Dear All,I have submitted static_tov simulation inside Cactus directory by
./simfactory/bin/sim submit static_tov --parfile=par/static_tov.par --procs=32
--walltime=8:0:0 --allocation=loni_cactus08
Inside Cactus directory ./simfactory/bin/sim list-simulations givesstatic_tov
[ACTIVE(FINISHED), restart 0000, job id 703467]But in
/scratch/ettest52/simulations/static_tov I found a log.txt file along with
output-0000, output-0000-active and SIMFACTORY directories. The log.txt file
contains following
[LOG:2013-08-04 11:09:54] self.create(simulationName, parfile)::Creating
simulation static_tov [LOG:2013-08-04 11:09:54] self.create(simulationName,
parfile)::Simulation directory: /scratch/ettest52/simulations/static_tov
[LOG:2013-08-04 11:09:54] self.create(simulationName, parfile)::Simulation
Properties: [LOG:2013-08-04 11:09:54] self.create(simulationName, parfile)::
[LOG:2013-08-04 11:09:54] self.create(simulationName, parfile)::[properties]
[LOG:2013-08-04 11:09:54] self.create(simulationName, parfile)::machine
= queenbee [LOG:2013-08-04 11:09:54] self.create(simulationName,
parfile)::simulationid =
simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.08.04-11.09.54-31394
[LOG:2013-08-04 11:09:54] self.create(simulationName, parfile)::sourcedir
= /home/ettest52/Cactus [LOG:2013-08-04 11:09:54] self.create(simulationName,
parfile)::configuration = sim [LOG:2013-08-04 11:09:54]
self.create(simulationName, parfile)::configid =
config-sim-qb4.loni.org-home-ettest52-Cactus [LOG:2013-08-04 11:09:54]
self.create(simulationName, parfile)::buildid =
build-sim-qb4.loni.org-ettest52-2013.07.18-07.25.24-12102 [LOG:2013-08-04
11:09:54] self.create(simulationName, parfile)::testsuite = False
[LOG:2013-08-04 11:09:54] self.create(simulationName, parfile)::executable
= /scratch/ettest52/simulations/static_tov/SIMFACTORY/exe/cactus_sim
[LOG:2013-08-04 11:09:54] self.create(simulationName, parfile)::optionlist
= /scratch/ettest52/simulations/static_tov/SIMFACTORY/cfg/OptionList
[LOG:2013-08-04 11:09:54] self.create(simulationName, parfile)::submitscript
= /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/SubmitScript
[LOG:2013-08-04 11:09:54] self.create(simulationName, parfile)::runscript
= /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/RunScript
[LOG:2013-08-04 11:09:54] self.create(simulationName, parfile)::parfile
= /scratch/ettest52/simulations/static_tov/SIMFACTORY/par/static_tov.par
[LOG:2013-08-04 11:09:54] self.create(simulationName, parfile)::
[LOG:2013-08-04 11:09:54] self.create(simulationName, parfile)::Simulation
static_tov created [LOG:2013-08-04 11:09:54] self.submit(submitScript)::Restart
for simulation static_tov created with restart id 0, long restart id 0000
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::Prepping for submission
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::No previous walltime
available to be used, using walltime 8:00:00 [LOG:2013-08-04 11:09:54]
self.submit(submitScript)::Defined substituion properties for submission
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::{'SIMULATION_ID':
'simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.08.04-11.09.54-31394',
'NODE_PROCS': 1, 'PPN_USED': 8, 'PPN': 8, 'ALLOCATION': 'loni_cactus08',
'WALLTIME_HH': '08', 'CPUFREQ': '2.33', 'USER': 'ettest52', 'RUNDIR':
'/scratch/ettest52/simulations/static_tov/output-0000', 'NODES': 4,
'SIMULATION_NAME': 'static_tov', 'WALLTIME': '8:00:00', 'NUM_THREADS': 8,
'EXECUTABLE':
'/scratch/ettest52/simulations/static_tov/SIMFACTORY/exe/cactus_sim',
'PROCS_REQUESTED': 32, 'EMAIL': '[email protected]', 'RESTART_ID': 0,
'CHAINED_JOB_ID': '', 'FROM_RESTART_COMMAND': '', 'NUM_SMT': 1,
'WALLTIME_SECONDS': 28800, 'SIMFACTORY':
'/home/ettest52/Cactus/simfactory/bin/sim', 'PROCS': 32, 'SUBMITSCRIPT':
'/scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/SubmitScript',
'WALLTIME_HOURS': 8.0, 'WALLTIME_MM': '00', 'PARFILE':
'/scratch/ettest52/simulations/static_tov/output-0000/static_tov.par',
'WALLTIME_SS': '00', 'QUEUE': 'checkpt', 'CONFIGURATION': 'sim', 'SOURCEDIR':
'/home/ettest52/Cactus', 'HOSTNAME': 'qb3.loni.org', 'NUM_PROCS': 4,
'SCRIPTFILE':
'/scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/SubmitScript',
'MEMORY': '8192', 'WALLTIME_MINUTES': 480, 'SHORT_SIMULATION_NAME':
'static_tov-0000'} [LOG:2013-08-04 11:09:54]
self.submit(submitScript)::self.Properties:
/scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/properties.ini
[LOG:2013-08-04 11:09:54] self.submit(submitScript):: [LOG:2013-08-04 11:09:54]
self.submit(submitScript)::[properties] [LOG:2013-08-04 11:09:54]
self.submit(submitScript)::machine = queenbee [LOG:2013-08-04 11:09:54]
self.submit(submitScript)::simulationid =
simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.08.04-11.09.54-31394
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::sourcedir =
/home/ettest52/Cactus [LOG:2013-08-04 11:09:54]
self.submit(submitScript)::configuration = sim [LOG:2013-08-04 11:09:54]
self.submit(submitScript)::configid =
config-sim-qb4.loni.org-home-ettest52-Cactus [LOG:2013-08-04 11:09:54]
self.submit(submitScript)::buildid =
build-sim-qb4.loni.org-ettest52-2013.07.18-07.25.24-12102 [LOG:2013-08-04
11:09:54] self.submit(submitScript)::testsuite = False [LOG:2013-08-04
11:09:54] self.submit(submitScript)::executable =
/scratch/ettest52/simulations/static_tov/SIMFACTORY/exe/cactus_sim
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::optionlist =
/scratch/ettest52/simulations/static_tov/SIMFACTORY/cfg/OptionList
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::submitscript =
/scratch/ettest52/simulations/static_tov/SIMFACTORY/run/SubmitScript
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::runscript =
/scratch/ettest52/simulations/static_tov/SIMFACTORY/run/RunScript
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::parfile =
/scratch/ettest52/simulations/static_tov/SIMFACTORY/par/static_tov.par
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::chainedjobid = -1
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::ppn = 8
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::procsrequested = 32
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::allocation =
loni_cactus08 [LOG:2013-08-04 11:09:54] self.submit(submitScript)::user
= ettest52 [LOG:2013-08-04 11:09:54] self.submit(submitScript)::numsmt
= 1 [LOG:2013-08-04 11:09:54] self.submit(submitScript)::walltime =
8:00:00 [LOG:2013-08-04 11:09:54] self.submit(submitScript)::numprocs =
4 [LOG:2013-08-04 11:09:54] self.submit(submitScript)::nodeprocs = 1
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::numthreads = 8
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::hostname =
qb3.loni.org [LOG:2013-08-04 11:09:54] self.submit(submitScript)::ppnused
= 8 [LOG:2013-08-04 11:09:54] self.submit(submitScript)::queue =
checkpt [LOG:2013-08-04 11:09:54] self.submit(submitScript)::cpufreq =
2.33 [LOG:2013-08-04 11:09:54] self.submit(submitScript)::procs = 32
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::memory = 8192
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::nodes = 4
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::pbsSimulationName=
static_tov-0000 [LOG:2013-08-04 11:09:54] self.submit(submitScript)::
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::saving substituted
submitscript contents to:
/scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/SubmitScript
[LOG:2013-08-04 11:09:54] self.submit(submitScript)::Executing submission
command: qsub
/scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/SubmitScript
[LOG:2013-08-04 11:09:54] self.makeActive()::Simulation static_tov with
restart-id 0 has been made active [LOG:2013-08-04 11:09:54] job_id =
self.extractJobId(output)::received raw output: 703467.qb2 [LOG:2013-08-04
11:09:54] job_id = self.extractJobId(output):: [LOG:2013-08-04 11:09:54] job_id
= self.extractJobId(output)::using submitRegex: (\d+)[.]qb2 [LOG:2013-08-04
11:09:54] self.submit(submitScript)::After searching raw output, it was
determined that the job_id is: 703467 [LOG:2013-08-04 11:09:54]
self.submit(submitScript)::Simulation static_tov, with restart id 0, and job id
703467 has been submitted [LOG:2013-08-04 11:11:02] ret = restart.load(sim,
activeId)::For simulation static_tov, loaded restart id 0, long restart id 0000
[LOG:2013-08-07 02:43:53] ret = restart.load(sim, activeId)::For simulation
static_tov, loaded restart id 0, long restart id 0000
Inside output-0000 there is not static_tov directory but contains SIMFACTORY
directory, static_tov.err and static_tov.out files. static_tov.err has [PBS:
exec of shell '' failed] and static_tov.out contains following
-------------------------------------- Running PBS prologue script
-------------------------------------- User and Job Data:
-------------------------------------- Job ID: 703467.qb2 Username:
ettest52 Group: lsuusers Date: 04-Aug-2013 11:10 Node: qb453
(6947) -------------------------------------- PBS has allocated the following
nodes:
qb453 qb452 qb451 qb450
A total of 32 processors on 4 nodes allocated
--------------------------------------------- Check nodes and clean them of
stray processes --------------------------------------------- Checking node
qb453 11:10:06 Checking node qb452 11:10:08 Checking node qb451 11:10:09
Checking node qb450 11:10:11 Done clearing all the allocated nodes
------------------------------------------------------ Concluding PBS prologue
script - 04-Aug-2013 11:10:11
------------------------------------------------------
------------------------------------------------------ Running PBS epilogue
script - 04-Aug-2013 11:10:12
------------------------------------------------------ Checking node qb453 (MS)
Checking node qb450 ok Checking node qb451 ok Checking node qb452 ok Checking
node qb453 ok ------------------------------------------------------ Concluding
PBS epilogue script - 04-Aug-2013 11:10:19
------------------------------------------------------ Exit Status: Job ID:
703467.qb2 Username: ettest52 Group: lsuusers Job
Name: static_tov-0000 Session Id: 6946 Resource Limits:
ncpus=1,nodes=4:ppn=8,walltime=08:00:00 Resources Used:
cput=00:00:00,mem=112kb,vmem=1416kb,walltime=00:00:00 Queue Used: checkpt
Account String: loni_cactus08 Node: qb453 Process id: 7476
------------------------------------------------------ How can I solve this
problem?
Udayaraj Khanal
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