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': '[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:2013-08-17 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 _______________________________________________
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