Users September 2019

users@lists.einsteintoolkit.org

21 participants
39 discussions

Failed installation
by Villani 25 Sep '19

25 Sep '19

I am trying to install Einstein ToolKit on my laptop following these instructions: https://nbviewer.jupyter.org/github/nds-org/jupyter-et/blob/master/CactusTu… but I run into errors when using the (last) command: ./simfactory/bin/sim build --mdbkey make'make -j2' --thornlist ../einsteintoolkit.th it seems that the computer cannot find the file ~/Cactus/configs/sim/config-data/make.thornlist what do I do?

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Fwd: Failed installation
by Haas, Roland 24 Sep '19

24 Sep '19

Begin forwarded message: Date: Tue, 24 Sep 2019 15:07:32 +0200 From: Villani <mattia.villani(a)uniurb.it> To: "Haas, Roland" <rhaas(a)illinois.edu> Subject: Re: [Users] Failed installation Thanks for the prompt answer. I did what you wrote, but I still get the same error. I am trying to install ET on a Ubuntu 16.04 machine, could it be a problem? Il 24/09/19 14:48, Haas, Roland ha scritto: > Hello Villani, > >> I am trying to install Einstein ToolKit on my laptop following these instructions: >> >> https://nbviewer.jupyter.org/github/nds-org/jupyter-et/blob/master/CactusTu… >> >> but I run into errors when using the (last) command: >> >> ./simfactory/bin/sim build --mdbkey make'make -j2' --thornlist ../einsteintoolkit.th >> >> it seems that the computer cannot find the file >> >> ~/Cactus/configs/sim/config-data/make.thornlist >> >> what do I do? > If you typed this in exactly as quoted, ie: > > ./simfactory/bin/sim build --mdbkey make'make -j2' ... > > > then please note that there should be a space " " between the "make" > and "'make -j2'" strings. Otherwise the shell will combine them. > > I would not have expected such a mistake to cause this kind of > behaviour though so that may well not be it. > > I am not quite sure what could have caused this other than maybe some > glitch on the file system. > > To check this I would try and start from scratch which you can do by > entering the following: > > !rm -r ~/Cactus/configs/sim > > into a cell and execute it. This completely removes the partially build > Cactus executable and you can start from scratch. > > 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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Fwd: Failed installation
by Haas, Roland 24 Sep '19

24 Sep '19

Begin forwarded message: Date: Tue, 24 Sep 2019 15:26:24 +0200 From: "Villani, Mattia" <mattia.villani(a)uniurb.it> To: "Haas, Roland" <rhaas(a)illinois.edu> Subject: Re: [Users] Failed installation I have tried everything you wrote, but nothing has changed. Il mar 24 set 2019, 15:23 Haas, Roland <rhaas(a)illinois.edu> ha scritto: > Hello Villani, > > > Thanks for the prompt answer. I did what you wrote, but I still get the > same error. > > > > I am trying to install ET on a Ubuntu 16.04 machine, could it be a > problem? > Ubuntu 16.04 should be find as we use that version as the base of our > tutorial server. > > Have you tried the > > !rm -r ~/Cactus/configs/sim > > line as well? It may be that after the first failed attempt, the build > is now in a strange state. > > Would you mind if I fowarded these emails to the mailing list as well > so that others now when / if the issue has been resolved? > > 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 . > -- 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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Question about GW150914 and other simulations
by 黎旭翔 19 Sep '19

19 Sep '19

Dear friends, We are trying to use those examples listed on the website to test if it works on our HPC. https://einsteintoolkit.org/gallery.html <https://einsteintoolkit.org/gallery.html> It goes well with a simple tov equation, which takes 2-5 min. But when we use it to simulate GW150914 BH merger or solve tov equation with high precision and long time, it seems that it will stop at an iteration point without any further output, even an error. What really confuses us is that for different tests it stops at different points. Could you please help us find out what goes wrong with the simulation? I will attach the log.txt and parameter files to this mail. Thanks for your time! Here we used a partition with 144 nodes. Sometimes with a specific —procs and —num-threads number in the shell file, the simulation finished successfully. In other time it came across the problem above. In the two neutron star output files, the job stoped at two different iteration points, and was cancelled due to time out or by hand. Yours, Xuxiang ————————————————————————————————————————————————————————— Xuxiang Li, School of Physics, Peking University Email: jukcoeng(a)pku.edu.cn <mailto:jukcoeng@pku.edu.cn>

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make <config>-utils failing with "RNS" error (ET_2019_03)
by Bernard Kelly 19 Sep '19

19 Sep '19

Hi. I have a working recent release of the ET (2019_03) that compiles & runs fine, but which fails when I try to build the associated utilities: --------------------- >make sim-utils Building utilities for sim make[1]: *** No rule to make target '/nobackupp2/bjkelly1/codes/Cactus/exe/sim/RNS', needed by 'utils'. Stop. Makefile:872: recipe for target 'sim-utils' failed --------------------- I'm left with about 50% of the utilities --- basically everything through "hdf5tobinary_slicer". But "hwloc-assembler" and all the other hwloc-related utilities haven't built. I have the ET_2018_03 release on the same machine, and that builds both the primary executable *and* all the utilities with no issues, even though the compilation options are identical between the two. Possibly relevant: (1) I don't know what the RNS refers to, but I am including the thorn GSFC_GRMHD_Initial/RNSID in my configuration (both old and new). (2) One difference between old and new configurations is that I'm not compiling CactusUtils/SystemTopology, as that gives me link-time errors with hwloc. Bernard -- ------------------------------------------------------------------ Bernard Kelly -- CRESST Assistant Research Scientist, NASA/GSFC Gravitational Astrophysics Laboratory --- Code 663 Phone: +1 (301) 286-7243 *** Fax: +1 (301) 286-2226 Web: http://science.gsfc.nasa.gov/sed/bio/bernard.j.kelly ORCID: orcid.org/0000-0002-3326-4454 ------------------------------------------------------------------

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meeting minutes for 2019-09-19
by Haas, Roland 19 Sep '19

19 Sep '19

Present: Bill, Chris, Helvi, Maria, Peter, Roland, Steve, Toni. Yosef, Yu Liu, Zach ET release: * Steve is reviewing Peter's self-force code, may open up ticket system in code repo * no one assigned yet to review Zach's Fishbone-Moncrief disk code, needs volunteer * DOI: proceed as planned * timeline for the release: freeze next week * name: Maria Goeppert Mayer (Physicist, Nobel prize 1963, 1972) KCL workshop review: * about 60 participants, 40 of them were new or beginning users * most slides are available on website, tutorials are in slack channel * video recordings of talks and lectures should be available in 1-2 weeks of time on Youtube * diverse topics from compact object mergers to exotic matter and mathematical topics * had a presentation by Niels Warburton on black hole perturbation theory * had fruitful discussion with GRChombo developers, plan to do code comparison project in the future * lessons learned: time for dedicated discussions was a bit short Unanswered questions: * for the manual topology issue Yosef will submit the patch that made things work for him, so that the issue is clearly spelled out * Steve provided some comments on http://lists.einsteintoolkit.org/pipermail/users/2019-August/006995.html based on his own experience with this, Yosef will forward to Carlos * http://lists.einsteintoolkit.org/pipermail/users/2019-September/007011.html * Steve suspects that http://lists.einsteintoolkit.org/pipermail/users/2019-September/007020.html may be caused by running out of memory and paging NRPy+ based BSSN code: * Zach has started to write a McLachlan equivalent BSSN code in NRPy+, and is making some progress as of the beginning of this week. Code is based on Lean so far. Will chat with Helvi about this. https://nbviewer.jupyter.org/github/zachetienne/nrpytutorial/blob/master/Tu… Gallery examples: * runners will be on DOI for this release only * BBH: Helvi et al. * Poisson: Helvi et al. * scalar wave: Helvi et al. * TOV: Helvi et al. * BNS: still an issue, originally assigned to Peter but would need help, will need to find an old ET release that produces the output shows on the gallery. Maria will try and help out with this. Ticket is: https://bitbucket.org/einsteintoolkit/tickets/issues/2119 Next week's call will be chaired by: Helvi 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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Re: [Users] HDF5 and submission/runtime issues on a PBS cluster
by Haas, Roland 19 Sep '19

19 Sep '19

Hello Vaishak, as usual, I would suggest addressing the mailing list. Would you mind if I forward this email to the list? Your point 3 sounds like either an incorrectly set-up cluster or (if this is a "private" cluster) missing passwordless ssh keys. I would contact your cluster administrators and show them the output of trying to run something like: mpirun -np 64 /usr/bin/hostname which tries to start 64 copies of the "hostname" command. Make sure that 64 is more cores than a single node can provide. Alternatively you can try and fix this yourself following for example https://www.open-mpi.org/faq/?category=rsh#ssh-keys but do leave the password blank (this implies you should only use this key-pair on the cluster and not do log into the cluster from the outside). Yours, Roland > Dear Sir, > > Thankyou very much for you reply. I will add the additional lines to > LDFLAGS and try. > > What do you think about the other issue point 3 in the document ? It looks > like simfactory is unable to login to more than one compute node on the > cluster. > > > I have an additional related questions. What is the variable 'LIBDIRS' used > for? > > > Thankyou for you support again > > Yours Sincerely > Vaishak > > On Fri, Sep 13, 2019 at 6:42 PM Haas, Roland <rhaas(a)illinois.edu> wrote: > > > Hello Vaishak, > > > > looking at you .ini and .cfg files you need to add extra options to > > make sure that the correct hdf5 libraries are found at runtime (not > > just at compile time). > > > > Often on clusters there will be "environment modules" that you should > > load to set the correct settings. The command to do so is the "module" > > command, which you can test using "module avail" and then add the > > correct "module load hdf5" command to the envsetup option in your ini > > file. Something like this: > > > > envsetup = <<EOT > > module load hdf5 > > EOF > > > > see eg the bluewaters.ini file in simfactory. > > > > If there are no modules or they don't work as expected or you would > > like to not use them, then you can also add the following bit to your > > LDFLAGS in your cfg file: > > > > -Wl,--rpath,/mnt/home/visitor/cvaishak/Installations/HDF5/hdf5-1.8.12/lib > > > > ie for each -L option that you have, add a "-Wl,--rpath," option (no > > space between the commas) to instruct the linker (-Wl) to add an RPATH > > (--rpath) value to the executable to tell it where to look for > > libraries at runtime. > > > > Yours, > > Roland > > > > > Dear all, > > > > > > I am herewith attaching a document ( etk_setup_errors) and some relevant > > > attachments concerning the issues I am facing in setting up ETK. > > > > > > I am looking forward to your help and support! > > > > > > > > > Thanks > > > > > > > > > > > -- > > 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 . > > > > -- 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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Postdoctoral position in numerical relativity at UIUC
by Witek, Helvi 16 Sep '19

16 Sep '19

Dear all, the Illinois Relativity Group (consisting of Professors Stuart Shapiro, Nico Yunes and, as of next January, myself as well as postdocs and PhD students) is opening a postdoctoral research position in numerical relativity and relativistic astrophysics. You can find more details below and here: https://hyperspace.uni-frankfurt.de/2019/09/04/postdoctoral-research-positi… We would appreciate it if you could circulate the information to interested candidates. Best wishes, Helvi ==== Postdoctoral Research Position in Numerical Relativity and Computational Astrophysics University of Illinois at Urbana-Champaign Applications are invited for a postdoctoral research position in the Illinois Relativity Group. The candidate should have expertise in numerical relativity and relativistic astrophysics. Some experience in computational hydrodynamics and/or computational MHD would be desirable. Applicants should go online at https://my.physics.illinois.edu/join/ to submit their application, which must include a cover letter, curriculum vitae, list of publications, brief description of research interests, and the names, mailing and email addresses of three references. Please contact Elisabeth Greifenkamp at greifenk(a)illinois.edu<mailto:greifenk@illinois.edu> if you have any questions. Applications should be posted by DEC 1, 2019 for full consideration. The starting date of the position is AUG 15, 2020. The successful applicant will join Professor Stuart Shapiro in developing and applying the tools of numerical relativity together with computational hydrodynamics, MHD, and/or stellar dynamics to tackle diverse problems in general relativity and astrophysics. Recent topics include the inspiral and coalescence of compact binaries, the generation of gravitational waves, magnetized neutron stars, magnetorotational stellar collapse, accretion onto isolated and binary black holes, the formation and cosmological growth of supermassive black holes in the early universe, and the dynamics of dark matter halos and spikes around black holes. Some of this work is geared to identifying astrophysically plausible, strong-field sources of gravitational waves and calculating gravitational waveforms detectable by LIGO/VIRGO, KAGRA, LISA and the PTA. For these “multimessenger” sources we are also exploring counterpart electromagnetic signals, including gamma-ray bursts and kilonovae, as well as neutrinos. In addition to Professor Shapiro, the Illinois Relativity Group includes Professors Nicolas Yunes and Helvi Witek, their postdocs, PhD and undergraduate research students. It maintains close interactions with UIUC colleagues in Physics, Astronomy and NCSA, in addition to several outside collaborators. The University of Illinois is an Affirmative Action/Equal Opportunity employer. -- =========================================== Dr. Helvi Witek Royal Society University Research Fellow Theoretical Particle Physics and Cosmology. Department of Physics King's College London ===========================================

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Error running nsns_test.par with file resu.d
by Atul Kedia 15 Sep '19

15 Sep '19

Hello, I am trying to do a test run with nsns_test.par from the default ETK package from directory /Cactus/repos/wvuthorns_diagnostics/NSNS_parameter_files/ and getting the following error: ERROR from host epycfe.crc.nd.edu process 1 while executing schedule bin HydroBase_Initial, routine Meudon_Bin_NS::Meudon_Bin_NS_initialise in thorn Meudon_Bin_NS, file /afs/ crc.nd.edu/user/i/isuh/astroph/Cactus/08132019/Cactus/configs/sim/build/Meu… : -> File "resu.d" does not exist. ABORTING cactus_sim: /afs/ crc.nd.edu/user/i/isuh/astroph/Cactus/08132019/Cactus/configs/sim/build/Car…: int Carpet::Abort(const cGH*, int): Assertion `0' failed. I obtained the file "resu.d" from http://astro.phys.wvu.edu/zetienne/resu.d but don't know where I should put the file. I think this is a Lorene data file (based on http://dspace-unipr.cineca.it/bitstream/1889/3328/1/Thesis_Maione.pdf). Does anyone know where to place it? Thank you, Atul Kedia, Physics Graduate student University of Notre Dame

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CarpetIOHDF5 recover failure with manual topology
by Yosef Zlochower 15 Sep '19

15 Sep '19

Hi, I have been trying to debug why some runs I was performing could not recover from a checkpoint file, but would otherwise proceed as normal. I attached a minimalist parfile showing the problem. A small grid is manually distributed over 8 processors and terminates at iteration 2. An attempt at recover fails with nans on grid::x. If the manual topology section is commented out, no problems are seen. -- 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 September 2019