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3984 discussions

-r & --redirect flags
by Scott Hawley 27 Jul '13

27 Jul '13

Has output redirection changed recently? >From my copy of the User's Guide: " -r[o|e|oe|eo] or--redirect=[o|e|oe|eo] Redirects the standard output (`o') and/or standard error (`e') of each processor to a le. By default, the standard outputs from processors other than processor 0 are discarded " Note that there is no space. But when I use either "-roe" or "--redirect=oe" I get Usage errors, e.g. /opt/local/bin/openmpirun -np 2 ./exe/cactus_bruiser --redirect=oe /Users/shawley/runs/cactus/bruiser/bruiser_test.par IN DIRECTORY: /Users/shawley/Cactus Usage: ./exe/cactus_bruiser [-h] [-O] [-o paramname] [-L n] [-W n] [-E n] [-r[o|e|oe|eo]] [--logdir <dir>] [-b <no|line|full>] [-S] [-T] [-t name] [--parameter-level <level>] [-v] <parameter_file_name> -------------------------------------------------------------------------- openmpirun noticed that the job aborted, but has no info as to the process that caused that situation. -------------------------------------------------------------------------- I must be doing something wrong. Any suggestions? Thanks, Scott

2 1

Einstein Toolkit Meeting Reminder
by Frank Loeffler 21 Jul '13

21 Jul '13

1 0

simulation problem
by Udayaraj Khanal 18 Jul '13

18 Jul '13

I found there is a directory /scratch/ettest52/simulations/static_tov. There are three directories and a file inside static_tov. They are output-0000, output-0000-active, SIMFACTORY and a file log.txt. Inside output-0000 there is a directory SIMFACTORY. There is not any log files. Inside SIMFACTORY there are three files properties.ini, simulation-1374132863.07 and SubmitScript. The log.txt file in /scratch/ettest52/simulations/static_tov contains following details. [LOG:2013-07-18 02:34:19] self.create(simulationName, parfile)::Creating simulation static_tov [LOG:2013-07-18 02:34:19] self.create(simulationName, parfile)::Simulation directory: /scratch/ettest52/simulations/static_tov [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::Simulation Properties: [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile):: [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::[properties] [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::machine = queenbee [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::simulationid = simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.07.18-02.34.19-19349 [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::sourcedir = /home/ettest52/Cactus [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::configuration = sim [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::configid = config-sim-qb4.loni.org-home-ettest52-Cactus [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::buildid = build-sim-qb4.loni.org-ettest52-2013.07.18-07.25.24-12102 [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::testsuite = False [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::executable = /scratch/ettest52/simulations/static_tov/SIMFACTORY/exe/cactus_sim [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::optionlist = /scratch/ettest52/simulations/static_tov/SIMFACTORY/cfg/OptionList [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::submitscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/SubmitScript [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::runscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/RunScript [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::parfile = /scratch/ettest52/simulations/static_tov/SIMFACTORY/par/static_tov.par [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile):: [LOG:2013-07-18 02:34:22] self.create(simulationName, parfile)::Simulation static_tov created [LOG:2013-07-18 02:34:22] self.submit(submitScript)::Restart for simulation static_tov created with restart id 0, long restart id 0000 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::Prepping for submission [LOG:2013-07-18 02:34:22] self.submit(submitScript)::No previous walltime available to be used, using walltime 8:00:00 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::Defined substituion properties for submission [LOG:2013-07-18 02:34:22] self.submit(submitScript)::{'SIMULATION_ID': 'simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.07.18-02.34.19-19349', '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:2013-07-18 02:34:22] self.submit(submitScript)::self.Properties: /scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/properties.ini [LOG:2013-07-18 02:34:22] self.submit(submitScript):: [LOG:2013-07-18 02:34:22] self.submit(submitScript)::[properties] [LOG:2013-07-18 02:34:22] self.submit(submitScript)::machine = queenbee [LOG:2013-07-18 02:34:22] self.submit(submitScript)::simulationid = simulation-static_tov-queenbee-qb3.loni.org-ettest52-2013.07.18-02.34.19-19349 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::sourcedir = /home/ettest52/Cactus [LOG:2013-07-18 02:34:22] self.submit(submitScript)::configuration = sim [LOG:2013-07-18 02:34:22] self.submit(submitScript)::configid = config-sim-qb4.loni.org-home-ettest52-Cactus [LOG:2013-07-18 02:34:22] self.submit(submitScript)::buildid = build-sim-qb4.loni.org-ettest52-2013.07.18-07.25.24-12102 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::testsuite = False [LOG:2013-07-18 02:34:22] self.submit(submitScript)::executable = /scratch/ettest52/simulations/static_tov/SIMFACTORY/exe/cactus_sim [LOG:2013-07-18 02:34:22] self.submit(submitScript)::optionlist = /scratch/ettest52/simulations/static_tov/SIMFACTORY/cfg/OptionList [LOG:2013-07-18 02:34:22] self.submit(submitScript)::submitscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/SubmitScript [LOG:2013-07-18 02:34:22] self.submit(submitScript)::runscript = /scratch/ettest52/simulations/static_tov/SIMFACTORY/run/RunScript [LOG:2013-07-18 02:34:22] self.submit(submitScript)::parfile = /scratch/ettest52/simulations/static_tov/SIMFACTORY/par/static_tov.par [LOG:2013-07-18 02:34:22] self.submit(submitScript)::chainedjobid = -1 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::ppn = 8 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::procsrequested = 32 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::allocation = NO_ALLOCATION [LOG:2013-07-18 02:34:22] self.submit(submitScript)::user = ettest52 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::numsmt = 1 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::walltime = 8:00:00 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::numprocs = 4 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::nodeprocs = 1 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::numthreads = 8 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::hostname = qb3.loni.org [LOG:2013-07-18 02:34:22] self.submit(submitScript)::ppnused = 8 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::queue = checkpt [LOG:2013-07-18 02:34:22] self.submit(submitScript)::cpufreq = 2.33 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::procs = 32 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::memory = 8192 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::nodes = 4 [LOG:2013-07-18 02:34:22] self.submit(submitScript)::pbsSimulationName= static_tov-0000 [LOG:2013-07-18 02:34:22] self.submit(submitScript):: [LOG:2013-07-18 02:34:22] self.submit(submitScript)::saving substituted submitscript contents to: /scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/SubmitScript [LOG:2013-07-18 02:34:22] self.submit(submitScript)::Executing submission command: qsub /scratch/ettest52/simulations/static_tov/output-0000/SIMFACTORY/SubmitScript [LOG:2013-07-18 02:34:22] self.makeActive()::Simulation static_tov with restart-id 0 has been made active [LOG:2013-07-18 02:34:23] job_id = self.extractJobId(output)::received raw output: Invalid allocation "NO_ALLOCATION". [LOG:2013-07-18 02:34:23] job_id = self.extractJobId(output)::===================== Allocation information for ettest52 ===================== [LOG:2013-07-18 02:34:23] job_id = self.extractJobId(output):: Proj. Name| Alloc| Balance| Deposited| %Used| Days Left| End [LOG:2013-07-18 02:34:23] job_id = self.extractJobId(output)::-------------------------------------------------------------------------------- [LOG:2013-07-18 02:34:23] job_id = self.extractJobId(output)::loni_cactus08|loni_cactus08 on @Dell_Cluster|106210.43| 250000.00| 57.52| 167|2014-01-01 [LOG:2013-07-18 02:34:23] job_id = self.extractJobId(output):: [LOG:2013-07-18 02:34:23] job_id = self.extractJobId(output)::Note: Balance and Deposit are measured in CPU-hours [LOG:2013-07-18 02:34:23] job_id = self.extractJobId(output)::qsub: submit filter returned an error code, aborting job submission. [LOG:2013-07-18 02:34:23] job_id = self.extractJobId(output):: [LOG:2013-07-18 02:34:23] job_id = self.extractJobId(output)::using submitRegex: (\d+)[.]qb2 [LOG:2013-07-18 02:34:23] self.submit(submitScript)::After searching raw output, it was determined that the job_id is: -1 [LOG:2013-07-18 02:34:23] self.submit(submitScript)::The regex did NOT match anything. No job_id means no control. [LOG:2013-07-18 02:35:29] ret = restart.load(sim, activeId)::For simulation static_tov, loaded restart id 0, long restart id 0000 I do not understand what these means. What I have to do to complete simulation? Udayaraj KhanalProfessorCentral Department of PhysicsTribhuvan UniversityKirtipur, Nepal

2 1

dependencies & CST warnings
by Kelly, Bernard J. (GSFC-660.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY] 17 Jul '13

17 Jul '13

Hi. I'm compiling an *extremely* simple cactus executable designed to run the testsuite "vectors" in LSUThorns/Vectors. If I were to believe the parameter file vectors.par, I should need exactly the following seven thorns: CartGrid3D CoordBase IOASCII IOUtil PUGH PUGHSlab Vectors However, if I begin to compile a minimal Cactus configuration using only these (in current ET stable release Gauss --- ET_2013_05), I quickly hit the warnings below, implying that I *also* need SymBase and Boundary. Now these are warnings, not errors; perhaps the code would compile fine and run OK anyway (I haven't tried). But surely trying to schedule a routine in a particular group or timebin means that the thorn responsible for such groups/timebins should be an actual dependency? Why are Boundary and SymBase not *required* in the interface.ccl of CartGrid3D? Bernard ------------------------------------------------------ Warnings were generated during execution of the CST ------------------------------------------------------ CST warning: -> Scheduling routine RegisterSymmetryBoundaries from thorn CartGrid3D in non-existent group or timebin SymmetryRegister HINT: If this routine should be scheduled check the spelling of the group or timebin name. Note that scheduling IN must be used to schedule a routine to run in a thorn-defined schedule group, whereas scheduling AT is used for a usual timebin. (Schedule IN may also be used with the usual timebins, but in this case the full name of the bin must be used, e.g. CCTK_EVOL and not EVOL) CST warning: -> Scheduling routine CartGrid3D_ApplyBC from thorn CartGrid3D in non-existent group or timebin BoundaryConditions HINT: If this routine should be scheduled check the spelling of the group or timebin name. Note that scheduling IN must be used to schedule a routine to run in a thorn-defined schedule group, whereas scheduling AT is used for a usual timebin. (Schedule IN may also be used with the usual timebins, but in this case the full name of the bin must be used, e.g. CCTK_EVOL and not EVOL)

3 2

New Thorn: LlamaWaveHyperboloidal
by Michael Jasiulek 17 Jul '13

17 Jul '13

Hello all, here is a new thorn: https://bitbucket.org/mjasiulek/llamawavehyperboloidal <https://bitbucket.org/mjasiulek/llamawavehyperboloidal> =============================================================================== LlamaWaveHyperboloidal =============================================================================== This thorn allows to evolve the scalar wave equation in 3D in Kerr spacetimes using Kerr-Schild coordinates which are horizon penetrating. At some transition radius the user can specify where the Kerr-Schild slicing becomes hyperboloidal, thus, 'bends up' to scri (future null infinity). Therefore, no outer (and inner) boundary conditions have to be set, radiation leaves the spacetime 'naturally' through the inner horizon and scri. The waveform at scri is readily computed during the evolution. It uses Llama's spherical 6-patch coordinates (r,u,v), the method-of-lines with 4th-order Runge-Kutta and 4th-,6th- or 8th-order spatial finite-differencing and matching Kreiss-Oliger dissipation. In http://arxiv.org/abs/1109.2513 <http://arxiv.org/abs/1109.2513> (or http://iopscience.iop.org/0264-9381/29/1/015008/ <http://iopscience.iop.org/0264-9381/29/1/015008/> ) I used this code to study QNMs, late-time tails in Kerr at scri and to test the novel hyperboloidal transformation used to smoothly attach the hyperboloidal slice. If you find this code useful, please cite the paper Class. Quantum Grav. 29 015008 (2012). =============================================================================== Enjoy, Michael Jasiulek .

1 0

New Thorn: LlamaWaveHyperboloidal
by Michael Jasiulek 17 Jul '13

17 Jul '13

Hello all, here is a new thorn: https://bitbucket.org/mjasiulek/llamawavehyperboloidal =============================================================================== LlamaWaveHyperboloidal =============================================================================== This thorn allows to evolve the scalar wave equation in 3D in Kerr spacetimes using Kerr-Schild coordinates which are horizon penetrating. At some transition radius the user can specify where the Kerr-Schild slicing becomes hyperboloidal, thus, 'bends up' to scri (future null infinity). Therefore, no outer (and inner) boundary conditions have to be set, radiation leaves the spacetime 'naturally' through the inner horizon and scri. The waveform at scri is readily computed during the evolution. It uses Llama's spherical 6-patch coordinates (r,u,v), the method-of-lines with 4th-order Runge-Kutta and 4th-,6th- or 8th-order spatial finite-differencing and matching Kreiss-Oliger dissipation. In http://arxiv.org/abs/1109.2513 <http://arxiv.org/abs/1109.2513> (or http://iopscience.iop.org/0264-9381/29/1/015008/ <http://iopscience.iop.org/0264-9381/29/1/015008/>) I used this code to study QNMs, late-time tails in Kerr at scri and to test the novel hyperboloidal transformation used to smoothly attach the hyperboloidal slice. If you find this code useful, please cite the paper Class. Quantum Grav. 29 015008 (2012). =============================================================================== Enjoy, Michael Jasiulek .

1 0

Einstein Toolkit: Minutes for 8 July
by Joshua Faber 15 Jul '13

15 Jul '13

Present: Josh, Vassileos, Frank, Ian, Erik, Philipp, (Peter?) McLachlan: *Erik and Ian want to make several changes to the code: -Allow arguments to be passed via scripts to generate multiple thorns in parallel, rather than sequentially - Design of more high level APIs to streamline declaration of new objects, e.g. tensors - Introduce master calculation for BSSN variables, and use filtering to isolate necessary code to be called in a specific run - Enable making parameters available at either runtime or Kranctime for greater flexibility - Additional Optimizations Carpet: Users are welcome to create their own branches to work on new features, but please use subdirectories as needed to keep the codebase clean. Incoming Thorns: *README has been updated with current status of several thorns and primary maintainer/developer, but some updates are needed from developers * MemSpeed likely moving to ET, but needs a testsuite * CartesianCoordinates requires use of Llama, which is not available in the ET yet

2 1

simulation time
by Udayaraj Khanal 14 Jul '13

14 Jul '13

Dear allI have created a batch queue script and submitted it to queue an example simulation static_tov as in tutorial for new user. Then I checked the status by ./simfactory/bin/sim list-simulations. I got static_tov [ACTIVE (FINISHED), restart 0000, job id -1]. Does this signifies the completion of the simulation?When I logged in by ssh -Y qb.loni.org and give command cd /scratch/ettest52/simulations/static_tov/output-0000/static_tovNo such file or directory. Is it due to not completion of the simulation?How much time does it take to complete a simulation? I have submitted it almost a week before. Udayaraj KhanalProfessorCentral Department of PhysicsTribhuvan UniversityKirtipur, Nepal

4 3

Einstein Toolkit Meeting Reminder
by Frank Loeffler 14 Jul '13

14 Jul '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#. In addition to anything that might be brought up at the meeting I would like to discuss the following points: - incoming Currently we do have quite a collection piling up in incoming. This is good. However, now it the best time to work on these, deciding about the faith of these contributions. Doing so means that they should get tested by someone else than someone from the contributing group, ideally multiple maintainers. If we could do so at least for some until Monday this would be great, but realistically we first probably need to remind everyone what these are actually about. So: I would like each author/contributor of the new modules to say just a few words about each of these. Also, please mention how well tested they are from the contributor's side (have they been built on a larger number of machines, or only on very few / are they used in production runs, ect) , and whether there exists sufficient documentation and testsuites to be able to include them as is. I created a README in the root of incoming where I would like to have a very short status indication of each of the contributions. We currently have in incoming: ADMDerivatives CartesianCoordinates CoreCollapseControl IDFileHydro MemSpeed PITTNullCode SphericalSlice Symmetry TOVSolverHot ZelmaniQuadWaveExtract In addition, there are tickets for inclusion of ZelmaniQuadWaveExtract [1], CartesianCoordiantes [2] and CoreCollapseControl [3], which each live in Zelmani [4]. Same goes here: please describe their current status (just very briefly). Please let me know if there is something else I missed for inclusion. - issues up for review There are currently 14 issues up for review, which is a rather high number. Issues up for review mean that someone already has put in enough time and work to come up with a solution that she/he thinks is worthy being considered as fix. What is not needed is a second pair of eyes to decide if this is ok, or should be changed in some way. Please consider going through that list [5] and help a few of these to finally pass. Frank Löffler [1] https://trac.einsteintoolkit.org/ticket/1356 [2] https://trac.einsteintoolkit.org/ticket/1357 [3] https://trac.einsteintoolkit.org/ticket/1358 [4] git://carpetcode.org/Zelmani.git [5] https://trac.einsteintoolkit.org/query?status=review&col=id&col=summary&col…

1 1

Re: [Users] [Commits] [svn:einsteintoolkit] TOVSolver/trunk/ (Rev. 137)
by Roland Haas 11 Jul '13

11 Jul '13

Hello all, > Log: > * remove option to have different gamma and K for different > stars. That's physically impossible. > * adjust test par files (will do so with GRHydro next) > * modify the way solutions are added so that atmosphere cuts > are applied after solutions are added. Otherwise one of the > stars will have the atmosphere added to it. This breaks symmetry. This commit (and the following ones) make the tests fail, at least in subversion (Zelmani is ok since the author *does* provide updated tests, just not in GRHydr/svn, so I could port over the change). I am personally generally unhappy about commits that require everybody to change/update their paramater files unless the change is required to prevent a bug from manifesting. Removing "[0]" from ones parameter file is not hard, but will break each and every single one of them. One of the nice things about Cactus has been that (some parts of it) are fairly stable and developers take care to not introduce changes that require each user to update their parameter files (unless the user wants/needs new features). I am also not sure I agree with the statement that one cannot have different Gama or K for different stars. Even if the same Gamma and K would be needed for all neutron stars (which I also don't fully understand, why should not a different Gamam or K be a better approximiation to NS of different massses?) there is still the possiblilty of setting up two different sorts of stars and evolve those. Note that I make no statement how to proceed with such an evolution past the point where the stars would touch. To my knowledge only Ian Hawke did such simulations in the past, and Ian effective advected the EOS parameters with the fluid if I remember correctly. If someone with more expterise would comment that would be helpful. I would like to revert parts of this patch (keeping the atmosphere treatment that prevents asymetries in the data setup and seems to be currently buggy) and restore the possibility to have different K and Gamma (indep of whether this is physical I don't see a point in removing this functionality). Please comment (in private or on the mailing list). Yours, Roland

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