Users July 2018

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15 participants
24 discussions

error after activating IllinoisGRMHD and VolumeIntegrals_GRMHD
by 林家暉 24 Jul '18

24 Jul '18

Dear whom it may concern, I tried to solve the tracking problem of unequal mass binary neutron (http://einsteintoolkit.org/gallery/bns/index.html ) star by using the thorn WVUThorns_Diagnostics / VolumeIntegrals_GRMHD . Therefore I activate both IllinoisGRMHD and VolumeIntegrals_GRMHD. However I met the error which showed in both .err file and .out file. In .err file: Thu Jul 12 08:03:04 2018: [unset]:_pmi_alps_init:alps_get_placement_info returned with error -1 Thu Jul 12 08:03:04 2018: [unset]:_pmi_init:_pmi_alps_init returned -1 In .out file: INFO (IllinoisGRMHD): Font fix failed! INFO (IllinoisGRMHD): i,j,k = 78 31 41, stats.failure_checker = 10000 x,y,z = -1.800000e+01 -7.593750e+00 1.068750e+01 , index=574610 st_i = -nan -nan -nan, rhostar = 2.902693e+243, Bi = 0.000000e+00 0.000000e+00 0.000000e+00, gij = 1.295702e+00 0.000000e+00 0.000000e+00 1.295702e+00 0.000000e+00 1.295702e+00, Psi6 = 1.474883e+00 INFO (IllinoisGRMHD): Couldn't find root from: -nan 2.902693e+243 -nan -nan -nan, rhob approx=1.968084e+243, rho_b_atm=1.000000e+200, Bx=0.000000e+00, By=0.000000e+00, Bz=0.000000e+00, gij_phys=1.295702e+00 0.000000e+00 0.000000e+00 1.295702e+00 0.000000e+00 1.295702e+00, alpha=8.746533e-01 I am not sure what these error exactly mean and how to solve it. Thanks. Chia-Hui

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meeting minutes for 2018-07-23
by Roland Haas 23 Jul '18

23 Jul '18

Present: Roland, Bhavesh, Gabrielle, Helvi, Miguel, Peter, Zach, Shawn, Qian, Antoni Ramos Buades Working group updates: * performance optimization: https://docs.einsteintoolkit.org/et-docs/images/8/88/wgopt-update-20180723.… * scheduling has been postponed due to PEARC * IllinoisGRMHD: https://docs.google.com/presentation/d/1ojZuRIbr28-sS5uKg7201D2rHcyZNnIAu6O… ** next telecon Thus July 26 2018, email Zach to be included in the hangout and google group * CosmoParticles: continue to explore what physics can be investigated, including alternative theories of gravity. No August meeting, but will have one in September with Isabelle Codero speaking * DataVault: currently upload of LIGO waveform files possible, automatic extraction of metadata and searching for waveforms in place on development laptop, but not yet in live version. Qian Zhang who has been the main developer is leaving NCSA end of the month so is in the process of writing documentation to enable a smooth handover Wiki * Peter will talk to LSU IT support * currently impossible to edit wiki without having a CCT account Tutorial server down: * NCSA needs to talk with NDS-Labs representative * was shut * also out of allocaton ET gallery examples: * Peter has updated setup for Mike: BBH and BNS. Roland to provide Peter with source code of release used to produce figures. * Shawn will do Poisson equation * scalar field and TOV example not yet done GiRaFFE review: * no news from actual review * tests are being reviewed internally * WVUDiagnostics update will also be included Release: * Zach confirms that ET works with Ubuntu 18 using the system gcc, is testing with Intel 2019 compiler Lean & Proca: * Erik was contacted but is busy for the next three weeks but could look a it after * Roland is concerned that this is very short before the release and there may be hidden (compiler) bugs triggered by running on a full set of ET machines: http://einsteintoolkit.org/testsuite_results/index.php but site is down and only the link to the repository with the raw data still exists Blockers for ET release: * BNS gallery * GiRaFFE * out of box support for OSX: Roland to test Steve's instructions and report back if they work. Bounce back if they fail. Questions on mailing list: * Miguel sees memory leak in high resolution runs, on three different machines incl. a laptop, a workstation and a cluster * Zach suggests to check that the memory increase is not due to grid separating as the objects move * Roland suggests using a memory profiler on the workstation and that Ian looked into them a couple of years ago and may remember what they were called. Using tcmalloc as Ian suggested can also help with both profiling and reducing memory fragmentation http://goog-perftools.sourceforge.net/doc/heap_profiler.html * Peter suggests looking at Carpet's output for memory in grid functions which is in carpetlib's memorystatistics output Yours, Roland -- 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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Reminder: Weekly users call.
by Peter Diener 21 Jul '18

21 Jul '18

Hi All, This is just a reminder that next week's Users Call will take place at the usual time (at 10:00am US Eastern time on Monday) and the usual place (https://bluejeans.com/194244555). If you have any items for the agenda please add them to the wiki (https://docs.einsteintoolkit.org/et-docs/meeting_agenda#Meeting_Agenda) or send them to me (diener(a)cct.lsu.edu). Cheers, Peter

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Queuing system and parameter file scripts on personal machine
by Federico G Lopez Armengol 18 Jul '18

18 Jul '18

Hello, I've been learning how to use the Toolkit for about a year. I've been reading public documentation and running individual simulations on my personal laptop. Now, I need to manage some set of simulations, and found some trouble: 1) it seems that I do not have a queuing system. Each time I submit a simulation, it starts running in parallel with previous ones and my laptop quickly collapses. I configured simfactory with: ./simfactory/bin/sim setup-silent --optionlist=ubuntu.cfg --runscript > debian.sh --submitscript debian.sub --runscript debian.sh 2) I've tried some scripting with .rpar files, but failed. For instance, if submitting: ./simfactory/bin/sim create-submit tov_multi --parfile par/tov.rpar no error displays, but the simulation is inmediately finished with no outputs. On the other hand, if running: ./simfactory/bin/sim create-run tov_multi --parfile par/tov.rpar I get the following error: Error: Parameter file script > '/home/fede/simulations/tov_multi/output-0000/tov.rpar' did not generate a > parameter file called '/home/fede/simulations/tov_multi/output-0000/tov.par' I changed the name of the parameter file created as asked, but just the last simulation of the script runs. I've tried this with every .rpar script that is included on the Toolkit. I use Linux Mint 18.1 Serena. Thanks in advance! Federico

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Working group updates in ET call Monday July 23rd
by Roland Haas 18 Jul '18

18 Jul '18

Hello all, this is a reminder for the working group leads that we will have the monthly status updates for the working groups in the next ET call Monday July 23rd. The current list of working groups can be found on the wiki: https://docs.einsteintoolkit.org/et-docs/Main_Page Established Groups: * Cosmology and Particles * Data Dependent Task Scheduler * IllinoisGRMHD * Performance Optimization Yours, Roland -- 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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Ubuntu 18.04
by Zach Etienne 16 Jul '18

16 Jul '18

Hi all, Good news: I was able to compile the development version of ETK on a fresh Ubuntu 18.04 (released Apr 2018), using the instructions on https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users (one exception: I used the Ubuntu OpenMPI MPI stack). Note that the Intel compiler does not yet support Ubuntu 18.04, so I found it a pleasant surprise that ETK compiled out of the box using GCC. Hooray! -Zach * * * Zachariah Etienne Assistant Professor of Mathematics West Virginia University *https://math.wvu.edu/~zetienne/ <https://math.wvu.edu/~zetienne/>* https://blackholesathome.net

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meeting minutes for 2018-07-16
by Roland Haas 16 Jul '18

16 Jul '18

Present: Peter, Roland, Sam, Zach, Helvi, Qian, Shawn * ET release ** BBH: maybe Steve or Sam ** Poisson equation: will be done Shawn Rosofsky ** Scalar field: Roland, will update description ** TOV: no update ** BNS: Peter, still compiling on Mike and debugging runtime issues * milestones: ** BNS example: Peter is working on them ** GiRaFFE: test are almost there, two of co-authors are working on it ** simfactory: should check what the current status is with Steve * Proca code: Peter will review * Lean code: no reviewer yet. Suggest to contact possible reviewers directly. Will update documentation.tex with information from paper (currently being written). * WVUDiagnostics: Steve may have volunteered to look into it ** Suggest to try and use only HydroBase variables ** generally this should be true for all non-evolution Hydro thorns that should only use HydroBase and ADMBase ** include this is thorn contribution guidelines maybe based on https://docs.einsteintoolkit.org/et-docs/Einstein_Toolkit_standards * ET one Mac requires specific version of gcc ** should provide information on expected error message if gcc does not match expectation ** shoudl provide instructions on how to fix this ** may want to auto-detect the correct one ** (possibly) we can use g++ (clang) with gfortran (see ticket by Steve in milestones) * unanswered questions ** http://lists.einsteintoolkit.org/pipermail/users/2018-July/006375.html should be responded to. Update instructions in tutorial wrt to "queuing system" in laptop. Helvi to respond. Yours, Roland -- 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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Reminder Weekly Users Call.
by Peter Diener 13 Jul '18

13 Jul '18

Hi All, This is just a reminder that next week's Users Call will take place at the usual time (at 10:00am US Eastern time) and the usual place (https://bluejeans.com/194244555). If you have any items for the agenda please add them to the wiki (https://docs.einsteintoolkit.org/et-docs/meeting_agenda#Meeting_Agenda) or send them to me (diener(a)cct.lsu.edu). Cheers, Peter

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Re: [Users] Users Digest, Vol 100, Issue 7
by Feyisso Sado 13 Jul '18

13 Jul '18

while build configuration sim I get the attached error in sim.out Please my dear help me!!!! *With Best Regards!!!* *-------------------------------------------------------------------* *Feyiso Sado Bedecha (PhD), Student* *Addis Ababa University, Department of Physics* *Cell Phone: +251910626090 <%2B251911089463>* *E-mail: bsfeyiso(a)gmail.com <bsfeyiso(a)gmail.com>* *P.O.Box: 1176* *Ethiopia* On Wed, Jul 11, 2018 at 8:00 PM, <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..." > > > Today's Topics: > > 1. Queuing system and parameter file scripts on personal machine > (Federico G Lopez Armengol) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 10 Jul 2018 17:24:46 -0300 > From: Federico G Lopez Armengol <fedelopezar(a)gmail.com> > Subject: [Users] Queuing system and parameter file scripts on personal > machine > To: users(a)einsteintoolkit.org > Message-ID: > <CAK3vroRxZbvF9+BePzYtoW2Z35E8rvxs4yO3VaNOR95N > 2bQNng(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I've been learning how to use the Toolkit for about a year. I've been > reading public documentation and running individual simulations on my > personal laptop. Now, I need to manage some set of simulations, and found > some trouble: > > 1) it seems that I do not have a queuing system. Each time I submit a > simulation, it starts running in parallel with previous ones and my laptop > quickly collapses. I configured simfactory with: > > ./simfactory/bin/sim setup-silent --optionlist=ubuntu.cfg --runscript > > debian.sh --submitscript debian.sub --runscript debian.sh > > > 2) I've tried some scripting with .rpar files, but failed. For instance, if > submitting: > > ./simfactory/bin/sim create-submit tov_multi --parfile par/tov.rpar > > > no error displays, but the simulation is inmediately finished with no > outputs. On the other hand, if running: > > ./simfactory/bin/sim create-run tov_multi --parfile par/tov.rpar > > > I get the following error: > > Error: Parameter file script > > '/home/fede/simulations/tov_multi/output-0000/tov.rpar' did not > generate a > > parameter file called '/home/fede/simulations/tov_ > multi/output-0000/tov.par' > > > I changed the name of the parameter file created as asked, but just the > last simulation of the script runs. I've tried this with every .rpar script > that is included on the Toolkit. > > I use Linux Mint 18.1 Serena. Thanks in advance! > > Federico >

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PeriodicCarpet question
by Yosef Zlochower 09 Jul '18

09 Jul '18

For periodiccarpet to work, is it necessary to demand that the upper and lower boundary widths are the same for boundaries not filled in via periodic BCs? This is enforced in periodic.cc on lines 493-496 for (int d = 0; d < dim; ++d) { assert(width[d] == width[d + 1]); stencil[d] = width[2 * d]; } Also, I think the test should be assert(width[2*d] == width[2*d + 1]);. -- Dr. Yosef Zlochower Center for Computational Relativity and Gravitation Associate Professor School of Mathematical Sciences Rochester Institute of Technology 85 Lomb Memorial Drive Rochester, NY 14623 Office:74-2067 Phone: +1 585-475-6103 yosef(a)astro.rit.edu CONFIDENTIALITY NOTE: The information transmitted, including attachments, is intended only for the person(s) or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and destroy any copies of this information.

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Users July 2018