installation Salome+CS+Syrthes via VM on ubuntu 15.10

[jgd23]

Hello,

I try to reinstall Syrthes with the modified "/usr/bin/mpicc" instead of "mpicc" for the wrapperC in the setup.ini file.
I have new errors. Syrthes in stand alone mode doesn't work.

ar xv /home/julien/Syrthes/syrthes4.3.0/arch/Linux_x86_64/lib/libsyrthes_mpi.a mainsyrthes.o
Makefile:15: recipe for target 'exe' failed
SYRTHES4 home directory: /home/julien/Syrthes/syrthes4.3.0/arch/Linux_x86_64
MPI home directory: /usr

-----------------------------------
Prepare SYRTHES execution directory
-----------------------------------

Building the executable file syrthes..
ar: /home/julien/Syrthes/syrthes4.3.0/arch/Linux_x86_64/lib/libsyrthes_mpi.a: Aucun fichier ou dossier de ce type
make: *** [exe] Error 9

Error during the compilation stage

Error during building syrthes executable.

Error during the prepration step (errno: 2
Stop Syrthes execution.

Maybe some new informations for you? Do you think that I have to reinstall everything now?

Best regards

Julien

[gbenefice]

Hello

I try to install Salome 7.6.0, Code Saturne 4.0.5 and Syrthes 4.3 via Oracle VM Virtual Box 5.1.0 on Ubuntu 16.04 LTS. So I have very carefully read your discussion.

The installation of Salome and CS is OK and I was able to launch the tutorial 1 (Simplified nuclear vessel with salome and without).

My problem is the installation and the utilization of Syrthes.
Like the Syrthes web site is offline, I have downloaded Syrthes on the Ubuntu website (http://packages.ubuntu.com/wily/syrthes). My setup.ini file is as an attachement. I have the following message:

Code: Select all

--> No such file or directory /home/benefice/Logiciels/Syrthes/syrthes-4.3.0-dfsg1/src//syrthes-gui/exe.linux-x86_64
 
function report
NO file ERREUR.log

---------------------------------------------------------
Before using SYRTHES, each user must source
the /home/benefice/Logiciels/Syrthes/syrthes-4.3.0-dfsg1/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/benefice/Logiciels/Syrthes/syrthes-4.3.0-dfsg1/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....

I have checked all log files and the installation is OK except for the syrthes-gui. It would seem that the Syrthes package is not complete. The exe.linux-x86_64 directory is missing in syrthes-4.3.0-dfsg1/src/syrthes-gui.
When I launch syrthe-gui, I have the following message:

Code: Select all

/home/benefice/Logiciels/Syrthes/syrthes-4.3.0-dfsg1/arch/Linux_x86_64/bin/syrthes.gui: ligne 3: /home/benefice/Logiciels/Syrthes/syrthes-4.3.0-dfsg1/arch/Linux_x86_64/lib/syrthes-GUI_exe/SyrthesMain: Aucun fichier ou dossier de ce type

Could you tell me how download the syrhtes-gui executable files ? Thanks

Julien, I think that it is necessary to put "mpicc" for the wrapperC in the setup.ini file. If you use "/usr/bin/mpicc", the program researchs the mpicc file in the /usr/bin/usr/bin directory and no in /usr/bin.

Best regard
Guillaume

[Yvan Fournier]

Hello,

The Web page to download Syrthes is now: https://www.edf.fr/en/the-edf-group/wor ... ciel=10818 (just press "cancel" for the login prompt which seems due to a bug in the shiny new EDF website).

Regards,

Yvan

[jgd23]

Hello,

Thank you both of you.

I have created a new VM ubuntu 15.10. I have installed CS4.2.1 and Syrthes4.3, both can run in serial and parallel.

I have again a problem to couple the 2 codes. I use the same setup files for CS and Syrthes that Yvan help me to write.

Coupling execution between:
o Code_Saturne [1 domain(s)];
o SYRTHES [1 domain(s)];


Code_Saturne
************

Version: 4.2
Path: /home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64

Result directory:
/home/julien/test_CS42/4-2Ddisks/case1/RESU_COUPLING/20160727-1120



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

SYRTHES4 home directory: /home/julien/syrthes43/syrthes4.3.0/arch/Linux_x86_64
MPI home directory: /usr
Building the executable file syrthes..

***** SYRTHES compilation and link completed *****
Single processor Code_Saturne simulation.
Single processor SYRTHES simulation.


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


SyrthesCase summary:

Name = solid
Data file = solid-coupling.syd
Update Data file = True
Do preprocessing = True
Debug = False
Case dir. = /home/julien/test_CS42/4-2Ddisks/case1/solid
Execution dir. = /home/julien/test_CS42/4-2Ddisks/case1/RESU_COUPLING/20160727-1120/solid
Data dir. = /home/julien/test_CS42/4-2Ddisks/case1/solid
Source dir. = /home/julien/test_CS42/4-2Ddisks/case1/solid
Post dir. = /home/julien/test_CS42/4-2Ddisks/case1/RESU_COUPLING/20160727-1120/solid/POST

Conduction mesh dir. = /home/julien/test_CS42/4-2Ddisks/mesh/solid
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-coupling.syd
Conduction mesh name = /home/julien/test_CS42/4-2Ddisks/mesh/solid/3rond2d.syr
Radiation mesh name = None
Result prefix. = resu2
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 23114 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/syrthes43/syrthes4.3.0/arch/Linux_x86_64/bin/syrthes4ensight -m "/home/julien/test_CS42/4-2Ddisks/mesh/solid/3rond2d.syr" -r "/home/julien/test_CS42/4-2Ddisks/case1/RESU_COUPLING/20160727-1120/solid/resu2.res" -o "resu2"
Traceback (most recent call last):
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/bin/code_saturne", line 76, in <module>
retcode = cs.execute()
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 89, in execute
return self.commands[command](options)
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 152, in run
return cs_run.main(options, self.package)
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_run.py", line 363, in main
return run(argv, pkg)[0]
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_run.py", line 351, in run
stages=stages)
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case.py", line 1868, in run
self.save_results()
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case.p Coupling execution between:
o Code_Saturne [1 domain(s)];
o SYRTHES [1 domain(s)];


Code_Saturne
************

Version: 4.2
Path: /home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64

Result directory:
/home/julien/test_CS42/4-2Ddisks/case1/RESU_COUPLING/20160727-1120



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

SYRTHES4 home directory: /home/julien/syrthes43/syrthes4.3.0/arch/Linux_x86_64
MPI home directory: /usr
Building the executable file syrthes..

***** SYRTHES compilation and link completed *****
Single processor Code_Saturne simulation.
Single processor SYRTHES simulation.


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


SyrthesCase summary:

Name = solid
Data file = solid-coupling.syd
Update Data file = True
Do preprocessing = True
Debug = False
Case dir. = /home/julien/test_CS42/4-2Ddisks/case1/solid
Execution dir. = /home/julien/test_CS42/4-2Ddisks/case1/RESU_COUPLING/20160727-1120/solid
Data dir. = /home/julien/test_CS42/4-2Ddisks/case1/solid
Source dir. = /home/julien/test_CS42/4-2Ddisks/case1/solid
Post dir. = /home/julien/test_CS42/4-2Ddisks/case1/RESU_COUPLING/20160727-1120/solid/POST

Conduction mesh dir. = /home/julien/test_CS42/4-2Ddisks/mesh/solid
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-coupling.syd
Conduction mesh name = /home/julien/test_CS42/4-2Ddisks/mesh/solid/3rond2d.syr
Radiation mesh name = None
Result prefix. = resu2
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 23114 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/syrthes43/syrthes4.3.0/arch/Linux_x86_64/bin/syrthes4ensight -m "/home/julien/test_CS42/4-2Ddisks/mesh/solid/3rond2d.syr" -r "/home/julien/test_CS42/4-2Ddisks/case1/RESU_COUPLING/20160727-1120/solid/resu2.res" -o "resu2"
Traceback (most recent call last):
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/bin/code_saturne", line 76, in <module>
retcode = cs.execute()
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 89, in execute
return self.commands[command](options)
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 152, in run
return cs_run.main(options, self.package)
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_run.py", line 363, in main
return run(argv, pkg)[0]
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_run.py", line 351, in run
stages=stages)
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case.py", line 1868, in run
self.save_results()
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case.py", line 1725, in save_results
d.copy_results()
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case_domain.py", line 1245, in copy_results
raise RunCaseError(err_str)
cs_case_domain.RunCaseError:
Error during SYRTHES postprocessing
y", line 1725, in save_results
d.copy_results()
File "/home/julien/Code_Saturne/4.2.1/code_saturne-4.2.1/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case_domain.py", line 1245, in copy_results
raise RunCaseError(err_str)
cs_case_domain.RunCaseError:
Error during SYRTHES postprocessing

Best regards

Julien

[Yvan Fournier]

Hello,

This seems to be the exact same issue as you encountered before...

I'll try to run more debugging tools with Syrthes some day, but I am already very busy with Code_Saturne development and support, and if I don't manage to reproduce the exact same issue, debugging will be difficult. I first need to check whether I upgraded my Ubuntu VM to 16.04 or am still on 15.10 (I don't use it much, my main home OS is Arch Linux, and work OSs are Debian). If I do still have it, I'll try to reproduce the issue... But probably not this week...

Otherwise, if anybody else who knows how to use a debugger is willing to help you first, they are welcome...

Finally, an interesting test would be to try the same case with Syrthess alone (replacing the coupled boundary conditions with heat exchange coefficients, with a user-defined coefficeint and external temperature). If you reproduce the crash on Syrthes alone, debugging will be much easier.

Regards,

Yvan

[jgd23]

Hello,

I will try to reinstall everything on debian 8.5.0 (amd64).

I don't know how to define a user defined coefficient heat transfert with syrthes for the test (user subroutine?). If you have an user subroutine I can compile it and test it.
I try only with constant values Syrthes in stand alone mode and it was working.

Best regards

Julien

[jgd23]

Hello,

I am on debian 8.5.0 now. I succeed to install salome 7.6.0, CS4.0.5, I can also launch code_saturne salome. It works on serial and parallel config.
I have difficulties with Syrthes4.3 for installing med (use=yes install=yes) and scotch (use=yes install=yes). Without installing and using these (using med308 from salome library) I can go to the end of the installation and launch the GUI but can't work with the mesh (due to wrong format of med308 -> syrthes 4.3 uses med307).

Where is the problem to install Syrthes?

Unzip med-3.0.7

***************************************************
* Installation MED *
***************************************************


cat: med.log: Aucun fichier ou dossier de ce type
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking how to create a ustar tar archive... gnutar
checking whether to compile using MPI... no
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for gcc option to accept ISO C99... -std=gnu99
checking whether to compile using MPI... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
configure: Can't find a parallel version of HDF.
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking absolute name of <H5public.h>... checking H5public.h usability... yes
checking H5public.h presence... yes
checking for H5public.h... yes
///home/julien/syrthes43/syrthes4.3.0/extern-libraries/opt/hdf5-1.8.14/arch/Linux_x86_64/include/H5public.h
checking absolute name of <H5Ipublic.h>... checking H5Ipublic.h usability... yes
checking H5Ipublic.h presence... yes
checking for H5Ipublic.h... yes
///home/julien/syrthes43/syrthes4.3.0/extern-libraries/opt/hdf5-1.8.14/arch/Linux_x86_64/include/H5Ipublic.h
checking for H5open in -lhdf5... no
configure: error: either use HDF5HOME env. var. or --with-hdf5=<path>
make: *** No rule to make target 'install'. Arrêt.
Error during make install of med-3.0.7

Best regards

Julien

[Yvan Fournier]

Hello,

To avoid those issues, tell Syrthes to use MED and HDF5, but not to install them: use the PATH=, to point either to SALOME's versions, or to the ones installed for Code_Saturne (if they are differrent from SALOME, you have the choice).

Regards,

Yvan

[jgd23]

Hello,

Ok it seems to work better, Syrthes works in serial and parallel but I can't postprocess in ensight format, only med
I use for Hdf5 med and scotch the library of Salome 7.6.0

I try the coupled case. I think that's it's a new error (goog news).

julien@debian:~/test_couplage/4-2Ddisks/case1$ ./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/test_couplage/4-2Ddisks/case1/RESU_COUPLING/20160728-1552


Single processor Code_Saturne simulation.
Single processor SYRTHES simulation.


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

SYRTHES4 home directory: /home/julien/syrthes43/syrthes4.3.0/arch/Linux_x86_64
MPI home directory: /usr
Building the executable file syrthes..

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

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

Error running the preprocessor.
Check the preprocessor.log file for details.


SyrthesCase summary:

Name = solid
Data file = solid-coupling.syd
Update Data file = True
Do preprocessing = True
Debug = False
Case dir. = /home/julien/test_couplage/4-2Ddisks/case1/solid
Execution dir. = /home/julien/test_couplage/4-2Ddisks/case1/RESU_COUPLING/20160728-1552/solid
Data dir. = /home/julien/test_couplage/4-2Ddisks/case1/RESU_COUPLING/20160728-1552/solid
Source dir. = /home/julien/test_couplage/4-2Ddisks/case1/RESU_COUPLING/20160728-1552/solid/src
Post dir. = /home/julien/test_couplage/4-2Ddisks/case1/RESU_COUPLING/20160728-1552/solid/POST

Conduction mesh dir. = /home/julien/test_couplage/4-2Ddisks/mesh/solid
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-coupling.syd
Conduction mesh name = /home/julien/test_couplage/4-2Ddisks/mesh/solid/3rond2d.syr
Radiation mesh name = None
Result prefix. = resu2
Restart = False
Coupling = True
Interpreted functions = False


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

Updating the mesh file name..
-> OK

Error in preprocessing stage.


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

Post-processing..
.syrthes --> med..
--> /home/julien/syrthes43/syrthes4.3.0/arch/Linux_x86_64/bin/syrthes4med30 -m "/home/julien/test_couplage/4-2Ddisks/mesh/solid/3rond2d.syr" -r "/home/julien/test_couplage/4-2Ddisks/case1/RESU_COUPLING/20160728-1552/solid/resu2.res" -o "resu2.med"
Traceback (most recent call last):
File "/home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64/bin/code_saturne", line 76, in <module>
retcode = cs.execute()
File "/home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 88, in execute
return self.commands[command](options)
File "/home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 150, in run
return cs_run.main(options, self.package)
File "/home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_run.py", line 304, in main
save_results=save_results)
File "/home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case.py", line 1779, in run
self.save_results()
File "/home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case.py", line 1694, in save_results
d.copy_results()
File "/home/julien/Code_Saturne/4.0.5/code_saturne-4.0.5/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case_domain.py", line 1200, in copy_results
raise RunCaseError(err_str)
cs_case_domain.RunCaseError:
Error during SYRTHES postprocessing

Best regards

Julien

[Yvan Fournier]

Hello,

Your syrthes.log states: Unable to open file /home/julien/test_couplage/4-2Ddisks/case1/RESU_COUPLING/20160728-1552/solid/resu2.res

Before I forge, I send you a simple patch, attached here (I'll let you add that to the Syrthes sources and recompile), to fix issues at the end of the calculation.

But the first error seems to occur during the preprocessing stage :

Error running the preprocessor.
Check the preprocessor.log file for detail

So I recommend checking that first (on the Code_Saturne side, probably a non-updated runcase or a missing mesh path in the GUI)

Regards,

Yvan