Trac April 2012

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[Einstein Toolkit] #745: the flesh allows two implemantion of the same interface to have different default values for restricted parameters
by Einstein Toolkit 05 Sep '12

05 Sep '12

#745: the flesh allows two implemantion of the same interface to have different default values for restricted parameters --------------------+------------------------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | --------------------+------------------------------------------------------- since the flesh creates paramters for all compiled in (rather than activated) thorns initially, this affects the default value that a thorn sees. Thorns seem to be initialized (and thus their parameter structures being created) in alphabetical order, which means that the thorn alphabetically '''last''' (How, I have no idea, the parameter handling logic seems a bit of a mess) will determine the default parameter value. Attached is a parameter file to demonstrate this with Carpet and PUGH who both declare parameters periodic and periodic_[xyz] but differ in their defaults. To demonstrate, create an executable with only Carpet compiled in and run the parameter file. Then look at the paramters in the checkpoint it creates eg. {{{ h5dump -r -d /Parameters\ and\ Global\ Attributes/All\ Parameters output/checkpoint.chkpt.it_0.h5 | grep periodic }}} Do the same with an executable that contains both PUGH and Carpet. Notice that parameter values are now PUGH's defaults. This can actually cause a runs to abort when recovering from a checkpoint when one switches from an executable with PUGH compiled in to one that does not. (Beyond the fact that some thorn might actually use it's parameters rather than the Carpet/PUGH pair where happily Carpet ignores these parameters and PUGH who actually used them gets to set the default). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/745> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #669: Rewrite users of deprecated HDF5 C++ API
by Einstein Toolkit 04 Sep '12

04 Sep '12

#669: Rewrite users of deprecated HDF5 C++ API ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: task | Status: new Priority: minor | Milestone: Component: Other | Version: Keywords: | ----------------------+----------------------------------------------------- The C++ API for HDF5 is decprecated. We should examine which code uses it, and rewrite it to use the C API instead. This would allow us to use more system-provided HDF5 installations. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/669> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #788: Produce movie about history of Einstein Toolkit
by Einstein Toolkit 17 Aug '12

17 Aug '12

#788: Produce movie about history of Einstein Toolkit ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: task | Status: new Priority: optional | Milestone: Component: Other | Version: Keywords: | ----------------------+----------------------------------------------------- Do this <https://www.youtube.com/watch?v=ZEAlhVOZ8qQ> for the Einstein Toolkit. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/788> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #531: Problem with adding/removing configuration.ccl files
by Einstein Toolkit 11 Aug '12

11 Aug '12

#531: Problem with adding/removing configuration.ccl files ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | ----------------------+----------------------------------------------------- Cactus doesn't handle well adding or removing configuration.ccl files. When a new configuration.ccl file is added, Cactus ignores it until the next "rebuild" (i.e. until another ccl file changes, until the thorn list changes, or until the user calls *-rebuild explicitly). When a configuration.ccl file is removed, make aborts with an error message, and a rebuild is forced. One way to remedy this would be to have (empty) configuration.ccl file in all thorns. After all, param.ccl and schedule.ccl files also need to be present even if they are empty. This would also remove a bit of complex logic from the Cactus make system. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/531> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #628: Configuring on Kraken leads to warnings
by Einstein Toolkit 11 Aug '12

11 Aug '12

#628: Configuring on Kraken leads to warnings -------------------------+-------------------------------------------------- Reporter: hinder | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- Using current simfactory to build on Kraken leads to the following warning during configuration: {{{ This is probably a Cray XT4 series system. Using known-architectures xt4-cray-linux This is an Cray XT4: you always need MPI! Forcing MPI to NATIVE. Unknown Linux f90 compiler. Please add appropriate information to /nics/d/home/hinder/Cactus/EinsteinToolkit/lib/make/known- architectures/linux and send the updated file to CactusMaint We will try anyway ... }}} Cactus should learn about this system. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/628> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #420: newest revision of simfactory 2.0 submit three instead of one job
by Einstein Toolkit 11 Aug '12

11 Aug '12

#420: newest revision of simfactory 2.0 submit three instead of one job ----------------------------------------------+----------------------------- Reporter: alexander.beck-ratzka@… | Owner: mthomas Type: defect | Status: new Priority: minor | Milestone: Component: SimFactory | Version: ET_2010_11 Keywords: | ----------------------------------------------+----------------------------- I am submitting a simulation using simfactory with the command: [snip] simfactory/bin/sim submit test-whisky-openmp --configuration test-whisky- openmp --parfile=whisky-openmp-test-ali.par --verbose --walltime=48:00:00 --procs=16 --ppn=4 --num-threads=4 --machine=damiana --queue=intel.q [snip] sim then comes with the messages: [snip] Info: Simfactory command: simfactory/bin/../lib/sim.py "submit" "test- whisky-openmp" "--configuration" "test-whisky-openmp" "--parfile=whisky- openmp-test-ali.par" "--verbose" "--walltime=48:00:00" "--procs=16" "-- ppn=4" "--num-threads=4" "--machine=damiana" "--queue=intel.q" Info: Version 1331M The Simulation Factory: Manage Cactus simulations Info: defs: /home/alibeck/programme/Cactus- Luca/Cactus/simfactory/etc/defs.ini Info: defs.local: /home/alibeck/programme/Cactus- Luca/Cactus/simfactory/etc/defs.local.ini Info: Cactus Directory: /home/alibeck/programme/Cactus-Luca/Cactus Info: simenv.COMMAND: submit Info: Executing command: submit Info: Assigned restart_id of: 0002 Info: Found the following restart_ids: [0, 1] Info: Maximum restart id determined to be: 0001 Assigned restart id: 2 Info: Simulation is inactive: submitting Info: Job allocation information: Info: System: nodes=170 cores/node=4 threads/process=4 Info: Requested: nodes=4 cores=16 cores/node=4 Info: Run: processes=4 threads=16 threads/process=4 Info: Distribution: processes/node=1 threads/node=4 Info: Ratio: threads/core=1.000 cores/thread=1.000 Info: writing to internalDir: /lustre/AEI/alibeck/simulations/test-whisky- openmp/output-0002/SIMFACTORY Info: saving substituted submitscript contents to: /lustre/AEI/alibeck/simulations/test-whisky- openmp/output-0002/SIMFACTORY/SubmitScript Executing submit command: qsub /lustre/AEI/alibeck/simulations/test- whisky-openmp/output-0002/SIMFACTORY/SubmitScript Submit finished, job id is 259460 Info: Restart 2 is active Info: Assigned restart_id of: 0003 Info: Found the following restart_ids: [0, 1, 2, 2] Info: Maximum restart id determined to be: 0002 Assigned restart id: 3 Info: Simulation is active: presubmitting Info: Job allocation information: Info: System: nodes=170 cores/node=4 threads/process=4 Info: Requested: nodes=4 cores=16 cores/node=4 Info: Run: processes=4 threads=16 threads/process=4 Info: Distribution: processes/node=1 threads/node=4 Info: Ratio: threads/core=1.000 cores/thread=1.000 Info: writing to internalDir: /lustre/AEI/alibeck/simulations/test-whisky- openmp/output-0003/SIMFACTORY Info: saving substituted submitscript contents to: /lustre/AEI/alibeck/simulations/test-whisky- openmp/output-0003/SIMFACTORY/SubmitScript Executing submit command: qsub /lustre/AEI/alibeck/simulations/test- whisky-openmp/output-0003/SIMFACTORY/SubmitScript Submit finished, job id is 259461 Info: Restart 2 is active Info: Assigned restart_id of: 0004 Info: Found the following restart_ids: [0, 1, 2, 2, 3] Info: Maximum restart id determined to be: 0003 Assigned restart id: 4 Info: Simulation is active: presubmitting Info: Job allocation information: Info: System: nodes=170 cores/node=4 threads/process=4 Info: Requested: nodes=4 cores=16 cores/node=4 Info: Run: processes=4 threads=16 threads/process=4 Info: Distribution: processes/node=1 threads/node=4 Info: Ratio: threads/core=1.000 cores/thread=1.000 Info: writing to internalDir: /lustre/AEI/alibeck/simulations/test-whisky- openmp/output-0004/SIMFACTORY Info: saving substituted submitscript contents to: /lustre/AEI/alibeck/simulations/test-whisky- openmp/output-0004/SIMFACTORY/SubmitScript Executing submit command: qsub /lustre/AEI/alibeck/simulations/test- whisky-openmp/output-0004/SIMFACTORY/SubmitScript Submit finished, job id is 259462 [snip] As a result three jobs are queued. [snip] qstat job-ID prior name user state submit/start at queue slots ja-task-ID ----------------------------------------------------------------------------------------------------------------- 259460 0.00000 test-whisk alibeck qw 04/29/2011 10:26:55 16 259461 0.00000 test-whisk alibeck hqw 04/29/2011 10:26:56 16 259462 0.00000 test-whisk alibeck hqw 04/29/2011 10:26:56 16 [snip] What is going wrong here? -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/420> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #380: AHFinderDirect failure with qc0-mclachlan.par
by Einstein Toolkit 10 Aug '12

10 Aug '12

#380: AHFinderDirect failure with qc0-mclachlan.par --------------------+------------------------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: major | Milestone: ET_2011_05 Component: Other | Version: Keywords: | --------------------+------------------------------------------------------- Trying to run the par/qc0-mclachlan.par in the ET trunk gives the following error: INFO (AHFinderDirect): proc 0: searching for horizons 1,5/6 WARNING level 0 in thorn CarpetInterp processor 0 host kop193.datura.admin (line 1683 of /home/ianhin/Cactus/etrelease/arrangements/Carpet/CarpetInterp/src/interp.cc): -> Grid function "AHFINDERDIRECT::ahmask" has only 1 active time levels on refinement level 1; this is not en ough for time interpolation See also #373, which might be related. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/380> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #676: GRHydro/MHD ist not fully multipatch aware yet
by Einstein Toolkit 10 Aug '12

10 Aug '12

#676: GRHydro/MHD ist not fully multipatch aware yet -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: GRHydro | -----------------------------------+---------------------------------------- eg. ReconstructPoly uses Bvec and vel directly. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/676> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #488: Reduce space taken by Formaline tarballs
by Einstein Toolkit 10 Aug '12

10 Aug '12

#488: Reduce space taken by Formaline tarballs -------------------------+-------------------------------------------------- Reporter: hinder | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: Formaline | -------------------------+-------------------------------------------------- When syncing lightweight data of simulations from a cluster, much of the time and disk space on the local system is taken with Formaline tarballs. It would be good to reduce this. I propose opportunistically replacing the generated tarballs with hard- links to existing tarballs on the same filesystem after Formaline has written them to the new output directory if the files compare equal. These could be from previous restarts of the same simulation when using simfactory. Then, if an entire simulation is rsynced with the appropriate options, hard-links will be transferred as hard-links, and the overall transfer time and disk space used will be significantly reduced. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/488> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #708: Cannot submit on Surveyor
by Einstein Toolkit 10 Aug '12

10 Aug '12

#708: Cannot submit on Surveyor ------------------------+--------------------------------------------------- Reporter: eschnett | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- Surveyor is a BlueGene/P, and the operating system apparently does not support hard links. Submitting a job via Simfactory fails: DISTRIBUTE: Executing: ./simfactory/bin/sim --remote surveyor create- submit testsuite-surveyor-2011.12.21-19.31.05 --testsuite --parfile=recover.par --walltime=2:00:00 --procs=4 --ppn-used=4 --num- threads=2 Skeleton Created Job directory: "/pvfs-surveyor/eschnett/simulations/testsuite- surveyor-2011.12.21-19.31.05" Executable: "/gpfs/home/eschnett/Cbeta/exe/cactus_sim" Option list: "/pvfs-surveyor/eschnett/simulations/testsuite- surveyor-2011.12.21-19.31.05/SIMFACTORY/cfg/OptionList" Submit script: "/pvfs-surveyor/eschnett/simulations/testsuite- surveyor-2011.12.21-19.31.05/SIMFACTORY/run/SubmitScript" Run script: "/pvfs-surveyor/eschnett/simulations/testsuite- surveyor-2011.12.21-19.31.05/SIMFACTORY/run/RunScript" Assigned restart id: 0 Copying testsuite data Traceback (most recent call last): File "/home/eschnett/Cbeta/simfactory/bin/../lib/sim.py", line 147, in ? main() File "/home/eschnett/Cbeta/simfactory/bin/../lib/sim.py", line 143, in main CommandDispatch() File "/home/eschnett/Cbeta/simfactory/bin/../lib/sim.py", line 105, in CommandDispatch module.main() File "/gpfs/home/eschnett/Cbeta/simfactory/lib/sim-manage.py", line 397, in main CommandDispatch() File "/gpfs/home/eschnett/Cbeta/simfactory/lib/sim-manage.py", line 376, in CommandDispatch exec("command_%s()" % command) File "<string>", line 1, in ? File "/gpfs/home/eschnett/Cbeta/simfactory/lib/sim-manage.py", line 161, in command_create_submit command_submit() File "/gpfs/home/eschnett/Cbeta/simfactory/lib/sim-manage.py", line 262, in command_submit restart.userSubmit(simulationName) File "/gpfs/home/eschnett/Cbeta/simfactory/lib/simrestart.py", line 346, in userSubmit self.submit(submitScript) File "/gpfs/home/eschnett/Cbeta/simfactory/lib/simrestart.py", line 739, in submit self.copyTestsuiteData() File "/gpfs/home/eschnett/Cbeta/simfactory/lib/simrestart.py", line 487, in copyTestsuiteData os.link(self.Properties.executable, os.path.join(testexe,simlib.BaseName(self.Properties.executable))) OSError: [Errno 95] Operation not supported Simfactory should catch this, and should copy the file if it cannot be linked. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/708> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac April 2012