Users August 2013

users@lists.einsteintoolkit.org

11 participants
22 discussions

Einstein Toolkit Meeting Reminder
by Frank Loeffler 17 Aug '13

17 Aug '13

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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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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

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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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Users August 2013