Trac August 2012

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[Einstein Toolkit] #1004: adding or removing thorns to a thorn list triggers what seems to be a full recompile
by Einstein Toolkit 11 Aug '12

11 Aug '12

#1004: adding or removing thorns to a thorn list triggers what seems to be a full recompile --------------------+------------------------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | --------------------+------------------------------------------------------- this seems to be due to the parameter file structures in {{{ configs/configname/bindings/include/CParameterStructNames.h }}} being regenerated. At least "make -d" lists them as newer as the C source file dependency files. There seems to be only one such file for the whole configuration. My unsubstantiated guess is that this is because CParameterStructNames.h was one of the files that were excluded from dependency tracking prior to #768 (see eg line 182 of lib/make/make.config.defn.in in https://trac.einsteintoolkit.org/attachment/ticket/768/NoThornIs12.patch). Classified as minor since it is just extra careful, but try adding thorns on kraken to see just how annoying this can be :-) I will try and see what happens if I reinstate the dependency exclusions, but input of the patch author would be helpful to understand why the exclusions were removed (I assume they should no longer be required). -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1004> 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] #1036: Implement Riemann symmetries in WeylScal4
by Einstein Toolkit 11 Aug '12

11 Aug '12

#1036: Implement Riemann symmetries in WeylScal4 -----------------------------------+---------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- WeylScal4 calculates 81 instead of 21 (or 20) components of the Riemann tensor. This makes code and run time about four times larger than necessary. https://github.com/ianhinder/Kranc/issues/81 describes what to do. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1036> 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] #1016: External library dependencies not taken into account
by Einstein Toolkit 10 Aug '12

10 Aug '12

#1016: External library dependencies not taken into account ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: major | Milestone: Component: Cactus | Version: Keywords: | ----------------------+----------------------------------------------------- I find that dependencies between external libraries are not taken into account when creating the library link order. That is, "REQUIRES" and "OPTIONAL" specifications are ignored. I believe I have isolated the problem and will propose a patch soon. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1016> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1032: change HDF5's file open options to close all sub-file objects when a file is closed
by Einstein Toolkit 10 Aug '12

10 Aug '12

#1032: change HDF5's file open options to close all sub-file objects when a file is closed --------------------------+------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: enhancement | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: CarpetIOHDF5 | --------------------------+------------------------------------------------- this is strictly speaking not necessary, since any need for it is caused by a HDF5 object leak. On the other hand it does not hurt either additionally one could overload H5Fclose and warn the user when there are still open objects when a file is closed, ie: {{{ ////////////////////////////////////////////////////////////////////////////// // Close HDF5 file checking for leaked objects ////////////////////////////////////////////////////////////////////////////// static herr_t H5Fclose (hid_t file) { DECLARE_CCTK_PARAMETERS; herr_t retval; int error_count = 0; hsize_t objectcount; HDF5_ERROR (objectcount = H5Fget_obj_count(file, H5F_OBJ_ALL | H5F_OBJ_LOCAL)); if (objectcount > 1) { std::vector<char> fn; hsize_t sz_fn; HDF5_ERROR (sz_fn = H5Fget_name(file, NULL, 0)); fn.resize(sz_fn+1); HDF5_ERROR (H5Fget_name(file, &fn[0], fn.size())); CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING, "%d open HDF5 objects when closing file '%s'", int(objectcount)-1, &fn[0]); } HDF5_ERROR (retval = ::H5Fclose (file)); return retval; } }}} -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1032> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1030: defer (re)opening checkpoint files until we need to
by Einstein Toolkit 10 Aug '12

10 Aug '12

#1030: defer (re)opening checkpoint files until we need to --------------------------+------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: enhancement | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: CarpetIOHDF5 | --------------------------+------------------------------------------------- this patch defers opening checkpoint files until we need to do so because either we need to browse them or open a dataset for reading. This speeds up open_one_file_at_a_time since it will not open a hdf5 file that was already parsed and does not contain useful datasets. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1030> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1029: support indices in sequential chunked output files
by Einstein Toolkit 10 Aug '12

10 Aug '12

#1029: support indices in sequential chunked output files --------------------------+------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: CarpetIOHDF5 | --------------------------+------------------------------------------------- this patch makes sure that even the sequential file writer writes correct index files. Right now this writer is (always) used when Carpet runs on a single process. Generated index files are currently invalid since the MetaData group is written but nothing else. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1029> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1028: do not re-parse file when using open_one_input_file_at_a_time
by Einstein Toolkit 10 Aug '12

10 Aug '12

#1028: do not re-parse file when using open_one_input_file_at_a_time -------------------------+-------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: enhancement | Status: new Priority: minor | Milestone: Component: Carpet | Version: Keywords: | -------------------------+-------------------------------------------------- this patch retains the patch map created when reading a file even when the file itself is closed due to open_one_input_file_at_a_time. Since parsing the file is slow this can considerably speed up open_one_input_file_at_a_time. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1028> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac August 2012