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Meeting Minutes
by Roland Haas 26 Aug '13

26 Aug '13

Present: Frank, Roland, Matt, Ian, Erik, Philipp, Steve, Peter * please review the outstanding tickets on track [1] * Roland introduced and fixed a bug in CarpetIOHDF5 that prevented recovering from checkpoints from Sun Aug 11 2013 to Sat Aug 17 2013 (fdadb2c to c02dd99) * Philipp will commit the cell centered vector potential code (bugfixes remain) after testing it with a dynamic simulation (TOV works) * Frank will contact Erik to learn how to run Cactus on the Phi processors Yours, Roland

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Meeting Minutes
by Roland Haas 21 Aug '13

21 Aug '13

Present: Frank, Roland, Peter, Erik, Matt, Ian, Josh, Yosef, Philipp, Oleg Cactus tutorial: * Oleg will give a short tutorial on Cactus at Nordita * suggest using current material from last workshop as basis * possibly more detailed tutorial later for interested parties * happy to have telecon with interested parties afterwards Point release: * there was a suggestion to have a point release with the accumulated patches * no support for this right now, instead will keep release branch and consider adding more bugfixes to it once we have a list of current bugs * suggest to add the word "backport" to ticket keywords when a bugfix should be backported to the release * Ian to create a list of bugfixes since the release (from the superrepository) * Ian to send around information on how to sign up for Jenkins (testing system) email Yours, Roland

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Simulation error
by Udayaraj Khanal 19 Aug '13

19 Aug '13

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(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:2013-08-17 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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Test status
by Ian Hinder 19 Aug '13

19 Aug '13

Hi, If you want to keep up with the current status of the automated build and test of the Einstein Toolkit, there are several options. 1. You can browse the test system at https://build.barrywardell.net/ 2. Follow the RSS feeds advertised on that page, and on the job-specific page. For example, the RSS feed for the EinsteinToolkit trunk is https://build.barrywardell.net/job/EinsteinToolkit/rssAll for all test runs, and https://build.barrywardell.net/job/EinsteinToolkit/rssFailed if you just want to know about failures. 3. Subscribe to the test mailing list at http://lists.einsteintoolkit.org/mailman/listinfo/test Note that occasionally you get some inaccurate items in the feed, for example if there is a problem with the test system. The test mailing list is very new, and we are still experimenting a bit with it. We currently have three "jobs" which are tested; the EinsteinToolkit trunk, EinsteinToolkitProposed, which includes some additional thorns and tests, and EinsteinToolkitRelease, which corresponds to the release branch. -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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Changes to release branch since the release
by Ian Hinder 19 Aug '13

19 Aug '13

Hi, The list of changes to the release branch since the release can be queried using the following URL: http://git.barrywardell.net/EinsteinToolkit.git/log/dac2e71fc0601829d992f79… Currently the list is: * simfactory c04079f...467325a (1): > supermuc-ibmmpi.sub: Change job class to 'micro' for jobs on <= 32 nodes * repos/CRL b11ce17...d9b0f3d (1): > fix uninitialized variable (typo), closes #1421 * flesh 85dd567...56632c4 (1): > fix implementation of 'complex' for c++0x, see #1374 * repos/CRL 8a48ebf...b11ce17 (1): > use 'old' git command syntax to change to different branch to be able to use old git versions We should probably go through all the changes since the release and decide if any are important enough to be backported. -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 17 Aug '13

17 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. One topic we had to leave out last week because of limited time was the idea of a point-release, which would include a selection of bugfixes that accumulated since the last release. Frank Löffler

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GetComponents: $old_url error (and version number)
by Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] 16 Aug '13

16 Aug '13

Hi. Having downloaded the current release (ET_2013_05) a while ago, I want now to use GetComponents to refresh what I have locally. However, I'm getting an error when trying to use it in this way. Specifically, I have the versions of GetComponents and einsteintoolkit.th pointed to from the "Tutorial for New Users" (https://docs.einsteintoolkit.org/et-docs/Tutorial_for_New_Users), though I've added other arrangements/thorns to the latter. In the normal way, I execute (and see) the following: --------------------------------------------------------------------------- ------------------------------------- > ./GetComponents einsteintoolkit.th Do you want to update all existing components? yes, no [no] : yes Use of uninitialized value $old_url in pattern match (m//) at ./GetComponents line 1316, <STDIN> line 1. Use of uninitialized value $old_url in concatenation (.) or string at ./GetComponents line 1321, <STDIN> line 1. Error: The URL for CactusArchive/ADM has changed, please perform a clean checkout. --------------------------------------------------------------------------- ------------------------------------- To my knowledge, the URL for CactusArchive/ADM has *not* changed. But anyway, removing this particular thorn from the results in a similar message from the next in line (CactusBase/Boundary), and so on. Given the actual "uninitialized value $old_url" warnings above, I think there's an issue in the script, one that doesn't manifest for fresh checkouts. Incidentally, I note that "GetComponents" itself has changed a bit since June 19, when I last downloaded it (same ET release, of course), but in both old and new versions quote the same version number (1.0.0). Perhaps this isn't a very meaningful number after all? Thanks, Bernard

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Release of SimulationTools for Mathematica
by Ian Hinder 15 Aug '13

15 Aug '13

15th August 2013 We present “SimulationTools for Mathematica” <http://simulationtools.org/>, available as free software under the GNU General Public License. SimulationTools is a Mathematica application for analysing data from numerical simulations. It has a modular design applicable to general grid-based numerical simulations, and contains specific support for the Cactus code, with a focus on the field of Numerical Relativity and the Einstein Toolkit. SimulationTools provides a functional, programmable interface to simulation data. A highly-optimised HDF5 module can be used for reading HDF5 data from production simulations, including 1D, 2D and 3D grid data produced by the Carpet code. Simulation details such as filenames, file formats, and details of parallel I/O are hidden from the user. Numeric data with attached coordinate information is manipulated using new data types. Many useful new functions are defined on these types, and most built-in numerical Mathematica functions such as +, -, *, /, Abs, Sin, Log and Max can be used transparently. There is also support for testing numerical convergence, with automatic resampling onto a common grid if desired. SimulationTools has generic functionality useful for analysis of many types of data, as well as explicit support for codes including Cactus, Carpet, Llama, SimFactory and many other components of the Einstein Toolkit. It provides an overview of the state of a simulation, including speed, memory usage, and physics (e.g. trajectories and waveforms from a binary system). The design is modular, and support for output from other codes can be added. Specific functionality for Numerical Relativity is available. Gravitational waveforms can be read from simulations using natural function semantics, and the waveforms can be manipulated, for example converting between Psi4 and strain and extrapolation to infinity. An abstraction for “binary systems” provides a convenient interface to the trajectories of members of a binary system tracked with codes from the Einstein Toolkit. Support for reading black hole masses and spins is also included. Data in the Numerical Relativity Data Format (as used in the NINJA and NR-AR projects) can be read using the same functions that are used for normal simulation data. More details are available on the SimulationTools website <http://simulationtools.org>, including an extensive feature summary, a list of capabilities and online documentation <http://simulationtools.org/Documentation/English/Tutorials/SimulationTools.…>. Tutorials and reference documentation are also available within the standard Mathematica documentation system. Code quality is maintained to a high standard with ~400 unit tests. SimulationTools has been in production use for over 5 years and has been used at several research institutions worldwide. We invite you to try out the code <http://simulationtools.org/download>, join the mailing list <http://simulationtools.org/mailman/listinfo/users> and freely use SimulationTools for your research. -- Ian Hinder and Barry Wardell http://numrel.aei.mpg.de/people/hinder http://barrywardell.net/

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Re: [Users] [Commits] [svn:einsteintoolkit] manifest/trunk/ (Rev. 245)
by Erik Schnetter 15 Aug '13

15 Aug '13

On 2013-08-14, at 18:56 , rhaas(a)tapir.caltech.edu wrote: > User: rhaas > Date: 2013/08/14 07:56 PM > > Modified: > /trunk/ > einsteintoolkit.th > > Log: > add Timers thorn (required by Carpet) I apologize for requiring the Timer thorn without due notice. I was debugging a particular memory allocation problem for about a week, and in the course of this, I cleanup up many stretches of code in Carpet and CarpetLib. I suspected that the timers were at fault, so I isolated the code and added parameters to disable the timers. Alas, the timers were not at fault. However, having the timers separated seemed like a good idea, and instead of throwing away all the clean-ups, or re-implementing the solution anew, I decided to push all clean-ups together with the work-around that avoids the problem. -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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Critical test failures
by Ian Hinder 15 Aug '13

15 Aug '13

Hi all, 25 of the ET tests started failing between 6th August and 15th August (the test system was down for maintenance during that time). The error is an assertion in LoopControl. I opened a ticket <https://trac.einsteintoolkit.org/ticket/1426> but also wanted to warn people that they might not want to update until this is fixed. -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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