Trac November 2013

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[Einstein Toolkit] #1473: Carpet segfaults in Shutdown
by Einstein Toolkit 16 May '14

16 May '14

#1473: Carpet segfaults in Shutdown --------------------+------------------------------------------------------- Reporter: knarf | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: development version Keywords: | --------------------+------------------------------------------------------- For high numbers of threads, Carpet segfaults in Shutdown for the testsuite CarpetWaveToyNewRecover_test_1proc. I tried this with gcc and intel on a Debian system. The machine I run this on (spine, with the default simfactory configurations) has 2 processors with 8 cores, and ht enabled. When I run this testsuite with 1 mpi process but certain numbers of threads (e.g. 9, 11, 16) I see this segfault. Which number triggers the bug seems to depend on the compiler, but seems to be consistent within tries. The backtrace I see is, e.g.,: {{{ 1. CarpetLib::signal_handler(int) [/home/knarf/ET_2013_11/exe/cactus_sim(_ZN9CarpetLib14signal_handlerEi+0xeb) [/home/knarf/ET_2013_11/configs/sim/build/CarpetLib/backtrace.cc:542] 2. /lib/x86_64-linux-gnu/libc.so.6(+0x324f0) [??:0] 3. /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x35) [??:0] 4. /lib/x86_64-linux-gnu/libc.so.6(abort+0x180) [??:0] 5. /lib/x86_64-linux-gnu/libc.so.6(+0x6d52b) [??:0] 6. /lib/x86_64-linux-gnu/libc.so.6(+0x76d76) [??:0] 7. /lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c) [??:0] 8. mem<double>::~mem() [/home/knarf/ET_2013_11/exe/cactus_sim(_ZN3memIdED1Ev+0x80) [/home/knarf/ET_2013_11/configs/sim/build/CarpetLib/mem.cc:185] 9. data<double>::free() [/home/knarf/ET_2013_11/exe/cactus_sim(_ZN4dataIdE4freeEv+0x4b) [/home/knarf/ET_2013_11/configs/sim/build/CarpetLib/data.cc:549] a. data<double>::~data() [/home/knarf/ET_2013_11/exe/cactus_sim(_ZN4dataIdED1Ev+0x27) [/home/knarf/ET_2013_11/configs/sim/build/CarpetLib/data.cc:487] b. data<double>::~data() [/home/knarf/ET_2013_11/exe/cactus_sim(_ZN4dataIdED0Ev+0x9) [/home/knarf/ET_2013_11/configs/sim/build/CarpetLib/data.cc:487] c. ggf::recompose_free(int) [/home/knarf/ET_2013_11/exe/cactus_sim(_ZN3ggf14recompose_freeEi+0x1ae) [/home/knarf/ET_2013_11/configs/sim/build/CarpetLib/ggf.cc:257] d. ggf::~ggf() [/home/knarf/ET_2013_11/exe/cactus_sim(_ZN3ggfD1Ev+0xde) [/home/knarf/ET_2013_11/configs/sim/build/CarpetLib/ggf.cc:70] e. gf<double>::~gf() [/home/knarf/ET_2013_11/exe/cactus_sim(_ZN2gfIdED0Ev+0x9) [/home/knarf/ET_2013_11/configs/sim/build/CarpetLib/gf.cc:30] f. Carpet::Shutdown(tFleshConfig*) [/home/knarf/ET_2013_11/exe/cactus_sim(_ZN6Carpet8ShutdownEP12tFleshConfig+0x3ad) [/home/knarf/ET_2013_11/configs/sim/build/Carpet/Shutdown.cc:102] 10. /home/knarf/ET_2013_11/exe/cactus_sim(main+0x49) [/home/knarf/ET_2013_11/configs/sim/build/Cactus/main/flesh.cc:92] 11. /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd) [??:0] 12. /home/knarf/ET_2013_11/exe/cactus_sim() [??:0] }}} Marking as minor because this is in Shutdown, however if something would actually check for this it might break workflows. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1473> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #590: McLachlan should allow other thorns to set the gauge
by Einstein Toolkit 28 Apr '14

28 Apr '14

#590: McLachlan should allow other thorns to set the gauge -----------------------------------+---------------------------------------- Reporter: bmundim | Owner: Type: defect | Status: new Priority: major | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: | -----------------------------------+---------------------------------------- The parameters lapse_evolution_method and shift_evolution_method are usually set to ML_BSSN in McLachlan. However they are never checked in the code. McLachlan indeed seems to ignore their values and overwrite whatever the values of lapse or shift set elsewhere, preventing therefore other thorns from setting them differently. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/590> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1495: Hopper doesn't pass test suite
by Einstein Toolkit 27 Apr '14

27 Apr '14

#1495: Hopper doesn't pass test suite ------------------------+--------------------------------------------------- Reporter: eschnett | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: Component: SimFactory | Version: development version Keywords: | ------------------------+--------------------------------------------------- There are many test suite failures on Hopper. The problem seems to be MPI errors when running on multiple nodes. I do not understand what is going wrong. I suspect a problem with our build or run options. I have asked NERSC for help. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1495> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1340: simfactory does not abort --testsuite submission process if rsync fails
by Einstein Toolkit 26 Apr '14

26 Apr '14

#1340: simfactory does not abort --testsuite submission process if rsync fails ------------------------+--------------------------------------------------- Reporter: rhaas | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: SimFactory | Version: Keywords: | ------------------------+--------------------------------------------------- when setting up testsuite runs simfactory uses rsync to copy the test suite data into the simulation folder. If this rsync fails (eg. because a user specified incorrect rsyncopts in defs.local.ini) the submission process does not abort and instead submits an emtpy test-suite run. {{{ rhaas@kraken-gsi2:~/ET_trunk> sim create-submit 2p6t --procs 12 --num- threads 6 --walltime 4:0:0 --tests uite --allocation TG-ASC120003 Skeleton Created Job directory: "/lustre/scratch/rhaas/simulations/2p6t" Option --testsuite given Executable: "/nics/c/home/rhaas/ET_trunk/exe/cactus_sim" Option list: "/lustre/scratch/rhaas/simulations/2p6t/SIMFACTORY/cfg/OptionList" Submit script: "/lustre/scratch/rhaas/simulations/2p6t/SIMFACTORY/run/SubmitScript" Run script: "/lustre/scratch/rhaas/simulations/2p6t/SIMFACTORY/run/RunScript" Assigned restart id: 0 Copying testsuite data rsync: --times=no: option does not take an argument rsync error: syntax or usage error (code 1) at main.c(1435) [client=3.0.9] Executing submit command: /opt/torque/2.5.7/bin/qsub /lustre/scratch/rhaas/simulations/2p6t/output-0000/SIMFACTORY/SubmitScript Submit finished, job id is 3236567.nid00016 rhaas@kraken-gsi2:~/ET_trunk> qdel 3236567.nid00016 }}} My rsynopts were: {{{ rsyncopts = --times=no --checksum --include 'configs/*/ThornList' --exclude 'configs/*/*' }}} which are bad for two reasons: 1.) kraken's rsync does not no --times-no (likely wants --notimes or so) 2.) --exclude 'configs/*/*' excludes cctk_MPI.h which is used by the test suite infrastructure to detect the presence of MPI Note that some of these options are obviously obsolete now that simfactory defaults to --times=no --checksum anyway. Still, simfactory should always check the exit status of any command it calls I think. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1340> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1359: add "read from file" option ot HydroBase's initial_data options
by Einstein Toolkit 25 Apr '14

25 Apr '14

#1359: add "read from file" option ot HydroBase's initial_data options -----------------------------------+---------------------------------------- Reporter: rhaas | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: EinsteinToolkit thorn | Version: Keywords: HydroBase | -----------------------------------+---------------------------------------- the attached patch adds a value "read from file" to HydroBase's initial_XXX options. This makes it possible to use IOUtils file reader with hydro data. This is somewhat similar to IDFileADM's extension of ADMBase's options, only we do not have to set any grid scalars. Needed to be able to reproduce the MHD paper's collapse test since Whisky_RNSID is not public. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1359> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1215: Source browsing not working
by Einstein Toolkit 24 Apr '14

24 Apr '14

#1215: Source browsing not working ----------------------------------+----------------------------------------- Reporter: hinder | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: EinsteinToolkit trac | Version: Keywords: | ----------------------------------+----------------------------------------- The repositories in the "Browse source" TRAC interface (https://trac.einsteintoolkit.org/browser) are not being updated. The last Cactus flesh commit visible there is from 10 months ago. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1215> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1493: testsuite Carpet/outer-buffers fails
by Einstein Toolkit 21 Apr '14

21 Apr '14

#1493: testsuite Carpet/outer-buffers fails --------------------+------------------------------------------------------- Reporter: knarf | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: ET_2014_05 Component: Carpet | Version: development version Keywords: | --------------------+------------------------------------------------------- The testsuite Carpet/outer-buffers fails because it sets the parameter Carpet::use_outer_buffer_zones which doesn't exist anymore. This testsuite was not usually run because a required thorn wasn't part of the toolkit. This now changed, triggering a failure in the regular builds and tests. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1493> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #849: Drop explicit support for Fortran 77 in Cactus
by Einstein Toolkit 19 Apr '14

19 Apr '14

#849: Drop explicit support for Fortran 77 in Cactus -------------------------+-------------------------------------------------- Reporter: eschnett | Owner: Type: enhancement | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | -------------------------+-------------------------------------------------- I suggest to drop explicit support for Fortran 77 in Cactus. Fortran 77 is, for all practical purposes, a subset of Fortran 90, and thus Fortran 77 code can be compiled by Fortran 90 compilers. There is currently no platform that has a Fortran 77 and no Fortran 90 compiler, and there is no Fortran source code in Cactus that cannot be compiled by a Fortran 90 compiler. In a way, supporting Fortran 77 as language is similar to supporting K&R C as a language. We don't do this either. I suggest to remove/ignore all configuration options regarding Fortran 77, and to compile .f77 and .F77 files with a Fortran 90 compiler. This change will simplify the configuration stage of Cactus. I don't expect any user to notice. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/849> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #882: Create ThornGuideHTML target
by Einstein Toolkit 14 Mar '14

14 Mar '14

#882: Create ThornGuideHTML target ----------------------+----------------------------------------------------- Reporter: eschnett | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: Keywords: | ----------------------+----------------------------------------------------- Barry Wardell suggests: The only issue is that there doesn't seem to be a HTML version of the configuration specific ThornGuide make target, so we should add this as a target at the same time as removing the patch. I'd imagine this would just be a matter of copy-and-paste from the existing ThornGuideHTML target. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/882> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1489: EinsteinExact (the arrangement) fails to build ThornGuideHTML
by Einstein Toolkit 14 Mar '14

14 Mar '14

#1489: EinsteinExact (the arrangement) fails to build ThornGuideHTML -----------------------------------+---------------------------------------- Reporter: knarf | Owner: Type: defect | Status: new Priority: major | Milestone: ET_2014_05 Component: EinsteinToolkit thorn | Version: development version Keywords: | -----------------------------------+---------------------------------------- EinsteinExact (the arrangement) fails to build ThornGuideHTML. The problem is the file spacetimes.tex which is included, but ThornGuideHTML is built outside of the doc directory, and cannot find it. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1489> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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Trac November 2013