[Users] Queuing system and parameter file scripts on personal machine
Federico G Lopez Armengol
fedelopezar at gmail.com
Wed Jul 18 12:12:02 CDT 2018
Dear Helvi,
I really appreciate your answer.
- About queing systems:
Indeed, queuing systems are used on clusters to manage a large number of
> simulations by different users. These are additional programs that are not
> usually installed on laptops and local desktops, and cannot be controlled
> by simfactory or the Einstein Toolkit. Therefore, every time you submitted
> a simulation it started running immediately, i.e., in parallel with those
> that you started before and presumably caused your laptop to crash
Thanks for clearing that up. I thought that maybe the queuing system was up
to Simfactory.
If you want to run multiple simulations simultaneously you will have to do
> so on a cluster. On your laptop you should be able to run small test
> simulations, and typically one at a time.
Actually my intention was to run one simulation at a time, but to submit
them all at once with parameter file scripts. Now I understand that I need
a cluster anyway.
- About my failure with parameter file scripting, let's take for
instance: Cactus/par/arXiv-1111.3344/tov/tov.rpar
Following Simfactory documentation: *"You can use a script in place of a
parameter file when invoking SimFactory. When a simulation is run, the
script will be executed and the resulting parameter file will be used by
Cactus. NB: Remember to use the full path of the original script when
determining the output filename, not just the base name."*
So I ran:
> sim create-run tovs --parfile par/arXiv-1111.3344/tov/tov.rpar --procs 4
And got:
> Parameter file:
> /home/fede/Documents/einstein_toolkit/Cactus/par/arXiv-1111.3344/tov/tov.rpar
> Skeleton Created
> Job directory: "/home/fede/simulations/tovs"
> Executable: "/home/fede/Documents/einstein_toolkit/Cactus/exe/cactus_sim"
> Option list: "/home/fede/simulations/tovs/SIMFACTORY/cfg/OptionList"
> Submit script: "/home/fede/simulations/tovs/SIMFACTORY/run/SubmitScript"
> Run script: "/home/fede/simulations/tovs/SIMFACTORY/run/RunScript"
> Parameter file: "/home/fede/simulations/tovs/SIMFACTORY/par/tov.rpar"
> Simulation name: tovs
> Assigned restart id: 0
> Running simulation tovs
> Error: Parameter file script
> '/home/fede/simulations/tovs/output-0000/tov.rpar' did not generate a
> parameter file called '/home/fede/simulations/tovs/output-0000/tov.par'
> Aborting Simfactory.
It seems that Simfactory is looking for a parameter file with the same name
as the script. This can also be seen from the 'log.txt' file, that I
attached. On the other hand, all the parameters files designed by
'tov.rpar' are properly created in the current directory, but not taken by
Simfactory for running.
Maybe I misunderstood the point of parameter file scripting. I understood
they serve for automatically create several parameter files, and
automatically run (or submit) the corresponding simulations.
Thanks again! Best,
Federico
On Wed, Jul 18, 2018 at 11:50 AM helvi witek <helvi.witek at kcl.ac.uk> wrote:
> Dear Federico,
>
> > it seems that I do not have a queuing system. Each time I submit a
> simulation, it starts running in parallel with previous ones and my laptop
> quickly collapses. I configured > simfactory with:
> Indeed, queuing systems are used on clusters to manage a large number of
> simulations by different users. These are additional programs that are not
> usually installed on laptops and local desktops, and cannot be controlled
> by simfactory or the Einstein Toolkit. Therefore, every time you submitted
> a simulation it started running immediately, i.e., in parallel with those
> that you started before and presumably caused your laptop to crash.
>
> If you want to run multiple simulations simultaneously you will have to do
> so on a cluster. On your laptop you should be able to run small test
> simulations, and typically one at a time.
>
> > I've tried some scripting with .rpar files, but failed...
> Could you please send us the parameter and logfiles? Otherwise it is
> difficult to access what goes wrong.
> I suspect that your runs overwrite each other, since they seem to have the
> same name and run in parallel. That is probably why only the last submitted
> simulation actually runs. As an easy check you could submit two small runs
> with different names.
>
> Best wishes,
> Helvi
>
>
>
> ===========================================
> Dr. Helvi Witek
> Royal Society University Research Fellow
> Theoretical Particle Physics and Cosmology
> Department of Physics
> King's College London
> ===========================================
>
> On Tue, Jul 10, 2018 at 8:24 PM, Federico G Lopez Armengol <
> fedelopezar at gmail.com> wrote:
>
>> Hello,
>>
>> I've been learning how to use the Toolkit for about a year. I've been
>> reading public documentation and running individual simulations on my
>> personal laptop. Now, I need to manage some set of simulations, and found
>> some trouble:
>>
>> 1) it seems that I do not have a queuing system. Each time I submit a
>> simulation, it starts running in parallel with previous ones and my laptop
>> quickly collapses. I configured simfactory with:
>>
>> ./simfactory/bin/sim setup-silent --optionlist=ubuntu.cfg --runscript
>>> debian.sh --submitscript debian.sub --runscript debian.sh
>>
>>
>> 2) I've tried some scripting with .rpar files, but failed. For instance,
>> if submitting:
>>
>> ./simfactory/bin/sim create-submit tov_multi --parfile par/tov.rpar
>>
>>
>> no error displays, but the simulation is inmediately finished with no
>> outputs. On the other hand, if running:
>>
>> ./simfactory/bin/sim create-run tov_multi --parfile par/tov.rpar
>>
>>
>> I get the following error:
>>
>> Error: Parameter file script
>>> '/home/fede/simulations/tov_multi/output-0000/tov.rpar' did not generate a
>>> parameter file called '/home/fede/simulations/tov_multi/output-0000/tov.par'
>>
>>
>> I changed the name of the parameter file created as asked, but just the
>> last simulation of the script runs. I've tried this with every .rpar script
>> that is included on the Toolkit.
>>
>> I use Linux Mint 18.1 Serena. Thanks in advance!
>>
>> Federico
>>
>> _______________________________________________
>> Users mailing list
>> Users at einsteintoolkit.org
>>
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>>
>
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[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::Creating simulation tovs
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::Simulation directory: /home/fede/simulations/tovs
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::Simulation Properties:
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::[properties]
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::machine = frankie
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::simulationid = simulation-tovs-frankie-frankie-fede-2018.07.18-13.46.53-16788
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::sourcedir = /home/fede/Documents/einstein_toolkit/Cactus
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::configuration = sim
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::configid = config-sim-frankie-home-fede-Documents-einstein_toolkit-Cactus
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::buildid = build-sim-frankie-fede-2018.07.02-23.54.38-17708
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::testsuite = False
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::executable = /home/fede/simulations/tovs/SIMFACTORY/exe/cactus_sim
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::optionlist = /home/fede/simulations/tovs/SIMFACTORY/cfg/OptionList
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::submitscript = /home/fede/simulations/tovs/SIMFACTORY/run/SubmitScript
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::runscript = /home/fede/simulations/tovs/SIMFACTORY/run/RunScript
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::parfile = /home/fede/simulations/tovs/SIMFACTORY/par/tov.rpar
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::Simulation tovs created
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::Creating new properties because this is an independant run, not a run following a submit
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::Determined the following properties
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::[properties]
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::machine = frankie
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::simulationid = simulation-tovs-frankie-frankie-fede-2018.07.18-13.46.53-16788
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::sourcedir = /home/fede/Documents/einstein_toolkit/Cactus
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::configuration = sim
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::configid = config-sim-frankie-home-fede-Documents-einstein_toolkit-Cactus
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::buildid = build-sim-frankie-fede-2018.07.02-23.54.38-17708
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::testsuite = False
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::executable = /home/fede/simulations/tovs/SIMFACTORY/exe/cactus_sim
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::optionlist = /home/fede/simulations/tovs/SIMFACTORY/cfg/OptionList
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::submitscript = /home/fede/simulations/tovs/SIMFACTORY/run/SubmitScript
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::runscript = /home/fede/simulations/tovs/SIMFACTORY/run/RunScript
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::parfile = /home/fede/simulations/tovs/SIMFACTORY/par/tov.rpar
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::numprocs = 1
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::nodeprocs = 1
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::numthreads = 4
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::hostname = frankie
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::ppn = 4
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::ppnused = 4
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::procsrequested = 4
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::pbsSimulationName= tovs-0000
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::cpufreq =
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::user = fede
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::memory = 0
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::nodes = 1
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::procs = 4
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::numsmt = 1
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::
[LOG:2018-07-18 13:46:53] self.makeActive()::Simulation tovs with restart-id 0 has been made active
[LOG:2018-07-18 13:46:53] self.run(debug)::Prepping for execution/run
[LOG:2018-07-18 13:46:53] checkpointing = self.PrepareCheckpointing(recover_id)::PrepareCheckpointing: max_restart_id: -1
[LOG:2018-07-18 13:46:53] self.run(debug)::Defined substitution properties for execution/run
[LOG:2018-07-18 13:46:53] self.run(debug)::{'SIMULATION_ID': 'simulation-tovs-frankie-frankie-fede-2018.07.18-13.46.53-16788', 'NODE_PROCS': 1, 'PPN_USED': 4, 'PPN': 4, 'CPUFREQ': None, 'USER': 'fede', 'RUNDIR': '/home/fede/simulations/tovs/output-0000', 'NODES': 1, 'SIMULATION_NAME': 'tovs', 'NUM_THREADS': 4, 'EXECUTABLE': '/home/fede/simulations/tovs/SIMFACTORY/exe/cactus_sim', 'PROCS_REQUESTED': 4, 'RESTART_ID': 0, 'NUM_SMT': 1, 'CONFIGURATION': 'sim', 'PROCS': 4, 'SUBMITSCRIPT': '/home/fede/simulations/tovs/SIMFACTORY/run/SubmitScript', 'MACHINE': 'frankie', 'PARFILE': '/home/fede/simulations/tovs/output-0000/tov.par', 'SOURCEDIR': '/home/fede/Documents/einstein_toolkit/Cactus', 'HOSTNAME': 'frankie', 'RUNDEBUG': 0, 'NUM_PROCS': 1, 'SCRIPTFILE': '/home/fede/simulations/tovs/SIMFACTORY/run/SubmitScript', 'MEMORY': '0', 'SHORT_SIMULATION_NAME': 'tovs-0000'}
-------------- next part --------------
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::Creating simulation tovs
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::Simulation directory: /home/fede/simulations/tovs
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::Simulation Properties:
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::[properties]
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::machine = frankie
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::simulationid = simulation-tovs-frankie-frankie-fede-2018.07.18-13.46.53-16788
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::sourcedir = /home/fede/Documents/einstein_toolkit/Cactus
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::configuration = sim
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::configid = config-sim-frankie-home-fede-Documents-einstein_toolkit-Cactus
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::buildid = build-sim-frankie-fede-2018.07.02-23.54.38-17708
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::testsuite = False
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::executable = /home/fede/simulations/tovs/SIMFACTORY/exe/cactus_sim
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::optionlist = /home/fede/simulations/tovs/SIMFACTORY/cfg/OptionList
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::submitscript = /home/fede/simulations/tovs/SIMFACTORY/run/SubmitScript
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::runscript = /home/fede/simulations/tovs/SIMFACTORY/run/RunScript
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::parfile = /home/fede/simulations/tovs/SIMFACTORY/par/tov.rpar
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::
[LOG:2018-07-18 13:46:53] restart.create(simulationName, parfile)::Simulation tovs created
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::Creating new properties because this is an independant run, not a run following a submit
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::Determined the following properties
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::[properties]
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::machine = frankie
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::simulationid = simulation-tovs-frankie-frankie-fede-2018.07.18-13.46.53-16788
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::sourcedir = /home/fede/Documents/einstein_toolkit/Cactus
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::configuration = sim
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::configid = config-sim-frankie-home-fede-Documents-einstein_toolkit-Cactus
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::buildid = build-sim-frankie-fede-2018.07.02-23.54.38-17708
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::testsuite = False
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::executable = /home/fede/simulations/tovs/SIMFACTORY/exe/cactus_sim
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::optionlist = /home/fede/simulations/tovs/SIMFACTORY/cfg/OptionList
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::submitscript = /home/fede/simulations/tovs/SIMFACTORY/run/SubmitScript
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::runscript = /home/fede/simulations/tovs/SIMFACTORY/run/RunScript
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::parfile = /home/fede/simulations/tovs/SIMFACTORY/par/tov.rpar
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::numprocs = 1
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::nodeprocs = 1
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::numthreads = 4
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::hostname = frankie
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::ppn = 4
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::ppnused = 4
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::procsrequested = 4
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::pbsSimulationName= tovs-0000
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::cpufreq =
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::user = fede
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::memory = 0
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::nodes = 1
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::procs = 4
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::numsmt = 1
[LOG:2018-07-18 13:46:53] restart.userRun(simulationName)::
[LOG:2018-07-18 13:46:53] self.makeActive()::Simulation tovs with restart-id 0 has been made active
[LOG:2018-07-18 13:46:53] self.run(debug)::Prepping for execution/run
[LOG:2018-07-18 13:46:53] checkpointing = self.PrepareCheckpointing(recover_id)::PrepareCheckpointing: max_restart_id: -1
[LOG:2018-07-18 13:46:53] self.run(debug)::Defined substitution properties for execution/run
[LOG:2018-07-18 13:46:53] self.run(debug)::{'SIMULATION_ID': 'simulation-tovs-frankie-frankie-fede-2018.07.18-13.46.53-16788', 'NODE_PROCS': 1, 'PPN_USED': 4, 'PPN': 4, 'CPUFREQ': None, 'USER': 'fede', 'RUNDIR': '/home/fede/simulations/tovs/output-0000', 'NODES': 1, 'SIMULATION_NAME': 'tovs', 'NUM_THREADS': 4, 'EXECUTABLE': '/home/fede/simulations/tovs/SIMFACTORY/exe/cactus_sim', 'PROCS_REQUESTED': 4, 'RESTART_ID': 0, 'NUM_SMT': 1, 'CONFIGURATION': 'sim', 'PROCS': 4, 'SUBMITSCRIPT': '/home/fede/simulations/tovs/SIMFACTORY/run/SubmitScript', 'MACHINE': 'frankie', 'PARFILE': '/home/fede/simulations/tovs/output-0000/tov.par', 'SOURCEDIR': '/home/fede/Documents/einstein_toolkit/Cactus', 'HOSTNAME': 'frankie', 'RUNDEBUG': 0, 'NUM_PROCS': 1, 'SCRIPTFILE': '/home/fede/simulations/tovs/SIMFACTORY/run/SubmitScript', 'MEMORY': '0', 'SHORT_SIMULATION_NAME': 'tovs-0000'}
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