Update scripts for new directory structure

bin/acme-amwg.sh

@@ -2,8 +2,42 @@
 
 set -e
 
-if [ $# -ne 1 ]; then
-    echo "Usage: $0 diag140804.csh"
+function usage () {
+    echo "Usage: $0 -case CASENAME -script diag140804.csh"
+}
+
+if [ $# -eq 0 ]; then
+    usage
+    exit 1
+fi
+
+while [ "$#" -ne 0 ]; do
+    case "$1" in
+        -case)
+            shift
+            CASENAME=$1
+            ;;
+        -script)
+            shift
+            SCRIPT=$1
+            ;;
+        *)
+            usage
+            exit 1
+            ;;
+    esac
+    shift
+done
+
+if [ -z "$CASENAME" ]; then
+    usage
+    echo "ERROR: Specify CASENAME"
+    exit 1
+fi
+
+if [ -z "$SCRIPT" ]; then
+    usage
+    echo "ERROR: Specify SCRIPT"
     exit 1
 fi
 
@@ -20,9 +54,7 @@ fi
 module load ncl
 module load nco
 
-# Chmod the templated script for this stage
-chmod 755 $1
+/bin/csh $PWD/$SCRIPT || true
 
-# Run the script on the service node
-./$1 || true
+exit 0
 

bin/acme-output.sh

@@ -3,7 +3,7 @@
 set -e
 
 function usage () {
-    echo "Usage: $0 -stage N"
+    echo "Usage: $0 -case CASENAME -stage N"
 }
 
 if [ $# -eq 0 ]; then
@@ -13,6 +13,10 @@ fi
 
 while [ $# -ne 0 ]; do
     case "$1" in
+        -case)
+            shift
+            CASENAME=$1
+            ;;
         -stage)
             shift
             STAGE=$1
@@ -25,36 +29,41 @@ while [ $# -ne 0 ]; do
     shift
 done
 
+if [ -z "$CASENAME" ]; then
+    echo "ERROR: Specify -casename"
+    usage
+    exit 1
+fi
+
 if [ -z "$STAGE" ]; then
     echo "ERROR: Specify -stage"
     usage
     exit 1
 fi
 
-# Get the case name
-CASE=$(./xmlquery CASE -valonly -silent)
-
-# Get the full path to the run directory
-RUNDIR=$(./xmlquery RUNDIR -valonly -silent)
-RUNDIR=$(cd $RUNDIR && pwd)
+CASEROOT=$PWD/$CASENAME
 
 # Get the workflow scratch directory
 DIR=$(pwd)
 
 # Make the stage output dir
-STAGEDIR=$DIR/${CASE}-stage${STAGE}
+STAGEDIR=$DIR/${CASENAME}-stage${STAGE}
 mkdir $STAGEDIR
 
+# Get the full path to the run directory
+RUNDIR=$(cd $CASEROOT && ./xmlquery RUNDIR -valonly -silent)
+RUNDIR=$(cd $RUNDIR && pwd)
+
 # Touch this file here so that it will always exist, even if it is empty
 # for the first stage
 touch outputs_to_ignore
 
 # For each of the new files
-for f in $(ls ${RUNDIR}/${CASE}.* ${RUNDIR}/*.log.*.gz ${RUNDIR}/rpointer.* | grep -v -f outputs_to_ignore); do
+for f in $(ls ${RUNDIR}/${CASENAME}.* ${RUNDIR}/*.log.*.gz ${RUNDIR}/rpointer.* | grep -v -f outputs_to_ignore); do
     # Symlink it to the output dir
     ln -s $f ${STAGEDIR}/$(basename $f)
 done
 
 # Update the ignore file to ignore outputs from the current stage
-ls ${RUNDIR}/${CASE}.* ${RUNDIR}/*.log.* > outputs_to_ignore
+ls ${RUNDIR}/${CASENAME}.* ${RUNDIR}/*.log.* > outputs_to_ignore
 

bin/acme-run.sh

-#!/bin/bash
+#!/bin/bash -l
 
 set -e
 
 function usage () {
-    echo "Usage: $0 [-continue] -stage N -stop STOP_OPTION -n STOP_N"
+    echo "Usage: $0 [-continue] -case CASENAME -stage N -stop STOP_OPTION -n STOP_N"
 }
 
 if [ $# -eq 0 ]; then
@@ -14,6 +14,10 @@ fi
 CONTINUE_RUN=FALSE
 while [ "$#" -ne 0 ]; do
     case "$1" in
+        -case)
+            shift
+            CASENAME=$1
+            ;;
         -continue)
             CONTINUE_RUN=TRUE
             ;;
@@ -37,11 +41,18 @@ while [ "$#" -ne 0 ]; do
     shift
 done
 
+echo CASENAME $CASENAME
 echo STOP_N $STOP_N
 echo STOP_OPTION $STOP_OPTION
 echo CONTINUE_RUN $CONTINUE_RUN
 echo STAGE $STAGE
 
+if [ -z "$CASENAME" ]; then
+    echo "ERROR: Specify -case"
+    usage
+    exit 1
+fi
+
 if [ -z "$STAGE" ]; then
     echo "ERROR: Specify -stage"
     usage
@@ -60,6 +71,14 @@ if [ -z "$STOP_OPTION" ]; then
     exit 1
 fi
 
+export CASENAME
+export CASEROOT=$PWD/$CASENAME
+
+cd $CASENAME
+
+# Make sure that the run directory is correct
+./xmlchange -file env_run.xml -id RUNDIR -val $CASEROOT/run
+
 # We never want to resubmit the jobs in the Pegasus workflow
 ./xmlchange -file env_run.xml -id RESUBMIT -val 0
 
@@ -78,12 +97,9 @@ fi
 ./xmlchange -file env_run.xml -id CHECK_TIMING -val FALSE
 ./xmlchange -file env_run.xml -id SAVE_TIMING -val FALSE
 
-# Get the case name
-CASE=$(./xmlquery CASE -valonly -silent)
-
 # This script often returns non-zero, so we need to mask the failure
 # We use exitcode.successmessage to detect failures
-./$CASE.run || true
+/bin/csh ./$CASENAME.run || true
 
 exit 0