Users April 2021

users@lists.einsteintoolkit.org

18 participants
33 discussions

Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 14 Apr '21

14 Apr '21

Hello, Please consider joining the weekly Einstein Toolkit phone call at 9:00 am US central time on Thursdays. For details on how to connect and what agenda items are to be discussed, use the link below. https://docs.einsteintoolkit.org/et-docs/Main_Page#Weekly_Users_Call --The Maintainers

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Need help building Einstein Toolkit: clang: error: unsupported option '-fopenmp'
by Murray Wolinsky 13 Apr '21

13 Apr '21

Hi All, Thanks so much for making the Einstein Toolkit software available! I'm using the CactusTutorial.ipynb that I got from your site. I'm trying to build ET on my 2015 Macbook Pro running OS 10.15.7. I'm stuck at the cell (after) *Building the Einstein Toolkit* . I modified that cell to get past issues with zlib . The cell now looks like: %%bash export ZLIB_DIR=/usr/local/opt/zlib/lib export LDFLAGS="-L/usr/local/opt/zlib/lib" export CPPFLAGS="-I/usr/local/opt/zlib/include" export PKG_CONFIG_PATH="/usr/local/opt/zlib/lib/pkgconfig" ./simfactory/bin/sim build -j2 --thornlist ../einsteintoolkit.th Running that cell eventually stops with the errors COMPILING CactusBase/CoordBase/src/Domain.c COMPILING configs/sim/bindings/build/ADMCoupling/cctk_ThornBindings.c clang: error: unsupported option '-fopenmp' make[3]: *** [Domain.c.o] Error 1 make[2]: *** [make.checked] Error 2 make[1]: *** [/Users/murray/Cactus/configs/sim/lib/libthorn_CoordBase.a] Error 2 make[1]: *** Waiting for unfinished jobs.... clang: error: unsupported option '-fopenmp' make[3]: *** [cctk_ThornBindings.c.o] Error 1 make[2]: *** [cctk_Bindings/make.checked] Error 2 make[1]: *** [/Users/murray/Cactus/configs/sim/lib/libthorn_ADMCoupling.a] Error 2 make: *** [sim] Error 2 Can you help? I'm confused by the error message coming from clang, since the ET seems to use gcc, but my attempt to force gcc, by including the exports below, made no difference: export CC=gcc-10 export CXX=gcc-10 I really appreciate any help you are able to provide! Thank you. Murray (Wolinsky) ______________________________________________________ Additional (likely irrelevant) notes: I used brew to install the prerequisites. It seemed to have gone more-or-less ok. Brew did issue a somewhat concerning message regarding hdf5: ==> Pouring hdf5-1.12.0_1.catalina.bottle.1.tar.gz Warning: hdf5 dependency gcc was built with a different C++ standard library (libstdc++ from clang). This may cause problems at runtime. But it didn't provide any guidance into fixing the potential problem. Itried brew reinstall hdf5 and brew no longer complains. I also had some issues with the subversion installation. But I don't think they're responsible for my current problem. Also, when I did the step *Configuring SimFactory for your machine*, I got the output: Here we will define some necessary Simulation Factory defaults. Determining local machine name: mw-3.local --------------------SUMMARY--------------------: [default] user = murray email = murray allocation = NO_ALLOCATION ------------------END SUMMARY------------------: Contents successfully written to /Users/murray/Cactus/repos/simfactory2/etc/defs.local.ini which looks OK, but the NO_ALLOCATION message seems like it might be of concern?

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3D Carpet component with one grid point along the z direction
by Gabriele Bozzola 13 Apr '21

13 Apr '21

Hello, one of my evolutions produced the attached file. What is interesting about this file is that refinement level 10 has a component that has shape (1, 53, 105). So, we have only one point along the z direction. I am not entirely sure how this came to be, but the problem is that the HDF5 attribute 'delta' reports a cell width of 0 along the z direction: In [12]: with h5py.File("alp.xyz.file_0.h5") as f: ...: print(f['ADMBASE::alp it=55296 tl=0 rl=10 c=0'].shape) (1, 53, 105) In [13]: with h5py.File("alp.xyz.file_0.h5") as f: ...: print(f['ADMBASE::alp it=55296 tl=0 rl=10 c=0'].attrs['delta']) [0.072 0.072 0. ] I would have expected the value of 0.072, even if the cell has only one grid point. Is this a bug? Thanks, Gabriele

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(virtual) ET school at UIUC 2021
by Roland Haas 13 Apr '21

13 Apr '21

Hello all, this year is UIUC's turn to organize a school and workshop for the ET. Given that COVID mandated safety measures still in place on campus and them not being lifted before fall semester (end of August) any such meeting will have to be virtual again. My plan would be to have a 1 week long school but each school day being only 3-4 hours long (say 8am US Central time to 1pm with a 35 minute break around 10am) which should allow students in the EU to join as well (8am Central being 3pm Central EU and 1pm being 8pm). The first order of business will be to find a week that is free of known competing meetings. As a first cut, please mark days that you know of a competing meeting in this document: https://docs.google.com/spreadsheets/d/1zNnN5kTh_X0_Le_UDCFbTlavOcjwLNh6pxR… Please all add conflicts that you are aware on by the time of the ET call this week (Thursday) so that a date can be decided on at that point. Please also forward suggestions for possible lecture topics and tutorials and interesting developments in and outside of the the ET you would like to hear about to me or any of the other maintainers. 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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Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 12 Apr '21

12 Apr '21

Please update the Wiki with agenda items for Thursday's meeting. Thanks! https://docs.einsteintoolkit.org/et-docs/meeting_agenda --The Maintainers

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Stopped making output
by Hee Il Kim 09 Apr '21

09 Apr '21

Hi, Though it might not be an issue of ET. Have you ever seen ET runs stopped making every output (even the stdout), even though the processes are running? I have seen this issue on new and old NVMe storages with various versions of OpenMPI. It happened in more than a day of runs. Oh, not all the processes are running. One process is in Dl state, so the every output stopped. Do you have any hints on this issue? There's no specific limits set for the files. The other write/read tasks on the disks are ok. Thanks for your help in advance. Hee Il

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Meeting Minutes 2021-04-08
by Steven Brandt 08 Apr '21

08 Apr '21

Present: Roland, Steve, Peter, Bill, Ken Sible, Indrani Banerjee, Miguel, Atul, Erik, Zach, Maria Chair: Peter Notes: Steve New machines added: deepbayou (db.hpc.lsu.edu) qb3 (qbc.loni.org) SPEC - GPL2 Release update POWER will be added Please verify your favorite machines in simfactory LORAINE vs LORAINE2 is an ongoing discussion. Which will be the default? Roland is putting together patches Roland started running testsuites and has uploaded the latest batch of results Maybe the hydro tests aren't the best? Please add tests to the testsuite. File names are machine__mpi_threads.txt. Results should be checked in to https://bitbucket.org/einsteintoolkit/testsuite_results Mailing list: User who can't login to the tutorial server was helped. Tickets: Peter looked at ticket 963 this week. Peter found that it affected performance dramatically. Test it out on the new McLachlan rewrite branch. The rewrite seems to not have the constraint damping terms. He suggests keeping the ticket open and considering putting these things into current master. Roland says he will put POWER into the master thornlist. It's just a single file. We have a cactus utilities repository that often refers to CVS, etc. Roland is cleaning up. Ticket 2516, different results for different number of cores. Peter says we should not forget about this one. Ken update on LaTex parser. BSSN tutorial notebook is finished. https://mybinder.org/v2/gh/zachetienne/nrpytutorial/HEAD?filepath=Tutorial-… https://www.youtube.com/watch?v=A9IWYpQe6Fo Parser was extracted from the root nrpy directory and will made availale through pip tomorrow. This should make it easier to use. Next week: Chair: Roland Minute Taker: Bill Two weeks: Chair: Bill Minute Taker: Atul

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Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 07 Apr '21

07 Apr '21

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Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 05 Apr '21

05 Apr '21

Please update the Wiki with agenda items for Thursday's meeting. Thanks! https://docs.einsteintoolkit.org/et-docs/meeting_agenda --The Maintainers

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Approved but can't log in.
by kkostaro＠physics.auth.gr 05 Apr '21

05 Apr '21

Hi there, I was just approved to use EinsteinToolkit . Trying to log in through https://cilogon.org/ , although my University, Aristotle University of Thessaloniki, is available in the drop down list it does say that I do not have the rights to enter. I guess the issue here is that i asked approval with the e-mail : kkostaro(a)physics.auth.gr and the login requests my kkostaro(a)auth.gr e-mail address. (Our uni provides us with 2 e-mail addresses one with and one without the 'physics' word). Could you please change my authorized address to kkostaro(a)auth.gr or guide me on how to log in with the already approved one? Thank you ! Kostaros Konstadinos

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Users April 2021