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TOPIC: ERROR IN T2DGEO
ERROR IN T2DGEO 2 years 9 months ago #39727
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Dear All,
I am new in using Telemac, I am using it in linux environment. I have succeed in compiling and installation. Nevertheless when I try to run the code in examples folders this error is appearing. I have tried with a couple of examples and the same error is appearing: examples/telemac2d/gouttedo/t2d_gouttedo.cas examples/telemac2d/malpasset/t2d_malpasset-fine.cas Does anyone knows how to fix it? Running your CAS file(s) for:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gfortranHPC:
+> Gfortran compiler 4.9.2 with open_mpi for a debian 8
+> root: /home/marcelo/my_opentelemac
+> module: ad / api / artemis / bief
damocles / gaia / gretel / hermes
identify_liq_bnd / khione / mascaret / metis-5.1.0
nestor / parallel / partel / postel3d
sisyphe / special / stbtel / telemac2d
telemac3d / tomawac / waqtel
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
... processing the steering file
... checking parallelisation
... handling temporary directories
copying: t2d_malpasset-fine.cas -> <root>/examples/telemac2d/malpasset/t2d_malpasset-fine.cas_2022-02-01-11h38min48s/T2DCAS
copying: telemac2d.dico -> <root>/examples/telemac2d/malpasset/t2d_malpasset-fine.cas_2022-02-01-11h38min48s/T2DDICO
copying: geo_malpasset-large.slf -> <root>/examples/telemac2d/malpasset/t2d_malpasset-fine.cas_2022-02-01-11h38min48s/T2DGEO
copying: geo_malpasset-large.cli -> <root>/examples/telemac2d/malpasset/t2d_malpasset-fine.cas_2022-02-01-11h38min48s/T2DCLI
... partitioning base files (geo, conlim, sections, zones and weirs)
+> /home/marcelo/my_opentelemac/builds/gfortranHPC/bin/partel < partel_T2DGEO.par >> partel_T2DGEO.log
STOP 1
Traceback (most recent call last):
File "/home/marcelo/my_opentelemac/scripts/python3/telemac2d.py", line 7, in <module>
main('telemac2d')
File "/home/marcelo/my_opentelemac/scripts/python3/runcode.py", line 279, in main
run_study(cas_file, code_name, options)
File "/home/marcelo/my_opentelemac/scripts/python3/execution/run_cas.py", line 169, in run_study
run_local_cas(my_study, options)
File "/home/marcelo/my_opentelemac/scripts/python3/execution/run_cas.py", line 31, in run_local_cas
my_study.partionning(options.use_link)
File "/home/marcelo/my_opentelemac/scripts/python3/execution/study.py", line 429, in partionning
run_partition(parcmd, self.cas, g_geo, g_fmt_geo, g_conlim,
File "/home/marcelo/my_opentelemac/scripts/python3/execution/run.py", line 51, in run_partition
run_partel(partel, geom, fmtgeom, conlim, ncsize, False,
File "/home/marcelo/my_opentelemac/scripts/python3/execution/run.py", line 133, in run_partel
raise TelemacException(
utils.exceptions.TelemacException: Could not split your file T2DGEO with the error as follows:
... The following command failed for the reason in the listing
/home/marcelo/my_opentelemac/builds/gfortranHPC/bin/partel < partel_T2DGEO.par >> partel_T2DGEO.log
Here is the log:
+-------------------------------------------------+
PARTEL/PARRES: TELEMAC METISOLOGIC PARTITIONER
REBEKKA KOPMANN & JACEK A. JANKOWSKI (BAW)
JEAN-MICHEL HERVOUET (LNHE)
CHRISTOPHE DENIS (SINETICS)
YOANN AUDOUIN (LNHE)
PARTEL (C) COPYRIGHT 2000-2002
BUNDESANSTALT FUER WASSERBAU, KARLSRUHE
METIS 5.0.2 (C) COPYRIGHT 2012
REGENTS OF THE UNIVERSITY OF MINNESOTA
BIEF V8P3 (C) COPYRIGHT 2012 EDF
+-------------------------------------------------+
MAXIMUM NUMBER OF PARTITIONS: 100000
+--------------------------------------------------+
--INPUT FILE NAME <INPUT_NAME>:
INPUT: T2DGEO
--INPUT FILE FORMAT <INPFORMAT> [MED,SERAFIN,SERAFIND]:
INPUT: SERAFIN
--BOUNDARY CONDITIONS FILE NAME:
INPUT: T2DCLI
--NUMBER OF PARTITIONS <NPARTS> [2 -100000]:
INPUT: 4
PARTITIONING METHOD <PMETHOD> [1 (METIS) OR 2 (SCOTCH)]:
--INPUT: 1
--CONTROL SECTIONS FILE NAME (OR RETURN) :
NO SECTIONS
--CONTROL ZONES FILE NAME (OR RETURN) :
NO ZONES
--WEIR FILE NAME (OR RETURN) :
NO WEIRS
--GEOMETRY FILE NAME <INPUT_NAME>:
INPUT: T2DGEO
--GEOMETRY FILE FORMAT <GEOFORMAT> [MED,SERAFIN,SERAFIND]:
INPUT: SERAFIN
--CONCATENATE FILES <YES-NO>:
CONCATENATE: NO
+---- PARTEL: BEGINNING -------------+
FICHIER:T2DGEO
ERROR 1016 DURING CALL OF PARTEL:OPENMESH:INP
ERROR TEXT: HERMES_INVALID_SERAFIN_FILE
ERROR IN T2DGEO: IDENTIFY_ENDIAN_TYPE:READ:LITTLE_ENDIAN
PLANTE: PROGRAM STOPPED AFTER AN ERROR
RETURNING EXIT CODE: 2kind regards, Marcelo |
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ERROR IN T2DGEO 2 years 9 months ago #39728
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Hello Marcelo,
Have you tried to run in sequential rather than in parallel? What is the size of the 2 geometry files? geo_gouttedo.slf is 181989 B and geo_malpasset-large.slf is 2097565 B If you do not have the same size, you may have forgotten to install git lfs extension. Hope this helps, Chi-Tuan |
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ERROR IN T2DGEO 2 years 9 months ago #39729
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Dear Chi-Tuan,
Thanks for the answer. I have run it as well on sequential. The error is the same. Apparently, it does not recognize the geometry file. MASTER PROCESSOR NUMBER 0 OF THE GROUP OF 1
EXECUTABLE FILE: /home/marcelo/my_opentelemac/examples/telemac2d/gouttedo/t2d_gouttedo.cas_2022-02-01-15h06min10s/A.EXE
LISTING OF TELEMAC2D------------------------------------------------------------------------------
TTTTT EEEEE L EEEEE M M AAAAA CCCCC
T E L E MM MM A A C
T EEE L EEE M M M AAAAA C
T E L E M M A A C
T EEEEE LLLLL EEEEE M M A A CCCCC
2D VERSION V8P3 FORTRAN 2003
~^~^~^~^~^~^~^~^~^~^~^^~^~^~^~^~^~
~ ~
\ ' o '
/\ o \ o
>=)'> ' /\ '
\/ \ >=)'> ~
/ /\ \/
~ >=)'> / .
\/ )
/ (
~ ) )
} ~ ( ( (
{ ) ) )
} } . ( ( (
{ { /^^^^^^^^^^^^
^^^^^^^^^\ /
^^^^^^^^^
WARNING IN DICTIONARY:
FOR KEYWORD: FINITE VOLUME SCHEME FOR TRACER DIFFUSION
THE NUMBER OF DEFAULT VALUES 1 IS DIFFERENT FROM THE DECLARED SIZE 2
DIFFERENT NUMBER OF PARALLEL PROCESSORS:
DECLARED BEFORE (CASE OF COUPLING ?): 1
TELEMAC-2D : 0
VALUE 1 IS KEPT
********************************************
* LECDON: *
* AFTER CALLING DAMOCLES *
* CHECKING OF DATA READ *
* IN THE STEERING FILE *
********************************************
EXITING LECDON. NAME OF THE STUDY:
TELEMAC 2D: DROPLET IN A BASIN
OPENING FILES FOR TELEMAC2D
OPENING: T2DGEO-geo_gouttedo.slf
ERROR 1016 DURING CALL OF BIEF_OPEN_FILES:OPEN_MESH
ERROR TEXT: HERMES_INVALID_SERAFIN_FILE
ERROR IN /home/marcelo/my_opentelemac/examples/telemac2d/gouttedo/t2d_gouttedo.cas_2022-02-01-15h06min10s/T2DGEO: IDENTIFY_ENDIAN_TYPE:READ:LITTLE_ENDIAN
PLANTE: PROGRAM STOPPED AFTER AN ERROR
RETURNING EXIT CODE: 2
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 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.
--------------------------------------------------------------------------
Traceback (most recent call last):
File "/home/marcelo/my_opentelemac/scripts/python3/telemac2d.py", line 7, in <module>
main('telemac2d')
File "/home/marcelo/my_opentelemac/scripts/python3/runcode.py", line 279, in main
run_study(cas_file, code_name, options)
File "/home/marcelo/my_opentelemac/scripts/python3/execution/run_cas.py", line 169, in run_study
run_local_cas(my_study, options)
File "/home/marcelo/my_opentelemac/scripts/python3/execution/run_cas.py", line 65, in run_local_cas
my_study.run(options)
File "/home/marcelo/my_opentelemac/scripts/python3/execution/study.py", line 637, in run
self.run_local()
File "/home/marcelo/my_opentelemac/scripts/python3/execution/study.py", line 465, in run_local
run_code(self.run_cmd, self.sortie_file)
File "/home/marcelo/my_opentelemac/scripts/python3/execution/run.py", line 182, in run_code
raise TelemacException('Fail to run\n'+exe)
utils.exceptions.TelemacException: Fail to runten
mpirun -machinefile MPI_HOSTFILE -np 1 /home/marcelo/my_opentelemac/examples/telemac2d/gouttedo/t2d_gouttedo.cas_2022-02-01-15h06min10s/out_user_fortranI have git lfs installed on my computer. I have not found neither the source path of this extension on the source.py script templates nor in the systel.cfg templates. Many thanks for the support! Regards, Marcelo |
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ERROR IN T2DGEO 2 years 9 months ago #39730
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Dear Marcelo,
Probably you forgot the option -fconvert=big-endian in your SYSTEL file (for cmd_obj and cmd_exe). See for example gitlab.pam-retd.fr/otm/telemac-mascaret/...s-ubuntu.cfg#L47-L48. Hope it helps, Luc |
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ERROR IN T2DGEO 2 years 9 months ago #39731
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Dear Luc,
This is my systel.cfg # _____ _______________________________
# ____/ TELEMAC Project Definitions /______________________________/
#
[Configurations]
configs: gfortran gfortranHPC
# _____ ____________________________________
# ____/ General /___________________________________/
# Global declarations that are set by default for all the configurations
[general]
language: 2
modules: system
version: v8p3
#
options: static api
#
f2py_name: f2py3
pyd_fcompiler: gnu95
#
sfx_zip: .gztar
sfx_lib: .a
sfx_obj: .o
sfx_mod: .mod
sfx_exe:
#
#
val_root: <root>/examples
#
val_rank: all
#
mods_all: -I <config>
#
incs_all:
#
libs_all:
#
cmd_obj_c: gcc -fPIC -c <srcName> -o <objName>
#
# _____ __________________________________
# ____/ Calibre9 _________________________________/
#
# Gfortran
#
[gfortran]
brief: Gfortran compiler 4.9.2
#
cmd_obj: gfortran -c -cpp -fallow-invalid-boz -fPIC -O2 -fconvert=big-endian -frecord-marker=4 -DHAVE_VTK <mods> <incs> <f95name>
cmd_lib: ar cru <libname> <objs>
cmd_exe: gfortran -fPIC -fconvert=big-endian -frecord-marker=4 -lpthread -lm -o <exename> <objs> <libs>
#
# Gfortran HPC
#
[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 -fallow-invalid-boz -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/lib -lmetis
# ____/ Ubuntu gfortran mpich2 /___________________________________/
[ubugfmpich2]
#
brief: parallel mode, using mpiexec directly (of the MPICH2 package).
The only difference with the scalar versions (debugged) is the presence
of the key mpi_cmdexec and the -DHAVE_MPI compilation directive.
Of course, you also need the key par_cmdexec.
Finally, note that this configuration also works whether
processor is 0 or 1.
#
options: hermes_only
#
f2py_name: f2py3
pyd_fcompiler: gfortran
#
mpi_cmdexec: /usr/bin/mpiexec -wdir <wdir> -n <ncsize> <exename>
#
cmd_obj: gfortran -c -cpp -g -fbounds-check -Wall -fbacktrace -finit-real=nan -DHAVE_AED2 -DHAVE_MPI -DHAVE_MUMPS -DHAVE_MED -fconvert=big-endian -frecord-marker=4 <mods> <incs> <f95name>
cmd_exe: /usr/bin/mpif90 -fconvert=big-endian -frecord-marker=4 -v -lm -o <exename> <objs> <libs>
#
incs_all: -I /usr/lib/mpich/include/ -I /home/telemac/mumps/MUMPS_5.0.0/include/ -I /home/telemac/aed2 -I /home/telemac/aed2/include -I /home/telemac/MED/include/
libs_all: /usr/lib/x86_64-linux-gnu/libmpich.so -L /home/telemac/mumps/MUMPS_5.0.0/lib -ldmumps -lmumps_common -lpord /home/telemac/mumps/SCALAPACK/libscalapack.a -L /home/telemac/mumps/BLAS-3.8.0 /home/telemac/mumps/BLAS-3.8.0/blas_LINUX.a /home/telemac/mumps/BLACS/LIB/blacs_MPI-LINUX-0.a /home/telemac/mumps/BLACS/LIB/blacsF77init_MPI-LINUX-0.a /home/telemac/mumps/BLACS/LIB/blacs_MPI-LINUX-0.a -lpthread /home/telemac/metis-5.0.2/libmetis.a /home/telemac/aed2/libaed2.a /home/telemac/MED/lib/libmed.so /home/telemac/hdf5-1.10.5/lib/libhdf5.so
#
# _____ _________________________________________
# ____/ Other Definitions /________________________________________/
#
#
# ____/ Ubuntu gfortran scalar /___________________________________/
[ubugfortrans]
#
brief: scalar mode, Fortran optimisation 3.
TELEMAC will work whether processor is 0 or 1
#
cmd_obj: gfortran -c -cpp -O3 -fconvert=big-endian -frecord-marker=4 <mods> <incs> <f95name>
cmd_exe: gfortran -fconvert=big-endian -frecord-marker=4 -v -o <exename> <objs> <libs>
#
#
# ____/ Ubuntu gfortran scalar debug/______________________________/
[ubugfortransdbg]
#
brief: scalar mode, Fortran debug mode.
TELEMAC will work whether processor is 0 or 1
#
cmd_obj: gfortran -c -cpp -g -fbounds-check -Wall -fbacktrace -finit-real=nan -fconvert=big-endian -frecord-marker=4 <mods> <incs> <f95name>
cmd_exe: gfortran -fconvert=big-endian -frecord-marker=4 -v -o <exename> <objs> <libs>
#
#
# _____ ________________________________________
# ____/ End of Definitions /_______________________________________/
#I checked this and all cmd_obj and cmd_exe have "-fconvert=big-endian". Anyway, I would appreciate if you check it. Maybe I have made a mistake. Kind regards, Marcelo |
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ERROR IN T2DGEO 2 years 9 months ago #39732
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Dear Marcelo,
I am not an expert of the SYSTEL file but probably you have a problem with the partitionner (METIS). Moreover you should probably have used a SYSTEL file closer to your configuration, such as systel.cis-debian.cfg. Did you set the environement variable $METISHOME ? Best Regards, Luc |
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ERROR IN T2DGEO 2 years 9 months ago #39738
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Dear all,
Be careful with systel.cis-XXX.cfg files, they may not be up to date and are not so often tested I think. I would rather advise to start from systel.edf.cfg and S9.gfortran or S9.gfortran.dyn configurations. There is one answer I would like to be sure, what are the sizes of geo_gouttedo.slf and geo_malpasset-large.slf files? Otherwise, can you run run_telfile.py scan geo_gouttedo.slf without any error? Can you visualize it with a post-treatment tool (e.g. Paraview, Blue Kenue or FUDAA PREPRO). @Luc, Marcelo has the same issue with Hermes when running in scalar, it is not a problem of parallelism. Chi-Tuan |
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ERROR IN T2DGEO 2 years 9 months ago #39744
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Dear Luc and Chi-Tuan
Yes I have the same problem with parallel and serial run. I have checked the size of the files geo_gouttedo.slf: version https://git-lfs.github.com/spec/v1
oid sha256:56e1d13117de3532a5f6306ea7dd76f9b113912c216c90ef7f1345999b434498
size 181989geo_malpasset-large.slf: version https://git-lfs.github.com/spec/v1
oid sha256:a068aaa8484f4abf9049525b4dc94a532bcc62bbe977d561b9d25ab52c17c6f9
size 2097565So, apparently it is not a problem with git lfs extension. I have ran "run_telfile.py scan geo_gouttedo.slf" and I have the same problem:
Warning: Using SerafinFile. It is recommended to compile Hermes api
Traceback (most recent call last):
File "/home/marcelo/my_opentelemac/scripts/python3/run_telfile.py", line 464, in <module>
main()
File "/home/marcelo/my_opentelemac/scripts/python3/run_telfile.py", line 372, in main
scan(options.tel_file, options.bnd_file, options.data)
File "/home/marcelo/my_opentelemac/scripts/python3/pretel/manip_telfile.py", line 26, in scan
res = TelemacFile(tel_file, bnd_file=bnd_file)
File "/home/marcelo/my_opentelemac/scripts/python3/data_manip/extraction/telemac_file.py", line 68, in __init__
SerafinFile.__init__(self,
File "/home/marcelo/my_opentelemac/scripts/python3/data_manip/formats/serafin_file.py", line 134, in __init__
self.__read()
File "/home/marcelo/my_opentelemac/scripts/python3/data_manip/formats/serafin_file.py", line 148, in __read
self.__endian = get_endian_from_char(self.__file, 80)
File "/home/marcelo/my_opentelemac/scripts/python3/data_manip/extraction/parser_selafin.py", line 485, in get_endian_from_char
raise TelemacException(
utils.exceptions.TelemacException: ... Cannot read 80 characters from your binary file +> Maybe it is the wrong file format ?It is a problem with the file format, how can I fix this ? Kind regards, Marcelo |
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ERROR IN T2DGEO 2 years 9 months ago #39750
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Hello Marcelo,
The sizes of the 2 geometry files are the expected ones. I have tried your systel configuration file and it worked for me (but I have had to delete the -fallow-invalid-boz option). I have succeeded in running the 2 examples. Hard for me to help you more as I cannot reproduce your issue. Chi-Tuan |
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ERROR IN T2DGEO 2 years 9 months ago #39763
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Dear all,
I have not really found the error. However I fixed it in another way. I did not use the version suggested on the installation link for linux, which is v8p3r0, instead I used the version v8p2r1, you can download it by typing the command line: svn co http://svn.opentelemac.org/svn/opentelemac/tags/v8p2r1 --username ot-svn-public --password telemac1*Moreover, I had to install metis library manually. my pysource.sh file is: This file is a template for a Linux environment file
# running "source pysource.template.sh" will position all
# the necessary environment variables for telemac
# To adapt to your installation replace word <word> by their local value
###
### TELEMAC settings -----------------------------------------------------------
###
# Path to telemac root dir
export HOMETEL=/home/marcelo/opentelemac-mascaret/v8p2r1
# Adding python scripts to PATH
export PATH=$HOMETEL/scripts/python3:.:$PATH
# Configuration file
export SYSTELCFG=$HOMETEL/configs/systel.cfg
# Name of the configuration to use
export USETELCFG=gfortranHPC
# Path to this file
export SOURCEFILE=$HOMETEL/configs
### Python
# To force python to flush its output
export PYTHONUNBUFFERED='true'
### API
export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH
export LD_LIBRARY_PATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$PYTHONPATH
###
### COMPILERS -----------------------------------------------------------
###
# Here are a few examples for external libraries
export SYSTEL=/data/projets/projets.002/systel.002
#export SYSTEL=$HOMETEL
### MPI -----------------------------------------------------------
export MPIHOME=$SYSTEL/LIBRARY/mpi/ifort.10.1.008
export PATH=$MPIHOME/bin:$PATH
export LD_LIBRARY_PATH=$MPIHOME/lib:$LD_LIBRARY_PATH
###
### EXTERNAL LIBRARIES -----------------------------------------------------------
###
### HDF5 -----------------------------------------------------------
export HDF5HOME=$SYSTEL/LIBRARY/hdf5-1.8.14/arch/C9
export LD_LIBRARY_PATH=$HDF5HOME/lib:$LD_LIBRARY_PATH
export LD_RUN_PATH=$HDF5HOME/lib:$MEDHOME/lib:$LD_RUN_PATH
### MED -----------------------------------------------------------
export MEDHOME=$SYSTEL/LIBRARY/med-3.2.0/arch/C9
export LD_LIBRARY_PATH=$MEDHOME/lib:$LD_LIBRARY_PATH
export PATH=$MEDHOME/bin:$PATH
### MUMPS -------------------------------------------------------------
export MUMPSHOME=$SYSTEL/LIBRARY/mumps/gnu
export SCALAPACKHOME=$SYSTEL/LIBRARY/scalapack/gnu
export BLACSHOME=$SYSTEL/LIBRARY/blacs/gnu
### METIS -------------------------------------------------------------
export METISHOME=$HOMETEL/sources/metis-5.1.0/build
export LD_LIBRARY_PATH=$METISHOME/lib:$LD_LIBRARY_PATHand my systel.cfg is: # _____ _______________________________
# ____/ TELEMAC Project Definitions /______________________________/
#
[Configurations]
configs: gfortran gfortranHPC
# _____ ____________________________________
# ____/ General /___________________________________/
# Global declarations that are set by default for all the configurations
[general]
language: 2
modules: clean system
version: v2p2r1
#
options: static api
#
f2py_name: f2py3
pyd_fcompiler: gnu95
#
sfx_zip: .gztar
sfx_lib: .a
sfx_obj: .o
sfx_mod: .mod
sfx_exe:
#
#
val_root: <root>/examples
#
val_rank: all
#
mods_all: -I <config>
#
incs_all:
#
libs_all:
#
cmd_obj_c: gcc -fPIC -c <srcName> -o <objName>
#
# _____ __________________________________
# ____/ Calibre9 _________________________________/
#
# Gfortran
#
[gfortran]
brief: Gfortran compiler 4.9.2
#
cmd_obj: gfortran -c -cpp -fallow-invalid-boz -fPIC -O2 -fconvert=big-endian -frecord-marker=4 -DHAVE_VTK <mods> <incs> <f95name>
cmd_lib: ar cru <libname> <objs>
cmd_exe: gfortran -fPIC -fconvert=big-endian -frecord-marker=4 -lpthread -lm -o <exename> <objs> <libs>
#
# Gfortran HPC
#
[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 -fallow-invalid-boz -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/lib -lmetis
libs_all: /home/marcelo/my_opentelemac/sources/metis-5.1.0/build/lib/libmetis.a
# _____ ____________________________________
# ____/ Ubuntu gfortran mpich2 /___________________________________/
[ubugfmpich2]
#
brief: parallel mode, using mpiexec directly (of the MPICH2 package).
The only difference with the scalar versions (debugged) is the presence
of the key mpi_cmdexec and the -DHAVE_MPI compilation directive.
Of course, you also need the key par_cmdexec.
Finally, note that this configuration also works whether
processor is 0 or 1.
#
options: hermes_only
#
f2py_name: f2py3
pyd_fcompiler: gfortran
#
mpi_cmdexec: /usr/bin/mpiexec -wdir <wdir> -n <ncsize> <exename>
#
cmd_obj: gfortran -c -cpp -g -fbounds-check -Wall -fbacktrace -finit-real=nan -DHAVE_AED2 -DHAVE_MPI -DHAVE_MUMPS -DHAVE_MED -fconvert=big-endian -frecord-marker=4 <mods> <incs> <f95name>
cmd_exe: /usr/bin/mpif90 -fconvert=big-endian -frecord-marker=4 -v -lm -o <exename> <objs> <libs>
#
incs_all: -I /usr/lib/mpich/include/ -I /home/telemac/mumps/MUMPS_5.0.0/include/ -I /home/telemac/aed2 -I /home/telemac/aed2/include -I /home/telemac/MED/include/
libs_all: /usr/lib/x86_64-linux-gnu/libmpich.so -L /home/telemac/mumps/MUMPS_5.0.0/lib -ldmumps -lmumps_common -lpord /home/telemac/mumps/SCALAPACK/libscalapack.a -L /home/telemac/mumps/BLAS-3.8.0 /home/telemac/mumps/BLAS-3.8.0/blas_LINUX.a /home/telemac/mumps/BLACS/LIB/blacs_MPI-LINUX-0.a /home/telemac/mumps/BLACS/LIB/blacsF77init_MPI-LINUX-0.a /home/telemac/mumps/BLACS/LIB/blacs_MPI-LINUX-0.a -lpthread /home/telemac/metis-5.0.2/libmetis.a /home/telemac/aed2/libaed2.a /home/telemac/MED/lib/libmed.so /home/telemac/hdf5-1.10.5/lib/libhdf5.so
# _____ ____________________________________
# ____/ Debian gfortran scalar /___________________________________/
[debgfortrans]
#
cmd_obj: gfortran -c -O3 -fconvert=big-endian -frecord-marker=4 <mods> <incs> <f95name>
cmd_lib: ar cru <libname> <objs>
cmd_exe: gfortran -fconvert=big-endian -frecord-marker=4 -v -o <exename> <objs> <libs>
#
# _____ ____________________________________
# ____/ Debian gfortran scalar debug /___________________________________/
[debgfortransdbg]
#
cmd_obj: gfortran -c -g -fbounds-check -Wall -fbacktrace -finit-real=nan -fconvert=big-endian -frecord-marker=4 <mods> <incs> <f95name>
cmd_lib: ar cru <libname> <objs>
cmd_exe: gfortran -fconvert=big-endian -frecord-marker=4 -v -o <exename> <objs> <libs>
#
# _____ ___________________________________
# ____/ Debian gfortran openMPI /__________________________________/
[debgfopenmpi]
#
par_cmdexec: <config>/partel < PARTEL.PAR >> <partel.log>
#
mpi_cmdexec: /usr/bin/mpiexec -wdir <wdir> -n <ncsize> <exename>
mpi_hosts:
#
cmd_obj: /usr/bin/mpif90 -c -O3 -DHAVE_MPI -fconvert=big-endian -frecord-marker=4 <mods> <incs> <f95name>
cmd_lib: ar cru <libname> <objs>
cmd_exe: /usr/bin/mpif90 -fconvert=big-endian -frecord-marker=4 -lpthread -v -lm -o <exename> <objs> <libs>
#
mods_all: -I <config>
#
libs_all: /usr/lib64/openmpi/lib/libmpi.so.0.0.2 /home/telemac/metis-5.0.2/build/Linux-x86_64/libmetis/libmetis.a
#
# _____ ___________________________________
# ____/ Debian gfortran openMPI debug /__________________________________/
[debgfopenmpidbg]
#
par_cmdexec: <config>/partel < PARTEL.PAR >> <partel.log>
#
mpi_cmdexec: /usr/bin/mpiexec -wdir <wdir> -n <ncsize> <exename>
mpi_hosts:
#
cmd_obj: /usr/bin/mpif90 -c -g -fbounds-check -Wall -fbacktrace -finit-real=nan -DHAVE_MPI -fconvert=big-endian -frecord-marker=4 <mods> <incs> <f95name>
cmd_lib: ar cru <libname> <objs>
cmd_exe: /usr/bin/mpif90 -fconvert=big-endian -frecord-marker=4 -lpthread -v -lm -o <exename> <objs> <libs>
#
mods_all: -I <config>
#
incs_all: -I /usr/include/mpi/
libs_all: /usr/lib64/openmpi/lib/libmpi.so.0.0.2 /home/telemac/metis-5.0.2/build/Linux-x86_64/libmetis/libmetis.a
#I have used the first two configurations "gfortran" "gfortranHPC". In addition my version of ubuntu is Ubuntu 20.04 LTS. I hope this help people that has faced the same problem. Kind regards, Marcelo |
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