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#2598: thornyflat - production run segmentation fault
by Maria 03 Mar '22

03 Mar '22

#2598: thornyflat - production run segmentation fault Reporter: Maria Status: new Milestone: Version: ET_2021_11 Type: bug Priority: major Component: Comment (by Maria): The helpdesk thinks that is an internal problem with Einstein Toolkit, bug or a bad software design, which has as result not checking for proper allocations. I suspect the problem is in the submit or run files. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2598/thornyflat-produc…

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#2578: Kranc, Cactus, and MPI linking issues
by Roland Haas 28 Feb '22

28 Feb '22

#2578: Kranc, Cactus, and MPI linking issues Reporter: Nicholas Hugh Olsen Status: closed Milestone: Version: ET_2021_05 Type: bug Priority: minor Component: Cactus Changes (by Roland Haas): status: closed (was new) Comment (by Roland Haas): Stale ticket. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2578/kranc-cactus-and-…

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#2590: Uninitialized variable in Perl code
by Roland Haas 28 Feb '22

28 Feb '22

#2590: Uninitialized variable in Perl code Reporter: Erik Schnetter Status: new Milestone: Version: development version Type: bug Priority: minor Component: Cactus Comment (by Roland Haas): Please apply. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2590/uninitialized-var…

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#2598: thornyflat - production run segmentation fault
by Maria 24 Feb '22

24 Feb '22

#2598: thornyflat - production run segmentation fault Reporter: Maria Status: new Milestone: Version: ET_2021_11 Type: bug Priority: major Component: Comment (by Maria): Again, the simulation gave me Segmentation Fault. In essence, the problem seems to be here: /scratch/mbh0012/simulations/tov/output-0000/SIMFACTORY/RunScript: line 24: 9372 Segmentation fault $core dumped$ mpiexec -n 1 -npernode 2 /scratch/mbh0012/simulations/tov/SIMFACTORY/exe/cactus\_etk -L 3 /scratch/mbh0012/simulations/tov/output-0000/static\_tov.par This can be traced to thornyflat.run, which is attached above. Most likely, there is an error in this line: mpiexec -n @NUM\_PROCS@ -npernode @$@PPN\_USED@ / @NUM\_THREADS@$@ @EXECUTABLE@ -L 3 @PARFILE@ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2598/thornyflat-produc…

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#2598: thornyflat - production run segmentation fault
by Maria 24 Feb '22

24 Feb '22

#2598: thornyflat - production run segmentation fault Reporter: Maria Status: new Milestone: Version: ET_2021_11 Type: bug Priority: major Component: Comment (by Maria): With the command: ./simfactory/bin/sim create-submit tov --configuration etk --machine=thornyflat --parfile=par/static\_tov.par --cores=10 ‌ I am getting the warnings: Warning: Current Working directory does not match Cactus sourcetree, changing to /users/mbh0012/Cactus … Warning: Too many threads per process specified: specified num-threads=20 $ppn-used is 40$ Warning: Total number of threads and number of threads per process are inconsistent: procs=10, num-threads=20 $procs\*num-smt must be an integer multiple of num-threads$ Warning: Total number of threads and number of cores per node are inconsistent: procs=10, ppn-used=40 $procs must be an integer multiple of ppn-used$ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2598/thornyflat-produc…

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#2597: Simfactory on Bridges2
by Maria 24 Feb '22

24 Feb '22

#2597: Simfactory on Bridges2 Reporter: Maria Status: new Milestone: Version: ET_2021_11 Type: task Priority: major Component: Comment (by Maria): Update: I changed the directories for MPI, HDF5, FFTW and OPENBLAS and the configuration built up to the end, when it gave this error: /ocean/projects/tra210033p/babiuc/Cactus/configs/etk/lib/libthorn\_IOHDF5.a$Write.c.o$: In function `IOHDF5_Write': /ocean/projects/tra210033p/babiuc/Cactus/arrangements/CactusPUGHIO/IOHDF5/src/Write.c:131: undefined reference to `H5Pset\_fapl\_mpio' /ocean/projects/tra210033p/babiuc/Cactus/configs/etk/lib/libthorn\_IOHDF5Util.a$DumpVar.c.o$: In function `WriteDataCollective': /ocean/projects/tra210033p/babiuc/Cactus/arrangements/CactusPUGHIO/IOHDF5Util/src/DumpVar.c:779: undefined reference to `H5Pset\_dxpl\_mpio' collect2: error: ld returned 1 exit status make\[1\]: \*\*\* \[/ocean/projects/tra210033p/babiuc/Cactus/lib/make/make.configuration:150: /ocean/projects/tra210033p/babiuc/Cactus/exe/cactus\_etk\] Error 1 make: \*\*\* \[Makefile:265: etk\] Error 2 -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2597/simfactory-on-bri…

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#2597: Simfactory on Bridges2
by Maria 22 Feb '22

22 Feb '22

#2597: Simfactory on Bridges2 Reporter: Maria Status: new Milestone: Version: ET_2021_11 Type: task Priority: major Component: Comment (by Maria): Oh, I'm sorry, I did not pay attention to that, and in fact the file I sent to you indeed did not have that header. The original file had the header [br012.ib.bridges2.psc.edu]. I changed it to [bridges2] and started to compile! ...only to stop at this error: MPI_DIR is set to a directory that does not exist (MPI_DIR = /opt/modulefiles/production/openmpi/4.0.5-gcc10.2.0.lua); continuing anyway No MPI compiler wrapper found beneath MPI_DIR (MPI_DIR = /opt/modulefiles/production/openmpi/4.0.5-gcc10.2.0.lua) ERROR: MPI could not be configured: neither automatic nor manual configuration succeeded CST error 1: -> Configuration script for thorn MPI returned exit code 5 Error message: 'MPI could not be configured: neither automatic nor manual configuration succeeded' The link seems correct, but it points to a file, not a directory. It seems that the file has the links to the library path. How shall I proceed? Maria -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2597/simfactory-on-bri…

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#2597: Simfactory on Bridges2
by Erik Schnetter 22 Feb '22

22 Feb '22

#2597: Simfactory on Bridges2 Reporter: Maria Status: new Milestone: Version: ET_2021_11 Type: task Priority: major Component: Comment (by Erik Schnetter): The file `bridges2.ini` is wrong. It is missing the section header `[bridges2]` in the beginning. Look at other ini files for examples. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2597/simfactory-on-bri…

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#2598: thornyflat - production run segmentation fault
by Maria 22 Feb '22

22 Feb '22

#2598: thornyflat - production run segmentation fault Reporter: Maria Status: new Milestone: Version: ET_2021_11 Type: bug Priority: major Component: Simfactory scripts for ThornyFlat give segmentation fault in production run. I am attaching the cfg, ini, run and sub scripts. In the simulations directory, the SIMFACTORY directory does not have inside the subdirectories: exe, cfg, run and par and NODES is empty. The only file is the properties.ini, which includes: \_\_\_\_ Loading torque version 6.1.3 : dev/torque/6.1.3 Loading openmpi version 4.1.2\_gcc112 : parallel/openmpi/4.1.2\_gcc112 Loading openblas version 0.3.19\_gcc112 : libs/openblas/0.3.19\_gcc112 \+ set -e \+ cd /scratch/mbh0012/simulations/bnsG2/output-0000-active \+ echo Checking: \+ pwd \+ hostname \+ date \+ cat \+ echo Environment: \+ export GMON\_OUT\_PREFIX=gmon.out \+ GMON\_OUT\_PREFIX=gmon.out \+ export CACTUS\_NUM\_PROCS=2 \+ CACTUS\_NUM\_PROCS=2 \+ export CACTUS\_NUM\_THREADS=20 \+ CACTUS\_NUM\_THREADS=20 \+ export OMP\_NUM\_THREADS=20 \+ OMP\_NUM\_THREADS=20 \+ env \+ sort \+ echo Starting: \+\+ date \+%s \+ export CACTUS\_STARTTIME=1642991790 \+ CACTUS\_STARTTIME=1642991790 \+ mpiexec -n 2 -npernode 2 /scratch/mbh0012/simulations/bnsG2/SIMFACTORY/exe/cactus\_nst -L 3 /scratch/mbh0012/simulations/bnsG2/output-0000/nsnstohmns.par \[trcis001:09698\] \*\*\* Process received signal \*\*\* \[trcis001:09698\] Signal: Segmentation fault $11$ \[trcis001:09698\] Signal code: $128$ \[trcis001:09698\] Failing at address: $nil$ \[trcis001:09698\] \[ 0\] /lib64/libpthread.so.0$\+0xf630$\[0x2b4fc7e60630\] \[trcis001:09698\] \[ 1\] /shared/software/parallel/openmpi/4.1.2\_gcc112/lib/libopen-rte.so.40$orte\_get\_attribute\+0x21$\[0x2b4fc6f4b101\] \[trcis001:09698\] \[ 2\] /shared/software/parallel/openmpi/4.1.2\_gcc112/lib/libopen-rte.so.40$orte\_plm\_base\_setup\_job\+0xf0$\[0x2b4fc6f83530\] \[trcis001:09698\] \[ 3\] /lib64/libevent\_core-2.0.so.5$event\_base\_loop\+0x774$\[0x2b4fc7a2f3a4\] \[trcis001:09698\] \[ 4\] mpiexec\[0x40133a\] \[trcis001:09698\] \[ 5\] /lib64/libc.so.6$\_\_libc\_start\_main\+0xf5$\[0x2b4fc808f555\] \[trcis001:09698\] \[ 6\] mpiexec\[0x40114e\] \[trcis001:09698\] \*\*\* End of error message \*\*\* /scratch/mbh0012/simulations/bnsG2/output-0000/SIMFACTORY/RunScript: line 24: 9698 Segmentation fault $core dumped$ mpiexec -n 2 -npernode 2 /scratch/mbh0012/simulations/bnsG2/SIMFACTORY/exe/cactus\_nst -L 3 /scratch/mbh0012/simulations/bnsG2/output-0000/nsnstohmns.par attachment: thornyflat.cfg (https://api.bitbucket.org/2.0/repositories/einsteintoolkit/tickets/issues/2…) attachment: thornyflat.ini (https://api.bitbucket.org/2.0/repositories/einsteintoolkit/tickets/issues/2…) attachment: thornyflat.run (https://api.bitbucket.org/2.0/repositories/einsteintoolkit/tickets/issues/2…) attachment: thornyflay.sub (https://api.bitbucket.org/2.0/repositories/einsteintoolkit/tickets/issues/2…) -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2598/thornyflat-produc…

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#2597: Simfactory on Bridges2
by Maria 22 Feb '22

22 Feb '22

#2597: Simfactory on Bridges2 Reporter: Maria Status: new Milestone: Version: ET_2021_11 Type: task Priority: major Component: Please help me set up simfactory in Bridges2, a PSC supercomputer. Works with SLURM. Here is the user guide: [https://www.psc.edu/resources/bridges-2/user-guide-2/](https://www.psc.edu/… My $PROJECT directory is /ocean/projects/tra210033p/babiuc and I think this is also where the simulations directory should reside. It does not have a “scratch“ directory. The command: `./simfactory/bin/sim setup-silent` creates a br012.ib.bridges2.psc.edu.ini file, which I renamed to bridges2.ini. I edited this file and created by hand bridges2.cgf, bridges2.sub and bridges2.run, which are attached. --- attachment: bridges2.cfg (https://api.bitbucket.org/2.0/repositories/einsteintoolkit/tickets/issues/2…) attachment: bridges2.ini (https://api.bitbucket.org/2.0/repositories/einsteintoolkit/tickets/issues/2…) attachment: bridges2.run (https://api.bitbucket.org/2.0/repositories/einsteintoolkit/tickets/issues/2…) attachment: bridges2.sub (https://api.bitbucket.org/2.0/repositories/einsteintoolkit/tickets/issues/2…) -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2597/simfactory-on-bri…

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