(Guys, I feel like an idiot for posting multiple messages per day to this list. I'm really trying to work these things out on my own before I post.....)
The TOV example works great on queenbee. :-)
After reading the Advanced Tutorial, I tried to run my own job, which I called "uni449_1". It's a Cactus run which works interactively... The command I used was
simfactory/sim create-submit uni449_1 --parfile=/home/shawley/runs/texmex/uni449.par --procs=8 --walltime=8:0:0 --num-threads=8 --ppn-used=1 --queue=workq
Several errors appeared, and it seems *Cactus itself* never even got started...but somehow the job used up 8 hours of wall clock time. ?
Does anyone have any suggestions? Errors and output log below.
Thanks, Scott
In /scratch/shawley/simulations/uni449_1/output-0000/ , the uni449_1.err file contained mention of several syntax errors: ... + for node in '$(cat ${MPD_NODEFILE})' + (( proc=0 )) + (( 0<0.125 )) /var/spool/torque/mom_priv/jobs/565273.qb2.SC: line 66: ((: 0<0.125: syntax error in expression (error token is ".125") + for node in '$(cat ${MPD_NODEFILE})' + (( proc=0 )) + (( 0<0.125 )) /var/spool/torque/mom_priv/jobs/565273.qb2.SC: line 66: ((: 0<0.125: syntax error in expression (error token is ".125") + for node in '$(cat ${MPD_NODEFILE})' + (( proc=0 )) + (( 0<0.125 )) /var/spool/torque/mom_priv/jobs/565273.qb2.SC: line 66: ((: 0<0.125: syntax error in expression (error token is ".125") + for node in '$(cat ${MPD_NODEFILE})' + (( proc=0 )) + (( 0<0.125 )) /var/spool/torque/mom_priv/jobs/565273.qb2.SC: line 66: ((: 0<0.125: syntax error in expression (error token is ".125") + for node in '$(cat ${MPD_NODEFILE})' + (( proc=0 )) + (( 0<0.125 )) /var/spool/torque/mom_priv/jobs/565273.qb2.SC: line 66: ((: 0<0.125: syntax error in expression (error token is ".125") + for node in '$(cat ${MPD_NODEFILE})' + (( proc=0 )) + (( 0<0.125 )) /var/spool/torque/mom_priv/jobs/565273.qb2.SC: line 66: ((: 0<0.125: syntax error in expression (error token is ".125") + for node in '$(cat ${MPD_NODEFILE})' + (( proc=0 )) + (( 0<0.125 )) /var/spool/torque/mom_priv/jobs/565273.qb2.SC: line 66: ((: 0<0.125: syntax error in expression (error token is ".125") + for node in '$(cat ${MPD_NODEFILE})' + (( proc=0 )) + (( 0<0.125 )) /var/spool/torque/mom_priv/jobs/565273.qb2.SC: line 66: ((: 0<0.125: syntax error in expression (error token is ".125") ++ date +%s + export CACTUS_STARTTIME=1312948714 + CACTUS_STARTTIME=1312948714 + /usr/local/packages/mvapich2/1.4/intel-11.1/bin/mpirun_rsh -np 1 -hostfile mpi_nodefile /bin/env MV2_ENABLE_AFFINITY=0 OMP_NUM_THREADS=8 ./SIMFACTORY/cactus_sim -L 3 uni449.par =>> PBS: job killed: walltime 28836 exceeded limit 28800
The output file didn't have any mention of Cactus:
[shawley@qb3 output-0000]$ cat uni449_1.out -------------------------------------- Running PBS prologue script -------------------------------------- User and Job Data: -------------------------------------- Job ID: 565273.qb2 Username: shawley Group: lsuusers Date: 09-Aug-2011 22:58 Node: qb528 (5373) -------------------------------------- PBS has allocated the following nodes:
qb528 qb502 qb493 qb472 qb463 qb441 qb215 qb149
A total of 64 processors on 8 nodes allocated --------------------------------------------- Check nodes and clean them of stray processes --------------------------------------------- Checking node qb528 22:58:19 Checking node qb502 22:58:21 Checking node qb493 22:58:23 Checking node qb472 22:58:25 Checking node qb463 22:58:27 Checking node qb441 22:58:29 Checking node qb215 22:58:30 Checking node qb149 22:58:32 Done clearing all the allocated nodes ------------------------------------------------------ Concluding PBS prologue script - 09-Aug-2011 22:58:32 ------------------------------------------------------ Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. Preparing: Checking: /scratch/shawley/simulations/uni449_1/output-0000-active qb528 Tue Aug 9 22:58:33 CDT 2011 PBS nodes: qb528 qb528 qb528 qb528 qb528 qb528 qb528 qb528 qb502 qb502 qb502 qb502 qb502 qb502 qb502 qb502 qb493 qb493 qb493 qb493 qb493 qb493 qb493 qb493 qb472 qb472 qb472 qb472 qb472 qb472 qb472 qb472 qb463 qb463 qb463 qb463 qb463 qb463 qb463 qb463 qb441 qb441 qb441 qb441 qb441 qb441 qb441 qb441 qb215 qb215 qb215 qb215 qb215 qb215 qb215 qb215 qb149 qb149 qb149 qb149 qb149 qb149 qb149 qb149 Environment: Starting: Terminated ------------------------------------------------------ Running PBS epilogue script - 10-Aug-2011 06:59:09 ------------------------------------------------------ Checking node qb528 (MS) Checking node qb149 ok Checking node qb215 ok Checking node qb441 ok Checking node qb463 ok Checking node qb472 ok Checking node qb493 ok Checking node qb502 ok Checking node qb528 ok ------------------------------------------------------ Concluding PBS epilogue script - 10-Aug-2011 06:59:32 ------------------------------------------------------ Exit Status: Job ID: 565273.qb2 Username: shawley Group: lsuusers Job Name: uni449_1-0000 Session Id: 5372 Resource Limits: ncpus=1,nodes=8:ppn=8,walltime=08:00:00 Resources Used: cput=08:00:33,mem=3700kb,vmem=124928kb,walltime=08:00:36 Queue Used: workq Account String: loni_cactus06 Node: qb528 Process id: 8870 ------------------------------------------------------
-- Scott H. Hawley, Ph.D. Asst. Prof. of Physics Chemistry & Physics Dept Office: Hitch 100D Belmont University Tel: +1-615-460-6206 Nashville, TN 37212 USA Fax: +1-615-460-5458 (Temporarily broken…xxxPGP Key at http://sks-keyservers.net)