Calculation starts only in single processor mode

[rodion]

Hello everyone,

I'm using Code_Saturne 5.0.3 on Ubuntu 16.04 in VirtualBox with 4 processors.
While installing CS5.0.3 I had the following settings in setup file:
compC /usr/bin/cc
mpiCompC auto
compCxx /usr/bin/c++
mpiCompCxx auto
hdf5 yes no /home/rodion/Code_Saturne/5.0.3/hdf5-1.8.17/arch/Linux_x86_64
cgns yes no /home/rodion/Code_Saturne/5.0.3/cgnslib-3.2.1/arch/Linux_x86_64
med yes no /home/rodion/Code_Saturne/5.0.3/med-3.2.1/arch/Linux_x86_64
scotch no no None
parmetis no no None
libxml2 auto no None

Then I have found that I don't have MPI in my OS and installed the following packages:
libopenmpi-dev
libopenmpi1.10
openmpi-bin
openmpi-common
libhdf5-openmpi-dev

File usr/include/openmpi/mpi/h exists.

In SCRIPTS/runcase it is written: \code_saturne run --param setup.xml --threads-per-task 2

But still Code_Saturne starts calculation only in single processor mode despite the number of threads per process imposed in GUI.
Does someone know what can be the problem in this case and how can I make Code_Saturne work in parallel mode?


Thanks in advance.
Best regards,
Rodion

[Yvan Fournier]

Hello,

The number of threads per task is a secondary parallel mode, which can be combined with MPI (though the speedup you will obtain depends on your hardware).

The MPI mode (number of tasks, or number of processes) should also appear in the GUI, unless MPI was not detected.

Could you post your config.log file from install ?

Regards,

Yvab

[rodion]

Thank you for your fast answer, Yvan.

Please find my config.log file from the folder called code_saturne-5.0.3.build attached.
By the way, I have found the following lines in it, so I suppose, CS was configured improperly. Is it possible to make things better or I need to reinstall Code_Saturne?

configure:25155: checking for MPI (MPI compiler wrapper test)
configure:25171: /usr/bin/cc -o conftest -std=c99 -fms-extensions -funsigned-char -pedantic -W -Wall -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wnested-externs -Wunused -Wfloat-equal -fdiagnostics-color=auto -fopenmp -D_POSIX_SOURCE -DNDEBUG -O -Wl,-export-dynamic -fopenmp conftest.c -ldl >&5
conftest.c:48:17: fatal error: mpi.h: No such file or directory
compilation terminated.
configure:25171: $? = 1
configure: failed program was:
| /* confdefs.h */

Best regards,
Rodion

[Yvan Fournier]

Hello,

Strange that "mpiCompC auto" and "mpiCompCxx auto" in your setup file are not enough to detect MPI (I'll need to check this).

Try "mpiCompC mpicc" and "mpiCompCxx mpicxx" instead in the setup file.

Regards,

Yvan

[rodion]

Thank you for your answer, Yvan.

Could you please specify if I should reinstall Code_Saturne?
If yes, how can I delete the previous instance from my Ubuntu?
And which MPI is better to use for Code_Saturne?

Best regards,
Rodion

[Yvan Fournier]

Hello,

Yes, you will need to reinstall it. To uninstall, things depend on how you installed it, so a summary of that may help. If you installed in a a given prefix, remove the directory. If you installed it in /usr/local, "make uninstall" from the install directory is safer.

Both OpenMPI and MPICH MPI libraries shoudl work well.

Regards,

Yvan

[rodion]

Thank you for your answer, Yvan.

I have reinstalled Code_Saturne after installation of OpenMPI. In GUI the option "Number of processes" appeared, but when I start CS with "sudo ./SaturneGUI" and choose 2 processes, for example, CS gives me the following error message:
--------------------------------------------------------------------------
mpiexec.openmpi has detected an attempt to run as root.
Running at root is *strongly* discouraged as any mistake (e.g., in
defining TMPDIR) or bug can result in catastrophic damage to the OS
file system, leaving your system in an unusable state.

You can override this protection by adding the --allow-run-as-root
option to your cmd line. However, we reiterate our strong advice
against doing so - please do so at your own risk.
--------------------------------------------------------------------------
Do you know how I can use CS with this key --allow-run-as-root?

I start CS with sudo because without sudo any attempt to start calculation gives me the following error message:

Traceback (most recent call last):
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/bin/code_saturne", line 76, in
retcode = cs.execute()
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 93, in execute
return self.commands[command](options)
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 168, in run
return cs_run.main(options, self.package)
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_run.py", line 387, in main
return run(argv, pkg)[0]
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_run.py", line 375, in run
stages=stages)
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case.py", line 1937, in run
retcode = self.prepare_data(force_id)
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case.py", line 1497, in prepare_data
d.compile_and_link()
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case_domain.py", line 599, in compile_and_link
shutil.copy2(src_file, dest_file)
File "/usr/lib/python2.7/shutil.py", line 130, in copy2
copyfile(src, dst)
File "/usr/lib/python2.7/shutil.py", line 82, in copyfile
with open(src, 'rb') as fsrc:
IOError: [Errno 13] Permission denied: '/home/rodion/TransfArc/Case3_Argon/SRC/cs_user_boundary_conditions.f90'

Best regards,
Rodion

[Yvan Fournier]

Hello,

No, I never run Code_Saturne as root.

Why should you use "sudo" to run the code ?

Regards,

Yvan

[rodion]

Thank you for you answer, Yvan.

I start CS with sudo because without sudo any attempt to start calculation gives me the following error message:

Traceback (most recent call last):
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/bin/code_saturne", line 76, in
retcode = cs.execute()
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 93, in execute
return self.commands[command](options)
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_script.py", line 168, in run
return cs_run.main(options, self.package)
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_run.py", line 387, in main
return run(argv, pkg)[0]
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_run.py", line 375, in run
stages=stages)
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case.py", line 1937, in run
retcode = self.prepare_data(force_id)
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case.py", line 1497, in prepare_data
d.compile_and_link()
File "/home/rodion/Code_Saturne/5.0.3/code_saturne-5.0.3/arch/Linux_x86_64/lib/python2.7/site-packages/code_saturne/cs_case_domain.py", line 599, in compile_and_link
shutil.copy2(src_file, dest_file)
File "/usr/lib/python2.7/shutil.py", line 130, in copy2
copyfile(src, dst)
File "/usr/lib/python2.7/shutil.py", line 82, in copyfile
with open(src, 'rb') as fsrc:
IOError: [Errno 13] Permission denied: '/home/rodion/TransfArc/Case3_Argon/SRC/cs_user_boundary_conditions.f90'

Do you know, what can be the reason?

Best regards,
Rodion

[Antech]

Hello, rodion.
IMHO, you just need to obtain rights for you case directory. When you are in your case directory (check with pwd), switch to root (su root) and then use chmod a+rwx ./* to eliminate access problems for any user. Please be careful while you're under root account. Changing access rights for the whole filesystem will make you OS unusabale so watch the directory you're now in! Be careful to not forget the dot before the slash when changing permissions! Or specify the dir explicitly, for example, like chmod a+rwx /home/user/Saturne/Case1/*