An XML based solution to mpirun output processing.

Author: hategan

src/psij/launchers/scripts/mpi_launch.sh

@@ -15,29 +15,53 @@ fi
 
 pre_launch
 
-filter_out() {
-    sed -nE 's/^\[[^]]+\]<stdout>:(.*)/\1/p'
-}
-
-filter_err() {
-    sed -nE 's/^\[[^]]+\]<stderr>:(.*)/\1/p'
+# We need to use a marker for when actual output starts because some mpi deployments add
+# banners at the beginning of the mpirun output. There are two seemingly reasonable
+# ways of extracting the output: --tag-output and --xml. Unfortunately, --tag-output is broken
+# and occasionally mashes two lines together in the form "part1<TAG>:part2" instead of
+# "<TAG>:part1part2". So we really only have XML
+process_line() {
+    LINE="$1"
+    if [[ "$LINE" =~ \<stdout ]]; then
+        FILE="$_PSI_J_STDOUT"
+    elif [[ "$LINE" =~ \<stderr ]]; then
+        FILE="$_PSI_J_STDERR"
+    else
+        return
+    fi
+    # We first remove </mpirun>, which can be found after </stdout>.
+    # The rest is about converting &#nnnn; entities to something that we can print with other
+    # POSIX tools. The %c specified does not work properly for the bash printf, since it requires
+    # an integer as input, but we can only supply strings. We can either use awk's printf or
+    #
+    P1=$(echo $LINE | sed -nE 's/<\/?mpirun>//g; s/&#0*/\&#/g; s/<std...[^>]*>([^<]*)<\/std...>/\1/g p')
+    FMT=$(echo "$P1" | sed 's/\\/\\\\/g;s/%/%%/g;s/&#[0-9]*;/%c/g;s/&gt;/>/g;s/&lt;/</g;s/&amp;/\&/g;s/"/\"/g')
+    NUMS=$(echo "$P1" | grep -o '&#[0-9]*;' | tr '&#;' '  ,' )
+    awk "BEGIN {printf \"$FMT%s\", $NUMS \"\"}" >>"$FILE"
 }
 
-filter_out_5() {
-    sed -nE 's/^\[[^]]+\]<stdout>: (.*)/\1/p'
+filter_out() {
+    while IFS= read LINE; do
+        process_line "$LINE"
+    done
+    # If the last line does not end in a newline, read will exit with a non-zero code but still
+    # set the variable to the contents of that line. Not sure how portable this is.
+    if [ "$LINE" != "" ]; then
+        process_line "$LINE"
+    fi
 }
 
-filter_err_5() {
-    sed -nE 's/^\[[^]]+\]<stderr>: (.*)/\1/p'
-}
+# truncate output since we append in the functions above
+> $_PSI_J_STDOUT
+> $_PSI_J_STDERR
 
 set +e
 if [ "$IS_OPENMPI_5" == "1" ]; then
-    mpirun --oversubscribe --output TAG -n $_PSI_J_PROCESS_COUNT "$@" \
-        1> >(filter_out_5 > $_PSI_J_STDOUT) 2> >(filter_err_5 > $_PSI_J_STDERR) <$_PSI_J_STDIN
+    mpirun --oversubscribe --output XML -n $_PSI_J_PROCESS_COUNT "$@" \
+      1> >(filter_out) <$_PSI_J_STDIN
 elif [ "$IS_OPENMPI" == "1" ]; then
-    mpirun --oversubscribe --tag-output -q -n $_PSI_J_PROCESS_COUNT "$@" \
-        1> >(filter_out > "$_PSI_J_STDOUT") 2> >(filter_err > $_PSI_J_STDERR) <$_PSI_J_STDIN
+    mpirun --oversubscribe -q -xml -n $_PSI_J_PROCESS_COUNT "$@" \
+      1> >(filter_out) <$_PSI_J_STDIN
 else
     mpirun -n $_PSI_J_PROCESS_COUNT "$@" 1>$_PSI_J_STDOUT 2>$_PSI_J_STDERR <$_PSI_J_STDIN
 fi