Issue runing 3D subduction

PyLith
1

Hello Brad, a time ago I ran 3D subduction examples without troubles in my laptop. But today I tried to run again in my computer and also in a remote server, however, in both I get an issue/error. I attach the comments:

#End of PETSc Option Table entries
Compiled without FORTRAN kernels
Compiled with full precision matrices (default)
sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 sizeof(PetscScalar) 8 sizeof(PetscInt) 4
Configure options: --prefix=/home/brad/pylith-binary/dist --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1 --with-shared-libraries=1 --with-64-bit-points=1 --with-large-file-io=1 --download-chaco=1 --download-ml=1 --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0 --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist --with-zlib=1 --LIBS=-lz --with-debugging=0 --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include -I/home/brad/pylith-binary/dist/include " LDFLAGS="-L/home/brad/pylith-binary/dist/lib -L/home/brad/pylith-binary/dist/lib64 -L/home/brad/pylith-binary/dist/lib -L/home/brad/pylith-binary/dist/lib64 " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS= PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith PETSC_ARCH=arch-pylith

Libraries compiled on 2019-07-02 18:55:01 on brad-centos-6.9-amd64
Machine characteristics: Linux-2.6.32-754.15.3.el6.x86_64-x86_64-with-centos-6.10-Final
Using PETSc directory: /home/brad/pylith-binary/dist
Using PETSc arch:

Using C compiler: mpicc -g -O2 -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -I/home/brad/pylith-binary/dist/include -I/home/brad/pylith-binary/dist/include

Using include paths: -I/home/brad/pylith-binary/dist/include

Using C linker: mpicc
Using libraries: -Wl,-rpath,/home/brad/pylith-binary/dist/lib -L/home/brad/pylith-binary/dist/lib -lpetsc -Wl,-rpath,/home/brad/pylith-binary/dist/lib -L/home/brad/pylith-binary/dist/lib -lml -lf2clapack -lf2cblas -lhdf5_hl -lhdf5 -lchaco -lstdc++ -ldl -lz

dcardenas@neculman:~/pylith2/src/pylith-2.2.2/examples/3d/subduction$

2

I don’t see any error message here. This looks like the output associated with --petsc.log_summary. Please attach the complete output and state exactly how you are running pylith (for example, what command line arguments are you using).

3

El 2021-05-12 10:35 pm, Brad Aagaard via Computational Infrastructure
for Geodynamics escribió:

baagaard [1]
May 13

I don’t see any error message here. This looks like the output
associated with --petsc.log_summary. Please attach the complete output
and state exactly how you are running pylith (for example, what
command line arguments are you using).

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Issue runing 3D subduction - #2 by baagaard
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Computational Infrastructure for Geodynamics
Hello Brad, I attached the running files *.cfg and the running script
document

The command line is: pylith step01.cfg mat_elastic.cfg

Regards,

step01.cfg (3.56 KB)

mat_elastic.cfg (2.08 KB)

pylithapp.cfg (6.61 KB)

(Attachment Running script document is missing)

4

El 2021-05-12 10:35 pm, Brad Aagaard via Computational Infrastructure
for Geodynamics escribió:

Running script document.txt (33.5 KB)

pylithapp.txt (6.61 KB)

step01.cfg (3.56 KB)

mat_elastic.cfg (2.08 KB)

5

I don’t see any error in your “Running script document.txt” file. The simulation proceeded as expected. The information at the end is the “PETSc performance summary” that will appear when you run with --petsc.log_summary.

1 Like
6

But pylith doesn’t complete the step01 run, and for example I don’t get the step01-progress.txt, and the step01.xmf / step01.h5 files, and I can’t open the entire step output in Paraview

7

What files are in your output directory?

1 Like
8

Thanks a lot Brad, I commented the last line of pylith.cfg script, and now it runs fine.

9

Thanks Willic3, I commented the last line of pylith.cfg script, and now it runs fine.