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Re: [Users] Users Digest, Vol 136, Issue 2
by Federico Cipolletta 03 Jul '21

03 Jul '21

Hello Konrad, To my understanding, it seems like the .cfg file has something wrong ( http://lists.einsteintoolkit.org/pipermail/users/2018-February/006103.html - i.e. the num-smt of your cluster should be 2, that should mean hyper threading - NOTE: I could be wrong with that). Moreover, you should use --procs=24 when submitting (from my experience this flag should be interpreted as the number of mpi task, that should correspond to the physical cores). I am only providing my experience, but for sure, some more experienced users/developers could drive you to the most correct answer. Regards, Federico Cipolletta. Il sab 3 lug 2021, 19:00 <users-request(a)einsteintoolkit.org> ha scritto: > Send Users mailing list submissions to > users(a)einsteintoolkit.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.einsteintoolkit.org/mailman/listinfo/users > or, via email, send a message with subject or body 'help' to > users-request(a)einsteintoolkit.org > > You can reach the person managing the list at > users-owner(a)einsteintoolkit.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Users digest..." > > > Today's Topics: > > 1. Submitting a simulation via simfactory on a cluster > (Konrad Topolski) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 3 Jul 2021 17:59:24 +0200 > From: Konrad Topolski <k.topolski2(a)student.uw.edu.pl> > Subject: [Users] Submitting a simulation via simfactory on a cluster > To: users(a)einsteintoolkit.org > Message-ID: > < > CAEx5SMHM6GszcaqE3_L0Rvx5+U29D6STMYH2d0PW777acyqrRA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi > > I am trying to get things right setting up simfactory on my cluster. > I have created the okeanos.ini and okeanos.cfg files, as well as built the > Cactus executable that's called cactus_okeanos. First I want to debug the > machine setup, then I hope to take care of the submission script. > > To submit a job, I use: > simfactory/bin/sim create-submit GW150914_4 --parfile > par/GW150914/GW150914.rpar --walltime 24:00:00 --configuration=okeanos > --machine=okeanos > > The error I am getting is the following: > > Warning: Too many threads per process specified: specified num-threads=48 > (ppn-used is 24) > Warning: Number of used cores per node, number of SMT threads, and number > of threads per process are inconsistent: ppn-used=24, num-smt=1, > num-threads=48_threads (ppn-used*num-smt must be an integer multiple of > num-threads) > Warning: Total number of threads and number of threads per process are > inconsistent: procs=1, num-threads=48 (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=24 (procs must be an integer multiple of > ppn-used) > > The relevant part of my machine .ini file looks like this: > cpu = Intel Xeon E5-2690 v3 > cpufreq = 2.6 > ppn = 24 # or more > max-num-threads = 48 # or more > num-threads = 48 # or more > nodes = 1084 > memory = 131072 #any node has 128GB ram > min-ppn = 24 > maxwalltime = 48:00:00 > > I know that each node in my cluster consists of 12 sockets for cpus, each > cpu has two cores and each core supports multithreading (=2), so it's > 12x2x2 = 48. > What am I getting wrong? > > > Best regards > Konrad Topolski >

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Submitting a simulation via simfactory on a cluster
by Konrad Topolski 03 Jul '21

03 Jul '21

Hi I am trying to get things right setting up simfactory on my cluster. I have created the okeanos.ini and okeanos.cfg files, as well as built the Cactus executable that's called cactus_okeanos. First I want to debug the machine setup, then I hope to take care of the submission script. To submit a job, I use: simfactory/bin/sim create-submit GW150914_4 --parfile par/GW150914/GW150914.rpar --walltime 24:00:00 --configuration=okeanos --machine=okeanos The error I am getting is the following: Warning: Too many threads per process specified: specified num-threads=48 (ppn-used is 24) Warning: Number of used cores per node, number of SMT threads, and number of threads per process are inconsistent: ppn-used=24, num-smt=1, num-threads=48_threads (ppn-used*num-smt must be an integer multiple of num-threads) Warning: Total number of threads and number of threads per process are inconsistent: procs=1, num-threads=48 (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=24 (procs must be an integer multiple of ppn-used) The relevant part of my machine .ini file looks like this: cpu = Intel Xeon E5-2690 v3 cpufreq = 2.6 ppn = 24 # or more max-num-threads = 48 # or more num-threads = 48 # or more nodes = 1084 memory = 131072 #any node has 128GB ram min-ppn = 24 maxwalltime = 48:00:00 I know that each node in my cluster consists of 12 sockets for cpus, each cpu has two cores and each core supports multithreading (=2), so it's 12x2x2 = 48. What am I getting wrong? Best regards Konrad Topolski

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meeting minutes for 2021-07-01
by Roland Haas 01 Jul '21

01 Jul '21

Present: Peter, David B,. Bill G., Roland, Leo, Yosef, SPEC: * no update Kuibit: * general agreement to include it, 2 explicit in favor, no objections, go ahead with inclusion at this point, bring up again next week * Roland mentioned that the paper may be in JOSS and thus reviewed Other codes to include: * RWZM self-force code could be ready for inclusion next release, by Sam Cupp * code is currently working for a circular effective source, currently testing fluxes and comparing to existing codes * Idaho (nee WVU) group may have an ID solver code that might be up for inclusion * LORENE2 update LORENE update: * no update yet, Roland to ping Josh New ET release manager: * postpone for a week ET school: * have heard back from most speakers confirming their slots * will most likely start 30min earlier than initially advertised * students can still register (to the last day), but no longer submit (new) talks * will finalize program and contributed talks today chair next weeks: Peter, Roland minutes next week: Leo, 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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Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 30 Jun '21

30 Jun '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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Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 28 Jun '21

28 Jun '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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Meeting minutes for 2021-06-24
by Atul Kedia 24 Jun '21

24 Jun '21

Present: Peter D, Roland H, Joshua Faber, Miguel G, Zach E, Maria H, Yosef Z, Atul K Chair: Peter D, Minutes: Atul K * Anything before the agenda? Roland - Lorene discussion with Josh. Roland - 2 years ago there were discussions about Lorene2 on ET. Did not get updated back then. Josh - Summary: Generating BNS ID, to increase catalog. Using Lorene from the website ( http://lorene.obspm.fr/). There are two versions (French and English) of the classes. Do essentially the same. French is older, and is used for JF’s BNS ID. English is slightly harder to use. French one is mostly usable with the Meudon_Bin_NS. Needs testing and cataloging of how to generate ID, and thorns that read it. Driver routines distinguish the French and English versions. There’s a directory which contains the files (executables?) for the two. Some of the math is different too. Roland - The one on ET only has (or compiles perhaps) classes that are needed for reading ID by ET. * SPEC benchmark contribution [https://bitbucket.org/einsteintoolkit/tickets/issues/2470] [RH, SB] Roland - They had a question about increasing runtime. We have to respond. * ET 2021 NA summer school [http://lists.einsteintoolkit.org/pipermail/users/2021-May/007944.html] [RH] Roland - Close to 200 participants. 18 lightning talks. Finalizing the program. Reaching out to Peter for LSU virtual machines. Peter - will talk with Steve. * Mugshots for ET gallery runners [RH] Roland - Will send email to gallery test runners for their mugshot to give them more visibility. This was discussed in an earlier ET meeting. Will (likely) add the mugshot of all the testers along with the maintainers page but not going to keep emeritus ET testers mugshots. * [https://www.einsteintoolkit.org/tools/unanswered.php unanswered question on mailing list] * [ https: //bitbucket.org/einsteintoolkit/tickets/issues?status=open&status=new&sort=- updated_on open tickets sorted by update time] #2539 Roland - installed on a new VM with no issues. Freshly installed. Want to include instructions on error reporting, and how to label the particular bugs. Can’t be “blocker” unless it causes issues to many machines. #2534 Roland gonna look into it. If only happening with things evolved with MoL, should cause issues with gridarrays. Yosef - does not make sense to evolve gridarrays in AMR. If it is AMR, it needs to be updated when the nearest grid element is updated. Makes doing everything very messy. #2413: Roland - Writing documentation remaining. Poisson, Single Stable neutron star, Binary Black hole : needs to be “resolved”. * [ https: //bitbucket.org/einsteintoolkit/tickets/issues?status=new&status=open&sort=- updated_on&q=Please%20review tickets ready for review] #332 : Roland - Old ticket by Bruno Mundim. Probably an ‘Enhancement’. Future chairs and minute takers: 1 July : Chair Peter, Minutes Roland. 8 July : Chair: -- , Minutes Miguel G. ---------------------------- End of Call ---------------------------- Atul Kedia PhD Candidate University of Notre Dame

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Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 23 Jun '21

23 Jun '21

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

21 Jun '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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Postdoctoral positions in computational relativity/cosmology/fluid dynamics (IBM, Daresbury, UK)
by eloisa.bentivegna 18 Jun '21

18 Jun '21

Dear colleagues, IBM Research is seeking to fill three postdoctoral positions, with start dates in the second half of 2021. Candidates with a background in any aspect of numerical relativity, computational cosmology, and/or fluid dynamics are invited to apply. Evidence of strong competence in large-scale scientific computing is required. Previous experience with optimization, AI/ML techniques, heterogeneous computing, or past involvement with industrial research projects would be an advantage. Applications should be submitted via our online system: https://careers.ibm.com/job/13128396/ and will be reviewed immediately. The deadline for full consideration is June 23, but the positions will remain open until suitable candidates are appointed. Applications from traditionally underrepresented groups are especially welcome. Best regards, Eloisa

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Issue with thorn Trigger
by Lorenzo Ennoggi 18 Jun '21

18 Jun '21

Dear all, I would like to restart a simulation from a checkpoint enlarging the finest refinement level in my grid. In particular, I would like to change CarpetRegrid2::radius_1[5] = 20.1 to CarpetRegrid2::radius_1[5] = 25. I tried to do that by making the parameter CarpetRegrid2::radius_1 always steerable and adding the following lines to my parameter file: ActiveThorns = "Trigger" Trigger::Trigger_Number = 1 Trigger::Trigger_Checked_Variable[0] = "hydrobase::rho" Trigger::Trigger_Relation[0] = ">" Trigger::Trigger_Checked_Value[0] = 1.e-4 Trigger::Trigger_Reduction[0] = "maximum" Trigger::Trigger_Reaction[0] = "steerparam" Trigger::Trigger_Steered_Parameter_Thorn[0] = "CarpetRegrid2" Trigger::Trigger_Steered_Parameter_Name[0] = "radius_1[5]" Trigger::Trigger_Steered_Parameter_Value[0] = "25." #New value of the above parameter Trigger::Trigger_Once[0] = 1 #It means "yes" Trigger::Trigger_Debug = 1 #It means "yes" In this way, the trigger should act immediately, as the maximum of rho is ~1e-3 in my case. Indeed, it looks like the trigger is working fine, as the standard output says [...] INFO (Trigger): Testing triggers INFO (Trigger): last_checked: -1 INFO (Trigger): reducing trigger 0 red_handle 2 varindex 428 INFO (Trigger): reducing was ok INFO (Trigger): trigger nr. 0 fullfilled for rho (0.000804>0.000100) INFO (Trigger): Steering parameter INFO (Trigger): Parameter steered [...] but unfortunately, looking at the 2D output with VisIt, the finest refinement level does not get enlarged (i.e. radius_1[5] does not appear to have been steered at all). Do you have any suggestions on how to get this trigger to work? Or, are you aware of other ways of obtaining the same result without using the thorn Trigger? I attach the parameter file in case you need it. Thank you very much in advance for your help. Sincerely, Lorenzo Ennoggi

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