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-xHost in edison.cfg
by Roland Haas 18 Sep '16

18 Sep '16

Hello all, NERSC's edison cluster specifies -xHost in its cfg file. However login nodes and compute nodes are actually different (Sandy Bridge vs. Ivy Bridge cpus). A quick test removing -xHost reveals a possible reason: without -xHost the compiled exectuables do not run on the head node. No for the actual question: is it worthwhile to claim cross compilation (and the requirement to have to specify endianess, type sizes etc manually) to possibly gain some more speed? Given that Ivy and Sandy Bridge are tick and tock I would not expect much of a gain (though maybe Ivy Bridge actually offers wider AVX instructions?). At least I will add a comment to edison.cfg explaining why either -xHost is used or why a cross compilation is required. 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.

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Problem with compiling Einstein Toolkit on Cray system
by L.S. Oswald 16 Sep '16

16 Sep '16

Hello I'm attempting to install the Einstein Toolkit on Dora, which is a Cray system supercomputer. In doing so I came across the following error: Configuration script for thorn MPI returned exit code 5 Error message: 'MPI could not be configured: neither automatic nor manual configuration succeeded' In addition the log stated that: No MPI compiler wrapper found beneath MPI_DIR (MPI_DIR = /usr) I subsequently discovered that it was looking in the wrong place for the MPI root directory and that the reason it was looking under /usr instead of /opt/cray/mpt/7.3.2/gni/mpich-cray/8.3 was because that was the setting in the ubuntu configuration file that I had used when configuring SimFactory. On a reattempt therefore I did not use the ubuntu.cfg file when configuring SimFactory, and got the following error instead: Configuring with flesh MPI Warning: use of flesh MPI via MPI option is deprecated and should be replaced with the thorn ExternalLibraries/MPI and its MPI_DIR option MPI selected, but no known MPI method - what is "/opt/cray/mpt/7.3.2/gni/mpich-cray/8.3" ? Attempts at altering the Makefile and the config-info file resulted in either no change, or more errors. Please would you be able to advise me on the correct way to specify the root directory for MPI? Many thanks, Lucy Oswald

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Continuation of problems downloading ET onto Dora
by L.S. Oswald 16 Sep '16

16 Sep '16

Hello again In previous emails I detailed the problems I was having downloading the Einstein Toolkit, first on the Dora supercomputer and then on a local computer. Following further efforts to solve my MPI issue on the Dora supercomputer I have come up against a new problem. This is the method I used to reach this point: I downloaded Cactus using the method described in https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users I created my own configuration file based on the debian.cfg file which I have attached. This file specifies the path for the MPI directory (and this solves the MPI issue) I configured Simfactory using the following command: ./simfactory/bin/sim setup --optionlist=dora.cfg --runscript debian.sh I built the Einstein Toolkit with the following command: ./simfactory/bin/sim build --mdbkey make 'make -j2' --thornlist=manifest/einsteintoolkit.th This is the error I got. It seems to be some kind of syntax error: /users/lsoswald/old/Cactus/arrangements/CactusTest/TestLoop/src/TestLoopPointwise.c: In function ‘TestLoopPointwise_All’: /users/lsoswald/old/Cactus/arrangements/CactusTest/TestLoop/src/TestLoopPointwise.c:31: error: expected ‘#pragma omp’ clause before ‘collapse’ Creating /users/lsoswald/old/Cactus/configs/sim/lib/libthorn_TestLocalInterp2.a /users/lsoswald/old/Cactus/arrangements/CactusTest/TestLoop/src/TestLoopPointwise.c: In function ‘TestLoopPointwise_Int’: /users/lsoswald/old/Cactus/arrangements/CactusTest/TestLoop/src/TestLoopPointwise.c:90: error: expected ‘#pragma omp’ clause before ‘collapse’ /users/lsoswald/old/Cactus/arrangements/CactusTest/TestLoop/src/TestLoopPointwise.c: In function ‘TestLoopPointwise_Bnd’: /users/lsoswald/old/Cactus/arrangements/CactusTest/TestLoop/src/TestLoopPointwise.c:158: error: expected ‘#pragma omp’ clause before ‘collapse’ /users/lsoswald/old/Cactus/arrangements/CactusTest/TestLoop/src/TestLoopPointwise.c: In function ‘TestLoopPointwise_IntBnd’: /users/lsoswald/old/Cactus/arrangements/CactusTest/TestLoop/src/TestLoopPointwise.c:231: error: expected ‘#pragma omp’ clause before ‘collapse’ make[3]: *** [TestLoopPointwise.c.o] Error 1 make[2]: *** [make.checked] Error 2 make[1]: *** [/users/lsoswald/old/Cactus/configs/sim/lib/libthorn_TestLoop.a] Error 2 make[1]: *** Waiting for unfinished jobs.... make: *** [sim] Error 2 Could you advise me on what the issue with this might be and how I may solve it? Many thanks, Lucy

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TwoPunctures::Newton_maxit
by Ian Hinder 14 Sep '16

14 Sep '16

Hi, What is the logic behind the parameter TwoPunctures::Newton_maxit? Its default is set to 5, and if the Newton iteration doesn't converge in this number of iterations, the solution is just used anyway. Shouldn't there be a fatal error in this case? Is it ever legitimate to use a solution which has not converged to within the tolerance? I think I would prefer to be told to specify a larger tolerance than to have a solution which does not meet the tolerance I set. -- Ian Hinder http://members.aei.mpg.de/ianhin

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Einstein Toolkit Meeting Reminder (not for today)
by Frank Loeffler 12 Sep '16

12 Sep '16

Hi No meeting happened today, leaving next Monday as the next time. I expect a lot on the agenda, and will send an email about that later this week. Let me know if you have something to put on it already now. Next Monday it will be again, as usual: Please consider joining the weekly Einstein Toolkit phone call at 9:30 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/ We use a Google hangout, with the URL: https://hangouts.google.com/call/5xt7voshalqmdcztr4zhfeox2ia Frank Loeffler

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OpenACC
by Christopher Ramirez 12 Sep '16

12 Sep '16

Hello, I've been trying to implement OpenACC, but have been getting the following error: COMPILING arrangements/Drewz/Spectral_dsincos/src/SpecDeriv.c PGC-F-0249-#error -- --- !!! UNKNOWN COMPILER: please provide a CUDA compatible definition for '__align__' !!! --- (/share/apps/cuda-toolkit/6.5/include/host_defines.h: 128) PGC/x86-64 Linux 15.7-0: compilation aborted make[3]: *** [SpecDeriv.c.o] Error 2 make[2]: *** [make.checked] Error 2 I'm not sure how to resolve this. Any assistance would be greatly appreciated. Thank you

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Limiting Carpet's Memory Usage
by Erik Schnetter 09 Sep '16

09 Sep '16

[I received a question on how to limit the amount of memory that Cactus uses.] You can try using "ulimit" to limit memory usage. You can also do that within an application by calling "setrlimit". There is also a parameter "CarpetLib::max_memory_size_MB" that does this. However, the Linux kernel is not good at enforcing memory limits, so this might turn out to be useless. There is also a parameter "CarpetLib::max_allowed_memory_MB" that Carpet checks for all the memory that it allocates. This ignores memory allocated by other thorns (hopefully not much) as well as by external libraries (MPI message buffers, HDF5 file caching, libc's malloc implementation, etc.). If one of these parameters is useful for you, please let me know. -erik -- Erik Schnetter <schnetter(a)gmail.com> http://www.perimeterinstitute.ca/personal/eschnetter/

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No Einstein Toolkit Meeting
by Frank Loeffler 05 Sep '16

05 Sep '16

Hi, There will *not* be an Einstein Toolkit meeting next Monday (today). The next meeting will be on Mon Sep 12th, 2016, at the usual time: 9:30am US central time). Why: https://en.wikipedia.org/wiki/Labor_Day Frank Loeffler

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Checkpointing with Cactus/Simfactory
by dumsani 31 Aug '16

31 Aug '16

Hi All, I have some very long BH simulations to run and I'd like to checkpoint for these. I haven't really done checkpointing before. But what I know is that chekpointing information can be specified in the parameter file (for use by Cactus), and also that Simfactory does seem to have some stuff to do with or handle checkointing ( "restart-id", etc...). Of course, scheduling systems (e.g. PBSPro) at HPCs would have support for checkpointing but I don't want to use that. Probably it is only best to use that to set the walltime. So, my main question is: Assuming I set a maximum walltime of 12 hours, and I set my simulation to dump checkpoints every 3hrs (in walltime units), how do I *restart* my job at the end of the 12 hrs using Simfactory in a way that the simulation starts off from the last checkpoint it droppped before terminating? What extra command line options should I pass to the sumbit command of SImfactory? Below is a segment of my parfile where checkpointing information is given, provides as a sample or as a basis for anyone who would want to advise me on how such information should be given. ##### Checkpointing ######### CarpetIOHDF5::checkpoint = yes IO::checkpoint_ID = yes IO::recover = autoprobe IO::checkpoint_every = 1024 IO::out_proc_every = 2 IO::checkpoint_keep = 3 IO::checkpoint_dir = $parfile Carpet::regrid_during_recovery = no CarpetIOHDF5::use_grid_structure_from_checkpoint = yes CarpetIOHDF5::open_one_input_file_at_a_time = yes Your advice and assistance will be highly appreciated. Best, Dumsani

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inutes for 2016-08-29
by Roland Haas 29 Aug '16

29 Aug '16

Present: Frank, Roland, Zach, Matt, Erik, Roberto di Pietro, * close ticket on floating release branch since it seems not straightforward to * Frank and Steve went through the piraha-everywhere branch and now are only minor issues left. It will most likely arrive on master soon. This will cause a force-rebuild to regenerate the ccl generated files * restart developer workshops (twice a year). Most likely focused on particular topics so that not everyone (needs to) attend. * monthly task-based remote developer's day so that there is minimum amount of progress on these topics. Initially try using google hangout for this. * please suggest topics that would require 3-4 hours of developer work ** update of the webpage to simplify navigation, a suggestion is to use bootstrap http://v4-alpha.getbootstrap.com/examples/ which uses javascript/css to ensure proper layout on desktops/phones/tablets. Uses javascript for menus, common include headers. Erik played around with http://jekyllrb.com which generates mostly static HTML pages from some markdown type source. ** make sure all example parfiles scattered throughout the ET work ** minor coding projects like writing a single HDF5 file of output rhather than 1 per variable or 1 per group 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.

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