Task #2699

Improved documentation; use -s instead of -p

CEP/LMWCommon/src/cexecms

@@ -7,60 +7,66 @@
 showhelp() 
 {
   echo ''
-  echo ' cexecms runs a command on cluster nodes for files matching'
-  echo ' the given file name glob pattern.'
+  echo ' cexecms runs a command or script on cluster nodes for files matching the'
+  echo ' given file name glob pattern. Placeholders in command or script are'
+  echo ' replaced by the actual file name.'
   echo ''
   echo ' usage:'
-  echo '    cexecms [-c cluster] command nameglob [arg1 arg2 ...]'
+  echo '    cexecms [-c cluster] [-d] [-s script] [-w workdir] command nameglob [arg1 arg2 ...]'
   echo ''
-  echo '      -c cluster    cluster name as defined for cexec'
+  echo '      -c cluster    Cluster name as defined for cexec.'
   echo '                    default is lce: if run on an lfe node, otherwise locus:'
-  echo '      -d            do a dryrun (i.e., do not execute, but only print the command)'
-  echo '      -i ids        List of ids to replace <ID> in the nameglob argument'
-  echo '                    A comma and/or blank can be used as separator'
+  echo '      -d            Do a dryrun.'
+  echo '                    (do not execute, but only print the command/script)'
+  echo '      -i ids        List of ids to replace <ID> in the nameglob argument.'
+  echo '                    A comma and/or blank can be used as separator.'
   echo '                    Ids can be given with parset range style (e.g. 33678..33683)'
-  echo '                    In this way the command can be executed for multiple observations'
-  echo '      -p parset     parset to be used by the command'
-  echo '                    It must b accessible on all nodes in the cluster'
-  echo '                    placeholders in the parset like <FN> are replaced'
-  echo '                    The parset will be used as the first argument for the command'
-  echo '      -w workdir    Working directory in remote process. Default is login directory'
-  echo '      command       command to be executed remotely'
+  echo '                    In this way the command can be executed for multiple observations.'
+  echo '      -s script     Script or parset file to be used by the command.'
+  echo '                    It must be accessible on all nodes in the cluster.'
+  echo '                    Placeholders (like <FN>) in the file are replaced.'
+  echo '                    It will be used as the first argument in the command.'
+  echo '      -w workdir    Working directory in remote process. Default is login directory.'
+  echo '      command       Command to be executed remotely.'
   echo '                    Quotes are needed if it contains spaces, etc.'
-  echo '      nameglob      file name glob pattern (# is a shorthand for [0-9])'
-  echo '                    E.g., one can use SB### for any subband'
-  echo '      arg1 arg2 ..  Optional extra arguments given to the command'
+  echo '                    Placeholders (like <FN>) in the command are replaced.'
+  echo '      nameglob      File name glob pattern (# is a shorthand for [0-9]).'
+  echo '                    E.g., one can use SB### meaning any subband.'
+  echo '      arg1 arg2 ..  Optional extra arguments to be given to command.'
   echo ''
   echo ' Using cexec, the script cexecms-part is executed on the given cluster'
   echo ' nodes. It looks for files matching the given file name glob pattern.'
   echo ' The glob pattern can be bash-style, thus *, ?, [], and {} are possible.'
   echo ' The given command will be executed for each matching file name.'
-  echo ' The actual file name can be made part of the command using:'
-  echo '     <FILENAME> or <FN>  for the full file name'
-  echo '     <BASENAME> or <BN>  for the basename part'
-  echo '     <DIRNAME>  or <DN>  for the directory part'
+  echo ' The actual file name can be made part of the command or script'
+  echo ' using one or more of the following placeholders:'
+  echo '     <FILENAME> or <FN>    for the full file name'
+  echo '     <BASENAME> or <BN>    for the basename part'
+  echo '     <DIRNAME>  or <DN>    for the directory part'
   echo ' The first two can be followed by a . (e.g. <FN.>) meaning that the'
   echo ' basename is used till the first dot (thus the extension is removed.)'
-  echo ' If no substitutions have been done, the command is executed like'
-  echo '     command filename arg1 arg2 ...'
-  echo ' otherwise like'
+  echo ''
+  echo ' If -s is given, the command is executed like:'
+  echo '     command script arg1 arg2 ..'
+  echo ' Otherwise, if no substitutions have been done the command is executed like:'
+  echo '     command <FN> arg1 arg2 ...'
+  echo ' Otherwise like'
   echo '     command arg1 arg2...'
   echo ''
   echo ' For example:'
-  echo '   cexecms "ls -d" "/data/scratch/pipeline/L2011_22663/*"'
+  echo '     cexecms "ls -d" "/data/scratch/pipeline/L2011_22663/*"'
   echo ' is a trivial example and could also be done with cexec. Note that'
-  echo '   cexecms "ls -d <FN>" "/data/scratch/pipeline/L2011_22663/*"'
+  echo '     cexecms "ls -d <FN>" "/data/scratch/pipeline/L2011_22663/*"'
   echo ' is doing the same.'
   echo ' The following example is more elaborate and creates a _sel.MS table'
   echo ' in another directory for each MS of subband 000 till 099.'
-  echo '   cexecms "taql '"'"'select from <FN> where ANTENNA1 in [0,1,2]'
-  echo '                 giving /data/scratch/diepen/<BN.>_sel.MS'"'"'"'
-  echo '           "/data/scratch/pipeline/L2011_22663/*SB0##*"'
+  echo '     cexecms "taql '"'"'select from <FN> where ANTENNA1 in [0,1,2]'
+  echo '                   giving /data/scratch/diepen/<BN.>_sel.MS'"'"'"'
+  echo '             "/data/scratch/pipeline/L2011_22663/*SB0##*"'
+  echo ' Note that quotes have to be used abundantly.'
   echo ''
   echo ' Sometimes a command can be dangerous or take a long time to run.'
-  echo ' In such a case it makes sense to execute it first on a single subband'
-  echo ' using a glob pattern with a specific subband or by using cexecms-part'
-  echo ' on a remote node'.
+  echo ' In such a case it makes sense to execute it first with the -d option.'
   echo ''
   echo ' Note that the current environment (paths, etc.) is copied. You should'
   echo ' have done "use LofIm" if you need LofIm in the (remote) command.'
@@ -76,7 +82,7 @@ if test $# -lt 2; then
     exit 1
 fi
 cluster=
-parset=
+script=
 ids=
 dryrun=
 workdir=
@@ -87,9 +93,9 @@ do
     shift
     cluster="$1"
     shift
-  elif test "$1" = "-p"; then
+  elif test "$1" = "-s"; then
     shift
-    parset="$1"
+    script="$1"
     shift
   elif test "$1" = "-i"; then
     shift
@@ -115,16 +121,6 @@ do
     esac
   fi
 done
-if test "$1" = "-p"; then
-    shift
-    parset="$1"
-    shift
-fi
-if test "$1" = "-c"; then
-    shift
-    cluster="$1"
-    shift
-fi
 if test $# -lt 2; then
     showhelp
     exit 1
@@ -188,18 +184,18 @@ nameglobnew=`echo "$nameglob" | sed \
     -e 's%{%:LBRACE:%g' \
     -e 's%}%:RBRACE:%g'`
 
-# Add -p is parset is used.
+# Add -s is script is used.
 # Same for -w.
-test "$parset"  = ""  ||   parset="-p $parset"
+test "$script"  = ""  ||   script="-s $script"
 test "$workdir" = ""  ||  workdir="-w $workdir"
 # Do a single run if no ids given, otherwise iterate over all ids.
 if test "$ids" = ""; then
-  cexec $cluster $pgmpath/cexecms-part $dryrun -e "$envfile" "$parset" "$workdir" "'$commandnew'" "$nameglobnew" "$@"
+  cexec $cluster $pgmpath/cexecms-part $dryrun -e "$envfile" "$script" "$workdir" "'$commandnew'" "$nameglobnew" "$@"
 else
   for id in $ids
   do
     nm=`echo "$nameglobnew" | sed -e "s%<ID>%$id%g"`
-    cexec $cluster $pgmpath/cexecms-part $dryrun -e "$envfile" "$parset" "$workdir" "'$commandnew'" "$nm" "$@"
+    cexec $cluster $pgmpath/cexecms-part $dryrun -e "$envfile" "$script" "$workdir" "'$commandnew'" "$nm" "$@"
   done
 fi
 rm -f "$envfile"

CEP/LMWCommon/src/cexecms-part

@@ -18,13 +18,13 @@
 
 showhelp()
 {
-  echo ' run like:   cexecms-part [-d] [-e envfile] [-w workdir] [-p parset] command nameglob [arg1 arg2 ...]'
+  echo ' run like:   cexecms-part [-d] [-e envfile] [-w workdir] [-s script] command nameglob [arg1 arg2 ...]'
   echo '     see cexecms for more information'
 }
 
 # Handle possible options.
 envfile=
-parset=
+script=
 dryrun=0
 workdir=
 while [ $# != 0 ]
@@ -33,9 +33,9 @@ do
     shift
     envfile="$1"
     shift
-  elif test "$1" = "-p"; then
+  elif test "$1" = "-s"; then
     shift
-    parset="$1"
+    script="$1"
     shift
   elif test "$1" = "-w"; then
     shift
@@ -121,7 +121,7 @@ command=`echo "$command" | sed \
     -e 's%:DOLLAR:%$%g'`
 
 # Process all files.
-# Substitute placeholders in the command and possible parset.
+# Substitute placeholders in the command and possible script.
 for fname in $names
 do
     # Form the various placeholder replacements.
@@ -143,9 +143,9 @@ do
 	-e "s%<FILENAME\.>%$fnamed%g" \
 	-e "s%<DIRNAME\.>%$dnamed%g" \
 	-e "s%<BASENAME\.>%$bnamed%g"`
-    if test "$parset" != ""; then
-        # A parset is given, replace placeholders in there as well.
-        psname=$HOME/`basename $parset`-$USER-$$
+    if test "$script" != ""; then
+        # A script is given, replace placeholders in there as well.
+        psname=$HOME/`basename $script`-$USER-$$
         sed \
 	-e "s%<FN>%$fname%g" \
 	-e "s%<DN>%$dname%g" \
@@ -159,7 +159,7 @@ do
 	-e "s%<FILENAME\.>%$fnamed%g" \
 	-e "s%<DIRNAME\.>%$dnamed%g" \
 	-e "s%<BASENAME\.>%$bnamed%g" \
-        $parset > $psname
+        $script > $psname
 	if test $dryrun = 1; then
 	    echo "Dryrun: " $commandnew $psname "$@"
 	    cat $psname