# Issue runing 3D subduction **URL:** \ **Category:** PyLith\ **Created:** [May 13, 2021, 2:07am UTC](https://community.geodynamics.org/t/issue-runing-3d-subduction/1833 "2021-05-13T02:07:31Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![DRCCGEO](https://yyz2.discourse-cdn.com/flex036/user_avatar/community.geodynamics.org/drccgeo/32/578_2.png) [@DRCCGEO](https://community.geodynamics.org/u/DRCCGEO)\ **Post date:** [May 13, 2021, 2:07am UTC](https://community.geodynamics.org/t/issue-runing-3d-subduction/1833/1 "2021-05-13T02:07:31Z")
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$ ---
**Author:** ![baagaard](https://yyz2.discourse-cdn.com/flex036/user_avatar/community.geodynamics.org/baagaard/32/615_2.png) [@baagaard](https://community.geodynamics.org/u/baagaard)\ **Post date:** [May 13, 2021, 2:25am UTC](https://community.geodynamics.org/t/issue-runing-3d-subduction/1833/2 "2021-05-13T02:25:25Z")
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). ---
**Author:** ![DRCCGEO](https://yyz2.discourse-cdn.com/flex036/user_avatar/community.geodynamics.org/drccgeo/32/578_2.png) [@DRCCGEO](https://community.geodynamics.org/u/DRCCGEO)\ **Post date:** [May 13, 2021, 2:46am UTC](https://community.geodynamics.org/t/issue-runing-3d-subduction/1833/3 "2021-05-13T02:46:48Z")
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). > > * * * > > Visit Topic [2] or reply to this email to respond. > > To unsubscribe from these emails, click here [3]. > > - > > ## Links: > > [1] [Profile - baagaard - Computational Infrastructure for Geodynamics](https://community.geodynamics.org/u/baagaard) > [2] > [Issue runing 3D subduction - #2 by baagaard](https://community.geodynamics.org/t/issue-runing-3d-subduction/1833/2) > [3] > [Computational Infrastructure for Geodynamics](https://community.geodynamics.org/email/unsubscribe/5e7d59782be43b539436e038cc009a402c6d781fe6090d8342f32bca8e9de34c) > 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](https://community.geodynamics.org/uploads/short-url/pLjcTIJT0SIQRaN1wjifCwxj5b6.cfg) (3.56 KB) [mat\_elastic.cfg](https://community.geodynamics.org/uploads/short-url/p6ZER1wCSNPxIbyXEvGmt55ECqc.cfg) (2.08 KB) [pylithapp.cfg](https://community.geodynamics.org/uploads/short-url/wVIAIU3qVbWfv9nKrQEihI4OPkG.cfg) (6.61 KB) (Attachment Running script document is missing) ---
**Author:** ![DRCCGEO](https://yyz2.discourse-cdn.com/flex036/user_avatar/community.geodynamics.org/drccgeo/32/578_2.png) [@DRCCGEO](https://community.geodynamics.org/u/DRCCGEO)\ **Post date:** [May 13, 2021, 2:55am UTC](https://community.geodynamics.org/t/issue-runing-3d-subduction/1833/4 "2021-05-13T02:55:35Z")
El 2021-05-12 10:35 pm, Brad Aagaard via Computational Infrastructure for Geodynamics escribió: [Running script document.txt](https://community.geodynamics.org/uploads/short-url/lNBFEkyrnmEpaXRxE0etggs5djP.txt) (33.5 KB) [pylithapp.txt](https://community.geodynamics.org/uploads/short-url/3H1ioXNHdoWgtIAME2VcZrzOjnH.txt) (6.61 KB) [step01.cfg](https://community.geodynamics.org/uploads/short-url/pLjcTIJT0SIQRaN1wjifCwxj5b6.cfg) (3.56 KB) [mat\_elastic.cfg](https://community.geodynamics.org/uploads/short-url/p6ZER1wCSNPxIbyXEvGmt55ECqc.cfg) (2.08 KB) ---
**Author:** ![baagaard](https://yyz2.discourse-cdn.com/flex036/user_avatar/community.geodynamics.org/baagaard/32/615_2.png) [@baagaard](https://community.geodynamics.org/u/baagaard)\ **Post date:** [May 13, 2021, 3:10am UTC](https://community.geodynamics.org/t/issue-runing-3d-subduction/1833/5 "2021-05-13T03:10:21Z")
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`. ---
**Author:** ![DRCCGEO](https://yyz2.discourse-cdn.com/flex036/user_avatar/community.geodynamics.org/drccgeo/32/578_2.png) [@DRCCGEO](https://community.geodynamics.org/u/DRCCGEO)\ **Post date:** [May 13, 2021, 3:26am UTC](https://community.geodynamics.org/t/issue-runing-3d-subduction/1833/6 "2021-05-13T03:26:15Z")
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 ---
**Author:** ![willic3](https://yyz2.discourse-cdn.com/flex036/user_avatar/community.geodynamics.org/willic3/32/598_2.png) [@willic3](https://community.geodynamics.org/u/willic3)\ **Post date:** [May 13, 2021, 6:40am UTC](https://community.geodynamics.org/t/issue-runing-3d-subduction/1833/7 "2021-05-13T06:40:50Z")
What files are in your output directory? ---
**Author:** ![DRCCGEO](https://yyz2.discourse-cdn.com/flex036/user_avatar/community.geodynamics.org/drccgeo/32/578_2.png) [@DRCCGEO](https://community.geodynamics.org/u/DRCCGEO)\ **Post date:** [May 13, 2021, 11:41am UTC](https://community.geodynamics.org/t/issue-runing-3d-subduction/1833/8 "2021-05-13T11:41:21Z")
Thanks a lot Brad, I commented the last line of pylith.cfg script, and now it runs fine. ---
**Author:** ![DRCCGEO](https://yyz2.discourse-cdn.com/flex036/user_avatar/community.geodynamics.org/drccgeo/32/578_2.png) [@DRCCGEO](https://community.geodynamics.org/u/DRCCGEO)\ **Post date:** [May 13, 2021, 11:41am UTC](https://community.geodynamics.org/t/issue-runing-3d-subduction/1833/9 "2021-05-13T11:41:44Z")
Thanks Willic3, I commented the last line of pylith.cfg script, and now it runs fine.