Users September 2013

users@lists.einsteintoolkit.org

14 participants
24 discussions

Einstein Toolkit Meeting Reminder
by Frank Loeffler 14 May '15

14 May '15

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ I short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. My agenda contains: - Fall workshop - PLEASE let us know if you come [1]! - Hotel booking - Release planning - release date: Mon Oct 24 2011 - freeze date: Mon Sep 26 - the day of the call! - branch name: ET_2011_10 - List of release-concerning bugs [2] - ET paper: proposed "freeze" by Oct 3rd (Mon after this call) As always: feel free to add to this list. Frank Loeffler [1] https://docs.einsteintoolkit.org/et-docs/ET_Workshop_Fall_2011#Fall_Einstei… [2] https://trac.einsteintoolkit.org/query?status=!closed&milestone=ET_2011_11&…

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Evolving grid arrays using MoL
by Ian Hinder 04 Nov '13

04 Nov '13

Hi, What is the current situation with evolving grid arrays with MoL? Over the past 7 years, this topic has come up repeatedly on the mailing lists, and some of the old information is probably out of date. Is there a way to do this without using any hacks, or are hacks still necessary? Is there an example somewhere of how to do this, or does someone have an example they would be willing to share? -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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Meeting Minutes
by Roland Haas 30 Sep '13

30 Sep '13

Present: Frank, Roland, Zach, Peter, Ian, Steve, Matt, Tanja Zach's UIUC code based MHD code: * code is ready, needs some minor cleanup * send email to Zach if you'd like a tarball * Zach will put into svn repository once he has access to the ET svn servers Next release: * Please have a look at the tickets marked for the next releas [1] * in particular the ones that were also present at the last release * next release is planned for November Test failures: * one test (TOVSolver/tov_carpet) failing since Roland's electric fence commits. Roland cannot reproduce this either on his workstation nor running manually within the jenkins VM. Will try to mimic more closely what Jenkins does. Ian will trigger a full rebuild. Jenkins: * currently have 3 build slaves: UCD, PI, Caltech * currently runs incremental builds since full builds take too long (~1hr) Yours, Roland [1] https://trac.einsteintoolkit.org/query?status=accepted&status=assigned&stat…

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hwloc inside virtual machine
by Roland Haas 29 Sep '13

29 Sep '13

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello all, I run a virtual machine (one of the slaves for Jenkins though I think it is hardly every used) inside of VirtualBox. I allocated 4 cores (and 4GB of RAM) for it. The host is a Intel(R) Core(TM) i7-2600 CPU which supports symmetric multithreading (ht in cpuinfo). hwloc detects this also inside the the virtual machine and thus sets the default number of threads to 4, however other places in the code disagree and I get a warning that more threads than physical SMT units are used: INFO (hwloc): Extracting CPU/cache/memory properties: There are 1 PUs per core (aka hardware SMT threads) There are 2 threads per core (aka SMT threads used) WARNING: This is larger than the number of hardware SMT threads VirtualBox apparently does not fully support this and indeed I end up with 8 concurrent threads which make the test unbearably slow (I had thought the ML tests were stuck). Explicitly setting OMP_NUM_THREADS=2 fixes the problem for me. If possible it would be nice though if hwloc detected this situation and did not start as many threads (useful eg for new users who use the ET virtual machine to try out Cactus). I attach the log file output. 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://keys.gnupg.net. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iEYEARECAAYFAlJI+CEACgkQTiFSTN7SboXvmgCgnpGcPH/2AIUxxB5lFUr9ZjO7 0oAAn04un6Kg41XAW5QXLkak/xBWVxxP =Xlnk -----END PGP SIGNATURE-----

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 29 Sep '13

29 Sep '13

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ET and Llama
by Erik Schnetter 24 Sep '13

24 Sep '13

We discussed the upcoming Einstein Toolkit release and the Llama infrastructure in yesterday's telecon. Unfortunately, my wireless connection was not well enough to support much of a discussion with me. When we (we = main Llama developers) released Llama earlier this year, we did so in the knowledge that the infrastructure supports high-quality production simulations, but lacks documentation and tutorials for newcomers. Our plan was (and is) to attract users who can help us add these tutorials, examples, documentation, and also help clean up the code. As you may imagine, Llama grew organically, and there are also some left-over pieces of unsuccessful sub-projects. Some pieces have also by now migrated into Cactus, and should now either be removed or rewritten and simplified. We intentionally did not submit Llama for inclusion into the Einstein Toolkit yet: Llama should not come "for free" with the Einstein Toolkit, but people should realize and acknowledge that Llama represents an independent project and significant amount of work. We are happy it if people find Llama useful and appreciate any contributions towards making it even more useful. Personally, I expect Llama to become part of the ET, but the code is not ready yet. In summary: - We (we = main Llama deveopers or users) should give a Llama tutorial soon, helping others to get started. - We are looking for a tutorial write-up and examples, in particular discussing some of the unexpected features (memory requirements, typical grid structures for binary systems, time step limitations, etc.) - A code review with the intent to better integrate Llama with the core of Cactus, to remove outdated parts, and consolidate the existing code would be in order. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/ 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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CarpetRegrid2 with nonexistent radii in some centres
by Ian Hinder 24 Sep '13

24 Sep '13

Hi, Suppose I want to set up a grid structure for a BBH evolution using CarpetRegrid2, but ensure that the outer levels never change. What I usually do is set up two box hierarchies centred on the two BHs, but this doesn't guarantee that the outer levels don't change. Instead, I would like to have three hierarchies, one for the outer levels, and two for the BHs, where the latter only contain boxes on the finest levels. I would implement this by not setting the coarser radii for the BH hierarchies, and leaving them at -1. I was under the impression that this used to be possible, but there is a check in CarpetRegrid2 which prevents this: -> The radius of refinement level 1 of region 2 is [-1,-1,-1], which is non-negative I can't see anything in the code which would make this necessary. Is it safe to disable this check? -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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Meeting Minutes
by Roland Haas 23 Sep '13

23 Sep '13

Present: Frank, Roland, Zach, Erik, Peter, Ian Zach's UIUC code based MHD code: * code is almost ready, needs some cleaning up * Frank to get into contact with Zach to set up a subversion repository within the ET Gallery (http://einsteintoolkit.org/about/gallery/): * want more examples * NSNS (with and without Llama): Roland * collapse (to BH or to NS): Roland, Philipp or Christian Reisswig * BBH and BH: Peter Important Tickets for next release: * #262 [1] concerns not being able to recover from a checkpoint if the number of timelevels does not match what prolongation_order_time requires also of interest might be #620 [2] which is an enhancement request to avoid having to specify the maximum number of timelevels. We will discuss this on the mailing list in more detail. * #1395 that contains a workaround for svn 1.7 and parallel checkouts [3]. Frank will take care of this. * with more git thorns in the ET ticket #393 [4] should also be adressed * documentation for GRHydro and PITTNull code should be updated GRHydro should include the relevant sections from the recent papers. PITTNull should contain some information in the "Physical system" section of the documentation * there was a suggestion to try and include Llama in next release however this seems to the too short notice since the code still needs cleanup etc and not all of the Llama authors have been contacted * if you have access to the newest Intel compiler, please test #1276 [5] to see if it still has problems with restrict in C code. * for the next workshop, consider "distributed" approach with several institutes broadcasting the lectures and organizing groups for the exercises, consider possibility of participants calling in (though this should be the exception and participants should try and attend as a group) * need to test whichever system might be used (video, slides, audio, questions from autience, chat). Suggestions were either bigbluebutton (most likely version 0.81 will be out by then) or the H323 (polycom) systems at AEI, Caltech, LSU, PI. Yours, Roland [1] https://trac.einsteintoolkit.org/ticket/626 [2] https://trac.einsteintoolkit.org/ticket/620 [3] https://trac.einsteintoolkit.org/ticket/1395 [4] https://trac.einsteintoolkit.org/ticket/392 [5] https://trac.einsteintoolkit.org/ticket/1276

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 21 Sep '13

21 Sep '13

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ In short: the number is (+1) 225-578-4942 or (+1) 866-573-0359 and the conference id is 118682#. As always, we will answer questions and hear comments that come up at the meeting. With the next release being about 2 months away it is time to discuss what we plan to include/develop/fix/extend in/for/until then/it - which is what I would like to talk about on Monday. Frank Löffler

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Recovery fails with out-of-memory
by Ian Hinder 21 Sep '13

21 Sep '13

Hi, Does anyone have a suggestion for how I can make a run recover if HDF5 claims to be out of memory? The original run was on 1056 cores of stampede. Recovery fails both on the same number of cores as well as on 2048. Would a newer version of HDF5 help? Is there some parameter I can set? I am already using CarpetIOHDF5::open_one_input_file_at_a_time = yes. I am using CarpetIOHDF5::compression_level = 9. I wonder if the problem is made worse by having to decompress when reading the file. Logically, I don't see any reason why HDF5 should need more memory to recover than the original run used. > HDF5-DIAG: Error detected in HDF5 (1.8.10-patch1) thread 0HDF5-DIAG: Error detected in HDF5 (1.8.10-patch1) thread 0: > #000: H5Dio.c line 174 in H5Dread(): can't read data > major: Dataset > minor: Read failed > #001: H5Dio.c line 449 in H5D__read(): can't read data > major: Dataset > minor: Read failed > #002: H5Dchunk.c line 1735 in H5D__chunk_read(): unable to read raw data chunk > major: Low-level I/O > minor: Read failed > #003: H5Dchunk.c line 2766 in H5D__chunk_lock(): data pipeline read failed > major: Data filters > minor: Filter operation failed > #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during read > major: Data filters > minor: Read failed > #005: H5Zdeflate.c line 136 in H5Z_filter_deflate(): memory allocation failed for deflate uncompression > major: Resource unavailable > minor: No space available for allocation > WARNING[L1,P254] (CarpetIOHDF5): : > HDF5 call 'H5Dread (dataset, datatype, memspace, filespace, xfer, cctkGH->data[patch->vindex][timelevel])' returned error code -1 -- Ian Hinder http://numrel.aei.mpg.de/people/hinder

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Users September 2013