Users April 2015

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14 participants
19 discussions

Problem with butch submission on XC30 CFCA.
by Max Barkov 20 Apr '15

20 Apr '15

Dear Sir or Madam, I have problem with submission of jobs on Cray XC30 in CFCA NAOJ. I used script which is similar to edison cluster (also XC30). Unfortunately, I have a problem if I submit the job ET/Cactus> simfactory/bin/sim run cir_1 --configuration whisky_15 --parfile=par/Collapsar.par --procs=48 --machine=cfca_intel I got the diagnostic: *Simulation name: cir_1* *Assigned restart id: 0 * *Running simulation cir_1* *ModuleCmd_Switch.c(172):ERROR:152: Module 'PrgEnv-cray' is currently not loaded* *Preparing:* *+ set -e* *+ cd /work/barkovmm/ET_simulations/cir_1/output-0000-active* *+ module list* *++ /opt/modules/3.2.6.7/bin/modulecmd <http://3.2.6.7/bin/modulecmd> bash list* *Currently Loaded Modulefiles:* * 1) modules/3.2.6.7 <http://3.2.6.7> 10) cray-libsci/13.0.1 19) alps/5.2.1-2.0502.8712.10.32.ari* * 2) eswrap/1.1.0-1.020200.1130.0 11) udreg/2.3.2-1.0502.8763.1.11.ari 20) rca/1.0.0-2.0502.51491.3.92.ari* * 3) switch/1.0-1.0502.51632.2.84.ari 12) ugni/5.0-1.0502.9037.7.26.ari 21) atp/1.7.5* * 4) craype-network-aries 13) pmi/5.0.5-1.0000.10300.134.8.ari 22) PrgEnv-intel/5.2.25* * 5) craype/2.2.0 14) dmapp/7.0.1-1.0502.9080.9.32.ari 23) cray-hdf5/1.8.13* * 6) pbs/12.2.3.141156 15) gni-headers/3.0-1.0502.9038.7.4.ari 24) cray-petsc/3.5.1.0 <http://3.5.1.0>* * 7) craype-haswell 16) xpmem/0.1-2.0502.51169.1.11.ari 25) fftw/3.3.4.0 <http://3.3.4.0>* * 8) cray-mpich/7.0.3 17) job/1.5.5-0.1_2.0502.52111.3.39.ari 26) gsl/115* * 9) intel/15.0.0.090 <http://15.0.0.090> 18) csa/3.0.0-1_2.0502.51200.1.108.ari 27) papi/5.3.2* *+ eval* *+ echo Checking:* *Checking:* *+ pwd* */work/barkovmm/ET_simulations/cir_1/output-0000-active* *+ hostname* *xc01* *+ date* *2015年 4月 20日月曜日 16:01:23 JST* *+ echo Environment:* *Environment:* *+ export CACTUS_NUM_PROCS=4* *+ CACTUS_NUM_PROCS=4* *+ export CACTUS_NUM_THREADS=12* *+ CACTUS_NUM_THREADS=12* *+ export GMON_OUT_PREFIX=gmon.out* *+ GMON_OUT_PREFIX=gmon.out* *+ export OMP_NUM_THREADS=12* *+ OMP_NUM_THREADS=12* *+ env* *+ sort* *+ export 'NODE_PROCS=-N 2'* *+ NODE_PROCS='-N 2'* *+ export 'SOCKET_PROCS=-S 1'* *+ SOCKET_PROCS='-S 1'* *+ export CORE_PROCS=* *+ CORE_PROCS=* *+ echo Starting:* *Starting:* *++ date +%s* *+ export CACTUS_STARTTIME=1429513283* *+ CACTUS_STARTTIME=1429513283* *+ aprun -cc numa_node -n 4 -d 12 -N 2 -S 1 /work/barkovmm/ET_simulations/cir_1/SIMFACTORY/exe/cactus_whisky_15 -L 3 /work/barkovmm/ET_simulations/cir_1/output-0000/Collapsar.par* */work/barkovmm/ET_simulations/cir_1/output-0000/SIMFACTORY/RunScript: line 39: aprun: command not found* *2015年 4月 20日月曜日 16:01:23 JST* *Simfactory Done at date: 0* As I understand, Runscript is launched not through qsub system. grep command can't find qsub word in the current configuration grep -irn qsub ./config/whisky_15/. In the machine configuration file I have: *submit = qsub @SCRIPTFILE@* *getstatus = qstat @JOB_ID@* *stop = qdel @JOB_ID@* *submitpattern = (\d+)[.]* *statuspattern = ^@JOB_ID@[. ]* *queuedpattern = " Q "* *runningpattern = " R "* *holdingpattern = " H "* *scratchbasedir = /work/@USER@* *exechost = qstat -f @JOB_ID@* Which additional information I can supply? Thank you in advance, Maxim Barkov.

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Llamacode.org
by Erik Schnetter 16 Apr '15

16 Apr '15

I hear that the Llamacode.org web site is down. Llama is hosted on Bitbucket, and the respective url <http://llamacode.bitbucket.org> is still working fine. Please go there for instructions, and to download the code. -erik -- Erik Schnetter <schnetter(a)cct.lsu.edu> http://www.perimeterinstitute.ca/personal/eschnetter/

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Minutes for 2015-04-13
by Roland Haas 13 Apr '15

13 Apr '15

Hi, Present were: Frank Loeffler, Christine Corbett Moran, Roland Haas, Matt Kinsey, Joshua Faber, Erik Schnetter, Steve Brandt Running Cactus on Windows: * Erik tried the instructions that were proposed and could not get it to work * tried instructions from GitHub wiki and found that the cygwin config file in there refers to very old things * Frank has a window installation that he may try * the major use case is that first time users can use their own workstation/laptop Release: * Problems with Ubuntu/Fedora: add -lnuma to Linux option lists * Stampede update: Erik will check * Include staggered operators: Roalnd to merge, check on commented out code in coeffs_restrict_3d_stagger.hh, mark as experimental * inconsistent parameter range syntax: Roland to provide more details * outdated supported machine page: Roland to replace with pointer to tested machines page Next call will be in two weeks, April 27 2015 Roland

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Einstein Toolkit Meeting Reminder
by Frank Loeffler 12 Apr '15

12 Apr '15

Hi Please consider joining the weekly Einstein Toolkit phone call at 10 am US central time on Mondays. As usual, you can find instructions how to join on the following web site: http://einsteintoolkit.org/community/support/ In short: the number is (+1) 225-578-4942 and the conference id is 118682#. Frank Löffler

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Question about configuration of ET on Cray XC30
by Max Barkov 09 Apr '15

09 Apr '15

Hello, I try to install ET on the NAOJ (Japan) CFCA XC30 cluster. My laptop configuration of ET works fine but I failed to compile it on XC30. The default configuration on XC30 is cray environment. I try to adopt edison configuration to reality of CFCA (paths are different, some libs are absent). Could you please find in attachment my configuration files? Any suggestions are very welcome. For calculation of my code on CFCA I used following butch script: --------------------------------------------------------- #PBS -N test #PBS -q large-b #PBS -j oe #PBS -l mppwidth=648 #PBS -meb #PBS -M maxim.barkov(a)riken.jp cd $PBS_O_WORKDIR time aprun -n 648 ./a.out >& log.txt ---------------------------------------------------------- Thank you in advance, Maxim Barkov

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Einstein Toolkit installation question
by Lizao Li 08 Apr '15

08 Apr '15

Dear all, I am new to Einstein Toolkit and am having some difficulty installing it. My system is minimal Ubuntu 14.04 with basic build toolchain . I followed the instructions given and ran: curl -kLO > https://raw.githubusercontent.com/gridaphobe/CRL/ET_2014_11/GetComponents > chmod a+x GetComponents > ./GetComponents --parallel > https://bitbucket.org/einsteintoolkit/manifest/raw/ET_2014_11/einsteintoolk… > cd Cactus > make test > I removed BLAS and LAPACK from Cactus/configs/build/Thornlist because it complains that OpenBLAS does the same thing. Then I ran: make > test > > The build fails at compiling GRHydro: /opt/Cactus/configs/test/build/GRHydro/Utils.f90:2897.10: > > pointer (pg11,g11), (pg12,g12), (pg13,g13), (pg22,g22), (pg23,g23), > (pg33,g33) > 1 > Error: Cray pointer declaration at (1) requires -fcray-pointer flag > /opt/Cactus/configs/test/build/GRHydro/Utils.f90:2900.8: > > pg11 = loc(gaa) > 1 > Error: Symbol 'pg11' at (1) has no IMPLICIT type > /opt/Cactus/configs/test/build/GRHydro/Utils.f90:2901.8: > > pg12 = loc(gab) > 1 > Error: Symbol 'pg12' at (1) has no IMPLICIT type > /opt/Cactus/configs/test/build/GRHydro/Utils.f90:2902.8: > > pg13 = loc(gac) > 1 > Error: Symbol 'pg13' at (1) has no IMPLICIT type > /opt/Cactus/configs/test/build/GRHydro/Utils.f90:2903.8: > > pg22 = loc(gbb) > 1 > Error: Symbol 'pg22' at (1) has no IMPLICIT type > /opt/Cactus/configs/test/build/GRHydro/Utils.f90:2904.8: > > pg23 = loc(gbc) > 1 > Error: Symbol 'pg23' at (1) has no IMPLICIT type > /opt/Cactus/configs/test/build/GRHydro/Utils.f90:2905.8: > > pg33 = loc(gcc) > 1 > Error: Symbol 'pg33' at (1) has no IMPLICIT type > make[3]: *** [Utils.F90.o] Error 1 > make[2]: *** [make.checked] Error 2 > make[1]: *** [/opt/Cactus/configs/test/lib/libthorn_GRHydro.a] Error 2 > make: *** [test] Error 2 > My Fortran compiler is from Ubuntu: # gfortran --version > GNU Fortran (Ubuntu 4.8.2-19ubuntu1) 4.8.2 Thanks in advance for the help~ -- Lizao (Larry) Li Univeristy of Minnesota

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No Einstein Toolkit Meeting
by Frank Loeffler 05 Apr '15

05 Apr '15

Hi, There will not be an Einstein Toolkit meeting coming Monday. The next meeting will be in about one week on Monday, April 13th, at the usual time. Happy Easter! Frank Löffler

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Einstein Toolkit Meeting Reminder
by Roland Haas 04 Apr '15

04 Apr '15

1 0

ET on SPARC system.
by Max Barkov 02 Apr '15

02 Apr '15

Hello, I am new user of ET. Recently a get access to FUJITSU Supercomputer PRIMEHPC FX100. FX100, with high performance processors SPARC64 XIfx. FX100 have sparc and intel mpi environment. Any one have experience to work with SPARC64 system? I would be very appreciated for any related information and/or config files. Thank you in advance, Maxim Barkov

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Users April 2015