installation Salome+CS+Syrthes via VM on ubuntu 15.10

[Yvan Fournier]

Hello,

Did you define boundary conditions based on the tutorial description, or use the example file already present ? There is missing info in the text, so starting from the file should work better (though it is less instructive).

Regards,

Yvan

[jgd23]

Hello,

The first part of 3disk2d tutorial works with CS and Syrthes in stand alone mode.
I don't understand which files I need to run the coupled calculation of CS and Syrthes.
I don't understand which file I have to use for CS? I try to put in this directory the file in the SCRIPTS or DATA from the fluid folder of CS but I have errors...
I have in the same folder the following files:

- solid.syd (configuration for a coupled study),

- a runcase file :
#!/bin/bash

# Ensure the correct command is found:
export PATH=/home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64/bin:$PATH

# Run command:
\code_saturne run --coupling coupling_parameters.py

- a py file named coupling_parameters.py:
# Define coupled domains

domains = [

{'solver': 'Code_Saturne',
'domain': 'fluid',
'script': 'runcase',
'n_procs_weight': None,
'n_procs_min': 1,
'n_procs_max': 1}

,
{'solver': 'SYRTHES',
'domain': 'solid',
'script': 'solid.syd',
'n_procs_weight': None,
'n_procs_min': 1,
'n_procs_max': 1,
'opt' : '-v ens'} # Additional SYRTHES options
# (ex.: postprocessing with '-v ens' or '-v med')

]

This is the terminal error message:

julien@julien-VirtualBox:~/3disks2D$ ./runcase
Coupling execution between:
o Code_Saturne [1 domain(s)];
o SYRTHES [1 domain(s)];


Code_Saturne is running
***********************

Version: 4.0
Path: /home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64

Result directory:
/home/julien/3disks2D/RESU_COUPLING/20160704-1656


Single processor Code_Saturne simulation.
Single processor SYRTHES simulation.


****************************
Preparing calculation data
****************************

SYRTHES4 home directory: /home/julien/Syrthes/syrthes4.3.0/arch/Linux_x86_64
MPI home directory: /home/julien/Syrthes/syrthes4.3.0/extern-libraries/opt/openmpi-1.8.3/arch/Linux_x86_64
Building the executable file syrthes..

***** SYRTHES compilation and link completed *****

***************************
Preprocessing calculation
***************************


SyrthesCase summary:

Name = solid
Data file = solid-alone.syd
Update Data file = True
Do preprocessing = True
Debug = False
Case dir. = /home/julien/3disks2D/solid
Execution dir. = /home/julien/3disks2D/RESU_COUPLING/20160704-1656/solid
Data dir. = /home/julien/3disks2D/RESU_COUPLING/20160704-1656/solid
Source dir. = /home/julien/3disks2D/RESU_COUPLING/20160704-1656/solid/src
Post dir. = /home/julien/3disks2D/RESU_COUPLING/20160704-1656/solid/POST

Conduction mesh dir. = /home/julien/3disks2D/MESH
Conduction mesh name = 3rond2d.syr

Total num. of processes = 1
Logfile name = syrthes.log
Echo = True
Parallel run = False
Do preprocessing = True

SyrthesParam summary
Param file name = solid-alone.syd
Conduction mesh name = /home/julien/3disks2D/MESH/3rond2d.syr
Radiation mesh name = None
Result prefix. = resu1
Restart = False
Coupling = True
Interpreted functions = False


---------------------------
Start SYRTHES preprocessing
---------------------------

Updating the mesh file name..
-> OK


**********************
Starting calculation
**********************

[julien-VirtualBox:11086] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 367
[julien-VirtualBox:11084] tcp_peer_recv_connect_ack: invalid header type: 946143232
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[14437,1],0]
Exit code: 1
--------------------------------------------------------------------------
solver script exited with status 1.

Error running the coupled calculation.

Either Code_Saturne or SYRTHES may have failed.

Check Code_Saturne log (listing) and SYRTHES log (syrthes.log)
for details, as well as error* files.


****************************
Saving calculation results
****************************

Post-processing..
.syrthes (.res) --> ensight...
--> /home/julien/Syrthes/syrthes4.3.0/arch/Linux_x86_64/bin/syrthes4ensight -m "/home/julien/3disks2D/MESH/3rond2d.syr" -r "/home/julien/3disks2D/RESU_COUPLING/20160704-1656/solid/resu1.res" -o "resu1"
.syrthes (.rdt) --> ensight...
--> /home/julien/Syrthes/syrthes4.3.0/arch/Linux_x86_64/bin/syrthes4ensight -m "/home/julien/3disks2D/MESH/3rond2d.syr" -r "/home/julien/3disks2D/RESU_COUPLING/20160704-1656/solid/resu1.rdt" -o "resu1_rdt"
Error in calculation stage.

Best regards

Julien

[Yvan Fournier]

Hello,

At this stage, the install is probably OK, but there may be an error in your setup.

Did you read the recommended log files ?

Regards,

Yvan

[jgd23]

Hello,

I don't know how to find these log files?

In the repertory RESU_COUPLING a created directory is here with new fluid and solid directories.
In the solid directory there is syrthes.log file telling that everything is normal, the same for the listing.bak file.
In the fluid directory, I have only 3 files; the xml file (I think), the mesh input file and the preprocessor.log file which indicate that everything is normal. I think that Code Saturne case definition is not well set up in the parent folder.

What files are supposed to exist to realize the coupling in the parent folder?

Best regards

Julien

[Yvan Fournier]

Hello,

You still have strange message in the script.

Did you use the same MPI library for Code_Saturne and Syrthes ?

Regards,

Yvan

[jgd23]

Hello,

No I used a different MPI for Syrthes. I modify the setup.ini like this:

mpi USE=yes PATH=/usr/bin

During installation I have the following message in the terminal:

Installation of syrthesmpi on architecture Linux_x86_64
mkdir: opérande manquant
Saisissez « mkdir --help » pour plus d'informations.
make -I /home/julien/Syrthes/syrthes4.3.0 -C ./syrthes-kernel/src clean
make[1]: Entering directory '/home/julien/Syrthes/syrthes4.3.0/src/syrthes-kernel/src'
mkdir: opérande manquant
Saisissez « mkdir --help » pour plus d'informations.
rm -rf /home/julien/Syrthes/syrthes4.3.0/build//*.o
make[1]: Leaving directory '/home/julien/Syrthes/syrthes4.3.0/src/syrthes-kernel/src'
make -I /home/julien/Syrthes/syrthes4.3.0 -C ./syrthes-kernel/src
make[1]: Entering directory '/home/julien/Syrthes/syrthes4.3.0/src/syrthes-kernel/src'
mkdir: opérande manquant
Saisissez « mkdir --help » pour plus d'informations.
/usr/bin/bin/mpicc -c -O3 -D _FILE_OFFSET_BITS=64 -D_SYRTHES_MPI_ -I/home/julien/Syrthes/syrthes4.3.0/src/syrthes-kernel/include -I/home/julien/Syrthes/syrthes4.3.0/src/syrthes-kernel/lib_material_syrthes utilitaire.c -o /home/julien/Syrthes/syrthes4.3.0/build//utilitaire.o
make[1]: /usr/bin/bin/mpicc: commande introuvable
Makefile:22: recipe for target '/home/julien/Syrthes/syrthes4.3.0/build//utilitaire.o' failed
make[1]: *** [/home/julien/Syrthes/syrthes4.3.0/build//utilitaire.o] Error 127
make[1]: Leaving directory '/home/julien/Syrthes/syrthes4.3.0/src/syrthes-kernel/src'
Makefile:27: recipe for target 'syrthesmpi' failed
make: *** [syrthesmpi] Error 2
mv: impossible d'évaluer «/home/julien/Syrthes/syrthes4.3.0/build/*»: Aucun fichier ou dossier de ce type

Installation of syrthescfd on architecture Linux_x86_64
mkdir: opérande manquant
Saisissez « mkdir --help » pour plus d'informations.
make CFD=yes -I /home/julien/Syrthes/syrthes4.3.0 -C ./syrthes-kernel/src clean
make[1]: Entering directory '/home/julien/Syrthes/syrthes4.3.0/src/syrthes-kernel/src'
mkdir: opérande manquant
Saisissez « mkdir --help » pour plus d'informations.
rm -rf /home/julien/Syrthes/syrthes4.3.0/build//*.o
make[1]: Leaving directory '/home/julien/Syrthes/syrthes4.3.0/src/syrthes-kernel/src'
make CFD=yes -I /home/julien/Syrthes/syrthes4.3.0 -C ./syrthes-kernel/src
make[1]: Entering directory '/home/julien/Syrthes/syrthes4.3.0/src/syrthes-kernel/src'
mkdir: opérande manquant
Saisissez « mkdir --help » pour plus d'informations.
/usr/bin/bin/mpicc -c -O3 -D _FILE_OFFSET_BITS=64 -D_SYRTHES_MPI_ -D_SYRTHES_CFD_ -I/home/julien/Syrthes/syrthes4.3.0/src/syrthes-kernel/include -I/home/julien/Syrthes/syrthes4.3.0/src/syrthes-kernel/lib_material_syrthes -I/home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64/include -I/home/julien/Syrthes/syrthes4.3.0/src/syrthes-kernel/include utilitaire.c -o /home/julien/Syrthes/syrthes4.3.0/build//utilitaire.o
make[1]: /usr/bin/bin/mpicc: commande introuvable
Makefile:22: recipe for target '/home/julien/Syrthes/syrthes4.3.0/build//utilitaire.o' failed
make[1]: *** [/home/julien/Syrthes/syrthes4.3.0/build//utilitaire.o] Error 127
make[1]: Leaving directory '/home/julien/Syrthes/syrthes4.3.0/src/syrthes-kernel/src'
Makefile:35: recipe for target 'syrthescfd' failed
make: *** [syrthescfd] Error 2
function report

---------------------------------------------------------
Before using SYRTHES, each user must source
the /home/julien/Syrthes/syrthes4.3.0/arch/Linux_x86_64/bin/syrthes.profile file before using the code.

The easiest way is to put the following lines in each of the users
'.profile' or '.bashrc' (depending on the shell)

syrthesprofile=/home/julien/Syrthes/syrthes4.3.0/arch/Linux_x86_64/bin/syrthes.profile
#(adjust path to your system)
if [ -f $syrthesprofile ] ; then
. $syrthesprofile
fi

---------------------------------------------------------
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Warning : installation of some composants failed
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Check log files for more information....


Best regards

Julien

[Yvan Fournier]

Hello,

You should not have:

mpi USE=yes PATH=/usr/bin

but (maybe):

mpi USE=yes PATH=/usr

As it seems Syrthes is installing its own MPI library, which may cause problems when coupling (as the coupling uses MPI, it should use the same library).

Regards,

Yvan

[jgd23]

Hello,

I restart with the new setup.ini file

mpi USE=yes PATH=/usr

The installation time is only 10 min, the first time I install Syrthes was maybe 1 hour, is it normal?

I join the log files for mpi and others

Best regards

Julien

[jgd23]

Hello,

I try to rerun the coupled case CS and Syrthes (tuto 3disks2d).


This is the setup of my coupling_parameter.py file:

# Define coupled domains

domains = [

{'solver': 'Code_Saturne',
'domain': 'fluid',
'script': 'runcase',
'n_procs_weight': None,
'n_procs_min': 1,
'n_procs_max': 1}

,
{'solver': 'SYRTHES',
'domain': 'solid',
'script': 'solid.syd',
'n_procs_weight': None,
'n_procs_min': 1,
'n_procs_max': 1,
'opt' : '-v ens'} # Additional SYRTHES options
# (ex.: postprocessing with '-v ens' or '-v med')

This the runcase file:

#!/bin/bash

# Ensure the correct command is found:
export PATH=/home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64/bin:$PATH

# Run command:
\code_saturne run --coupling coupling_parameters.py

The solid.syd file is joined.

I have the following error in the terminal:

julien@julien-VirtualBox:~/3disks2D$ ./runcase
Coupling execution between:
o Code_Saturne [1 domain(s)];
o SYRTHES [1 domain(s)];


Code_Saturne is running
***********************

Version: 4.0
Path: /home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64

Result directory:
/home/julien/3disks2D/RESU_COUPLING/20160706-0857


Single processor Code_Saturne simulation.
Single processor SYRTHES simulation.


****************************
Preparing calculation data
****************************

SYRTHES4 home directory: /home/julien/Syrthes/syrthes4.3.0/arch/Linux_x86_64
MPI home directory: /usr
Building the executable file syrthes..

***** SYRTHES compilation and link completed *****

***************************
Preprocessing calculation
***************************


SyrthesCase summary:

Name = solid
Data file = solid-alone.syd
Update Data file = True
Do preprocessing = True
Debug = False
Case dir. = /home/julien/3disks2D/solid
Execution dir. = /home/julien/3disks2D/RESU_COUPLING/20160706-0857/solid
Data dir. = /home/julien/3disks2D/RESU_COUPLING/20160706-0857/solid
Source dir. = /home/julien/3disks2D/RESU_COUPLING/20160706-0857/solid/src
Post dir. = /home/julien/3disks2D/RESU_COUPLING/20160706-0857/solid/POST

Conduction mesh dir. = /home/julien/3disks2D/MESH
Conduction mesh name = 3rond2d.syr

Total num. of processes = 1
Logfile name = syrthes.log
Echo = True
Parallel run = False
Do preprocessing = True

SyrthesParam summary
Param file name = solid-alone.syd
Conduction mesh name = /home/julien/3disks2D/MESH/3rond2d.syr
Radiation mesh name = None
Result prefix. = resu1
Restart = False
Coupling = True
Interpreted functions = False


---------------------------
Start SYRTHES preprocessing
---------------------------

Updating the mesh file name..
-> OK


**********************
Starting calculation
**********************

--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 SPLIT FROM 0
with errorcode 1.

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.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec.openmpi noticed that process rank 0 with PID 1828 on node julien-VirtualBox exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
solver script exited with status 139.

Error running the coupled calculation.

Either Code_Saturne or SYRTHES may have failed.

Check Code_Saturne log (listing) and SYRTHES log (syrthes.log)
for details, as well as error* files.


****************************
Saving calculation results
****************************

Post-processing..
.syrthes (.res) --> ensight...
--> /home/julien/Syrthes/syrthes4.3.0/arch/Linux_x86_64/bin/syrthes4ensight -m "/home/julien/3disks2D/MESH/3rond2d.syr" -r "/home/julien/3disks2D/RESU_COUPLING/20160706-0857/solid/resu1.res" -o "resu1"
.syrthes (.rdt) --> ensight...
--> /home/julien/Syrthes/syrthes4.3.0/arch/Linux_x86_64/bin/syrthes4ensight -m "/home/julien/3disks2D/MESH/3rond2d.syr" -r "/home/julien/3disks2D/RESU_COUPLING/20160706-0857/solid/resu1.rdt" -o "resu1_rdt"
Error in calculation stage.

I am not sure that the coupling is done correctly. And maybe also a problem with MPI

Best regards

Julien

[jgd23]

This is the listing file