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Problem on running validate_telemac.py on ubuntu 20.04
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TOPIC: Problem on running validate_telemac.py on ubuntu 20.04

Problem on running validate_telemac.py on ubuntu 20.04 3 years 11 months ago #37285

  • GuillaumeDt
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Hi,
I compiled the version 8p2r0 on an ubuntu 20.04 machine. The compilation was ok and the api was built.
When i try to validate telemac with validate_telemac.py, i have the following errors:
import _hermes
ImportError: ~/telemac-mascaret/v8p2r0/builds/gfortran/wrap_api/lib/_hermes.cpython-38-x86_64-linux-gnu.so: undefined symbol: _gfortran_st_close
unable to load the dynamic library _hermes.so
You can check the environment variable: PYTHONPATH
~/telemac-mascaret/v8p2r0/builds/gfortran/wrap_api/lib/_hermes.cpython-38-x86_64-linux-gnu.so: undefined symbol: _gfortran_st_close

I can not fix the problem, if anyone can help ...

Thanks
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Problem on running validate_telemac.py on ubuntu 20.04 3 years 11 months ago #37287

  • yugi
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Hi,

Can you try adding -lgfortran to libs_all in your systel.cfg under [general] and in the parallel config.

That might solve the issue
There are 10 types of people in the world: those who understand binary, and those who don't.
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Problem on running validate_telemac.py on ubuntu 20.04 3 years 11 months ago #37288

  • GuillaumeDt
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Thanks! It solves the initial problem but i have a parallel inconsistency now:
Parallel inconsistency:
+> you may be using an inappropriate configuration: gfortran
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Problem on running validate_telemac.py on ubuntu 20.04 3 years 11 months ago #37290

  • GuillaumeDt
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Thanks! It solves the initial problem but for parallel config i receive the following error
In ~/telemac-mascaret/v8p2r0/examples/artemis/G8M/vnv_g8m/vnv_1/gfortranHPC/tmp_vnv_1:
mpirun -machinefile MPI_HOSTFILE -np 1 ~/telemac-mascaret/v8p2r0/examples/artemis/G8M/vnv_g8m/vnv_1/gfortranHPC/tmp_vnv_1/out_user_fortran

[Laptop:246576] *** An error occurred in MPI_Comm_rank
[Laptop:246576] *** reported by process [1989607425,0]
[Laptop:246576] *** on communicator MPI_COMM_WORLD
[Laptop:246576] *** MPI_ERR_COMM: invalid communicator
[Laptop:246576] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[Laptop:246576] *** and potentially your MPI job)

utils.exceptions.TelemacException: Fail to run
mpirun -machinefile MPI_HOSTFILE -np 1 ~/telemac-mascaret/v8p2r0/examples/artemis/G8M/vnv_g8m/vnv_1/gfortranHPC/tmp_vnv_1/out_user_fortran
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Problem on running validate_telemac.py on ubuntu 20.04 3 years 11 months ago #37297

  • yugi
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Hi,

I think there is a conflict with you MPI.
Try replacing you parallel configuration by the following:
[gfortranHPC]
brief: Gfortran compiler 4.9.2 with open_mpi for a debian 8
#
mpi_cmdexec: mpirun -machinefile MPI_HOSTFILE -np <ncsize> <exename>
#
cmd_obj:    mpif90 -c -cpp -fPIC -O2 -fconvert=big-endian -frecord-marker=4 -DHAVE_MPI -DHAVE_VTK <mods> <incs> <f95name>
cmd_lib:    ar cru <libname> <objs>
cmd_exe:    mpif90 -fPIC -fconvert=big-endian -frecord-marker=4 -lpthread -lm -o <exename> <objs> <libs>
#
libs_all: -L$METISHOME/libmetis -lmetis -lgfortran

and run compile_telemac.py --clean -c gfortranHPC
There are 10 types of people in the world: those who understand binary, and those who don't.
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Problem on running validate_telemac.py on ubuntu 20.04 3 years 11 months ago #37303

  • GuillaumeDt
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Hi,
the compilation of the code is OK.
Running the validation on 1 core seems to be OK (at least for the 1St case).
Problem with parallelization on 4 cores:
MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD
with errorcode 2.
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.
[Laptop:20283] 3 more processes have sent help message help-mpi-api.txt / mpi-abort
[Laptop:20283] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

There is always a conflict with my MPI configuration but i don't know where ...
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Problem on running validate_telemac.py on ubuntu 20.04 3 years 11 months ago #37305

  • yugi
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Can you have a look at the PE*.LOG that should be in the temporary folder.

Also can you give the return of the following commands:
- which mpif90
- which mpirun
There are 10 types of people in the world: those who understand binary, and those who don't.
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Problem on running validate_telemac.py on ubuntu 20.04 3 years 11 months ago #37306

  • GuillaumeDt
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I have 3 PE*.LOG (similar) related to the case that crashes.
command "which mpif90" returns /usr/bin/mpif90
command "which mpirun" returns /usr/bin/mpirun
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Problem on running validate_telemac.py on ubuntu 20.04 3 years 11 months ago #37308

  • yugi
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Hi,

Could you repost the file and change the extentision in .txt otherwise I cannot open it.
There are 10 types of people in the world: those who understand binary, and those who don't.
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The following user(s) said Thank You: GuillaumeDt

Problem on running validate_telemac.py on ubuntu 20.04 3 years 11 months ago #37309

  • GuillaumeDt
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Sorry, the file in .txt
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Problem on running validate_telemac.py on ubuntu 20.04

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