Users

users@lists.einsteintoolkit.org

3 participants
3984 discussions

Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 05 Oct '20

05 Oct '20

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

1 0

Postdoc positions at Perimeter Institute
by Daniel Siegel 02 Oct '20

02 Oct '20

Dear all, The Strong Gravity Group at Perimeter Institute is inviting applications for Postdoctoral Research positions. Successful candidates will be part of the newly established Gravitational Waves Initiative (https://www.perimeterinstitute.ca/research/research-initiatives/gravitation… <https://www.perimeterinstitute.ca/research/research-initiatives/gravitation…>) that brings together expertise in analytical and numerical approaches to studying the nonlinear regime of gravity, data analysis for gravitational wave observations, relativistic astrophysics, and connections to particle physics and cosmology. Perimeter Institute offers a dynamic, multi-disciplinary environment with maximum research freedom and opportunity to collaborate. We welcome all candidates to apply by November 9, 2020 but applications will be considered until all positions are filled. For more information and to apply, please visit the Perimeter Postdoctoral Program 2021 website (https://www.perimeterinstitute.ca/about/careers/positions/perimeter-postdoc…). Best wishes, Daniel -- Daniel Siegel Assistant Professor Perimeter Institute for Theoretical Physics 31 Caroline St N Waterloo, ON Canada, N2L 2Y5 http://www.perimeterinstitute.ca/people/daniel-siegel

1 0

Meeting Minutes 2020-10-01
by Cupp, Samuel D. 01 Oct '20

01 Oct '20

Present: Beyhan, Samuel Cupp, Helvi Witek, Peter Diener, Kenneth Sible, Roland Haas, Steven Brandt, Alois Peter Schaffarczyk, Miguel Gracia, Zachariah Etienne, Maria Hamilton, Yosef E Zlochower Chair: Helvi Minutes: Samuel Chairs and minute takers for next two weeks were decided. 10/8 Meeting Chair: Steve Minute taker: Miguel 10/15 Meeting Chair: Peter Minute taker: Roland SPEC Benchmarks: The Einstein Toolkit submission to the SPEC benchmark was discussed again. The deadline for submission is February 21st, so the code should be submitted before this date. Since this submission date is soon after winter break, the code should be prepared for submission prior to the break if possible. Submission requires a standalone version of the code, which will likely consist of an ML_BSSN McLachlan code. Roland offered to create an Overleaf document with information on SPEC benchmark submission process, and he will send the link to the document to those on the call, so others can assist with preparation for submission. Erik Schnetter was previously submitted to SPEC, so he will be contacted to provide input on the Toolkit's previous submissions to this program. Moving off the Jenkins server: An intern at NCSA is working to port the testing features on Jenkins over to Github Actions. One goal is to move the continuous integration tests to an external system that does not require as much maintenance by Toolkit maintainers. Also, Github should not have the security issues that were present with the Jenkins server. The solutions to these issues prevented Jenkins from being easily accessible to anyone outside of NCSA, so moving to Github should allow the testing and testing results to be more publicly visible. Currently, the Github port can compile and run the tests. It also caches compiled code so compilation time is minimized. The demo page is available at https://mojamil.github.io/einsteintoolkit/. It currently has limited UI and presentability, as the first goal is ensuring functionality. Roland requested input for suggestions and feedback, especially about any features that are missing from the prior testing system or improvements that could be made. Helvi requested listing the unrunnable tests explicitly on the webpage. Roland explained the cause of most unrunnable tests and suggested adding a clickable UI to show details for those tests. Another future goal is to provide data from previous tests. The information about old test results is kept; it simply needs to be accessible via this interface. Upcoming release: The release still needs a release coordinator (7 weeks till release!). The individual release tasks have been itemized by Roland and Steve, but they haven't yet given estimates for the time commitment for each task. They aim to have this soon so that people will volunteer for these roles. Helvi offered some time and/or students for testing the new release. NRPyPN ticket 2417: This needs to be reviewed for the next release. Peter has begun the process of review and doesn't expect any major issues. Postdoc position announcement: Helvi announced a postdoc position with herself and Roland at University of Illinois at Urbana-Champaign. An official solicitation email is pending, and the solicitation is linked below. https://hyperspace.uni-frankfurt.de/2020/09/30/postdoctoral-postion-with-fo… User questions: Beyhan asked about an error occurring specifically with non-equal mass simulations. The error does not occur with equal mass. For these simulations, he is using McLachlan + GRHydro. At some point, the lapse goes negative, and this ends the simulation. Zach suggested setting the minimum lapse to a small positive value, though the default setting for this parameter is 0. He also suggested being more conservative with the trigger for adding refinement levels, as they may need to be introduced slightly sooner for accurate data. Another suggestion was to check if the horizon finder is the source of the error. If so, having the finder not search until further into the simulation may help. Interpolation early in the simulation may result in values which aren't a problem for the simulation but could cause errors in the horizon finder.

1 0

Stuck compiling dh.cc
by Chris Stevens 29 Sep '20

29 Sep '20

Hi everyone, I've managed to get this compiling and have just completed the example BBH run simulating the system of the first detection, however now that I have left it for a few weeks and come back, naturally nothing works. The error I now have is with MPI_UB and dh.cc when building through simfactory. I get the following output: In file included from /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dist.hh:12, from /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/vect.hh:13, from /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/bbox.hh:11, from /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:10: /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: In function ‘ompi_datatype_t* mpi_datatype(const dh::light_dboxes&)’: /opt/openmpi4/include/mpi.h:337:63: error: expected ‘}’ before ‘;’ token #define THIS_SYMBOL_WAS_REMOVED_IN_MPI30(symbol, new_symbol) 0; static_assert(0, #symbol " was removed in MPI-3.0. Use " #new_symbol " instead.") ^ /opt/openmpi4/include/mpi.h:1131:24: note: in expansion of macro ‘THIS_SYMBOL_WAS_REMOVED_IN_MPI30’ # define MPI_UB THIS_SYMBOL_WAS_REMOVED_IN_MPI30(MPI_UB, MPI_Type_create_resized); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2195:23: note: in expansion of macro ‘MPI_UB’ {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}}; ^~~~~~ /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2195:9: note: to match this ‘{’ {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}}; ^ In file included from /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dist.hh:12, from /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/vect.hh:13, from /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/bbox.hh:11, from /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:10: /opt/openmpi4/include/mpi.h:337:63: error: expected ‘}’ before ‘;’ token #define THIS_SYMBOL_WAS_REMOVED_IN_MPI30(symbol, new_symbol) 0; static_assert(0, #symbol " was removed in MPI-3.0. Use " #new_symbol " instead.") ^ /opt/openmpi4/include/mpi.h:1131:24: note: in expansion of macro ‘THIS_SYMBOL_WAS_REMOVED_IN_MPI30’ # define MPI_UB THIS_SYMBOL_WAS_REMOVED_IN_MPI30(MPI_UB, MPI_Type_create_resized); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2195:23: note: in expansion of macro ‘MPI_UB’ {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}}; ^~~~~~ /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2188:46: note: to match this ‘{’ dist::mpi_struct_descr_t const descr[] = { ^ In file included from /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dist.hh:12, from /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/vect.hh:13, from /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/bbox.hh:11, from /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:10: /opt/openmpi4/include/mpi.h:337:79: error: static assertion failed: MPI_UB was removed in MPI-3.0. Use MPI_Type_create_resized instead. #define THIS_SYMBOL_WAS_REMOVED_IN_MPI30(symbol, new_symbol) 0; static_assert(0, #symbol " was removed in MPI-3.0. Use " #new_symbol " instead.") ^ /opt/openmpi4/include/mpi.h:1131:24: note: in expansion of macro ‘THIS_SYMBOL_WAS_REMOVED_IN_MPI30’ # define MPI_UB THIS_SYMBOL_WAS_REMOVED_IN_MPI30(MPI_UB, MPI_Type_create_resized); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2195:23: note: in expansion of macro ‘MPI_UB’ {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}}; ^~~~~~ /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2195:29: error: expected primary-expression before ‘,’ token {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}}; ^ /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2188:36: warning: unused variable ‘descr’ [-Wunused-variable] dist::mpi_struct_descr_t const descr[] = { ^~~~~ /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2177:23: warning: unused variable ‘newtype’ [-Wunused-variable] static MPI_Datatype newtype; ^~~~~~~ /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2195:50: warning: no return statement in function returning non-void [-Wreturn-type] {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}}; ^ /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: At global scope: /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2197:5: error: ‘newtype’ does not name a type; did you mean ‘iswctype’? newtype = dist::create_mpi_datatype(sizeof descr / sizeof descr[0], descr, ^~~~~~~ iswctype /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2208:5: error: ‘initialised’ does not name a type; did you mean ‘MPI_Initialized’? initialised = true; ^~~~~~~~~~~ MPI_Initialized /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2209:3: error: expected declaration before ‘}’ token } ^ /maybehome/cstevens/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2177:23: warning: ‘newtype’ defined but not used [-Wunused-variable] static MPI_Datatype newtype; ^~~~~~~ make[3]: *** [/maybehome/cstevens/Cactus/configs/CTGD_Testing/config-data/make.config.rules:281: dh.cc.o] Error 1 make[2]: *** [/maybehome/cstevens/Cactus/lib/make/make.thornlib:113: make.checked] Error 2 make[1]: *** [/maybehome/cstevens/Cactus/lib/make/make.configuration:181: /maybehome/cstevens/Cactus/configs/CTGD_Testing/lib/libthorn_CarpetLib.a] Error 2 make: *** [Makefile:260: CTGD_Testing] Error 2 I did find the following thread: http://lists.einsteintoolkit.org/pipermail/users/2018-October/006566.html and I've done a clean compilation but same deal. I'm using OpenMPI 4.0.5 and gcc/g++ etc 8.3.1. I've confirmed which mpicc etc points to the right place, and what I think the relevant lines in the option list file are: CPPFLAGS = -DOMPI_SKIP_MPICXX FPPFLAGS = -traditional CFLAGS = -g3 -std=gnu11 -Wunused-variable CXXFLAGS = -g3 -std=gnu++11 -Wunused-variable F77FLAGS = -g3 -fcray-pointer -ffixed-line-length-none F90FLAGS = -g3 -fcray-pointer -ffixed-line-length-none# -Wextra -Wimplicit-interface#-fallow-argument-mismatch MPI_DIR = /opt/openmpi4/ MPI_LIB_DIRS = /opt/openmpi4/lib MPI_INC_DIRS = /opt/openmpi4/include MPI_LIBS = mpi open-rte open-pal I have added CPP = ... CXX = ... etc which point to the appropriate places. I also have cstevens@skynet:~/Cactus$ mpic++ --showme g++ -I/opt/openmpi4/include -pthread -Wl,-rpath -Wl,/opt/openmpi4/lib -Wl,--enable-new-dtags -L/opt/openmpi4/lib -lmpi Any help would be greatly appreciated. Thanks, Chris -- Dr Chris Stevens Postdoctoral Fellow Rm 310A Department of Mathematics and Statistics University of Otago Ph: +64 3 479 4567 http://www.chrisdoesmaths.com http://gravity.otago.ac.nz

3 2

Postdoctoral Positions in Computational Relativistic Astrophysics at Penn State
by Radice, David 29 Sep '20

29 Sep '20

The Department of Physics at The Pennsylvania State University is seeking to fill one postdoctoral scholar positions in computational relativistic astrophysics. The successful candidate will work on the development of a new numerical relativity code for neutron star mergers and supernovae in collaboration with David Radice. This position requires a Ph.D. in mathematics, physics, astronomy, or a closely related field. Applications must be submitted electronically at this url<https://psu.wd1.myworkdayjobs.com/PSU_Academic/job/University-Park-Campus/P…> and include a cover letter, a CV, and a statement of research interests. Applicants should arrange for three recommendation letters to be submitted to dur566(a)psu.edu<mailto:dur566@psu.edu> indicating the appropriate job number in the subject line. Applications received before December 1, 2020 will be given full consideration. The expected start date is September 1, 2021, although alternative start dates will also be considered. For more information, please visit https://www.gravity.psu.edu/. This is a fixed-term appointment funded for one year from date of hire with possibility of re-funding on a yearly basis for up to three years. CAMPUS SECURITY CRIME STATISTICS: For more about safety at Penn State, and to review the Annual Security Report which contains information about crime statistics and other safety and security matters, please go to http://www.police.psu.edu/clery, which will also provide you with detail on how to request a hard copy of the Annual Security Report. Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran status. Questions can be directed to Dr. David Radice (dur566(a)psu.edu<mailto:dur566@psu.edu>).

1 0

Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 28 Sep '20

28 Sep '20

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

1 0

Problem with the installation of the ET on the Marconi A3 machine
by Lorenzo Ennoggi 26 Sep '20

26 Sep '20

Dear ET users' support team, I'm new to the Einstein Toolkit and I'm experiencing an issue with the installation of the 2020 ET release on the Marconi A3 machine at CINECA, Italy. I'm using the 2017 Intel family compilers and libraries, as required in the /Cactus/simfactory/mdb/optionlists/marconiA3.cfg file. The installation seems to end up successfully, but running the "HelloWorld" test simulation results in errors related to the fact that GLIBCXX_3.4.21, needed by /simulations/HelloWorld/SIMFACTORY/exe/cactus_sim, is not found. In fact, the command strings /cineca/prod/opt/compilers/intel/pe-xe-2017/binary/inspector/lib64/libstdc++.so.6 | grep GLIBCXX gives the following output: GLIBCXX_3.4 GLIBCXX_3.4.1 GLIBCXX_3.4.2 GLIBCXX_3.4.3 GLIBCXX_3.4.4 GLIBCXX_3.4.5 GLIBCXX_3.4.6 GLIBCXX_3.4.7 GLIBCXX_3.4.8 GLIBCXX_3.4.9 GLIBCXX_3.4.10 GLIBCXX_3.4.11 GLIBCXX_3.4.12 GLIBCXX_3.4.13 GLIBCXX_3.4.14 GLIBCXX_3.4.15 GLIBCXX_3.4.16 GLIBCXX_3.4.17 GLIBCXX_3.4.18 GLIBCXX_3.4.19 GLIBCXX_3.4.20 GLIBCXX_FORCE_NEW GLIBCXX_DEBUG_MESSAGE_LENGTH 'GLIBCXX_3.4.21' does not appear. This version of GLIBCXX is only available within the 2019 and 2020 Intel families, but these are not compatible with many of the libraries needed by the ET and available on Marconi A3. What can I do to get the ET to work? The modules I have loaded on Marconi A3 are the following: 1) profile/base 2) profile/advanced 3) profile/archive 4) gnu/6.1.0 5) cmake/3.12.0 6) intel/pe-xe-2017--binary 7) intelmpi/2017--binary 8) zlib/1.2.8--gnu--6.1.0 9) szip/2.1--gnu--6.1.0 10) hdf5/1.8.17--intel--pe-xe-2017--binary 11) papi/5.7.1 12) git/2.17 13) hwloc/1.11.3--gnu--6.1.0 14) mkl/2017--binary 15) blas/3.6.0--intel--pe-xe-2017--binary 16) lapack/3.6.1--intel--pe-xe-2017--binary 17) gsl/2.2.1--intel--pe-xe-2017--binary 18) fftw/3.3.4--intelmpi--2017--binary 19) boost/1.61.0--intelmpi--2017--binary 20) python/3.6.4 The config-info file and a snapshot of the error messages generated by running the "HelloWorld" simulation are attached to the e-mail. Thanks in advance for your support. Best regards, Lorenzo Ennoggi

1 1

Postdoctoral positions in general relativistic magneto-hydrodynamics simulations at CCRG@RIT
by Carlos Lousto 25 Sep '20

25 Sep '20

As part of several NASA and NSF collaborative projects, RIT’s Center for Computational Relativity and Gravitation (CCRG) is currently seeking to fill one or two postdoctoral research positions with highly qualified individuals interested in pursuing research in the fields of numerical relativity, theoretical and computational astrophysics, with an emphasis on general relativistic magneto-hydrodynamics simulations. We are particularly interested in relativistic magneto-hydrodynamics simulations of accretion disks around supermassive black hole mergers, and binary neutron star coalescences from prior to merger through to the formation of disks and/or collapse of the merged remnant, the production of jets, and launching of outflows. We are also interested to perform “event-based” simulations, using parameters informed by specific LIGO/Virgo detections, and thereby permitting much closer comparison with observables, in order to interpret current and future multi-messenger observations by a wide array of current and future detectors. The group is involved in several large collaborations, including the LIGO Scientific Collaboration (LSC), The Einstein Toolkit Consortium (einsteintoolkit.org <http://einsteintoolkit.org/>) and a NASA Theoretical and Computational Astrophysics Network (TCAN) (compact-binaries.org <http://compact-binaries.org/>). CCRG researchers have access to several computing cluster facilities at national computing centers such as XSEDE and the TACC’s Frontera Supercomputer, as well as a dedicated over 3500-cores cluster and large storage pool hosted at the Center. The successful postdoctoral candidates will be Fellows of the “Frontier in Gravitational-Wave Astrophysics” (FGWA) Program hosted by CCRG (ccrg.rit.edu <http://ccrg.rit.edu/>) and our broader Institute of Astrophysics (aspire.rit.edu <http://aspire.rit.edu/>). Initially appointed for three years, the Fellows can renewable for up to five years depending on satisfactory performance and the availability of funds. Applications should consist of a cover letter, a brief statement of research interests, a curriculum vitae including publication list, and at least three letters of recommendation. All materials should be sent electronically as soon as possible to: manuela[AT]astro[dot]rit[dot]edu with a copy to ccrg-postdoc[AT]ccrg.rit.edu <http://ccrg.rit.edu/>. More information about the CCRG is available at http://ccrg.rit.edu/ <http://ccrg.rit.edu/>. And about Rochester at http://en.wikipedia.org/wiki/Rochester,_New_York <http://en.wikipedia.org/wiki/Rochester,_New_York> Please see the full advertisement at https://jobregister.aas.org/ad/7f61e5ff <https://jobregister.aas.org/ad/7f61e5ff>

1 0

Meeting Minutes 2020-09-24
by Hamilton, Maria 24 Sep '20

24 Sep '20

Present: Roland, Steve, Alois Peter, Liu, Sam, Zach, Ken, Helvi, Atul, Peter, Maria Chair: Peter Minutes: Maria Peter opened the meeting remarking that the agenda for Today is very short and asked if anybody wants to talk about things that are not currently on the agenda. There were three items added. 1. Maria mentioned failing to compile the development ETK version on OSX, while the stable version works just fine. Roland remarked that it might be a link problem and suggested compiling with j1, for a more explicit error output. 2. Zach reported new work done on the NRPy LaTeX interpreter, namely the Kronecker Delta is implemented now, which is very useful for coding the analytic metric. 3. Helvi announced that the Einstein Toolkit tutorial presented by Erik in the first week of the semester-long workshop at the ICERM was very well received and there is interest in having more tutorials like that, on a regular basis, while the workshop is running. Peter continued with the first urgent item on the agenda, namely the SPEC benchmark contribution. Steve admits that he did not do anything about it and will look into it, to see when the items are due. Helvi asked for clarifications on what exactly SPEC benchmark is, and Steve explained that it’s an acronym for Standard Performance Evaluation Corporation and there are a series of benchmarks to run based on science codes. Cactus ADM standard benchmark was given as an example. The next item on the agenda is the upcoming release planning. Roland emphasized that this is a serious issue, there are only two months until the planning release and there is not a lot of time, so things need to move along fast to get this going. First, everything that needs reviewed should be completed, then the release manager needs to be chosen, and he needs to come up with list of tasks to be executed. Roland and Steve would try to be released managers, since Yosef said no. Peter went on to the next item, the unanswered questions on the mailing list. Atul reported about the issue he is having with restarting simfactory, and the help he is getting from Erik. Helvi came up with very good suggestions that might fix the problem. Next item was open tickets, and Roland explained that there are only two big issues, related to Blas and OpenMPI, and a third one, related to the reduction interface. He and Steve will handle them. As the release date approaches, minor tickets and bug fixes will be addressed in the order of importance to the release. Lastly, Peter asked for chair and minutes taker for the next meeting. Helvi offered as chair, and Sam was encouraged to take minutes. The meeting adjourned. _______________________ 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

1 0

Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 21 Sep '20

21 Sep '20

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

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

Users