[Swift-commit] r2811 - in usertools/cio: bin libexec libexec/falkon libexec/zoid science/blast tools

Fri Apr 3 15:45:53 CDT 2009

Author: aespinosa
Date: 2009-04-03 15:45:49 -0500 (Fri, 03 Apr 2009)
New Revision: 2811

Added:
   usertools/cio/libexec/zoid/
Removed:
   usertools/cio/tools/zoid/
Modified:
   usertools/cio/bin/ciologic-bgp.sh
   usertools/cio/libexec/falkon/falkon-start-bgp.sh
   usertools/cio/libexec/zoid/logging-script.sh
   usertools/cio/science/blast/tc.data
Log:
Inserted ZeptOS logging code in core ciologic.  Moved zoid scripts to libexec

Modified: usertools/cio/bin/ciologic-bgp.sh
===================================================================

--- usertools/cio/bin/ciologic-bgp.sh	2009-04-02 22:34:13 UTC (rev 2810)
+++ usertools/cio/bin/ciologic-bgp.sh	2009-04-03 20:45:49 UTC (rev 2811)
@@ -19,7 +19,7 @@
 LD_LIBRARY_PATH=/lib:/fuse/lib:/fuse/usr/lib
 PATH=/fuse/bin:/fuse/usr/bin:$PATH
 
-/home/iskra/ZeptoOS/packages/cnip/prebuilt/cn-ipfwd.2409 &
+/home/iskra/ZeptoOS/packages/cnip/prebuilt/cn-ipfwd &
 while [ ! -f /tmp/ifconfig.cmd ]; do
     sleep 1
 done

Modified: usertools/cio/libexec/falkon/falkon-start-bgp.sh
===================================================================
--- usertools/cio/libexec/falkon/falkon-start-bgp.sh	2009-04-02 22:34:13 UTC (rev 2810)
+++ usertools/cio/libexec/falkon/falkon-start-bgp.sh	2009-04-03 20:45:49 UTC (rev 2811)
@@ -24,7 +24,7 @@
   exit 1
 fi
 
-PROFILE_NAME="zeptocn"
+PROFILE_NAME="zeptocn-swift"
 QUEUE_NAME=$1
 NUM_NODES=$2
 let NUM_ION=NUM_NODES/64
@@ -46,7 +46,7 @@
    STR=$6
 fi 
 
-cp ${FALKON_HOME}/bin/zoid-user-script.sh ${HOME}/zoid-user-script.sh
+cp $CIOROOT/libexec/zoid/logging-script.sh ${HOME}/zoid-user-script.sh
 chmod +x ${HOME}/zoid-user-script.sh
 
 FALKON_JOB_ID=`falkon-id-get.sh N/A`                   
@@ -61,23 +61,19 @@
 
 
 WORKER_SCRIPT=$CIOROOT/bin/ciologic-$CIOARCH.sh
-ZOID_JOB_ID=`cqsub -q ${QUEUE_NAME} -k ${PROFILE_NAME} -C ${HOME} -t \
+SUBMIT_CMD="cqsub -q ${QUEUE_NAME} -k ${PROFILE_NAME} -C ${HOME} -t \
     ${MAX_TIME_MIN} -n ${NUM_NODES} \
 	-e LD_LIBRARY_PATH=/lib:/fuse/lib:/fuse/usr/lib:CIOROOT=$CIOROOT:CIOARCH=$CIOARCH:CHIRPROOT=$CHIRPROOT  \
 	/bgsys/linux/1.2.020080512/bin/bash $WORKER_SCRIPT \
 	${SERVICE_IP} ${SERVICE_PORT1} ${SERVICE_PORT2} ${WORKERS_PER_NODE} \
 	${USER} ${FALKON_JOB_ID} ${FALKON_ROOT} \
-    $NUM_NODES $DATA_NUM $STR` # MTIO parameters
+    $NUM_NODES $DATA_NUM $STR" # MTIO parameters
 
+ZOID_JOB_ID=`$SUBMIT_CMD`
 EXIT_CODE=$? 
 
 if [ "${EXIT_CODE}" -ne "0" ]; then
-  echo "Error in submitting job to Cobalt.. 'cqsub -q ${QUEUE_NAME} \
-       -k ${PROFILE_NAME} -C ${HOME} -t ${MAX_TIME_MIN} -n ${NUM_NODES} \
-       -e LD_LIBRARY_PATH=/lib:/fuse/lib:/fuse/usr/lib \
-       /bgsys/linux/1.2.020080512/bin/bash $WORKER_SCRIPT \
-       ${SERVICE_IP} ${SERVICE_PORT1} ${SERVICE_PORT2} \
-       ${WORKERS_PER_NODE} ${USER} ${FALKON_JOB_ID} ${FALKON_ROOT}' "
+  echo "Error in submitting job to Cobalt.. $SUBMIT_CMD"
   exit ${EXIT_CODE}
 fi
 
@@ -157,6 +153,9 @@
   exit 1
 fi
 
+echo $ZOID_JOB_ID $FALKON_JOB_ID $QUEUE_NAME \
+    $NUM_NODES $MAX_TIME_MIN $WORKERS_PER_NODE >>$HOME/.falkonjobs
+
 echo "Succesfully submitted the job to Cobalt, and setup job specific Falkon tree!"
 echo "To monitor the job status, type 'cqstat | grep ${USER}'; once it is in running state, you can use the Falkon specific command ...."
 echo "To submit your Falkon-based workload, type: ....; you can do this any time, the falkon workload will wait for the resources to come online, and will only be submitted when everything is ready; the script is run in the background, so the workload will run even if the ssh session gets disconnected."

Copied: usertools/cio/libexec/zoid (from rev 2810, usertools/cio/tools/zoid)

Modified: usertools/cio/libexec/zoid/logging-script.sh
===================================================================
--- usertools/cio/tools/zoid/logging-script.sh	2009-04-02 22:34:13 UTC (rev 2810)
+++ usertools/cio/libexec/zoid/logging-script.sh	2009-04-03 20:45:49 UTC (rev 2811)
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # Added GPFS activity  logging of IO calls -ame
-COBALT_JOBID=`echo $ZOID_JOB_ENV | sed 's/^.*COBALT_JOBID=\([^:]*\)/\1/'`
+COBALT_JOBID=`echo $ZOID_JOB_ENV | sed 's/^.*COBALT_JOBID=\([^:]*\)*/\1/' | cut -f 1 -d ':'`
 
 TARGET_DIR=$HOME/performance/$COBALT_JOBID
 
@@ -10,8 +10,7 @@
 echo -n $TARGET_DIR/gpfs.`hostname` >/tmp/gpfs_log_name.new
 touch $TARGET_DIR/gpfs.`hostname` || exit 1
 mv /tmp/gpfs_log_name.new /tmp/gpfs_log_name
-echo -n $TARGET_DIR/zoid.`hostname` >/tmp/zoid_log_name.new
-mv /tmp/zoid_log_name.new /tmp/zoid_log_name
+/bin.rd/statquery 60 >$TARGET_DIR/zoid.`hostname` &
 # end addition
 
 #startup

Modified: usertools/cio/science/blast/tc.data
===================================================================
--- usertools/cio/science/blast/tc.data	2009-04-02 22:34:13 UTC (rev 2810)
+++ usertools/cio/science/blast/tc.data	2009-04-03 20:45:49 UTC (rev 2811)
@@ -17,9 +17,7 @@
 localhost 	paste 		/bin/paste	INSTALLED	INTEL32::LINUX	null
 
 # BLAST binaries
-localhost	blastall	/home/aespinosa/science/blast/ncbi.communicado/bin/blastall	INSTALLED	INTEL32::LINUX	null
-localhost	mockblast	/home/aespinosa/cio/science/blast/mockblast.sh	INSTALLED	INTEL32::LINUX	null
-# TERAPORT
-TERAPORT	blastall	/home/aespinosa/science/blast/ncbi.teraport/bin/blastall	INSTALLED	INTEL32::LINUX	null
-# RANGER
-RANGER	blastall	/share/home/01035/tg802895/ncbi/bin/blastall	INSTALLED	INTEL32::LINUX	null
+communicado	blastall	/home/aespinosa/science/blast/ncbi.communicado/bin/blastall	INSTALLED	INTEL32::LINUX	null
+communicado	mockblast	/home/aespinosa/cio/science/blast/mockblast.sh	INSTALLED	INTEL32::LINUX	null
+surveyor	blastall	/home/espinosa/science/blast/ncbi.communicado/bin/blastall	INSTALLED	INTEL32::LINUX	null
+surveyor	mockblast	/home/espinosa/cio/science/blast/mockblast.sh	INSTALLED	INTEL32::LINUX	null


