Trac May 2011

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[Einstein Toolkit] #285: python simfactory submit does not remove active link after job execution has finished
by Einstein Toolkit 11 Jul '11

11 Jul '11

#285: python simfactory submit does not remove active link after job execution has finished ----------------------------------------------+----------------------------- Reporter: alexander.beck-ratzka@… | Type: defect Status: new | Priority: major Milestone: | Component: Other Version: | Keywords: ----------------------------------------------+----------------------------- The python version of simfactory does not remove the active link output-xxxx-active in the simulation directory, after a job has finished. As a consequence the next submit fails with the error message, that more then one active link has been found. Removing the link manually enables a poper submit of the next job. The problem occurs on a lustre file system. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/285> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #419: CarpetRegrid2 sets up grids which are not consistent
by Einstein Toolkit 06 Jul '11

06 Jul '11

#419: CarpetRegrid2 sets up grids which are not consistent --------------------+------------------------------------------------------- Reporter: knarf | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: | --------------------+------------------------------------------------------- The attached parfile creates a grid using CarpetRegrid2 (hg version), which CarpetReduce later warns about: INFO (CarpetReduce): Simulation domain volume: 4096 INFO (CarpetReduce): Reduction weight sum: 4468.125 WARNING[L1,P0] (CarpetReduce): Simulation domain volume and reduction weight sum differ The grid info is: INFO (Carpet): Grid structure (superregions, grid points): [0][0][0] exterior: [0,0,0] : [21,21,21] ([22,22,22] + PADDING) 10648 [1][0][0] exterior: [3,3,3] : [40,40,40] ([38,38,38] + PADDING) 54872 [2][0][0] exterior: [9,9,9] : [42,42,42] ([34,34,34] + PADDING) 39304 [3][0][0] exterior: [21,21,21] : [52,52,52] ([32,32,32] + PADDING) 32768 [4][0][0] exterior: [45,45,45] : [72,72,72] ([28,28,28] + PADDING) 21952 INFO (Carpet): Grid structure (superregions, coordinates): [0][0][0] exterior: [-48,-48,-48] : [288,288,288] : [16,16,16] [1][0][0] exterior: [-24,-24,-24] : [272,272,272] : [8,8,8] [2][0][0] exterior: [-12,-12,-12] : [120,120,120] : [4,4,4] [3][0][0] exterior: [-6,-6,-6] : [56,56,56] : [2,2,2] [4][0][0] exterior: [-3,-3,-3] : [24,24,24] : [1,1,1] -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/419> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #381: Cannot log in to Kraken using default simfactory configuration
by Einstein Toolkit 06 Jul '11

06 Jul '11

#381: Cannot log in to Kraken using default simfactory configuration ------------------------+--------------------------------------------------- Reporter: hinder | Owner: mthomas Type: defect | Status: new Priority: major | Milestone: ET_2011_05 Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- SimFactory uses the gsissh method to connect to Kraken. This requires a "proxy" to be created locally via the myproxy-logon command. There is currently logic in Perl simfactory's mdb.pm file to automatically run myproxy-logon and prompt for the passphrase. This does not work for me. I get the error Failed to receive credentials. ERROR from myproxy-server (myproxy.teragrid.org): PAM authentication failed: Permission denied (see below for the full output). If I remove the localsshsetup key, I can run the myproxy-logon command manually and then connect using simfactory. Looking at the full output below, it seems that it is trying to run myproxy-logon with my local username (ian) instead of the remote one (hinder). If I replace the @USER@ in the myproxy-logon command with my Kraken username, everything works as expected. MacBook:etrelease ian$ sim login kraken Simulation Factory: Executing: { mkdir -p /Users/ian/Cactus/etrelease/.globus && : >> /Users/ian/Cactus/etrelease/.globus/proxy-teragrid && chmod go-rwx /Users/ian/Cactus/etrelease/.globus/proxy-teragrid && export X509_USER_PROXY=/Users/ian/Cactus/etrelease/.globus/proxy-teragrid && : mkdir -p /Users/ian/Cactus/etrelease/.globus/certificates-teragrid && : export X509_CERT_DIR=/Users/ian/Cactus/etrelease/.globus/certificates- teragrid && { { grid-proxy-info -issuer -file /Users/ian/Cactus/etrelease/.globus /proxy-teragrid 2>/dev/null | grep "^/C=US/O=National Center for Supercomputing Applications/" >/dev/null 2>/dev/null && test $(grid-proxy-info -timeleft -file /Users/ian/Cactus/etrelease/.globus/proxy-teragrid 2>/dev/null) -gt 0 2>/dev/null } || { { grid-proxy-destroy 2>/dev/null || true; } && myproxy-logon -p 7514 -s myproxy.teragrid.org -T -l ian -o /Users/ian/Cactus/etrelease/.globus/proxy-teragrid } } && { globus-update-certificate-dir > /dev/null 2>&1 || true; }; } && gsissh -t hinder(a)kraken-gsi2.nics.teragrid.org '{ source /etc/profile; } && cd /nics/b/home/hinder/Cactus/etrelease && $SHELL -l' Enter MyProxy pass phrase: Failed to receive credentials. ERROR from myproxy-server (myproxy.teragrid.org): PAM authentication failed: Permission denied -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/381> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #113: Simfactory should be able to run the Cactus testsuites
by Einstein Toolkit 05 Jul '11

05 Jul '11

#113: Simfactory should be able to run the Cactus testsuites -------------------------+-------------------------------------------------- Reporter: knarf | Owner: mthomas Type: enhancement | Status: new Priority: critical | Milestone: ET_2011_06 Component: SimFactory | Version: Keywords: | -------------------------+-------------------------------------------------- ... in the python version, before the next ET release. The scripts at http://einsteintoolkit.org/release-info/ might help with implementing that. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/113> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #372: Accept comments in multi-line strings in parameter files
by Einstein Toolkit 02 Jul '11

02 Jul '11

#372: Accept comments in multi-line strings in parameter files -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- The attached patch modifies the parameter file parser to accept comments in multi-line strings. These comments extend from a "#" character to the end of the line. This makes it much easier to comment out variables in output strings. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/372> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #349: pyc files when syncing
by Einstein Toolkit 23 Jun '11

23 Jun '11

#349: pyc files when syncing ---------------------------+------------------------------------------------ Reporter: barry.wardell | Owner: mthomas Type: defect | Status: new Priority: major | Milestone: Component: SimFactory | Version: Keywords: | ---------------------------+------------------------------------------------ When I use 'sim sync' to copy files to a machine, it often rsyncs several .pyc files in the SimFactory directory. This happens every time I sync after running a simfactory command on the remote machine. I think these files should probably be excluded from the sync process. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/349> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #442: Restructure grid hierarchy properties
by Einstein Toolkit 14 Jun '11

14 Jun '11

#442: Restructure grid hierarchy properties -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: eschnett Type: enhancement | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: | -------------------------+-------------------------------------------------- Some time ago, someone (can't find the email right now) reported problems with CarpetRegrid2, where the grid structure may be inconsistent. I have restructured the code, but since this is a fairly invasive change I would like this to be thoroughly tested before committing it. This change may lead to Carpet using a (slightly) different grid structure than before. The differences are not "important"; what potentially changes is the order in which consistency conditions are applied. I expect that, in most cases, there will be no differences. The list of consistency conditions is: - ensure proper nesting (level must be larger than next finer level) - add buffer zones (only once, not really a consistency condition) - combine regions into a single box (if this is efficient) - apply rotating 90/180 symmetry (if requested) - clip at outer boundary (so that boxes that are too large or are outside are cut off) I attach a patch and four new files that implement this restructuring. Give it a try if you are interested. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/442> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #441: Use LoopControl in WeylScal4
by Einstein Toolkit 08 Jun '11

08 Jun '11

#441: Use LoopControl in WeylScal4 -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- I suggest to use LoopControl in WeylScal4: $ svn diff Index: WeylScal4.m =================================================================== --- WeylScal4.m (revision 73) +++ WeylScal4.m (working copy) @@ -296,6 +296,7 @@ Calculations -> calculations, DeclaredGroups -> declaredGroupNames, PartialDerivatives -> derivatives, + UseLoopControl -> True, KeywordParameters -> keywordParameters, RealParameters -> realParameters, InheritedImplementations -> {"admbase", "methodoflines"}]; -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/441> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #316: Checkpoint recovery nonfunctional
by Einstein Toolkit 23 May '11

23 May '11

#316: Checkpoint recovery nonfunctional ------------------------+--------------------------------------------------- Reporter: hinder | Owner: mthomas Type: defect | Status: new Priority: blocker | Milestone: Component: SimFactory | Version: Keywords: regression | ------------------------+--------------------------------------------------- Checkpoint recovery is nonfunctional in SimFactory 2 (it has broken since it was last fixed in ticket #60). Using the attached parameter file, I submit a simulation on Datura: simfactory2/bin/sim --machine datura --config sim2_datura create-submit parfiles/cptest.par 12 1:00:00 This parameter file terminates the Cactus run after 1 minute and dumps a checkpoint file. I then manually remove the output-0000-active symlink, as the automatic cleanup in the main() function is cleaning up restarts that are attempting to run, so I have disabled it, and manual cleanup doesn't work (see ticket #315). I then resubmit the simulation simfactory2/bin/sim --machine datura submit parfiles/cptest.par and observe that the checkpoint files from the first restart are never hardlinked into the output directory. The job does not recover, and instead starts from initial data. Log file is attached. Looking at the code, it appears that the checkpoint linking is conditional on the from-restart-id parameter being passed to simfactory, which I think is something to do with job-chaining. I can't see anywhere in the code which sets this option, so this is probably why the linking is not happening. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/316> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #435: double instead of CCTK_REAL in two routines in GRHydro
by Einstein Toolkit 23 May '11

23 May '11

#435: double instead of CCTK_REAL in two routines in GRHydro -----------------------------------+---------------------------------------- Reporter: jtao | Owner: Type: enhancement | Status: new Priority: optional | Milestone: ET_2011_11 Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- There are two places in GRHydro code that variables are declared using double. It will be better to use CCTK_REAL instead. It makes it easier to check various things by setting REAL_PRECISION in the config file. GRHydro/src/GRHydro_Con2PrimM_pt.c: register double ftmp,gtmp; GRHydro/src/GRHydro_Con2PrimM_pt.c: double gam_m1_o_gam = ((gammaeos-1.)/gammaeos); -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/435> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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