-sysv.txt
-${PLIST.linux}share/openmpi/help-opal-timer-linux.txt
 share/openmpi/help-opal-util.txt
 share/openmpi/help-opal-wrapper.txt
 share/openmpi/help-opal_info.txt

Index: pkgsrc/parallel/openmpi/distinfo
diff -u pkgsrc/parallel/openmpi/distinfo:1.23 pkgsrc/parallel/openmpi/distinfo:1.24
--- pkgsrc/parallel/openmpi/distinfo:1.23       Thu Aug 25 22:09:14 2022
+++ pkgsrc/parallel/openmpi/distinfo    Wed Apr 17 14:50:01 2024
@@ -1,8 +1,8 @@
-$NetBSD: distinfo,v 1.23 2022/08/25 22:09:14 thor Exp $
+$NetBSD: distinfo,v 1.24 2024/04/17 14:50:01 adam Exp $
 
-BLAKE2s (openmpi-4.1.4.tar.bz2) = 0d98f1b9404f2a4328288c01d614421ca0a409f7e8550164664a5d692209b4b4
-SHA512 (openmpi-4.1.4.tar.bz2) = c70a92c9b16b8c76a871183f9b180d60861186e64140da897d206d53bc06213f31ea93b31734645f580f4bf28dda5605d85dbce2417e4596955384d961bed653
-Size (openmpi-4.1.4.tar.bz2) = 10042839 bytes
+BLAKE2s (openmpi-4.1.6.tar.bz2) = 5333eb0abe9b0bd794c9849e694fb2f5538650b964b4591d4352a62d68674ba4
+SHA512 (openmpi-4.1.6.tar.bz2) = 0ef3240f9c436fb19b67e836cac376eafeb7825d12de3387dad04329dee9f182799d17d785ea23eba763810f479015bb5230593c28950b616b2f0aa1c0a81e71
+Size (openmpi-4.1.6.tar.bz2) = 10017002 bytes
 SHA1 (patch-ak) = 1dba883fb533df57f5869b743e499a3117339529
 SHA1 (patch-config_opal__setup__wrappers.m4) = c3fe3cb5ff7cedcb5c847f25eea129d4299dd5d2
 SHA1 (patch-configure) = bb6373289ffa2beabccedb6ead679367c85dbe1e

Added files:

Index: pkgsrc/parallel/openmpi/PLIST.Darwin
diff -u /dev/null pkgsrc/parallel/openmpi/PLIST.Darwin:1.1
--- /dev/null   Wed Apr 17 14:50:01 2024
+++ pkgsrc/parallel/openmpi/PLIST.Darwin        Wed Apr 17 14:50:01 2024
@@ -0,0 +1,2 @@
+@comment $NetBSD: PLIST.Darwin,v 1.1 2024/04/17 14:50:01 adam Exp $
+lib/pmix/mca_gds_ds21.la

Index: pkgsrc/parallel/openmpi/PLIST.Linux
diff -u /dev/null pkgsrc/parallel/openmpi/PLIST.Linux:1.3
--- /dev/null   Wed Apr 17 14:50:01 2024
+++ pkgsrc/parallel/openmpi/PLIST.Linux Wed Apr 17 14:50:01 2024
@@ -0,0 +1,5 @@
+@comment $NetBSD: PLIST.Linux,v 1.3 2024/04/17 14:50:01 adam Exp $
+lib/openmpi/mca_pstat_linux.la
+lib/openmpi/mca_reachable_netlink.la
+lib/pmix/mca_gds_ds21.la
+share/openmpi/help-opal-timer-linux.txt

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