Users October 2020

users@lists.einsteintoolkit.org

18 participants
23 discussions

Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 19 Oct '20

19 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

Setting procs
by Robert Kopp 19 Oct '20

19 Oct '20

I have run CactusTutorial.ipynb and obtained output for Hello World. However, when the characteristics of my computer (i9-7940X) were guessed, apparently something went wrong. I obtained the following output: Warning: Too many threads per process specified: specified num-threads=14 (ppn-used is 14)Warning: Total number of threads and number of threads per process are inconsistent: procs=1, num-threads=14 (procs*num-smt must be an integer multiple of num-threads)Warning: Total number of threads and number of cores per node are inconsistent: procs=1, ppn-used=14 (procs must be an integer multiple of ppn-used)+ set -e+ cd /home/robert/simulations/helloworld/output-0000-active+ echo Checking:+ pwd+ hostname+ date+ echo Environment:+ export CACTUS_NUM_PROCS=1+ export CACTUS_NUM_THREADS=14+ export GMON_OUT_PREFIX=gmon.out+ export OMP_NUM_THREADS=14 I can reduce the number of threads, but I'd rather not. I don't know enough yet about how this software works to set procs, though: it is not explicitly mentioned as such in the machine database. How would I do this?

2 2

Poisson equation
by Taishi Ikeda 17 Oct '20

17 Oct '20

Dear all Hello, I’m a user of EinsteinToolkit. Now, I’m trying to solve Poisson's equation using ctthorn as initial data before time evolution on EinsteinToolkit. The boundary condition is 1/r. I already implemented my thorns for the source term of the equation, and solved the equation using "CT_MutiLevel”. I checked if the final solution is real solution of the original equation, but it is not good solution. I changed the resolution, but it is not improved. So, I may misunderstand how to use CT_MutiLevel thorns, and I have questions relate to "CT_MutiLevel" : 1) In order to understand correct behavior, I want to try test simulation using poisson.par, which is one of the example parameter file. But, it does not work. The output told me the grid structure is inconsistent, and I also try another example, but it also has same error. Are there other available par file for CT_MutiLevel ? 2) To solve the elliptic equation with 1/r boundary condition, is CT_MutiLevel the best way ? If there are another thorn to solve elliptic equation in EinsteinToolkit, let me know. Since I want to use Carpet, the thorn should be compatible with Carpet. 3) After solving elliptic equation, I want to solve time evolution. Since CT_MutiLevel is a solver using MultiGrid method, we must prepare several Carpet grids on whole domain. But, is it consist with time evolution ? If there is an example par file, let me know. Best. Taishi. ************************************ Taishi Ikeda Physics Department Sapienza University of Rome (Italy) taishi.ikeda(a)uniroma1.it ************************************ -- ________________________________________________________ Le informazioni contenute in questo messaggio di posta elettronica sono strettamente riservate e indirizzate esclusivamente al destinatario. Si prega di non leggere, fare copia, inoltrare a terzi o conservare tale messaggio se non si è il legittimo destinatario dello stesso. Qualora tale messaggio sia stato ricevuto per errore, si prega di restituirlo al mittente e di cancellarlo permanentemente dal proprio computer. The information contained in this e mail message is strictly confidential and intended for the use of the addressee only. If you are not the intended recipient, please do not read, copy, forward or store it on your computer. If you have received the message in error, please forward it back to the sender and delete it permanently from your computer system. --

2 2

meeting minutes for 2020-10-15
by Roland Haas 15 Oct '20

15 Oct '20

Present: Roland, Peter D, Steve, Sam, Peter S., Bill, Yosef, Zach, Maria, Atul ICERM tutorial: * Steve, could need help for 2pm EDT session today. Transition cactuscode to GitHub pages * request to LSU DNS amdins sent by Steve * paperwork needed for this to happen Release planning: * Steve created release timeline * Roland started testing on clusters, no (major) unexpected failures. Steve will add Roland to new LSU allocations for QB and Mike/Shelob. ** CT_MultiLevel/boostedpuncture test fails on most clusters ** twopunctures test is failing on many clusters but is new * Roland will update long timeline plan to reflect 2 weeks of feature freeze but starting testing on clusters 1 month before NRPY_PN: * reviewed by Peter * Roland had some comments about not being able to find all information looking for inclusion vote in the ticket * Zach mentioned validation tests in NRPyPN which is tested in Travis right now, could be incorporated to Jenkins * Zach and Roland will work on GetComponents setup (if possible), add to ET repos * plan to have inclusion vote 2 weeks from now Questions: * CT_MultiLevel question http://lists.einsteintoolkit.org/pipermail/users/2020-October/007633.html no one on call is very familiar with CT_MutliLevel. Roland says that 1/r boundary conditions are not currently supported by CT_MultLevel Will try and ping Eloisa. * Cartoon2D/Carpet question http://lists.einsteintoolkit.org/pipermail/users/2020-September/007609.html not clear what is causing this. Peter might have some time to look at it. Open tickets: * no noteworthy tickets * Roland will poke those who were poked before about tickets whose content is ready to be included 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 .

1 0

Poisson equation
by Taishi Ikeda 15 Oct '20

15 Oct '20

1 0

Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 12 Oct '20

12 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

Einstein Toolkit at ICERM 2020 Fall workshop, October 15th
by Roland Haas 12 Oct '20

12 Oct '20

Hello all, Due to popular demand, there will be an Einstein Toolkit tutorial part II on Thursday, October 15th with the following schedule: (12 - 2 EDT) NRPy+ (Zach Etienne). NRPy+ is an open-source Python code that converts expressions written in Einstein-like notation into highly optimized C/C++ code, using the powerful computer algebra package SymPy as a backend. The NRPy+ tutorial will review a number of interactive Jupyter notebooks, which use NRPy+ to generate both small, efficient standalone NR codes and useful Einstein Toolkit thorns. A new, in-progress LaTeX interpreter interface for NRPy+ will also be briefly introduced, whereby tensorial equations pasted into NRPy+ from LaTeX paper source can be directly converted into SymPy symbolic expressions, which can then be converted into C/C++/Mathematica codes. (2:15 - 4 EDT) Writing your own Einstein Toolkit thorns (Steve Brandt). This tutorial will show you how to extend the Einstein Toolkit by writing your own thorns. Jupyter notebooks will cover the wave and heat equations. This tutorial requires an RSVP so the tutorial runners can adequately prepare the necessary computational resources. Please complete this form if you intend to attend any part of this tutorial. https://forms.gle/7MFap2kkhzJYQEbg7 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 .

1 0

Reg. HDF5 output of QuasiLocalMeasures variables part II
by Vaishak P 11 Oct '20

11 Oct '20

Dear All, This is regarding the output of QuasiLocalMeasures variables in HDF5 format in a BBH simulation similar to the gallery one. I am unable to output QLM data in HDF5 format using the "IOHDF5:out_vars" option for this run. I had previously opened a ticket at https://bitbucket.org/einsteintoolkit/tickets/issues/2451 where the issue is related to using "IOHDF5:out2d_vars" (and out_1dvars), which is now fixed. Please note that I am not facing this issue with "qlm-ks-outvars.par" test case (details in the above ticket). This issue is only with the gallery run. Also, I only face this issue when I request any QuasiLocalMeasures variables to be output using "IOHDF5:out_vars" option. I I am attaching the par files, the er and out files and the backtrace from one of the procs. The error is : *'std::out_of_range' what(): vector::_M_range_check: __n (which is 0) >= this->size() (which is 0)* Thanking you in anticipation -- P. Vaishak PhD Scholar, Shyama Prasad Mukherjee Fellow Inter-University Center for Astronomy and Astrophysics (IUCAA) Pune, India

3 3

TmunuBase requires Exact thorn in ET_2020_05?
by Bernard Kelly 11 Oct '20

11 Oct '20

Hi. I just did a fresh download of the latest stable release, "Turing" (ET_2020_05), and during an initial minimal compile, I had a failure during the "parsing schedule files" stage -- see below. Should EinsteinBase::TmunuBase be requiring EinsteinInitialData::Exact? It doesn't show up in the dependencies of TmunuBase, I don't recall it being true in previous releases, and I don't normally compile Exact. (More generally, should *any* thorn in EinsteinBase depend on other Einstein***** arrangements?) Thanks, Bernard ---------- error output below ------ ******************************************************************************** Running configuration script for thorn HDF5: Additional requested language support: Fortran HDF5 selected, but HDF5_DIR not set. Checking pkg-config ... HDF5 not found. Checking standard paths ... HDF5 not found. Using bundled HDF5... 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... CST error in /gpfsm/dnb31/bjkelly1/codes/Cactus/repos/flesh/lib/sbin/CreateScheduleBindings.pl (at 819) -> Schedule error: Thorn TmunuBase - group exact::Exact_pars_real doesn't exist. CST error in /gpfsm/dnb31/bjkelly1/codes/Cactus/repos/flesh/lib/sbin/CreateScheduleBindings.pl (at 819) -> Schedule error: Thorn TmunuBase - group exact::decoded_exact_model doesn't exist. Creating function bindings... Generating arguments... CST error in /gpfsm/dnb31/bjkelly1/codes/Cactus/arrangements/EinsteinBase/TmunuBase/schedule.ccl (at 101) -> Error in TmunuBase_SetTmunu schedule. Check variable or group 'EXACT::decoded_exact_model' and verify correct implementation/thorn name and variable name. CST error in /gpfsm/dnb31/bjkelly1/codes/Cactus/arrangements/EinsteinBase/TmunuBase/schedule.ccl (at 101) -> Error in TmunuBase_SetTmunu schedule. Check variable or group 'EXACT::exact_pars_real' and verify correct implementation/thorn name and variable name. ------------------------------------------------------ There were 4 errors during execution of the CST These must be corrected before compilation can proceed ------------------------------------------------------ ------------------------------------------------------ Warnings were generated during execution of the CST ------------------------------------------------------ CST error in /gpfsm/dnb31/bjkelly1/codes/Cactus/repos/flesh/lib/sbin/CreateScheduleBindings.pl (at 819) -> Schedule error: Thorn TmunuBase - group exact::Exact_pars_real doesn't exist. HINT: Check thorn TmunuBase inherits from implementation exact CST error in /gpfsm/dnb31/bjkelly1/codes/Cactus/repos/flesh/lib/sbin/CreateScheduleBindings.pl (at 819) -> Schedule error: Thorn TmunuBase - group exact::decoded_exact_model doesn't exist. HINT: Check thorn TmunuBase inherits from implementation exact CST error in /gpfsm/dnb31/bjkelly1/codes/Cactus/arrangements/EinsteinBase/TmunuBase/schedule.ccl (at 101) -> Error in TmunuBase_SetTmunu schedule. Check variable or group 'EXACT::decoded_exact_model' and verify correct implementation/thorn name and variable name. HINT: Is exact::decoded_exact_model a correctly declared variable? CST error in /gpfsm/dnb31/bjkelly1/codes/Cactus/arrangements/EinsteinBase/TmunuBase/schedule.ccl (at 101) -> Error in TmunuBase_SetTmunu schedule. Check variable or group 'EXACT::exact_pars_real' and verify correct implementation/thorn name and variable name. HINT: Is exact::Exact_pars_real a correctly declared variable? ------------------------------------------------------ -- ------------------------------------------------------------------ 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 ------------------------------------------------------------------

2 1

Meeting Minutes 2020-10-08
by Gracia Linares, Miguel 08 Oct '20

08 Oct '20

Present: Peter D., Roland H., Miguel G., Steven B., Alois S., Atul K., William G., Kenneth S., Samuel C., Yosef Z., Zach E. Maria H., Chair: Steven B. Minutes: Miguel G. * SPEC benchmark contribution [RH, SB] Roland created a list of the needed tasks task<https://bitbucket.org/einsteintoolkit/tickets/issues/2470> . Erick E. and Jian T. have files for the SPEC CPU 2017 that they’re going to share. Only Scalar McLachlan would be included, should compile on every mainly OSs. Steve is going to look for the old SPEC repo and check if there’s something that could be recycled. * Transition cactuscode.org<http://cactuscode.org> to github pages [RH, SB] [Steve ] No update this week [Roland] The transition should be done by the end of the month if we want to have it ready for November’s release. Steve is going to talk with IT people about the migration. Roland pointed out that there are changes to be made like changing the name of the latest ETK release. * Upcoming release planning (7 weeks to go, 3 weeks to feature freeze, 2 weeks to have everything reviewed) [RH] A list of release tasks for November’s release can be find here: List of tasks and time estimates<https://docs.einsteintoolkit.org/et-docs/Release_Process> . Reminders on the weekly telecom and look for volunteers to split the tasks because there won’t be a release coordinator. Steve will create the schedule and the link for ET_2020_11 release. * NRPyPN<https://nbviewer.jupyter.org/github/zachetienne/nrpytutorial/blob/master/NR…>: ticket 2417<https://bitbucket.org/einsteintoolkit/tickets/issues/2417>, Peter Diener is reviewer. [RH ] Peter is finishing reviewing NRPyPN and will talk with Zach about some questions he has. * Unanswered questions: Qlm h5 output issue: Zach has responded with a work around. Still need to look for the cause of the problem. Cartoon2d issue: Roland is going to ping Helvi about the follow up of this problem. * Tickets: Ticket #2432. The Baikal version on the master branch does not fail as reported but Zach is going to look for a better fix. Ticket # 2463. Discussion about running the test suite in parallel. Steve is going to comment on the ticket. * Extra: On October 15, Zach and Steve are giving tutorials for the ICERM workshop. Should be advertised on the ETK mailing list. Kent S. gave a LaTeX interpreter update and talked about the symbolic derivative feature. The next step is adding arbitrary coordinate systems. * Coming Chair/Minutes: October 22 Chair: Maria H. Minutes: William G. October 29 Chair: Zach E. Minutes: Maria H.

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

Users October 2020