Trac February 2014

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141 discussions

[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] #1549: jobs starting/ending on stampede do not send emails
by Einstein Toolkit 30 Apr '14

30 Apr '14

#1549: jobs starting/ending on stampede do not send emails ------------------------+--------------------------------------------------- Reporter: anonymous | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: SimFactory | Version: development version Keywords: | ------------------------+--------------------------------------------------- jobs starting/ending on stampede do not send emails because stampede.sub lacks a line like: #SBATCH --mail-user= -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1549> Einstein Toolkit <http://einsteintoolkit.org> The Einstein Toolkit

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[Einstein Toolkit] #1541: WaveToy2D outputs what looks like unitiialized data
by Einstein Toolkit 28 Apr '14

28 Apr '14

#1541: WaveToy2D outputs what looks like unitiialized data --------------------------+------------------------------------------------- Reporter: rhaas | Owner: Type: defect | Status: new Priority: minor | Milestone: Component: Cactus | Version: development version Keywords: WaveToy2DF77 | --------------------------+------------------------------------------------- the test test_WaveToy2D in WaveToy2DF77 in the CactusExamples arrangement fails for me (with a [mostly] clean checkout): {{{ WaveToy2DF77: test_WaveToy2D Failure: 7 files compared, 6 differ, 6 differ significantly }}} attached are diff log and one of the data files. This happens with current trunk. It looks to me as if I am seeing poison. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1541> 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] #1497: CarpetInterp/waveinterp_1p and CarpetInterp/waveinterp_2p tests are failing
by Einstein Toolkit 26 Apr '14

26 Apr '14

#1497: CarpetInterp/waveinterp_1p and CarpetInterp/waveinterp_2p tests are failing --------------------+------------------------------------------------------- Reporter: hinder | Owner: eschnett Type: defect | Status: new Priority: minor | Milestone: Component: Carpet | Version: development version Keywords: | --------------------+------------------------------------------------------- The old tests CarpetInterp/waveinterp_1p and CarpetInterp/waveinterp_2p, which are almost identical apart from running on 1 or 2 processes, are both failing with the error {{{ ---------------------------------------------------------------- Iteration Time | WAVEMOL::phi | *VEMOL::phit | *VEMOL::phix | norm2 | norm2 | norm2 ---------------------------------------------------------------- 0 0.138 | -nan | -nan | -nan WARNING level 0 in thorn CarpetLib processor 0 host caltechcactusjenkins.spdns.org (line 428 of /home/jenkins/workspace/EinsteinToolkit/arrangements/Carpet/CarpetLib/src/gdata.cc): -> Internal error: extrapolation in time. variable=WAVEMOL::phi time=0.20000000000000001 times=[0.40000000000000002,0.67500000000000004,0.27500000000000002] WARNING level 0 in thorn CarpetLib processor 0 host caltechcactusjenkins.spdns.org (line 428 of /home/jenkins/workspace/EinsteinToolkit/arrangements/Carpet/CarpetLib/src/gdata.cc): -> Internal error: extrapolation in time. variable=WAVEMOL::phi time=0.20000000000000001 times=[0.40000000000000002,0.67500000000000004,0.27500000000000002] }}} This test is newly failing because the dependent thorn WaveMoL has only just been added to the toolkit. The tests had a parameter setting WaveMoL::num_timelevels = 3 which didn't correspond to any WaveMoL parameter, so previously the tests would crash earlier. I removed that parameter setting, and now the tests fail with this "extrapolation in time" error. I don't understand this failure. The times array seems to be non-monotonic [0.4, 0.675, 0.275] perhaps indicating that it might not have been initialised correctly? The coarse grid timestep should be 0.1*0.25 = 0.025, so I don't see where these times come from during iteration 1. The NaNs in the norms are probably poison, which probably wasn't enabled when this test was written, so nobody noticed. -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1497> 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] #1550: Carpet Timer object gives 0 the first time it is read
by Einstein Toolkit 25 Apr '14

25 Apr '14

#1550: Carpet Timer object gives 0 the first time it is read --------------------+------------------------------------------------------- Reporter: hinder | Owner: eschnett Type: defect | Status: new Priority: major | Milestone: ET_2014_05 Component: Carpet | Version: development version Keywords: | --------------------+------------------------------------------------------- The getTime method of the Carpet Timer object returns a value of 0 the first time it is read. The following test demonstrates the problem: {{{ SCHEDULE Timer_TestTimer at startup { LANG: C } "Test the timers" }}} {{{ #include <unistd.h> extern "C" int Timer_TestTimer() { Timer timer("Test"); timer.start(); unsigned int reason = sleep(1); double val = timer.getTime(); assert(reason != 0 || val > 0.5); timer.stop(); } }}} This is a regression since the original version of the Timer class, possibly introduced during the move of the class from Carpet to Timers. A symptom is that the evolution timer tree shows "inf" for the percentage of the total time the first time it is used, since the Evolve timer used to normalise the time values has been read as zero. The underlying Cactus timers do not suffer from this problem, so there is something wrong in the logic for the Timer class. The following test passes: {{{ SCHEDULE Timer_TestCactusTimers at startup { LANG: C } "Test the Cactus timers" }}} {{{ extern "C" int Timer_TestCactusTimers() { int handle = CCTK_TimerCreate("TestTimer"); cout << "handle == " << handle << endl; assert(handle >= 0); CCTK_TimerStartI (handle); unsigned int reason = sleep(1); CCTK_TimerStopI (handle); static cTimerData * timer = 0; if (not timer) timer = CCTK_TimerCreateData (); assert (timer); CCTK_TimerI (handle, timer); const cTimerVal* tv = CCTK_GetClockValue("gettimeofday", timer); assert(tv); double val = CCTK_TimerClockSeconds(tv); assert(reason != 0 || val > 0.5); return 0; } }}} -- Ticket URL: <https://trac.einsteintoolkit.org/ticket/1550> 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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Trac February 2014