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Einstein Toolkit Meeting Reminder
by Frank Loeffler 12 Aug '13

12 Aug '13

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ In short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. As always, we will answer questions and hear comments that come up at the beginning of the meeting. After that, and because of the long discussion last week, I would like to get to a conclusion about 1) possible rearrangement of ET repositories (combine repositories) 2) possible conversion of some ET thorns from svn to git Arguments for both topics can be voiced on a wiki page (thanks to Ian Hinder for creating it, even with a quite wrong name imho): https://docs.einsteintoolkit.org/et-docs/Version_control#Reasons_to_Change We will handle these two topics in that order, and as separate as possible. Frank Löffler

3 2

ExternalLibraries without tarballs
by Erik Schnetter 11 Aug '13

11 Aug '13

ExternalLibraries thorns containing tarballs can be very large, in particular if the history of the thorn grows and contains multiple tarballs. I have just tested storing the source tree instead of the tarball in ExternalLibraries/Boost. This seems to work surprisingly well. For example, boost_1_54_0.tar.gz (the current version) has 66 MByte, while a git repository containing the last five versions of Boost as uncompressed source trees has 75 MByte. Clearly, this is very good. Other advantages of storing source trees are: - this is what we do for every thorn, so why not for ExternalLibraries (d'oh) - one can easily look at the source code of an external library - no need to untar and later delete the source tree while building - no need to apply patches -- the changes can be made directly in the source tree In my opinion, this is the way to go. I am currently setting up a new repository of ExternalLibraries/Boost in this way. (Obviously, it is not possible to keep the current repository, since its history is already at 406 MB.) -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/ My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu/.

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Meeting Minutes
by Roland Haas 08 Aug '13

08 Aug '13

Present: Josh, Roland, Frank, Erik, Ian, Matt, Peter, Steve, Barry, Philipp, Bruno svn to git transition of ET thorns: * LSU has domain name, has ssl certificates for domain * LSU will update OS on virtual machines in near future, hold off with transition until then * Ian Hinder already has git repositories for the ET thorns which could serve as the basis for the git repositories * leave svn running in read only mode afterwards * git server to use: plain git, gitolite (Ian has experience with that)? * Open question: few large repositories (or even one) or one repository per thorn ** no agreement on what to do. Two views are presented to either have fine granularity (one repo per thorn) or being able to make consistent changes in several thorns at the same time (few repos) ** Roland and Ian to describe arguments for fine granularity repos, for experience with large/small repos on the wiki (everyone else of course is welcome to comment as well) ** question on which (if this is done) thorns to collect in repositories: by arrangement, by institution, by type of code, how tightly they are coupled? ** Ian and Barry have been using a git super-repo to track several individual repos which can be used as a per-user solution for a large repository, it is however not yet ready for public use ** single repository makes it easy to keep several thorns in sync, and to get a global overview of what has changed, there are also nicer GUIs available ** multiple repositories make it easier to pick only bugfixes for a thorn but but new features from another in the same repository ** Barry mentioned git subtree (https://github.com/apenwarr/git-subtree) as an alternative for single users ** likely need to modify GetComponents to handle git repositories more similar like svn workshop report: * we had David Rideout gave a talk on how to use Cactus with causal sets, notes are on the wiki https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Summer_2013_(Developer… * Ellipitic solver: Eloisa Bentivegna's elliptic solver (multigrid, works with Carpet grids) is available and described in print and on the wiki ** supports Dirichlet and Robin like boundary conditions ** invite Eloisa to give a ET seminar in one of the next calls * Chemora (see wiki): meet in Atlanta, wait for confirmation of grant * ML rewrite: make it easier to rearrange equations so that calculations can be split if needed to improve performance ** improvement to flow back to Kranc * Erik reported on new bboxset2 class which improves scaling, paper on wiki * Erik reported on parameter file generator for benchmarks using simfactory, Ian added performance regression tests on top of this to Jenkins * Steve added code coverage tests MHD: * Philipp has working cell centred A-field evolution code, working on cleaning it up Yours, Roland

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simulation problem
by Udayaraj Khanal 07 Aug '13

07 Aug '13

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': 'urkhanal(a)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:2013-08-04 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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Einstein Toolkit Meeting Reminder
by Frank Loeffler 04 Aug '13

04 Aug '13

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ In short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. Besides feedback or questions from users, I would like to go through achievements of the developers workshop last week, with two goals in mind. First, people that were not present should be informed, and secondly we should follow-up on some topics. Be prepared to say a few sentences about what you worked on. Also, we need to decide about including a new thorn to the ET: the (external) boost library thorn. See trac for details [1]. This would be not build by default, mainly because of the size and time it requires. Frank Löffler [1] https://trac.einsteintoolkit.org/ticket/1410

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Re: [Users] Users Digest, Vol 41, Issue 2
by David Bradley 03 Aug '13

03 Aug '13

On 08/03/2013 05:37 AM, users-request(a)einsteintoolkit.org wrote: > Send Users mailing list submissions to > users(a)einsteintoolkit.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.einsteintoolkit.org/mailman/listinfo/users > or, via email, send a message with subject or body 'help' to > users-request(a)einsteintoolkit.org > > You can reach the person managing the list at > users-owner(a)einsteintoolkit.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Users digest..." > > > ./simfactory/bin/sim submit static_tov --parfile=par/static_tov.par --procs=1 --walltime=8:0:0 > Today's Topics: > > 1. simulation problem (Udayaraj Khanal) > > > > _______________________________________________ > Users mailing list > Users(a)einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users > 1. For QueenBee, what did you use for UDB.pm for setting up your allocation 2, In your email, I noticed 'NO_ALLOCATION'. Could you provide the command line used to start the simulation. I believe at least '1' is needed, on my linux system. QueenBee may need more. 3. The Following is my submission, under linuxmint 15: ./simfactory/bin/sim submit static_tov --parfile=par/static_tov.par --procs=1 --walltime=8:0:0 I hope this may be helpfull Dave

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simulation problem
by Udayaraj Khanal 03 Aug '13

03 Aug '13

Dear All,I have submitted two simulations. In Cactus directory ./simfactory/bin/sim list-simulations gives ks-mclachlan [ACTIVE (FINISHED), restart 0000, job id 702161]static_tov [ACTIVE (FINISHED), restart 0001, job id 701299]In /scratch/ettest52/simulations three directories CACHE, ks-mclachlan and static_tov are present. Inside static_tov there are four directories(output-0000, output-0001, output-0001-active,SIMFACTORY) and one file log.txt, which contains following details.[LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::Creating simulation static_tov [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::Simulation directory: /scratch/ettest52/simulations/static_tov [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::Simulation Properties: [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile):: [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::[properties] [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::machine = queenbee [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::simulationid = simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.07.21-11.10.48-15714 [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::sourcedir = /home/ettest52/Cactus [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::configuration = sim [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::configid = config-sim-qb4.loni.org-home-ettest52-Cactus [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::buildid = build-sim-qb4.loni.org-ettest52-2013.07.18-07.25.24-12102 [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::testsuite = False [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::executable = /scratch/ettest52/simulations/static_tov/SIMFACTORY/exe/cactus_sim [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::optionlist = /scratch/ettest52/simulations/static_tov/SIMFACTORY/cfg/OptionList [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::submitscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/SubmitScript [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::runscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/RunScript [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::parfile = /scratch/ettest52/simulations/static_tov/SIMFACTORY/par/static_tov.par [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile):: [LOG:2013-07-21 11:10:48] self.create(simulationName, parfile)::Simulation static_tov created [LOG:2013-07-21 11:10:48] self.submit(submitScript)::Restart for simulation static_tov created with restart id 0, long restart id 0000 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::Prepping for submission [LOG:2013-07-21 11:10:48] self.submit(submitScript)::No previous walltime available to be used, using walltime 8:00:00 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::Defined substituion properties for submission [LOG:2013-07-21 11:10:48] self.submit(submitScript)::{'SIMULATION_ID': 'simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.07.21-11.10.48-15714', 'NODE_PROCS': 1, 'PPN_USED': 8, 'PPN': 8, 'ALLOCATION': 'NO_ALLOCATION', '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(a)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:2013-07-21 11:10:48] self.submit(submitScript)::self.Properties: /scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/properties.ini [LOG:2013-07-21 11:10:48] self.submit(submitScript):: [LOG:2013-07-21 11:10:48] self.submit(submitScript)::[properties] [LOG:2013-07-21 11:10:48] self.submit(submitScript)::machine = queenbee [LOG:2013-07-21 11:10:48] self.submit(submitScript)::simulationid = simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.07.21-11.10.48-15714 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::sourcedir = /home/ettest52/Cactus [LOG:2013-07-21 11:10:48] self.submit(submitScript)::configuration = sim [LOG:2013-07-21 11:10:48] self.submit(submitScript)::configid = config-sim-qb4.loni.org-home-ettest52-Cactus [LOG:2013-07-21 11:10:48] self.submit(submitScript)::buildid = build-sim-qb4.loni.org-ettest52-2013.07.18-07.25.24-12102 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::testsuite = False [LOG:2013-07-21 11:10:48] self.submit(submitScript)::executable = /scratch/ettest52/simulations/static_tov/SIMFACTORY/exe/cactus_sim [LOG:2013-07-21 11:10:48] self.submit(submitScript)::optionlist = /scratch/ettest52/simulations/static_tov/SIMFACTORY/cfg/OptionList [LOG:2013-07-21 11:10:48] self.submit(submitScript)::submitscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/SubmitScript [LOG:2013-07-21 11:10:48] self.submit(submitScript)::runscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/RunScript [LOG:2013-07-21 11:10:48] self.submit(submitScript)::parfile = /scratch/ettest52/simulations/static_tov/SIMFACTORY/par/static_tov.par [LOG:2013-07-21 11:10:48] self.submit(submitScript)::chainedjobid = -1 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::ppn = 8 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::procsrequested = 32 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::allocation = NO_ALLOCATION [LOG:2013-07-21 11:10:48] self.submit(submitScript)::user = ettest52 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::numsmt = 1 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::walltime = 8:00:00 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::numprocs = 4 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::nodeprocs = 1 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::numthreads = 8 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::hostname = qb3.loni.org [LOG:2013-07-21 11:10:48] self.submit(submitScript)::ppnused = 8 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::queue = checkpt [LOG:2013-07-21 11:10:48] self.submit(submitScript)::cpufreq = 2.33 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::procs = 32 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::memory = 8192 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::nodes = 4 [LOG:2013-07-21 11:10:48] self.submit(submitScript)::pbsSimulationName= static_tov-0000 [LOG:2013-07-21 11:10:48] self.submit(submitScript):: [LOG:2013-07-21 11:10:48] self.submit(submitScript)::saving substituted submitscript contents to: /scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/SubmitScript [LOG:2013-07-21 11:10:48] self.submit(submitScript)::Executing submission command: qsub /scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/SubmitScript [LOG:2013-07-21 11:10:48] self.makeActive()::Simulation static_tov with restart-id 0 has been made active [LOG:2013-07-21 11:10:49] job_id = self.extractJobId(output)::received raw output: Invalid allocation "NO_ALLOCATION". [LOG:2013-07-21 11:10:49] job_id = self.extractJobId(output)::===================== Allocation information for ettest52 ===================== [LOG:2013-07-21 11:10:49] job_id = self.extractJobId(output):: Proj. Name| Alloc| Balance| Deposited| %Used| Days Left| End [LOG:2013-07-21 11:10:49] job_id = self.extractJobId(output)::-------------------------------------------------------------------------------- [LOG:2013-07-21 11:10:49] job_id = self.extractJobId(output)::loni_cactus08|loni_cactus08 on @Dell_Cluster|106210.43| 250000.00| 57.52| 164|2014-01-01 [LOG:2013-07-21 11:10:49] job_id = self.extractJobId(output):: [LOG:2013-07-21 11:10:49] job_id = self.extractJobId(output)::Note: Balance and Deposit are measured in CPU-hours [LOG:2013-07-21 11:10:49] job_id = self.extractJobId(output)::qsub: submit filter returned an error code, aborting job submission. [LOG:2013-07-21 11:10:49] job_id = self.extractJobId(output):: [LOG:2013-07-21 11:10:49] job_id = self.extractJobId(output)::using submitRegex: (\d+)[.]qb2 [LOG:2013-07-21 11:10:49] self.submit(submitScript)::After searching raw output, it was determined that the job_id is: -1 [LOG:2013-07-21 11:10:49] self.submit(submitScript)::The regex did NOT match anything. No job_id means no control. [LOG:2013-07-21 11:11:26] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 0, long restart id 0000 [LOG:2013-07-22 10:23:47] restart.load(simulationName, active_id)::For simulation static_tov, loaded restart id 0, long restart id 0000 [LOG:2013-07-22 10:23:47] restart.load(simulationName, active_id)::For simulation static_tov, loaded restart id 0, long restart id 0000 [LOG:2013-07-22 10:23:47] restart.finish()::For simulation static_tov, Finishing restart 0000 [LOG:2013-07-22 10:23:47] restart.finish()::Force option: False [LOG:2013-07-22 10:23:47] restart.finish()::Job ID: -1, Job Status: U [LOG:2013-07-22 10:23:47] restart.finish()::Cleaning up simulation static_tov, restart 0, with job_status U [LOG:2013-07-22 10:23:47] restart.finish()::Simulation static_tov, restart 0, with job id -1 has been successfully cleaned up [LOG:2013-07-22 10:23:47] self.submit(submitScript)::Restart for simulation static_tov created with restart id 1, long restart id 0001 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::Prepping for submission [LOG:2013-07-22 10:23:47] self.submit(submitScript)::No previous walltime available to be used, using walltime 8:00:00 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::Defined substituion properties for submission [LOG:2013-07-22 10:23:47] self.submit(submitScript)::{'SIMULATION_ID': 'simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.07.21-11.10.48-15714', '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-0001', '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(a)tucdp.edu.np', 'RESTART_ID': 1, '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-0001/SIMFACTORY/SubmitScript', 'WALLTIME_HOURS': 8.0, 'WALLTIME_MM': '00', 'PARFILE': '/scratch/ettest52/simulations/static_tov/output-0001/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-0001/SIMFACTORY/SubmitScript', 'MEMORY': '8192', 'WALLTIME_MINUTES': 480, 'SHORT_SIMULATION_NAME': 'static_tov-0001'} [LOG:2013-07-22 10:23:47] self.submit(submitScript)::self.Properties: /scratch/ettest52/simulations/static_tov/output-0001/SIMFACTORY/properties.ini [LOG:2013-07-22 10:23:47] self.submit(submitScript):: [LOG:2013-07-22 10:23:47] self.submit(submitScript)::[properties] [LOG:2013-07-22 10:23:47] self.submit(submitScript)::machine = queenbee [LOG:2013-07-22 10:23:47] self.submit(submitScript)::simulationid = simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.07.21-11.10.48-15714 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::sourcedir = /home/ettest52/Cactus [LOG:2013-07-22 10:23:47] self.submit(submitScript)::configuration = sim [LOG:2013-07-22 10:23:47] self.submit(submitScript)::configid = config-sim-qb4.loni.org-home-ettest52-Cactus [LOG:2013-07-22 10:23:47] self.submit(submitScript)::buildid = build-sim-qb4.loni.org-ettest52-2013.07.18-07.25.24-12102 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::testsuite = False [LOG:2013-07-22 10:23:47] self.submit(submitScript)::executable = /scratch/ettest52/simulations/static_tov/SIMFACTORY/exe/cactus_sim [LOG:2013-07-22 10:23:47] self.submit(submitScript)::optionlist = /scratch/ettest52/simulations/static_tov/SIMFACTORY/cfg/OptionList [LOG:2013-07-22 10:23:47] self.submit(submitScript)::submitscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/SubmitScript [LOG:2013-07-22 10:23:47] self.submit(submitScript)::runscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/RunScript [LOG:2013-07-22 10:23:47] self.submit(submitScript)::parfile = /scratch/ettest52/simulations/static_tov/SIMFACTORY/par/static_tov.par [LOG:2013-07-22 10:23:47] self.submit(submitScript)::chainedjobid = -1 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::ppn = 8 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::procsrequested = 32 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::allocation = loni_cactus08 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::user = ettest52 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::numsmt = 1 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::walltime = 8:00:00 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::numprocs = 4 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::nodeprocs = 1 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::numthreads = 8 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::hostname = qb3.loni.org [LOG:2013-07-22 10:23:47] self.submit(submitScript)::ppnused = 8 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::queue = checkpt [LOG:2013-07-22 10:23:47] self.submit(submitScript)::cpufreq = 2.33 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::procs = 32 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::memory = 8192 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::nodes = 4 [LOG:2013-07-22 10:23:47] self.submit(submitScript)::pbsSimulationName= static_tov-0001 [LOG:2013-07-22 10:23:47] self.submit(submitScript):: [LOG:2013-07-22 10:23:47] self.submit(submitScript)::saving substituted submitscript contents to: /scratch/ettest52/simulations/static_tov/output-0001/SIMFACTORY/SubmitScript [LOG:2013-07-22 10:23:47] self.submit(submitScript)::Executing submission command: qsub /scratch/ettest52/simulations/static_tov/output-0001/SIMFACTORY/SubmitScript [LOG:2013-07-22 10:23:47] self.makeActive()::Simulation static_tov with restart-id 1 has been made active [LOG:2013-07-22 10:23:48] job_id = self.extractJobId(output)::received raw output: 701299.qb2 [LOG:2013-07-22 10:23:48] job_id = self.extractJobId(output):: [LOG:2013-07-22 10:23:48] job_id = self.extractJobId(output)::using submitRegex: (\d+)[.]qb2 [LOG:2013-07-22 10:23:48] self.submit(submitScript)::After searching raw output, it was determined that the job_id is: 701299 [LOG:2013-07-22 10:23:48] self.submit(submitScript)::Simulation static_tov, with restart id 1, and job id 701299 has been submitted [LOG:2013-07-22 10:26:43] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 1, long restart id 0001 [LOG:2013-07-23 00:12:00] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 1, long restart id 0001 [LOG:2013-07-23 10:29:21] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 1, long restart id 0001 [LOG:2013-07-27 10:12:50] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 1, long restart id 0001 [LOG:2013-07-27 10:25:09] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 1, long restart id 0001 [LOG:2013-07-31 00:59:46] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 1, long restart id 0001 [LOG:2013-08-01 10:58:25] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 1, long restart id 0001 [LOG:2013-08-03 04:34:24] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 1, long restart id 0001 The directory output-oooo contains only SIMFACTORY but output-0001 contains SIMFACTORY directory and two files static_tov.err and static_tov.out but static_tov is not present, which is required. static_tov.err contains (PBS: exec of shell " failed) and static_tov.out contains following details.-------------------------------------- Running PBS prologue script -------------------------------------- User and Job Data: -------------------------------------- Job ID: 701299.qb2 Username: ettest52 Group: lsuusers Date: 22-Jul-2013 10:23 Node: qb223 (19932) -------------------------------------- PBS has allocated the following nodes: qb223 qb218 qb217 qb216 A total of 32 processors on 4 nodes allocated --------------------------------------------- Check nodes and clean them of stray processes --------------------------------------------- Checking node qb223 10:23:55 Checking node qb218 10:23:57 Checking node qb217 10:23:59 Checking node qb216 10:24:01 Done clearing all the allocated nodes ------------------------------------------------------ Concluding PBS prologue script - 22-Jul-2013 10:24:01 ------------------------------------------------------ ------------------------------------------------------ Running PBS epilogue script - 22-Jul-2013 10:24:01 ------------------------------------------------------ Checking node qb223 (MS) Checking node qb216 ok Checking node qb217 ok Checking node qb218 ok Checking node qb223 ok ------------------------------------------------------ Concluding PBS epilogue script - 22-Jul-2013 10:24:08 ------------------------------------------------------ Exit Status: Job ID: 701299.qb2 Username: ettest52 Group: lsuusers Job Name: static_tov-0001 Session Id: 19931 Resource Limits: ncpus=1,nodes=4:ppn=8,walltime=08:00:00 Resources Used: cput=00:00:00,mem=428kb,vmem=1416kb,walltime=00:00:01 Queue Used: checkpt Account String: loni_cactus08 Node: qb223 Process id: 20454 ------------------------------------------------------ Similarly the directory ks-mclachlan contains three directories(output-0000, output-0000-active and SIMFACTORY) and a log.txt file, which contains following details[LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::Creating simulation ks-mclachlan [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::Simulation directory: /scratch/ettest52/simulations/ks-mclachlan [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::Simulation Properties: [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile):: [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::[properties] [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::machine = queenbee [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::simulationid = simulation-ks-mclachlan-queenbee-qb3.loni.org-ettest52-2013.07.27-10.19.03-7922 [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::sourcedir = /home/ettest52/Cactus [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::configuration = sim [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::configid = config-sim-qb4.loni.org-home-ettest52-Cactus [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::buildid = build-sim-qb4.loni.org-ettest52-2013.07.18-07.25.24-12102 [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::testsuite = False [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::executable = /scratch/ettest52/simulations/ks-mclachlan/SIMFACTORY/exe/cactus_sim [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::optionlist = /scratch/ettest52/simulations/ks-mclachlan/SIMFACTORY/cfg/OptionList [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::submitscript = /scratch/ettest52/simulations/ks-mclachlan/SIMFACTORY/run/SubmitScript [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::runscript = /scratch/ettest52/simulations/ks-mclachlan/SIMFACTORY/run/RunScript [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::parfile = /scratch/ettest52/simulations/ks-mclachlan/SIMFACTORY/par/ks-mclachlan.par [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile):: [LOG:2013-07-27 10:19:03] self.create(simulationName, parfile)::Simulation ks-mclachlan created [LOG:2013-07-27 10:19:03] self.submit(submitScript)::Restart for simulation ks-mclachlan created with restart id 0, long restart id 0000 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::Prepping for submission [LOG:2013-07-27 10:19:03] self.submit(submitScript)::No previous walltime available to be used, using walltime 8:00:00 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::Defined substituion properties for submission [LOG:2013-07-27 10:19:03] self.submit(submitScript)::{'SIMULATION_ID': 'simulation-ks-mclachlan-queenbee-qb3.loni.org-ettest52-2013.07.27-10.19.03-7922', 'NODE_PROCS': 1, 'PPN_USED': 8, 'PPN': 8, 'ALLOCATION': 'loni_cactus08', 'WALLTIME_HH': '08', 'CPUFREQ': '2.33', 'USER': 'ettest52', 'RUNDIR': '/scratch/ettest52/simulations/ks-mclachlan/output-0000', 'NODES': 4, 'SIMULATION_NAME': 'ks-mclachlan', 'WALLTIME': '8:00:00', 'NUM_THREADS': 8, 'EXECUTABLE': '/scratch/ettest52/simulations/ks-mclachlan/SIMFACTORY/exe/cactus_sim', 'PROCS_REQUESTED': 32, 'EMAIL': 'urkhanal(a)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/ks-mclachlan/output-0000/SIMFACTORY/SubmitScript', 'WALLTIME_HOURS': 8.0, 'WALLTIME_MM': '00', 'PARFILE': '/scratch/ettest52/simulations/ks-mclachlan/output-0000/ks-mclachlan.par', 'WALLTIME_SS': '00', 'QUEUE': 'checkpt', 'CONFIGURATION': 'sim', 'SOURCEDIR': '/home/ettest52/Cactus', 'HOSTNAME': 'qb3.loni.org', 'NUM_PROCS': 4, 'SCRIPTFILE': '/scratch/ettest52/simulations/ks-mclachlan/output-0000/SIMFACTORY/SubmitScript', 'MEMORY': '8192', 'WALLTIME_MINUTES': 480, 'SHORT_SIMULATION_NAME': 'ks-mclachlan-00'} [LOG:2013-07-27 10:19:03] self.submit(submitScript)::self.Properties: /scratch/ettest52/simulations/ks-mclachlan/output-0000/SIMFACTORY/properties.ini [LOG:2013-07-27 10:19:03] self.submit(submitScript):: [LOG:2013-07-27 10:19:03] self.submit(submitScript)::[properties] [LOG:2013-07-27 10:19:03] self.submit(submitScript)::machine = queenbee [LOG:2013-07-27 10:19:03] self.submit(submitScript)::simulationid = simulation-ks-mclachlan-queenbee-qb3.loni.org-ettest52-2013.07.27-10.19.03-7922 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::sourcedir = /home/ettest52/Cactus [LOG:2013-07-27 10:19:03] self.submit(submitScript)::configuration = sim [LOG:2013-07-27 10:19:03] self.submit(submitScript)::configid = config-sim-qb4.loni.org-home-ettest52-Cactus [LOG:2013-07-27 10:19:03] self.submit(submitScript)::buildid = build-sim-qb4.loni.org-ettest52-2013.07.18-07.25.24-12102 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::testsuite = False [LOG:2013-07-27 10:19:03] self.submit(submitScript)::executable = /scratch/ettest52/simulations/ks-mclachlan/SIMFACTORY/exe/cactus_sim [LOG:2013-07-27 10:19:03] self.submit(submitScript)::optionlist = /scratch/ettest52/simulations/ks-mclachlan/SIMFACTORY/cfg/OptionList [LOG:2013-07-27 10:19:03] self.submit(submitScript)::submitscript = /scratch/ettest52/simulations/ks-mclachlan/SIMFACTORY/run/SubmitScript [LOG:2013-07-27 10:19:03] self.submit(submitScript)::runscript = /scratch/ettest52/simulations/ks-mclachlan/SIMFACTORY/run/RunScript [LOG:2013-07-27 10:19:03] self.submit(submitScript)::parfile = /scratch/ettest52/simulations/ks-mclachlan/SIMFACTORY/par/ks-mclachlan.par [LOG:2013-07-27 10:19:03] self.submit(submitScript)::chainedjobid = -1 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::ppn = 8 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::procsrequested = 32 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::allocation = loni_cactus08 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::user = ettest52 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::numsmt = 1 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::walltime = 8:00:00 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::numprocs = 4 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::nodeprocs = 1 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::numthreads = 8 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::hostname = qb3.loni.org [LOG:2013-07-27 10:19:03] self.submit(submitScript)::ppnused = 8 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::queue = checkpt [LOG:2013-07-27 10:19:03] self.submit(submitScript)::cpufreq = 2.33 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::procs = 32 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::memory = 8192 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::nodes = 4 [LOG:2013-07-27 10:19:03] self.submit(submitScript)::pbsSimulationName= ks-mclachlan-00 [LOG:2013-07-27 10:19:03] self.submit(submitScript):: [LOG:2013-07-27 10:19:03] self.submit(submitScript)::saving substituted submitscript contents to: /scratch/ettest52/simulations/ks-mclachlan/output-0000/SIMFACTORY/SubmitScript [LOG:2013-07-27 10:19:03] self.submit(submitScript)::Executing submission command: qsub /scratch/ettest52/simulations/ks-mclachlan/output-0000/SIMFACTORY/SubmitScript [LOG:2013-07-27 10:19:03] self.makeActive()::Simulation ks-mclachlan with restart-id 0 has been made active [LOG:2013-07-27 10:19:04] job_id = self.extractJobId(output)::received raw output: 702161.qb2 [LOG:2013-07-27 10:19:04] job_id = self.extractJobId(output):: [LOG:2013-07-27 10:19:04] job_id = self.extractJobId(output)::using submitRegex: (\d+)[.]qb2 [LOG:2013-07-27 10:19:04] self.submit(submitScript)::After searching raw output, it was determined that the job_id is: 702161 [LOG:2013-07-27 10:19:04] self.submit(submitScript)::Simulation ks-mclachlan, with restart id 0, and job id 702161 has been submitted [LOG:2013-07-27 10:25:09] ret = restart.load(sim, activeId)::For simulation ks-mclachlan, loaded restart id 0, long restart id 0000 [LOG:2013-07-31 00:59:45] ret = restart.load(sim, activeId)::For simulation ks-mclachlan, loaded restart id 0, long restart id 0000 [LOG:2013-08-01 10:58:25] ret = restart.load(sim, activeId)::For simulation ks-mclachlan, loaded restart id 0, long restart id 0000 [LOG:2013-08-03 04:34:24] ret = restart.load(sim, activeId)::For simulation ks-mclachlan, loaded restart id 0, long restart id 0000 Inside output-0000 a directory SIMFACTORY and two files ks-mclachlan.err and ks-mclachlan.out are present. ks-mclachlan.err contains (PBS: exec of shell " failed) and ks-mclachlan.out contains the following-------------------------------------- Running PBS prologue script -------------------------------------- User and Job Data: -------------------------------------- Job ID: 702161.qb2 Username: ettest52 Group: lsuusers Date: 28-Jul-2013 01:20 Node: qb215 (24943) -------------------------------------- PBS has allocated the following nodes: qb215 qb184 qb151 qb130 A total of 32 processors on 4 nodes allocated --------------------------------------------- Check nodes and clean them of stray processes --------------------------------------------- Checking node qb215 01:20:30 Checking node qb184 01:20:31 Checking node qb151 01:20:33 Checking node qb130 01:20:35 Done clearing all the allocated nodes ------------------------------------------------------ Concluding PBS prologue script - 28-Jul-2013 01:20:35 ------------------------------------------------------ ------------------------------------------------------ Running PBS epilogue script - 28-Jul-2013 01:20:35 ------------------------------------------------------ Checking node qb215 (MS) Checking node qb130 ok Checking node qb151 ok Checking node qb184 ok Checking node qb215 ok ------------------------------------------------------ Concluding PBS epilogue script - 28-Jul-2013 01:20:43 ------------------------------------------------------ Exit Status: Job ID: 702161.qb2 Username: ettest52 Group: lsuusers Job Name: ks-mclachlan-00 Session Id: 24942 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: qb215 Process id: 25465 ------------------------------------------------------ The directory output-0000-active also contains the same details. I am wondering where I made mistake. Udayaraj Khanal

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database maintenance - 6pm CST - 9pm CST]
by Frank Loeffler 31 Jul '13

31 Jul '13

Hi, There will be a short outage of LSUThorns repositories this evening. See below for details. Frank ----- Forwarded message from Adam Yates <yates(a)cct.lsu.edu> ----- Date: Wed, 31 Jul 2013 15:27:18 -0500 From: Adam Yates <yates(a)cct.lsu.edu> To: allcct(a)cct.lsu.edu Subject: [Allcct] database maintenance - 6pm CST - 9pm CST Hi everyone; We will be performing some database maintenance this evening from 6pm CST to 9pm CST. During this time, some of the following services will be intermittently available: CCT's main website custom database / web applications group websites subversion wikis webmail * any other service not mentioned that accesses db.cct.lsu.edu. If you experience any difficulties after 9pm CST with any of the above services, please let us know. Thanks! Adam -- Adam Yates Manager of Information Technology Center for Computation and Technology (CCT) 231 Johnston Hall Baton Rouge, LA 70803 225.578.8235 _______________________________________________

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Automated Interactive Tutorial for ET
by Dennis Castleberry 29 Jul '13

29 Jul '13

Dear users, In preparation for the user workshop, I had created a Virtualbox virtual machine (VM) with a pre-compiled ET and several other utilities (see ticket #780: https://trac.einsteintoolkit.org/ticket/780) installed to facilitate use of the ET for new users. Unfortunately, another VM had been deployed at the workshop for that same purpose before the existence of my own VM was made known to the organizers; thus mine never saw use. Here are the links to it: https://www.cct.lsu.edu/~dcastl2/etk/etk_2.2.zip<https://www.cct.lsu.edu/~dcastl2/etk/etk_2.2.zip.md5.txt> https://www.cct.lsu.edu/~dcastl2/etk/etk_2.2.zip.md5.txt https://www.cct.lsu.edu/~dcastl2/etk/etk_2.2.vdi.md5.txt<https://www.cct.lsu.edu/~dcastl2/etk/etk_2.2.zip.md5.txt> I would like to propose re-purposing my VM for an automated tutorial. For an (unrelated) automated testing project, I created a system which can automatically detect sub-images within a screen shot and move the mouse cursor to click on the sub-image (see here: http://www.youtube.com/watch?v=0xck7w-UeX8). It can also do automated keyboard entry. I would like to port this system to my ET VM to follow tutorials for setting up ET, running the WaveToy demo, thorn writing, etc. The tutorials would be interactive in the sense that they could be paused to allow for the user to give input. Such a system would provide an interactive ET tutorial which is accessible to everyone. Please let me know if you think this would be a worthwhile endeavor. If so, feel free to make any suggestions toward its development and feature set. Regards, Dennis Castleberry dcastl2(a)tigers.lsu.edu

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problems with Visit 2.6.* and CarpetHDF5
by Bruno Giacomazzo 29 Jul '13

29 Jul '13

Hi, I have some issues using the latest version of Visit. When visualizing data in CarpetHDF5 format for some reasons VisIt does not show properly all the values, i.e., values below a certain threshold are visualized using the same color of the minimum in the colorbar. I have attached two images to make it more clear: rho_visit_263.jpeg shows the density using version 2.6.3, while rho_visit_232.jpeg shows the same quantity but using version 2.3.2. As you can see, 2.6.3 does not show properly the values below ~1e-6 (they all get the same color of 1e-10). I tried both the binary and source versions of visit 2.6.3 and they both show the same problem. I also tried the 2.6.0 binary version and it shows the same problem too. Any idea of what's going on? Thanks, Bruno Dr. Bruno Giacomazzo JILA - University of Colorado 440 UCB Boulder, CO 80309 USA Tel. : +1 303-492-5170 Fax : +1 303-492-5235 email : bruno.giacomazzo(a)jila.colorado.edu web: http://www.brunogiacomazzo.org ---------------------------------------------------------------------- There are only 10 types of people in the world: Those who understand binary, and those who don't ----------------------------------------------------------------------

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