When running scirpt: Files not found

[stobbe...@gmail.com]

Hello, I installed Mofem today and wanted to start the "Time dependent nonlinear mix formulation (unsaturated flow) simulation".
Unfortunately, I got the error that some files couldn't be found (e.g: ../../tools/mofem_part)
But I checked that the file is there. Adding the file extension .cpp, I could also open it.
I was also suprised that my script do_vtk.sh had the extension .sh.in
I then changed it to .sh and now I get 

I share my error message below.
I would be glad if anyone could help me :)

PS: I installed on WSL and installed through spack and installed all prequisites (afterwards).

Regards
Adrian

adrian:~/um_view/mix_transport$ ./run_uf.sh soil_impermeable.cub unsaturated.cfg 4 0.001 1 0

./run_uf.sh: line 47: ../../tools/mofem_part: No such file or directory

[0]MOAB ERROR: --------------------- Error Message ------------------------------------

[0]MOAB ERROR: out.h5m: No such file or directory!

[0]MOAB ERROR: serial_load_file() line 567 in src/Core.cpp

[0]MOAB ERROR: --------------------- Error Message ------------------------------------

[0]MOAB ERROR: Failed in step PARALLEL READ PART!

[0]MOAB ERROR: load_file() line 612 in src/ReadParallel.cpp

[0]MOAB ERROR: load_file() line 263 in src/ReadParallel.cpp

[0]MOAB ERROR: load_file() line 503 in src/Core.cpp

[0]MoFEM ERROR: --------------------- MoFEM Error Message ---------------------------------------------------

[0]MoFEM ERROR: MoFEM version 0.9.1 (MOAB 5.1.0 Petsc Release Version 3.11.3, Jun, 26, 2019 )

[0]MoFEM ERROR: MoFEM git commit id d7f7af40db97c6f08c21f029863f086e77fc8e30

[0]MoFEM ERROR: See http://mofem.eng.gla.ac.uk/mofem/html/guidelines_bug_reporting.html for bug reporting.

[0]MoFEM ERROR: Write to https://groups.google.com/forum/#!forum/mofem-group to seek help.

[0]MoFEM ERROR: MOAB error (16) MB_FAILURE

[0]MoFEM ERROR: #1 main() line 133 in /home/adrian/spack/var/spack/stage/mofem-users-modules-0.9.1-lmaoro3yhew4fz4wyqh2piitlp5rchxx/spack-src/basic_finite_elements/mix_transport/unsaturated_transport.cpp

#PETSc Option Table entries:

-configure unsaturated.cfg

-how_often_output 5

-ksp_type gmres

-my_file out.h5m

-my_max_post_proc_ref_level 0

-my_order 0

-pc_factor_mat_solver_package mumps

-pc_type lu

-snes_atol 1e-7

-snes_converged_reason

-snes_linesearch_damping 1.

-snes_linesearch_max_it 3

-snes_linesearch_minlambda 1e-3

-snes_linesearch_type l2

-snes_max_it 32

-snes_rtol 1e-4

-snes_stol 0

-snes_type newtonls

-ts_adapt_basic_safety 0.8

-ts_adapt_dt_max 0.005

-ts_adapt_dt_min 0.0001

-ts_adapt_monitor

-ts_adapt_type basic

-ts_alpha_adapt false

-ts_atol 0.01

-ts_dt 0.001

-ts_error_if_step_fails false

-ts_final_time 1

-ts_max_reject -1

-ts_max_snes_failures -1

-ts_monitor

-ts_rtol 0.01

-ts_theta_adapt false

-ts_type beuler

#End of PETSc Option Table entries

[0]MoFEM ERROR: -- MoFEM End of Error Message -- send entire error message to mofem...@googlegroups.com --

--------------------------------------------------------------------------

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD

with errorcode 110.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.

You may or may not see output from other processes, depending on

exactly when Open MPI kills them.

--------------------------------------------------------------------------

out_*h5m convert to out_*h5m

[0]MOAB ERROR: --------------------- Error Message ------------------------------------

[0]MOAB ERROR: out_*h5m: No such file or directory!

[0]MOAB ERROR: serial_load_file() line 567 in src/Core.cpp

[0]MOAB ERROR: load_file() line 514 in src/Core.cpp

Failed to load "out_*h5m".

Error code: MB_FILE_DOES_NOT_EXIST (7)

Error message: out_*h5m: No such file or directory

[Lukasz Kaczmraczyk]

Hello Adrian,

You have to edit run_ud.sh file, at line 47, location of mofem_part is different in your installation. You will find file mofem_part in $HOME/um_view/bin/mofem_part

.# Partition mesh

#../../tools/mofem_part  -my_file $MESHFILE -meshsets_config $CONFIGFILE -my_nparts $NBPROCS

$HOME/um_view/bin/mofem_part  -my_file $MESHFILE -meshsets_config $CONFIGFILE -my_nparts $NBPROCS

Regards,

Lukasz