Users June 2021

users@lists.einsteintoolkit.org

19 participants
26 discussions

Re: [Users] problems compiling ETK on OSX Big Sur
by Hamilton, Maria 05 Jun '21

05 Jun '21

Roland, It looks like I'm seeing exactly the problem you resolved in the ticket you mentioned. Has it been backported? If not, will you please remind me how to do the pull request? In my notes I have something like this: 1. Change to the correct directory 2. git fetch origin 3. git fetch && git checkout origin/<patch> I am stuck at point 1: what is the correct directory for this pull? thanks, Maria _______________________ Maria C. Babiuc Hamilton, Ph.D. Professor, Department of Physics College of Science, Marshall University, 1 John Marshall Drive, Huntington, WV, 25755 Room S 257, Phone: (304)696-2754 ________________________________ From: Roland Haas Sent: Friday, June 4, 2021 3:26 PM To: Hamilton, Maria Cc: users(a)einsteintoolkit.org Subject: Re: [Users] problems compiling ETK on OSX Big Sur Hello Maria, > I've been trying to compile the new stable version of the ETK Lorentz > on osx Big Sur and I got all kinds of problems. This is x86 or M1? I could compile Lorentz fine on OSX BigSur (x86 in a VM) using both macports and homebrew. Note that both might have updated their default compilers (to gcc-11) since you last tried. The instructions to compile are in the jupyter notebook: https://github.com/nds-org/jupyter-et/blob/master/CactusTutorial.ipynb I just tried following those instructions on BigSur 11.4, HomeBrew, both freshly updated and things worked ok (taking into account the bugfix in https://bitbucket.org/einsteintoolkit/tickets/issues/2537/sim-setup-silent-… ). Here's my OS information and installed packages: % sw_vers ProductName: macOS ProductVersion: 11.4 BuildVersion: 20F71 % brew list --versions apr 1.7.0_2 apr-util 1.6.1_3 fftw 3.3.9_1 gcc 11.1.0_1 gettext 0.21 gmp 6.2.1 gsl 2.7 hdf5 1.12.0_4 hwloc 2.4.1 isl 0.24 jpeg 9d libevent 2.1.12 libmpc 1.2.1 lz4 1.9.3 mpfr 4.1.0 open-mpi 4.1.1_2 openssl(a)1.1 1.1.1k pkg-config 0.29.2_3 readline 8.1 sqlite 3.35.5 subversion 1.14.1_2 szip 2.1.1_1 utf8proc 2.6.1 zstd 1.5.0 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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problems compiling ETK on OSX Big Sur
by Hamilton, Maria 04 Jun '21

04 Jun '21

Hello, I've been trying to compile the new stable version of the ETK Lorentz on osx Big Sur and I got all kinds of problems. 1) using simfactory I get this error: ./simfactory/bin/sim setup-silent Error: value for key ppn in section BabiucMacBook15.local is not of required type int Aborting Simfactory 2) using make with gcc-11 I get this error: /Users/babiuc/ETKStable/Cactus/configs/ET/build/IOJpeg/JPEG.c:10:10: fatal error: jconfig.h: No such file or directory 10 | #include "jconfig.h" | ^~~~~~~~~~~ compilation terminated. 3) using make without any option I get this error: CST error 1: -> Configuration script for thorn PTHREADS returned exit code 1 Error message: 'Did not find PTHREADS' Not sure what happened, Things used to work really smooth! Maria _______________________ Maria C. Babiuc Hamilton, Ph.D. Professor, Department of Physics College of Science, Marshall University, 1 John Marshall Drive, Huntington, WV, 25755 Room S 257, Phone: (304)696-2754

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Inclusion of kuibit in the Einstein Toolkit
by Gabriele Bozzola 04 Jun '21

04 Jun '21

Hello, congratulations to the release team for the new version of the Einstein Toolkit! Looking forward, I would like to propose the inclusion of kuibit in the Einstein Toolkit. kuibit is a Python package for post-processing simulations. The tool comes with several features for analysis and visualization. For some of the most common operations (e.g., 2D plot of a grid variable, extraction of gravitational waves, ...), users can directly obtain the result without writing any code. The number of such ready-made scripts grows with every release of kuibit. For everything else, kuibit has a large number of features ( https://sbozzolo.github.io/kuibit/features.html) that can be used in scripts or notebooks. kuibit is designed to be user-friendly: it has rich documentation ( https://sbozzolo.github.io/kuibit/), examples ready to be used, and tutorials. kuibit is also designed to be developer- and maintainer- friendly: it is thoroughly commented, and it implements several continuous integration pipelines to test, document, and publish the package automatically. The high quality of kuibit is also recognized by its publication in the Journal of Open Source Software (https://joss.theoj.org/papers/10.21105/joss.03099). kuibit is largely inspired by Wolfgang Kastaun's PyCactus. kuibit shares the same overall design with PyCactus, and in some cases, the implementation details too. kuibit would not exist without PyCactus. As far as I know, 5-10 people are actively using kuibit as their main tool to interface with the output of simulations. The feedback I got is overwhelmingly positive: users that are new to the Einstein Toolkit praise the simplicity of use and the comfort of working in Python; experienced users claim that kuibit allows them to focus on the science instead of the technical details. The next release of the Einstein Toolkit is far in the future, so there is time to incorporate any feedback/suggestion that the community might have. I will be happy to work towards the goal of including kuibit in the Einstein Toolkit. kuibit repo: https://github.com/Sbozzolo/kuibit Best, Gabriele

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Meeting Minutes 2021-06-03
by Miguel Gracia 03 Jun '21

03 Jun '21

Present: Bruno G., Peter D., Miguel G., Roland H., Steven B., Zach E., Atul K., Yosef Z., William G., Leonardo W, Maria H. Chair: Steven B. Minutes: Miguel G. * Latest release discussion. Gallery examples: [Atul] Tested the BNS gallery example after release and he experienced an error (Ticket #2176), seems to be a problem with simfactory python script, he will investigate more about the source of the error. [Roland] BBH gallery example webpage is missing the date the gallery was tested. Other: [Zach] Created some documentation about tasks that the release coordinator should follow. This should improve the next release process. Zach pointed out that only Steve has access to Zenodo, and Roland is the only one that has access to the release repositories. These make things a little more complicated for the release coordinator. * SPEC benchmark contribution no updates. * Other comments: Cactus.org<http://Cactus.org> has a certificate problem. Roland is going to run some tests and try to fix the Cactus website and mailing list problems. * Tickets/unanswered questions: No discussion. * Future chair and minute taker June 17th Chair: Roland H. Minutes: William G — end of the meeting

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Re: [Users] Compiling on DiRAC DIaL
by Elley, Matthew 03 Jun '21

03 Jun '21

Hi Roland, both of your suggestions worked, thanks! Matt ________________________________ From: Roland Haas Sent: Wednesday, May 19, 2021 6:31 PM To: Elley, Matthew Cc: users(a)einsteintoolkit.org Subject: Re: [Users] Compiling on DiRAC DIaL Hello Matt, > Cactus/arrangements/ExternalLibraries/PAPI/src/stats.c(20): catastrophic error: cannot open source file "papi.h" > #include <papi.h> > > I cannot find the header file anywhere (i.e. in ET or /usr/include) > so I am not sure how to proceed. Is PAPI a necessary library for ET > function? If you use PAPI_DIR=BUILD to make Cactus build PAPI itself (which you seem to do) then it will install the created PAPI library to Cactus/configs/ET_dirac/scratch/external/PAPI and the include file would be there. Cactus at that point should set up a include search path to find files there, which you can check in: Cactus/configs/ET_dirac/bindings/Configuration/Capabilities/make.PAPI.defn > Compiling with it excluded from the thornlist gives me > > /usr/bin/ld: cannot find -lsz > make[1]: *** > [/lustre/dirac/home/dc-elle1/ET/Cactus/exe/cactus_ET_dirac] Error 1 > > which I am not sure is connected as I am compiling from scratch. That one I suspect is actually being pulled in by HDF5 which can use the sz library but I have seen systems (Windows using MSYS admittedly) where the sz library was called szip. The actual line that cases the failure is probably this one: https://github.com/EinsteinToolkit/ExternalLibraries-HDF5/blob/abf8dbf78e76… You could try two things to avoid this: 1. build your own HDF5 by setting HDF5_DIR=BUILD 2. find out where libsz.so or libsz.a are located (by using he "module show" command on the HDF5 module or asking the admins) and adding that directory to HDF5_LIB_DIRS Please see https://www.einsteintoolkit.org/thornguide/ExternalLibraries/HDF5/documenta… and https://www.einsteintoolkit.org/usersguide/UsersGuide.html#x1-21000B2.2 for details on these option list variables. Yours, Roland > > Thanks, > > Matt > -- 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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Postdoc position in computational astrophysics
by Agnieszka Janiuk 01 Jun '21

01 Jun '21

Dear colleagues, I am looking for a postdoctoral researcher working in the area of computational astrophysics. The main focus of the planned research is on collapsing massive stars and gamma ray bursts engines. The post-doc will contribute to our group projects related to the Kerr metric evolution in collapsars, with constraints imposed by the realistic models of the stellar structure. The position will be for 3 years. The starting date is negotiable, and funding is available immediately. Planned starting date can be in October 2021. The formal job advertisement has been put on AAS Job register and on the EAS website. Please forward this email to anybody who you think might be interested! Contact address for further questions: agnes @ cft.edu.pl regards Agnieszka Janiuk -- -- prof. dr hab. Agnieszka Janiuk | tel. +48 22 116 20 06 Center for Theoretical Physics | fax. +48 22 843 13 69 Polish Academy of Sciences | www: http://www.cft.edu.pl/astrofizyka Al. Lotnikow 32/46 | 02-668 Warsaw, Poland |

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Users June 2021