Dear All, I submitted a simulation from Cactus directory as ./simfactory/bin/sim submit static_tov --parfile=par/static_tov.par --procs=32 --walltime=8:0:0 --allocation=loni_cactus08
Then ./simfactory/bin/sim list-simulations gives
static_tov [ACTIVE(FINISHED), restart 0000, job id 705851]
I found in /scratch/ettest52/simulations/static_tov/output-0000 there is a folder SIMFACTORY and two file static_tov.err and static_tov.out but static_tov directory is not present as mentioned in Tutorial for New Users. File static_tov.err contains {PBS: exec of shell failed} and file static_tov.out contains following details, -------------------------------------- Running PBS prologue script -------------------------------------- User and Job Data: -------------------------------------- Job ID: 705851.qb2 Username: ettest52 Group: lsuusers Date: 17-Aug-2013 13:52 Node: qb031 (11969) -------------------------------------- PBS has allocated the following nodes:
qb031 qb030 qb029 qb028
A total of 32 processors on 4 nodes allocated --------------------------------------------- Check nodes and clean them of stray processes --------------------------------------------- Checking node qb031 13:52:20 Checking node qb030 13:52:21 Checking node qb029 13:52:23 Checking node qb028 13:52:25 Done clearing all the allocated nodes ------------------------------------------------------ Concluding PBS prologue script - 17-Aug-2013 13:52:25 ------------------------------------------------------ ------------------------------------------------------ Running PBS epilogue script - 17-Aug-2013 13:52:26 ------------------------------------------------------ Checking node qb031 (MS) Checking node qb028 ok Checking node qb029 ok Checking node qb030 ok Checking node qb031 ok ------------------------------------------------------ Concluding PBS epilogue script - 17-Aug-2013 13:52:33 ------------------------------------------------------ Exit Status: Job ID: 705851.qb2 Username: ettest52 Group: lsuusers Job Name: static_tov-0000 Session Id: 11968 Resource Limits: ncpus=1,nodes=4:ppn=8,walltime=08:00:00 Resources Used: cput=00:00:00,mem=428kb,vmem=3884kb,walltime=00:00:00 Queue Used: checkpt Account String: loni_cactus08 Node: qb031 Process id: 12492 ------------------------------------------------------
I also found a log.txt file in /scratch/ettest52/simulations/static_tov which contains,
[LOG:2013-08-17 04:21:54] self.create(simulationName, parfile)::Creating simulation static_tov [LOG:2013-08-17 04:21:54] self.create(simulationName, parfile)::Simulation directory: /scratch/ettest52/simulations/static_tov [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::Simulation Properties: [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile):: [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::[properties] [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::machine = queenbee [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::simulationid = simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.08.17-04.21.54-5675 [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::sourcedir = /home/ettest52/Cactus [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::configuration = sim [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::configid = config-sim-qb4.loni.org-home-ettest52-Cactus [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::buildid = build-sim-qb4.loni.org-ettest52-2013.08.17-09.01.14-32035 [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::testsuite = False [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::executable = /scratch/ettest52/simulations/static_tov/SIMFACTORY/exe/cactus_sim [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::optionlist = /scratch/ettest52/simulations/static_tov/SIMFACTORY/cfg/OptionList [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::submitscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/SubmitScript [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::runscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/RunScript [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::parfile = /scratch/ettest52/simulations/static_tov/SIMFACTORY/par/static_tov.par [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile):: [LOG:2013-08-17 04:21:56] self.create(simulationName, parfile)::Simulation static_tov created [LOG:2013-08-17 04:21:56] self.submit(submitScript)::Restart for simulation static_tov created with restart id 0, long restart id 0000 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::Prepping for submission [LOG:2013-08-17 04:21:56] self.submit(submitScript)::No previous walltime available to be used, using walltime 8:00:00 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::Defined substituion properties for submission [LOG:2013-08-17 04:21:56] self.submit(submitScript)::{'SIMULATION_ID': 'simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.08.17-04.21.54-5675', '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': 'urkhanal@tucdp.edu.np', '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:2013-08-17 04:21:56] self.submit(submitScript)::self.Properties: /scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/properties.ini [LOG:2013-08-17 04:21:56] self.submit(submitScript):: [LOG:2013-08-17 04:21:56] self.submit(submitScript)::[properties] [LOG:2013-08-17 04:21:56] self.submit(submitScript)::machine = queenbee [LOG:2013-08-17 04:21:56] self.submit(submitScript)::simulationid = simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.08.17-04.21.54-5675 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::sourcedir = /home/ettest52/Cactus [LOG:2013-08-17 04:21:56] self.submit(submitScript)::configuration = sim [LOG:2013-08-17 04:21:56] self.submit(submitScript)::configid = config-sim-qb4.loni.org-home-ettest52-Cactus [LOG:2013-08-17 04:21:56] self.submit(submitScript)::buildid = build-sim-qb4.loni.org-ettest52-2013.08.17-09.01.14-32035 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::testsuite = False [LOG:2013-08-17 04:21:56] self.submit(submitScript)::executable = /scratch/ettest52/simulations/static_tov/SIMFACTORY/exe/cactus_sim [LOG:2013-08-17 04:21:56] self.submit(submitScript)::optionlist = /scratch/ettest52/simulations/static_tov/SIMFACTORY/cfg/OptionList [LOG:2013-08-17 04:21:56] self.submit(submitScript)::submitscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/SubmitScript [LOG:2013-08-17 04:21:56] self.submit(submitScript)::runscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/RunScript [LOG:2013-08-17 04:21:56] self.submit(submitScript)::parfile = /scratch/ettest52/simulations/static_tov/SIMFACTORY/par/static_tov.par [LOG:2013-08-17 04:21:56] self.submit(submitScript)::chainedjobid = -1 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::ppn = 8 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::procsrequested = 32 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::allocation = loni_cactus08 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::user = ettest52 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::numsmt = 1 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::walltime = 8:00:00 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::numprocs = 4 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::nodeprocs = 1 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::numthreads = 8 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::hostname = qb3.loni.org [LOG:2013-08-17 04:21:56] self.submit(submitScript)::ppnused = 8 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::queue = checkpt [LOG:2013-08-17 04:21:56] self.submit(submitScript)::cpufreq = 2.33 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::procs = 32 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::memory = 8192 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::nodes = 4 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::pbsSimulationName= static_tov-0000 [LOG:2013-08-17 04:21:56] self.submit(submitScript):: [LOG:2013-08-17 04:21:56] self.submit(submitScript)::saving substituted submitscript contents to: /scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/SubmitScript [LOG:2013-08-17 04:21:56] self.submit(submitScript)::Executing submission command: qsub /scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/SubmitScript [LOG:2013-08-17 04:21:56] self.makeActive()::Simulation static_tov with restart-id 0 has been made active [LOG:2013-08-17 04:21:56] job_id = self.extractJobId(output)::received raw output: 705851.qb2 [LOG:2013-08-17 04:21:56] job_id = self.extractJobId(output):: [LOG:2013-08-17 04:21:56] job_id = self.extractJobId(output)::using submitRegex: (\d+)[.]qb2 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::After searching raw output, it was determined that the job_id is: 705851 [LOG:2013-08-17 04:21:56] self.submit(submitScript)::Simulation static_tov, with restart id 0, and job id 705851 has been submitted [LOG:2013-08-17 04:23:24] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 0, long restart id 0000 [LOG:2013-08-17 11:46:32] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 0, long restart id 0000 [LOG:2013-08-18 10:18:50] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 0, long restart id 0000 [LOG:2013-08-18 11:40:56] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 0, long restart id 0000
How can I complete the simulation?
Udayaraj Khanal