Upgrade MPIs on linux

linx64/mpi/openmpi/bin/hwloc-compress-dir

@@ -0,0 +1,170 @@
+#!/bin/sh
+#-*-sh-*-
+
+#
+# Copyright © 2013-2021 Inria.  All rights reserved.
+# See COPYING in top-level directory.
+#
+
+HWLOC_VERSION="2.7.1"
+prefix="/home/admin/Documents/code/projects/cpp-thirdparty-src/mpi/openmpi/install/5.0.7"
+exec_prefix="${prefix}"
+bindir="${exec_prefix}/bin"
+# this will be changed into $bindir/... during make install
+localhwlocdiff="$bindir/hwloc-diff"
+localhwlocpatch="$bindir/hwloc-patch"
+
+verbose=0
+reverse=0
+
+error()
+{
+	echo $@ 2>&1
+}
+
+usage()
+{
+	echo `basename $0`" [options] <inputdir> <outputdir>"
+	echo "  Compress topologies from <inputdir> into <outputdir>"
+	echo "Options:"
+	echo "  -R --reverse        Uncompress instead of compressing"
+	echo "  -v --verbose        Display verbose messages"
+	echo "  --version           Report version and exit"
+	echo "  -h --help           Show this usage"
+}
+
+while test $# -gt 0 ; do
+	case "$1" in
+	-R|--reverse)
+		reverse=1
+		;;
+	-v|--verbose)
+		verbose=1
+		;;
+	--version)
+	    echo `basename $0`" $HWLOC_VERSION"
+	    exit 0
+	    ;;
+	-h|--help)
+		usage
+		exit 0
+		;;
+	-*)
+		error "Unrecognized option: $1"
+		usage
+		exit 1
+		;;
+	*)
+		break
+		;;
+	esac
+	shift
+done
+
+if test $# -lt 2 ; then
+    usage
+    exit 1
+fi
+
+inputdir="$1"
+test x`echo $inputdir | sed -e 's/^\///'` = x$inputdir && inputdir="$PWD/$inputdir"
+outputdir="$2"
+test x`echo $outputdir | sed -e 's/^\///'` = x$outputdir && outputdir="$PWD/$outputdir"
+
+if ! cd "$outputdir" ; then
+    echo "Cannot enter output directory $outputdir"
+    exit 1
+fi
+
+if test x$reverse = x0; then
+    # compress
+
+    alreadycompressed=0
+    alreadynoncompressed=0
+    newlycompressed=0
+    newlynoncompressed=0
+
+    inputs=`ls -1 "$inputdir"`
+    for input in $inputs ; do
+	name=`echo $input | sed -e 's/.xml$//'`
+
+	if test "x${name}.xml" != "x$input"; then
+	    test x$verbose = x1 && echo "Ignoring non-XML file $input"
+	    continue
+	fi
+	if test -f "$outputdir/${name}.xml" ; then
+	    test x$verbose = x1 && echo "$name already non-compressed, skipping"
+	    alreadynoncompressed=`expr $alreadynoncompressed + 1`
+	    continue
+	fi
+	if test -f  "$outputdir/${name}.diff.xml" ; then
+	    test x$verbose = x1 && echo "$name already compressed, skipping"
+	    alreadycompressed=`expr $alreadycompressed + 1`
+	    continue
+	fi
+
+	found=
+	outputs=`ls -1 "$outputdir"`
+	for output in $outputs ; do
+	    outputname=`echo $output | sed -e 's/.xml$//' | sed -e 's/.diff$//'`
+	    test -f "${outputdir}/${outputname}.diff.xml" && continue
+
+	    if $localhwlocdiff "$outputdir/${outputname}.xml" "$inputdir/${name}.xml" "$outputdir/${name}.diff.xml" >/dev/null 2>/dev/null; then
+		echo "Compressed $name on top of $outputname"
+		newlycompressed=`expr $newlycompressed + 1`
+		found=1
+		break
+	    fi
+	done
+
+	if test x$found = x ; then
+	    echo "Could not compress $name, keeping non-compressed"
+	    newlynoncompressed=`expr $newlynoncompressed + 1`
+	    cp "$inputdir/${name}.xml" "$outputdir/${name}.xml"
+	fi
+    done
+
+    echo "Compressed $newlycompressed new topologies ($alreadycompressed were already compressed)"
+    echo "Kept $newlynoncompressed new topologies non-compressed ($alreadynoncompressed were already non-compressed)"
+
+else
+    # uncompress
+
+    newlyuncompressed=0
+    newlynoncompressed=0
+    alreadyuncompressed=0
+
+    inputs=`ls -1 "$inputdir"`
+    for input in $inputs ; do
+
+	name=`echo $input | sed -e 's/.xml$//' | sed -e 's/.diff$//'`
+
+	if test "x${name}.xml" != "x$input" -a "x${name}.diff.xml" != "x$input"; then
+	    test x$verbose = x1 && echo "Ignoring non-XML and non-diff-XML file $input"
+	    continue
+	fi
+	if test -f "$outputdir/${name}.xml" ; then
+	    test x$verbose = x1 && echo "$name already uncompressed, skipping"
+	    alreadyuncompressed=`expr $alreadyuncompressed + 1`
+	    continue
+	fi
+
+	if test "x${name}.xml" = "x$input"; then
+	    # non-compressed
+	    cp "$inputdir/${name}.xml" "$outputdir/${name}.xml"
+	    echo "Copied $name, wasn't compressed"
+	    newlynoncompressed=`expr $newlynoncompressed + 1`
+	else
+	    # compressed
+	    if (cd $outputdir && $localhwlocpatch refname "$inputdir/${name}.diff.xml" "${name}.xml"); then
+		echo "Uncompressed $name"
+		newlyuncompressed=`expr $newlyuncompressed + 1`
+	    else
+		echo "Failed to uncompress $inputdir/${name}.diff.xml" 1>&2
+	    fi
+	fi
+    done
+
+    echo "Uncompressed $newlyuncompressed new topologies, copied $newlynoncompressed non-compressed topologies ($alreadyuncompressed were already uncompressed)"
+
+fi

linx64/mpi/openmpi/bin/hwloc-gather-topology

@@ -0,0 +1,349 @@
+#!/bin/sh
+#-*-sh-*-
+
+#
+# Copyright © 2009 CNRS
+# Copyright © 2009-2021 Inria.  All rights reserved.
+# Copyright © 2009-2012 Université Bordeaux
+# Copyright © 2014 Cisco Systems, Inc.  All rights reserved.
+# See COPYING in top-level directory.
+#
+
+HWLOC_VERSION="2.7.1"
+prefix="/home/admin/Documents/code/projects/cpp-thirdparty-src/mpi/openmpi/install/5.0.7"
+exec_prefix="${prefix}"
+bindir="${exec_prefix}/bin"
+localstatedir="${prefix}/var"
+runstatedir="${localstatedir}/run"
+# this will be changed into $bindir/lstopo during make install
+lstopo="$bindir/lstopo-no-graphics"
+hgcpuid="$bindir/hwloc-gather-cpuid"
+
+# make sure we use default numeric formats
+LANG=C
+LC_ALL=C
+export LANG LC_ALL
+
+# don't let ls append special chars after symlinks etc
+unalias -a ls
+
+gathercpuid=1
+gatherio=0
+gatherdmi=0
+keep=0
+
+if [ ! -x "$lstopo" ]
+then
+    error "Could not find lstopo executable in the install or build dir."
+    exit 1
+fi
+
+error()
+{
+    echo $@ 2>&1
+}
+
+usage()
+{
+   echo `basename $0`" [options] <savepath>"
+   echo "  Saves the Linux topology files (/sys, /proc, ...) under <savepath>.tar.bz2"
+   echo "  and the corresponding lstopo verbose output under <savepath>.output"
+   echo "Options:"
+   echo "  --io        Gather I/O files (takes much longer and generates much larger tarball)"
+   echo "  --dmi       Gather SMBIOS files. Works only when run as root. Requires dmi-sysfs kernel module"
+   echo "  --no-cpuid  Do not gather x86 CPUID using hwloc-gather-cpuid"
+   echo "  --keep      Keep the temporary copy of dumped files"
+   echo "  --version   Report version and exit"
+   echo "  -h --help   Show this usage"
+   echo "Example:"
+   echo "  $0 /tmp/\$(uname -n)"
+}
+
+while [ x`echo "$1" | cut -c1` = x- ] ; do
+  case $1 in
+  --io) gatherio=1;;
+  --dmi) gatherdmi=1;;
+  --no-cpuid) gathercpuid=0;;
+  --keep) keep=1;;
+  --version) echo `basename $0`" $HWLOC_VERSION"; exit 0;;
+  -h|--help) usage; exit 0;;
+  *) echo "Unrecognized option: $1"; usage; exit 1;;
+  esac
+  shift
+done
+
+if test $# -lt 1 -o x$1 = x; then
+  usage
+  exit 1
+fi
+name="$1"
+basename=`basename "$name"`
+dirname=`dirname "$name"`
+
+if [ x$gatherio = x0 ]; then
+  echo "I/O files won't be saved (--io not given)."
+fi
+if [ x$gatherdmi = x0 ]; then
+  echo "DMI files won't be saved (--dmi not given)."
+fi
+
+echo
+echo "*** Note that this tool may be slow on large nodes or when I/O is enabled. ***"
+echo
+
+if ! mkdir -p "$dirname" ; then
+    error "Failed to create directory $dirname."
+    exit 1
+fi
+
+if [ ! -w  "$dirname" ] ; then
+    echo "$dirname is not writable."
+    exit 1
+fi
+
+destdir=`mktemp -d --tmpdir hwloc-gather-topology.XXXXXXXX`
+
+# Use cat so that we properly get proc/sys files even if their
+# file length is wrong
+_savefile() {
+  local dest="$1"
+  local file="$2"
+  if test -r "$file"; then
+    dir=`dirname "$file"`
+    mkdir -p "$dest/$dir" 2>/dev/null
+    cat "$file" > "$dest/$file" 2>/dev/null
+  fi
+}
+
+_savelink() {
+  local dest="$1"
+  local file="$2"
+  dir=`dirname "$file"`
+  mkdir -p "$dest/$dir" 2>/dev/null
+  cp -P "$file" "$dest/$file"
+}
+
+# Get a file
+savefile() {
+  local dest="$1"
+  local file="$2"
+  echo " file $file"
+  _savefile "$dest" "$file"
+}
+
+# Get all files from the given directory
+# Ignore errors since some files may be missing, and some may be
+# restricted to root (but we don't need them).
+savedir() {
+  local dest="$1"
+  local path="$2"
+  echo " directory $path"
+  # gather all directories, including empty ones
+  find "$path" -type d 2>/dev/null | while read -r dir ; do
+    mkdir -p "$dest/$dir" 2>/dev/null
+  done
+  # gather all files now
+  find "$path" -type f 2>/dev/null | while read -r file ; do
+    test -e "$dest/$file" || _savefile "$dest" "$file"
+  done
+  # gather symlinks
+  find "$path" -type l 2>/dev/null | while read -r link ; do
+    test -e "$dest/$link" || _savelink "$dest" "$link"
+  done
+}
+
+# Save a class directory, including symlink targets (except in /devices/pci) and their device symlinks if any
+saveclassdir() {
+  local dest="$1"
+  local classname="$2"
+
+  test -d /sys/class/$classname/ || return
+
+  savedir "$dest" /sys/class/$classname/
+
+  for dev in $(ls /sys/class/$classname/); do
+    target=$(readlink /sys/class/$classname/$dev 2>/dev/null | grep -v /devices/pci)
+    if test "x$target" != x; then
+       savedir "$dest" "/sys/class/$classname/$target"
+    fi
+    device=$(readlink /sys/class/$classname/$target/device 2>/dev/null | grep -v /devices/pci)
+    if test "x$device" != x; then
+       savedir "$dest" "/sys/class/$classname/$target/$device"
+    fi
+  done
+}
+
+# Save a bus devices directory, include symlinks target (except in /devices/pci) with a possible relative path, and their device symlink if any
+savebusdir() {
+  local dest="$1"
+  local busname="$2"
+  local relpath="$3"
+
+  test -d /sys/bus/$busname/devices/ || return
+
+  savedir "$dest" /sys/bus/$busname/devices/
+
+  for dev in $(ls /sys/bus/$busname/devices/); do
+    target=$(readlink /sys/bus/$busname/devices/$dev 2>/dev/null | grep -v /devices/pci)
+    if test "x$target" != x; then
+       savedir "$dest" "/sys/bus/$busname/devices/$target/$relpath"
+    fi
+    device=$(readlink /sys/bus/$busname/devices/$target/$relpath/device 2>/dev/null | grep -v /devices/pci)
+    if test "x$device" != x; then
+       savedir "$dest" "/sys/bus/$busname/devices/$target/$relpath/$device"
+    fi
+  done
+}
+
+# savedir "$destdir/$basename" /sys/bus/dax/devices/
+# readlink /sys/bus/dax/devices/* 2>/dev/null | grep -v /devices/pci | while read -r path ; do savedir "$destdir/$basename" "/sys/bus/dax/devices/$path/.." ; done
+
+# Get an entire mount point, after decoding its path
+# we don't support path with \n since it would break in 'find ... | while read ..." above
+savemntpnt() {
+  local encodedpath=$1
+  if echo "$1" | grep "\\012" ; then
+    echo "Ignoring mount point whose filename contains an end of line."
+    return
+  fi
+  local path=$(echo "$1" | sed -e 's@\\134@\\@g' -e 's@\\040@ @g' -e 's@\\011@	@g')
+  savedir "$destdir/$basename" "${path}/"
+}
+
+#
+# Main stuff
+#
+echo "Gathering main files and directories..."
+
+# Gather the following list of files
+savefile "$destdir/$basename" /proc/cmdline
+savefile "$destdir/$basename" /proc/cpuinfo
+savefile "$destdir/$basename" /proc/meminfo
+savefile "$destdir/$basename" /proc/mounts
+savefile "$destdir/$basename" /proc/stat
+savefile "$destdir/$basename" /proc/version
+savefile "$destdir/$basename" /proc/self/cpuset
+savefile "$destdir/$basename" /proc/self/cgroup
+savefile "$destdir/$basename" /proc/driver/nvidia
+
+# Gather cpu and node information
+# (no need for savebusdir since we already gather the target /sys/devices/system/{cpu,node} explicitly)
+savedir "$destdir/$basename" /sys/devices/system/cpu/
+savedir "$destdir/$basename" /sys/bus/cpu/devices/
+savedir "$destdir/$basename" /sys/devices/system/node/
+savedir "$destdir/$basename" /sys/bus/node/devices/
+
+# Gather DMI IDs
+# (no need for aveclassdir since we only want "id" and it usually points to /sys/devices/virtual/dmi/id/)
+savedir "$destdir/$basename" /sys/class/dmi/id/
+savedir "$destdir/$basename" /sys/devices/virtual/dmi/id/
+
+# Gather hugepage information
+savedir "$destdir/$basename" /sys/kernel/mm/hugepages/
+
+# Gather the default /var/run/hwloc (in case it was created by a system-wide hwloc-dump-hwdata)
+if test -d /var/run/hwloc; then
+  savedir "$destdir/$basename" /var/run/hwloc
+fi
+# Then, gather what the current hwloc installation could have created in a different $runstatedir
+if test "$runstatedir" != "/var/run" -a -d "$runstatedir/hwloc"; then
+  savedir "$destdir/$basename" "$runstatedir/hwloc/"
+  mkdir -p "$destdir/$basename/var/run"
+  ln -sr "$destdir/$basename/$runstatedir/hwloc" "$destdir/$basename/var/run/hwloc.runstatedir"
+fi
+# And gather what custom $HWLOC_DUMPED_HWDATA_DIR
+if test "x$HWLOC_DUMPED_HWDATA_DIR" != x -a -d "$HWLOC_DUMPED_HWDATA_DIR"; then
+  savedir "$destdir/$basename" "$HWLOC_DUMPED_HWDATA_DIR"
+  mkdir -p "$destdir/$basename/var/run"
+  ln -sr "$destdir/$basename/$HWLOC_DUMPED_HWDATA_DIR" "$destdir/$basename/var/run/hwloc.HWLOC_DUMPED_HWDATA_DIR"
+fi
+# Now link to /var/run/hwloc (used by default in lstopo -i) to something sane if needed
+if ! test -d "$destdir/$basename/var/run/hwloc"; then
+  if test -e "$destdir/$basename/var/run/hwloc.HWLOC_DUMPED_HWDATA_DIR"; then
+    ln -sr "$destdir/$basename/var/run/hwloc.HWLOC_DUMPED_HWDATA_DIR" "$destdir/$basename/var/run/hwloc"
+  else if test -e "$destdir/$basename/$runstatedir/hwloc"; then
+    ln -sr "$destdir/$basename/var/run/hwloc.runstatedir" "$destdir/$basename/var/run/hwloc"
+  fi fi
+fi
+
+# Gather cgroup/cpuset mntpnts
+cat /proc/mounts | while read -r dummy1 mntpath mnttype mntopts dummy2 ; do
+  [ x$mnttype = xcpuset ] && savemntpnt "$mntpath"
+  [ x$mnttype = xcgroup ] && echo $mntopts | grep -w cpuset >/dev/null && savemntpnt "$mntpath"
+  [ x$mnttype = xcgroup2 ] && savemntpnt "$mntpath"
+done
+
+#
+# Optionally gather I/O directories too
+#
+if [ x$gatherio = x1 ]; then
+  echo "Gathering I/O files..."
+  # gather all PCI stuff, lots of links (/sys/bus/pci/devices/* and /sys/class/foo/*) point there
+  savedir "$destdir/$basename" /sys/bus/pci/devices/
+  savedir "$destdir/$basename" /sys/bus/pci/slots/
+  ls -d /sys/devices/pci* 2>/dev/null | while read -r path ; do savedir "$destdir/$basename" "$path" ; done
+  # gather class and bus links, we'll parse that the target path for PCI busids
+  saveclassdir "$destdir/$basename" block
+  saveclassdir "$destdir/$basename" dax
+  savebusdir "$destdir/$basename" dax ..
+  saveclassdir "$destdir/$basename" dma
+  saveclassdir "$destdir/$basename" drm
+  saveclassdir "$destdir/$basename" infiniband
+  saveclassdir "$destdir/$basename" net
+  saveclassdir "$destdir/$basename" ve
+  saveclassdir "$destdir/$basename" bxi
+  saveclassdir "$destdir/$basename" mic
+  # udev block data
+  ls -d /run/udev/data/b* 2>/dev/null | while read -r path ; do savefile "$destdir/$basename" "$path" ; done
+fi
+
+#
+# Optionally gather DMI directories too
+#
+if [ x$gatherdmi = x1 ]; then
+  echo "Gathering DMI files..."
+  savedir "$destdir/$basename" /sys/firmware/dmi/
+fi
+
+#
+# Export /proc/hwloc-nofile-info during lstopo (needs HWLOC_DUMP_NOFILE_INFO with HWLOC_THISSYSTEM=1)
+#
+echo "Exporting /proc/hwloc-nofile-info"
+export HWLOC_DUMP_NOFILE_INFO="$destdir/$basename/proc/hwloc-nofile-info"
+"$lstopo" - >/dev/null
+# disable HWLOC_DUMP_NOFILE_INFO for next lstopo invocation
+export HWLOC_DUMP_NOFILE_INFO=
+
+#
+# Export cpuid if available
+#
+if [ x$gathercpuid = x1 -a -e "$hgcpuid" ]; then
+  echo
+  echo "Exporting x86 CPUID using hwloc-gather-cpuid"
+  $hgcpuid --silent "$destdir/$basename/cpuid"
+fi
+
+# Create the archive and optionally keep the tree in /tmp for testing
+echo
+( cd "$destdir/" && tar cfj "$basename.tar.bz2" "$basename" )
+mv "$destdir/$basename.tar.bz2" "$dirname/$basename.tar.bz2"
+if test x$keep = x1; then
+  echo "Topology files gathered in $dirname/$basename.tar.bz2 and kept in $destdir/$basename/"
+else
+  echo "Topology files gathered in $dirname/$basename.tar.bz2"
+  rm -rf "$destdir"
+fi
+
+# Generate the output as well
+# we need "Topology not from this system" in the output so as to make test-topology.sh happy
+export HWLOC_THISSYSTEM=0
+"$lstopo" - -v > "$dirname/$basename.output"
+echo "Expected topology output stored in $dirname/$basename.output"
+"$lstopo" -.xml --whole-io --disallowed > "$dirname/$basename.xml"
+echo "XML topology stored in $dirname/$basename.xml"
+
+echo
+echo "WARNING: Do not post these files on a public list or website unless you"
+echo "WARNING: are sure that no information about this platform is sensitive."
+
+exit 0

linx64/mpi/openmpi/bin/hwloc-ls

@@ -0,0 +1 @@
+lstopo-no-graphics

linx64/mpi/openmpi/bin/mpiexec

@@ -1 +1 @@
-orterun
+mpirun

linx64/mpi/openmpi/bin/mpirun

@@ -1 +0,0 @@
-orterun

linx64/mpi/openmpi/bin/ompi-clean

@@ -1 +0,0 @@
-orte-clean

linx64/mpi/openmpi/bin/ompi-server

@@ -1 +0,0 @@
-orte-server

linx64/mpi/openmpi/bin/ortecc

@@ -1 +0,0 @@
-opal_wrapper

linx64/mpi/openmpi/bin/oshrun

@@ -0,0 +1 @@
+mpirun

linx64/mpi/openmpi/bin/prterun

@@ -0,0 +1 @@
+prte