Users October 2019

users@lists.einsteintoolkit.org

19 participants
28 discussions

Stop MoL after tolerance is reached
by Erik Rodrígo Jiménez Vázquez 22 Oct '19

22 Oct '19

Dear all I'm trying to construct Brill wave initial data by transforming the elliptic pde equation for the conformal factor in to a wave-like equation with a source. After reaching a stationary state, I want to stop the evolution and give the stationary state as an initial data for the BSSN system. I'm evolving the wave-like equation with MoL and my question is, How can I stop the MoL evolution if the solution reaches the numerical tolerance and then pass it as initial data? Erik

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meeting minutes for 2019-10-17
by Haas, Roland 17 Oct '19

17 Oct '19

Present: Bill, Chris, Erik, Maria, Peter, Philipp, Roland, Steve, Yosef, Zach ET release * scheduled for Oct 27th * BBH, Poisson equation still in the works * BNS, needs to be re-run. Maria and Roland will do so, Roland to push fixes in pull requests needed * testsuite status: no unexpected failures * Fishbone-Moncrief disk: reviewed acceptable * Self-Force code: ** Peter fixed scons 2.7 issue ** serial build only so far due to scons limitation ** consider (based on suggestion by Barry Wardell) to include scon copy in repository ** changes to be done before deep-freeze ** would be happy to have second person look at it * blocker tickets: ** Roland to push assuming he tested them * ICERM meeting ** should into this, still a bit out since it only starts 1 year from now * https://bitbucket.org/einsteintoolkit/tickets/issues/1371/ needs reviewing, other milestone tickets are old, or coincide with "blockers" or gallery tests. Roles: * try and rotate roles, so as to not rely on the same persons. Eg leading the meeting, taking notes 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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compilation fails on SuperMUC due to a missing link to library
by Ficarra, Giuseppe 11 Oct '19

11 Oct '19

Dear all, I am trying to compile the Einstein Toolkit on SuperMUC-NG and I get the following error at the very end of the compilation: -------------------------------------------------------------------- ld: warning: libpsm_infinipath.so.1, needed by /usr/lib64/libfabric.so.1, not found (try using -rpath or -rpath-link) fatal: bad revision 'HEAD' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_ep_num_devunits' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_init' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_ep_connect' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_epaddr_getctxt' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_error_get_string' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_mq_send' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_am_get_parameters' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_mq_cancel' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_finalize' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_mq_test' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_mq_finalize' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_epaddr_setctxt' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_mq_init' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_mq_ipeek' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_mq_irecv' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_ep_open' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_am_request_short' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_error_register_handler' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_ep_epid_lookup' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_ep_open_opts_get_defaults' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_am_reply_short' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_ep_close' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_mq_iprobe' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_mq_isend' ld: /usr/lib64/libfabric.so.1: undefined reference to `psm_am_register_handlers' make[1]: *** [/dss/dsshome1/00/di39wog2/EinsteinToolkit/Cactus/exe/cactus_ET_SUPERMUC_NG] Error 1 make: *** [ET_SUPERMUC_NG] Error 2 ------------------------------------------------------------------------- I have tried to link this library using its path on the cluster in the configuration script as: ———————————————————————— LDFLAGS = -rdynamic -xCORE-AVX2 -Wl,--rpath,-L/usr/lib64/psm2-compat/libpsm_infinipath.so.1 ———————————————————————— Unfortunately I have not much experience in linking libraries so I hope someone can help me with this. I attach log files and configurations script so you can cross-check. Regards, Giuseppe

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meeting minutes for 2019-10-10
by Haas, Roland 10 Oct '19

10 Oct '19

Present: Bill, Chris, Maria, Roland, Yosef, Zach upcoming ET release Timeline: https://docs.einsteintoolkit.org/et-docs/Release_Details * gallery examples other than BNS ** all assigned to Helvi's group, who are working on them * BNS gallery example ** Zach had a look at results, agrees that it is likely as good as we can expect ** has seems similar unpredictable behaviour wrt to the number of oscillations observed in his own runs, can be a numerical issue given the resolution used * status of test suites ** no new unexplained failures since last release (CT_MultiLevel only) ** can compile on MacPorts again, seem to be able to compile on HomeBrew * status of Fishbone-Moncrief disk thorn ** Zach and Steve working on getting thorn ready for inclusion * status of self-force code ** no updates since Peter and Steve are not on call * suggestion to provide docker image for ET release ** would opt for fully compiled ** have einsteintoolkit docker organization ** do not aim for cluster support ** would need portable instructions on how to run with parfile living outside of container and write data to location outside of container (need at least OSX, Linux, Windows) ** an alternative would be a purely static executable, which is not always easy to produce * testing OSX Catalina, which is not yet supported by MacPorts ** no official support yet, will try and see what happens if one uses Mojava version CarpetIOHDF5 recover failure with manual topology * Yosef made patch available * needs to be looked at to check if this is the correct way to fix it running BNS example * Maria will re-run with extra debug output for RotatingSymmetry180 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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Unsubscribe from mailing list
by Sinead Mannion 09 Oct '19

09 Oct '19

Hello, Could I please unsubscribe from mailing list please for einsteinstoolkit.org<http://einsteinstoolkit.org>. Kind regards, Sinéad

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Possible performance issue
by Vaishak P 09 Oct '19

09 Oct '19

Dear All, I am running the simulation GW150914 using the parameter file available at the ETK gallery at (GW150914-ETK gallery <https://einsteintoolkit.org/gallery/bbh/index.html>) using 128 cores. Each compute node consists of 2 X 16 Cores Intel SkyLake ( Intel(R) Xeon(R) Gold 6142 CPU @ 2.60GHz) and 384 GB RAM . I have compiled and am running Einstein Toolkit without OpenMP and using mpich-3.3.1. The issue is that the simulation seems to be running at a very slow pace. The number of physical time per hour that it is completing is only about 1.3 units. At this rate to complete 1700 units, it would take about 54 days, in contrast to 2.8 days on (Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz) as per the details at the example run of GW150914 available at the gallery (GW150914-ETK gallery <https://einsteintoolkit.org/gallery/bbh/index.html>). I have also tried using intel mpi (impi) but with simular results. I am also attaching the out file from the simulation. Looking forward to your inputs. Thanks and regards, Vaishak P PhD Scholar, Shyama Prasad Mukherjee Fellow Inter-University Center for Astronomy and Astrophysics (IUCAA) Pune, India

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Postdoctoral Fellow in Numerical Relativity at WVU
by Zach Etienne 09 Oct '19

09 Oct '19

Dear friends, The Department of Physics & Astronomy at West Virginia University is seeking applications for a Postdoctoral Fellow in the field of Computational Relativistic Astrophysics/Numerical Relativity. The successful candidate will: * Develop next-generation numerical relativity software. * Perform state-of-the-art simulations; analyze and visualize simulation data; and write scientific papers summarizing work. * Work with a multi-institution network of collaborators on a variety of numerical relativity projects such as: - Supercomputer simulations of magnetized binary neutron star mergers with IllinoisGRMHD (https://illinoisgrmhd.net) and realistic equations of state. - A volunteer-computing project called BlackHoles@Home ( https://blackholesathome.net), which is aimed at unlocking the consumer-grade desktop computer as a core tool for numerical relativity simulations of black holes and black hole binaries. The preferred start date is August 15, 2020, though earlier start dates are acceptable. This position may be renewed in annualized increments for up to three years, contingent upon performance, need, and funding. The screening process will begin on December 15, 2019 and will continue until the position is filled. *To apply, please use the following link: * *https://wvu.taleo.net/careersection/wvu_research/jobdetail.ftl?job=13139* <https://wvu.taleo.net/careersection/wvu_research/jobdetail.ftl?job=13139> Any questions about this position should be directed to me via email, at *zbetienne *at* mail.wvu.edu <http://mail.wvu.edu>* -={ *Qualifications* }=- * Ph.D. in Physics or a related field required. * Strong programming skills (C and Python, or closely related languages). * Experience in high-performance computing and large-scale data analysis. * Excellent ability to communicate research to both experts and non-experts. -={ *Requirements* }=- * CV * Cover letter * Three letters of recommendation West Virginia University Research Corporation is an Equal Opportunity/Affirmative Action Employer. The Corporation values diversity among its employees and invites applications from all qualified individuals, including minorities, females, individuals with disabilities and veterans. -Zach * * * Prof. Zachariah Etienne Physics & Astronomy Dept. West Virginia University http://astro.phys.wvu.edu/zetienne/ http://blackholesathome.net <https://blackholesathome.net>

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Err logs like "[83bdcfc58a2e:19025] Read -1, expected 4096, errno = 1" when running ET.
by ZhiChao Zhao 09 Oct '19

09 Oct '19

Hello everyone, I am trying to write a par file and run it. I use simfactory and the command is : > ./simfactory/bin/sim create-submit bnstest --procs=28 --num-threads=2 > --parfile=./my_par/bnstest.par I am workiing on a PC computer with ubuntu (in fact, is a ubuntu docker in a PC computer with host OS centos). This pc has two cpus. Each cpu has 28 cores. I found there are so much error logs: > + date +%s > + export CACTUS_STARTTIME=1567761511 > + [ 14 = 1 ] > + mpirun -np 14 /home/zhaozc/simulations/bnstest/SIMFACTORY/exe/cactus_sim > -L 3 /home/zhaozc/simulations/bnstest /output-0000/bnstest.par > [83bdcfc58a2e:19025] Read -1, expected 4096, errno = 1 > [83bdcfc58a2e:19027] Read -1, expected 4096, errno = 1 > [83bdcfc58a2e:19029] Read -1, expected 4096, errno = 1 > [83bdcfc58a2e:19024] Read -1, expected 4096, errno = 1 > [83bdcfc58a2e:19026] Read -1, expected 4096, errno = 1 > [83bdcfc58a2e:19028] Read -1, expected 4096, errno = 1 > [83bdcfc58a2e:19032] Read -1, expected 4096, errno = 1 > [83bdcfc58a2e:19034] Read -1, expected 4096, errno = 1 > [83bdcfc58a2e:19036] Read -1, expected 4096, errno = 1 > [83bdcfc58a2e:19030] Read -1, expected 4096, errno = 1 > [83bdcfc58a2e:19023] Read -1, expected 4096, errno = 1 ...... but those errors will not terminate the task. Is it safe to ignore those errors?

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compilation fails on supermuc-ng due to hdf5 library
by Ficarra, Giuseppe 08 Oct '19

08 Oct '19

Hi all, I am trying to compile the Einstein toolkit on the SuperMUC-NG cluster but I am having some issues with the HDF5 libraries and I don’t understand whether it is a problem of the cluster itself or if there is any workaround that maybe some of you know. I first this warning message when the CST is running on the HDF5 section: ******************************************************************************** Running configuration script for thorn HDF5: Additional requested language support: Fortran WARNING in HDF5 configuration: None of H5pubconf.h H5pubconf-64.h H5pubconf-32.h found in Automatic detection of szip/zlib compression not possible Finished running configuration script for thorn HDF5. Checking consistency... Creating Thorn-Flesh bindings... Creating implementation bindings... Creating parameter bindings... Creating variable bindings... Creating schedule bindings... Creating function bindings... CST finished. ******************************************************************************** Then the compilation goes on until it fails when there’s the first call to the HDF5 library: ******************************************************************************** dss/dsshome1/00/di39wog2/EinsteinToolkit/Cactus/arrangements/EinsteinAnalysis/AHFinderDirect/src/patch/patch_system.cc<http://patch_system.cc>(87): catastrophic error: cannot open source file "hdf5.h" # include <hdf5.h> ^ /dss/dsshome1/00/di39wog2/EinsteinToolkit/Cactus/arrangements/EinsteinAnalysis/AHFinderDirect/src/patch/patch_system.cc<http://patch_system.cc>(87): catastrophic error: cannot open source file "hdf5.h" # include <hdf5.h> ^ compilation aborted for /dss/dsshome1/00/di39wog2/EinsteinToolkit/Cactus/configs/ET_SUPERMUC_NG/build/AHFinderDirect/patch/patch_system.cc<http://patch_system.cc> (code 4) make[3]: *** [patch_system.cc.o] Error 4 make[2]: *** [patch/make.checked] Error 2 make[1]: *** [/dss/dsshome1/00/di39wog2/EinsteinToolkit/Cactus/configs/ET_SUPERMUC_NG/lib/libthorn_AHFinderDirect.a] Error 2 make: *** [ET_SUPERMUC_NG] Error 2 ******************************************************************************** I attach here both log and error file of the compilation and my configuration script if you need it. I have already tried every possible hdf5 module they have on the cluster. They all lead to the same exact error. Please let me know if anything else is needed. Best regards, Giuseppe

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LSU ETK meeting
by Steven R. Brandt 08 Oct '19

08 Oct '19

So I've been looking into dates which can be used for the LSU ETK workshop. Due to various summer camps, the logical dates are either May 25-29 or Aug 3-7. Does anyone have a preference for one set of dates over the other? Thanks. --Steve

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Users October 2019