Users October 2014

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11 participants
20 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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ET test failures on Stampede
by Erik Schnetter 05 Nov '14

05 Nov '14

I've begun to run the automated tests for the ET on our production machines. Things look very good almost everywhere, except on Stampede, one of the machines that is most important to us. It seems that there are many test failures for GRHydro, and these seem to be caused by segfaults. Does anybody volunteer to investigate? -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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Proposal: Modify HydroBase to Support Staggered A-Fields
by Zach Etienne 02 Nov '14

02 Nov '14

Dear ET folks, I have written a small thorn that converts HydroBase and ADMBase variables into the variables IllinoisGRMHD needs to perform a GRMHD evolution. This conversion works just fine on all variables... except the vector potential. As you may be aware, IllinoisGRMHD requires that A_t (=\sqrt{\gamma} \Phi), A_x, A_y, and A_z each be staggered differently (a la Table I of http://arxiv.org/abs/1007.2848). However, HydroBase does not support defining such staggered A-fields. Thus it is currently impossible to modify/create GRMHD initial data thorns so that vector potential data produced by them can be directly read in by IllinoisGRMHD. For example, if an initial data thorn only outputs the vector potential on grid vertices, then an interpolation will need to be performed to staggered gridpoints. This will introduce truncation errors that, depending on the A-field structure and needed grid resolutions, may be severe. I conclude that this is _not_ The Right Strategy. The Right Strategy would not break any existing thorn as a first step, either. So as a first step, I believe we should modify HydroBase so that 1) A new set of four, 3-timelevel groups are defined, one for each component of the vector potential 2) The prolongation type can be specified differently for each of the four vector potential gridfunction groups, allowing for arbitrary staggerings of the single variable within each of these groups. Variables in these groups will be read in by IllinoisGRMHD and can be used directly for evolutions. Regarding the longer-term strategy, we could either 1) modify Carpet so that different components of Avec() (the current 3-vector potential group in HydroBase) can accept different prolongation/restriction operators (then modifying IllinoisGRMHD to accept this new vector gridfunction), or 2) just keep the four, 3-timelevel groups and phase out Avec() and Aphi altogether. Even the latter strategy would not be difficult to implement in current publicly available thorns: After a simple grep, I could only find a single initial data thorn that actually sets Avec, so the needed changes to public initial data thorns should be minimal. Further, I am under the impression that Avec evolutions are not yet supported in GRHydro anyway, and found only about 40 references to the Avec() gridfunctions within GRHydro, so renaming these variables to a new style would be trivial. Please let me know your thoughts regarding this proposal. The IllinoisGRMHD code announcement paper is nearing completion, and at least having the infrastructure for this code in place by the next ET release would be great. In this regard, I have already asked Erik if he would be willing to merge the staggered prolongation/restriction code into the mainline Carpet for the next ET release. The soft freeze is Nov 10, these new features affect none of Carpet's other functionality, and I have thoroughly tested these new features with GRMHD evolutions, verifying that they work well. Please consider the possibility of adding these small infrastructure enhancements prior to the freeze. Sincerely, -Zach * * * Zachariah Etienne Assistant Professor of Mathematics West Virginia University

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Meeting Minutes for 2014-10-27
by Roland Haas 29 Oct '14

29 Oct '14

Present: Frank, Peter, Steve, Matt, Roland, Ian, Erik, Yosef * intel compiler miscompiles NewRad ** Peter tried intel 15 ** Ian or Roland to try with intel 15 on datura ** Steve found and fixed some issues in compiler test * svn checkouts out of private repositories requiring login: ask Bruno for patch, we initially introduced non-interactive flag to cope with svn asking permission to accept new ssl certificates and seeming to stall since the user did not see the prompt * OpenBLAS as replacement for LAPACK and BLAS ** desire to build OpenBLAS rather than use a system installed reference LAPACK which is very slow ** difficult to detect exactly what the system installed LAPACK library is since some optimized versions keep parts of the reference library intact ** issue only arises on user workstations/laptops and possibly private clusters where simfactory does not explicitly provide a "good" LAPACK library installation ** balance between compilation speed and execution speed (and reputation of Cactus being slow when using PETSc due to slow LAPACK) ** decision: come up with way to auto-detect in the next 6 months then decide what to do ** decision: keep OpenBLAS in thornlist but keep it commented out for now Upcoming release: * change group separator in output file names from "::" to "-" after the release * example to solve Poisson equation using CactusPetsc ** works with unigrid only (PUGH and Carpet), no mesh refinement, no multi-patch ** currently has no test case but may not need one given that it itself is an example ** needs documentation ** in test there are NaN values on the outer edges of the residual grid function that should be set to something harmless instead * testing: ** Erik ran tests using simfactory's distribute script ** no major issues so far ** send out call to mailing list for user to send in option lists for cluster they use but that are not in simfactory, in particular European ones (Ian and Roland have access to the RZG machine in Munich but they are Max-Planck machines so not public, have yet to hand in a PRACE allocation request for the XSEDE equivalent) Yours, Roland

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 27 Oct '14

27 Oct '14

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#. Notice that "summer time" ended in several countries over the weekend (like Germany), but it didn't yet in the US, which means that the meeting time might be different for you right now compared to "usually". For Germany for instance it will be 16:00 instead of the usual 17:00. (Some) noteworthy tickets: - 1276: Intel Compiler and __restrict__ Some versions of the Intel compiler (we believe) miscompile code. Steve was looking into the issue, but could find a (relevant) error in our standalone test case - 1338: (Some of) Cactus' output file names will change ('::' to '-') after the release; parameter for this already present in release - 1677 (review): nonnull - 1682 (review): new thorn Poisson - 1680: GetComponents and interactive password promt for checkout/update Frank Loeffler

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Moving SimFactory to git
by Erik Schnetter 23 Oct '14

23 Oct '14

I want to move the Simfactory svn repository to Bitbucket. Does anybody object? -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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cctk_ash versus cctk_lsh
by Yosef Zlochower 21 Oct '14

21 Oct '14

Hi, Is it the case that cctk_ash[i] = cctk_lsh[i] (i=0..3) if VECTORISE_ALIGNED_ARRAYS= no? I want to update and test a code that assumed the GF sizes were given by cctk_lsh. Is there a way to force cctk_ash to be larger than cctk_lsh in order to test the update. Thanks -- Dr. Yosef Zlochower Center for Computational Relativity and Gravitation Associate Professor School of Mathematical Sciences Rochester Institute of Technology 85 Lomb Memorial Drive Rochester, NY 14623 Office:74-2067 Phone: +1 585-475-6103 yosef(a)astro.rit.edu CONFIDENTIALITY NOTE: The information transmitted, including attachments, is intended only for the person(s) or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and destroy any copies of this information.

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MPI thorn doesn't output error messages
by Erik Schnetter 20 Oct '14

20 Oct '14

I am seeing this error message from thorn MPI: Running configuration script for thorn MPI: MPI could not be configured. CST error 1: -> Configuration script for thorn MPI returned exit code 5 (no error message) Finished running configuration script for thorn MPI. That's not good enough, I really need to see either an error message, or at least a line number. The previous MPI configuration script echoed all commands to stderr, so that it was easy to see where things fail. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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Meeting Minutes for 2014-10-20
by Roland Haas 20 Oct '14

20 Oct '14

Present: Frank, Roland, Peter, Steve, Josh, Ian, Matt, Erik, Philipp Carpet move to bitbucket: * move seems sucessful * still write access to old repository, ask current authors (Ian Hinder, Roland Haas) to migrate their branches Using OpenBLAS to provide BLAS and LAPACK: * no objections * new thorn will be called BLAS_LAPACK Intel 13 miscompiling newrad: * desire to have autoconf test that detects this and then aborts with useful error message * need to find out which version are affected * compile with intel 15 to check if still affected include CT_Multilevel in ET: * license is GPL v2+ * Ian will champion inclusion, Eloisa Bentivegna is author and will provide support * code was tried at Caltech to remove MHD divergence but does not quite fit the needs wrt to exactly controlling the discretization and the desire to use preconditioning * we do however want some sort of elliptic solver in the toolkit * ask to have example run with example results for example the data already in the paper on the poisson problem * decision: include in toolkit, add example to gallery and/or wiki page Fall release: * tentative schedule: soft freeze (no major changes) Nov 10th, hard freeze and release about 14 days after * check on milestone tickets in trac * test MoL changes for speed and correctness by running qc0 * ML rewrite branch: ** test with qc0 ** make backwards compatible options Jenkins build slaves: * update to Ubuntu 14.04 Yours, Roland

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Cannot create build slave
by Erik Schnetter 20 Oct '14

20 Oct '14

I am trying to create a build slave, and I receive this error message that I don't understand: -erik $ sudo ./create-build-slave-vm build DNS domain cannot be determined automatically; please set VM_DOMAIN VM_LANGUAGE=en_CA:en VM_LOCALE=en_US VM_UBUNTU_VERSION=precise VM_UBUNTU_HOSTNAME=archive.ubuntu.com VM_UBUNTU_DIRECTORY=/ubuntu VM_DOMAIN= VM_PASSWORD_HASH=$1$nd.xreKj$oQjMMP0b6/Wdu4gptOI71. VM_TIMEZONE=America/Toronto VM_HOME=/xfs1/eschnetter/vms [Mon, 20 Oct 2014 12:34:44 virt-install 19915] DEBUG (cli:227) Launched with command line: /usr/bin/virt-install -d -n build -r 2048 --vcpus=4 --disk path=/xfs1/eschnetter/vms/build/root.qcow2,format=qcow2,bus=virtio,size=50 --location=http://archive.ubuntu.com//ubuntu/dists/precise/main/installer-amd64/ --accelerate --network network=default,model=virtio --connect=qemu:///system --vnc -v --extra-args=auto=true priority=critical initrd=/install/initrd.gz --initrd-inject=/xfs1/eschnetter/vms/build/preseed.cfg --noautoconsole [Mon, 20 Oct 2014 12:34:44 virt-install 19915] DEBUG (cli:332) Requesting libvirt URI qemu:///system [Mon, 20 Oct 2014 12:34:44 virt-install 19915] DEBUG (cli:334) Received libvirt URI qemu:///system [Mon, 20 Oct 2014 12:34:44 virt-install 19915] DEBUG (virt-install:258) Requesting virt method 'hvm', hv type 'default'. [Mon, 20 Oct 2014 12:34:44 virt-install 19915] DEBUG (virt-install:469) Received virt method 'hvm' [Mon, 20 Oct 2014 12:34:44 virt-install 19915] DEBUG (virt-install:470) Hypervisor name is 'kvm' [Mon, 20 Oct 2014 12:34:44 virt-install 19915] DEBUG (cli:959) --graphics compat generated: vnc [Mon, 20 Oct 2014 12:34:44 virt-install 19915] ERROR (cli:445) Format cannot be specified for unmanaged storage. [Mon, 20 Oct 2014 12:34:44 virt-install 19915] DEBUG (cli:448) Traceback (most recent call last): File "/usr/bin/virt-install", line 1014, in <module> sys.exit(main()) File "/usr/bin/virt-install", line 999, in main guest = build_guest_instance(conn, options) File "/usr/bin/virt-install", line 529, in build_guest_instance options.disksize, options.sparse, need_storage) File "/usr/bin/virt-install", line 164, in get_disks get_disk(disklist[idx], sizelist[idx], sparse, guest, is_file_path) File "/usr/bin/virt-install", line 137, in get_disk dev, size = cli.parse_disk(guest, diskopts) File "/usr/lib/python2.7/dist-packages/virtinst/cli.py", line 1621, in parse_disk format=fmt) File "/usr/lib/python2.7/dist-packages/virtinst/VirtualDisk.py", line 669, in __init__ self.__validate_params() File "/usr/lib/python2.7/dist-packages/virtinst/VirtualDisk.py", line 1322, in __validate_params self.__set_format() File "/usr/lib/python2.7/dist-packages/virtinst/VirtualDisk.py", line 1101, in __set_format raise RuntimeError(_("Format cannot be specified for " RuntimeError: Format cannot be specified for unmanaged storage. -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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Users October 2014