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Patch for 3D hdf5 output files
by Francesco Zappa 13 Sep '21

13 Sep '21

Hallo everybody, I am Francesco Zappa, a PhD student at the Jena university. I am using a Cactus-based code and I am running simulations on Hawk cluster. Unfortunately, recent policy of Hawk have severe restrictions in terms of number of files that can be produced at the same time. The problem is that running several mpi processes generate many hdf5 output files and I would like to have them packed somehow. I have tried to use the option CarpetIOHDF5::one_file_per_proc = "yes" which works fine for 2D data files but it does not seem to work on 3D data files (which have the form <variable>.file_<process>.h5). I have been aware of the fact that it exists a patch for the Carpet Thorn to have these files packed together somehow. Could you please help me with this issue? Best regards, Francesco Zappa ------------------------------------- Friedrich-Schiller-Universität Jena Theoretisch-Physikalisches Institut Fröbelstieg 1, Office 219, Phone Number 0049-3641-9-47133 D-07743 Jena

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meeting minutes for 2021-09-09
by Roland Haas 09 Sep '21

09 Sep '21

Present: Peter D., Yosef, Roland, Steve, Atul, Miguel, Helvi, Leo, Zach, Gabriele SPEC benchmark: * need to provide parameters for 1 min short and full node long run Next ET release: * Steve updated timeline, template: https://docs.einsteintoolkit.org/et-docs/Release_Process instance: https://docs.einsteintoolkit.org/et-docs/Release_Details * past date of adding new thorns * current time intersects with SC2021, which Steve is attending, but is a quiet week with just gallery examples being due * Students in Helvi's group are testing galleries Jenkins updates: * Roland will migrate away from dedicated Jenkins VM to GitHub actions based setup developed by UIUC REU students * reported on at 2021-04-29 and demo on https://mojamil.github.io/einsteintoolkit Emails: * Intel compiler question: Gabriele responded to the email and could run with modern intel compilers but just BBH, in Hee Il's email it is a BNS, Yosef had used Intel 19 but could not get it simulate BNS, Intel 18 worked (but this was a while ago) * THC thorn issues: conversation is between Konrad and David * PITTNull compilation failures: Intel compiler issue when it tries to optimize large Maple generated code chunks. Yosef suggests adding options (pragma), is working with a student on a leaner version of the code Tickets: * init_3_timelevels: https://bitbucket.org/einsteintoolkit/tickets/issues/2554/init_3_timelevels… some nans on past timelevels but not everywhere. Steve suggests trying to run with presync tests enabled to see if it reports sometthing useful. Chair next week (Sept 16): Helvi Minute taker next week (Sept 16): Bill 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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Multiple postdoc openings at Penn State
by Radice, David 09 Sep '21

09 Sep '21

Dear all: The Department of Physics at The Pennsylvania State University is seeking to fill two postdoctoral scholar positions in numerical relativity and high-energy astrophysics. The first position will be funded by NASA and is dedicated to the study of binary black holes for LISA in collaboration with David Radice: https://tinyurl.com/eucfauc4 The second position will be funded by NSF and is dedicated to the modeling of high-energy emission from merging neutron stars in collaboration with David Radice and Kohta Murase: https://tinyurl.com/4uncwsxk Additionally, there will be ample opportunity to collaborate with other members of the Institute for Gravitation and the Cosmos, which includes, among others, Abhay Ashtekar, Eugenio Bianchi, Martin Bojowald, Chad Hanna, Sarah Shandera, and B.S. Sathyaprakash. These position requires a Ph.D. in mathematics, physics, astronomy, or a closely related field. Please, refer to the URL above for the application details. Questions can be directed to David Radice (dur566(a)psu.edu). We specifically seek applications from women and from members of groups traditionally underrepresented among scholars in higher education. Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applications without regards to race, color, religion, age, sex, sexual orientation, gender identify, national origin, disability or protected veteran status. With best wishes, David Radice (he/him) Assistant Professor Department of Physics The Pennsylvania State University 104 Davey Lab, Box 113 University Park, PA 16802-6300

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Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 08 Sep '21

08 Sep '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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Compilation error with ifort
by Lorenzo Ennoggi 08 Sep '21

08 Sep '21

Hi, I am trying to compile the Einstein Toolkit on MarconiA3 and I am getting the following error: ifort: error #10106: Fatal error in /marconi/prod/opt/compilers/intel/pe-xe-2018/binary/compilers_and_libraries_2018.5.274/linux/bin/intel64/fortcom, terminated by kill signal compilation aborted for /marconi/home/userexternal/lennoggi/ET_2020_11/Cactus/configs/Spritz_UpwindCT/build/NullConstr/NullConstr_R00.f90 (code 1) I have tried to compile both at O3 and O2, but that makes no difference. I am attaching the optionlist I am using. Do you have any clue about what may be causing the error? Thank you, Lorenzo

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Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 06 Sep '21

06 Sep '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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Fwd: ICASU Inaugural Conference
by Helvi Witek 03 Sep '21

03 Sep '21

Dear all, I hope you are doing well! Please consider joining us for the Inaugural Conference of our new "Illinois Center for Advanced Studies of the Universe" (ICASU) in May 2022. Please find more details below. Best wishes Helvi --------------------------------------------- Dr. Helvi Witek Assistant Professor Department of Physics University of Illinois at Urbana-Champaign 247 Loomis Lab 1110 W Green St Urbana, IL 61801 --------------------------------------------- -------- Forwarded Message -------- Subject: [icasu-members] ICASU Inaugural Conference Date: Tue, 31 Aug 2021 15:35:18 +0000 From: Yunes, Nicolas <nyunes(a)illinois.edu> Reply-To: icasu-members(a)lists.illinois.edu To: Icasu-members(a)lists.illinois.edu <Icasu-members(a)lists.illinois.edu> Dear all, I hope this finds you well. We will be hosting the ICASU Inaugural Conference from May 19 - 21, 2022, and we hope you’ll be able to attend. There is no registration fee, but the deadline for registration is April 1, 2022. You can find more details about our inaugural conference at this website: https://icasu.illinois.edu/inaugural-conference. I hope you and your students and postdocs will attend. Please help us announce this event widely. With kind regards, n. ---------------------------------------------------------------------------------------------------------- | NICOLAS YUNES, | | Founding Director of the | | Illinois Center for Advanced Studies of the Universe, | | Professor of Physics, | | Department of Physics, | | University of Illinois Urbana-Champaign, | | 1110 W Green St, 249 Loomis Laboratory, Tel: (814) 883-2069 | | Urbana, IL 61801 Email: nyunes(a)illinois.edu | ----------------------------------------------------------------------------------------------------------

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ETK Meeting Minutes - Sep. 02, 2021
by Hamilton, Maria 02 Sep '21

02 Sep '21

Present: Yosef Zlochower, Maria Hamilton, Roland Haas, William Gabella, Atul Kedia, Leo Werneck, Gabrielle Bozzola, Miguel Garcia, Zach Etienne, Helvi Witek, Steve Brandt Chair: Yosef Zlochower Minutes: Maria Hamilton * pre-Agenda : loss of power due to Hurricane/Post-Tropical Cyclone Ida * SPEC benchmark contribution: * Roland gives an update, looking good. * next ET release: * Steve is released chair, helped by Roland and Yosef * Release Process <https://docs.einsteintoolkit.org/et-docs/Release_Process> * Details <https://docs.einsteintoolkit.org/et-docs/Release_Details> * Unanswered mailing list queries: * Intel Compiler issue - related to an older one? Compiler too aggressive. * THC thorn issues with Boundaries - old! * Unanswered mailing list queries: * #2549: FLRWSolver - Helvi reviewer - nothing to report * #2538: Kuibit - Yosef reviewer - nothing to report * #2561: Update simfactory for Expanse: Gabriele explains * .... * * #2554 init_3_times produces nans in the initial time slice * Tickets ready to review * #963: improved McLaughlin accuracy * #2364: multiple HDF5 files opening and closing during output * https://github.com/EinsteinToolkit/ExternalLibraries-HDF5/pull/4/files * Steve explains backslash issues...."((\\.|[^"\\])*)" * Sep. 27 meeting: Minutes: Steve; Chair: Roland 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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Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 01 Sep '21

01 Sep '21

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Einstein Toolkit and modern AMD supercomputer
by Gabriele Bozzola 30 Aug '21

30 Aug '21

Hello, Last week I opened a PR to add the configuration files for Expanse to simfactory. Expanse is an example of the new generation of AMD supercomputers. Others are Anvil, one of the other new XSEDE machines, or Puma, the newest cluster at The University of Arizona. I have some experience with Puma and Expanse and I would like to share some thoughts, some of which come from interacting with the admins of Expanse. The problem is that I am finding terrible multi-node performance on both these machines, and I don't know if this will be a common thread among new AMD clusters. These supercomputers have similar characteristics. First, they have very high cores/node count (typically 128/node) but low memory per core (typically 2 GB / core). In these conditions, it is very easy to have a job killed by the OOM daemon. My suspicion is that it is rank 0 that goes out of memory, and the entire run is aborted. Second, depending on the MPI implementation, MPI collective operations can be extremely expensive. I was told that the best implementation is mvapich 2.3.6 (at the moment). This seems to be due to the high core count. I found that the code does not scale well. This is possibly related to the previous point. If your job can fit on a single node, it will run wonderfully. However, when you perform the same simulation on two nodes, the code will actually be slower. This indicates that there's no strong scaling at all from 1 node to 2 (128 to 256 cores, or 32 to 64 MPI ranks). Using mvapich 2.3.6 improves the situation, but it is still faster to use fewer nodes. (My benchmark is a par file I've tested extensively on Frontera) I am working with Expanse's support staff to see what we can do, but I wonder if anyone has had a positive experience with this architecture and has some tips to share. Gabriele

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