"Preprocessing stage required but no mesh is given"

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senartcon
Posts: 37
Joined: Wed May 08, 2013 6:46 pm

"Preprocessing stage required but no mesh is given"

Post by senartcon »

Dear All,

I am facing the problem upon running code_saturne as the title says:

Code: Select all

cs_case_domain.RunCaseError: Preprocessing stage required but no mesh is given
although I have ensured that the mesh path is correctly given.

Since after a fresh install of Ubuntu 18.04, Salome and CS 6.0.0 I am facing this issue. To my knowledge there were no issues in installation - please see attached files - setup.txt and install_saturne.log.

For a typical case the run.bat looks normal as i learnt from this forum:

Code: Select all

#!/bin/bash

# Ensure the correct command is found:
export PATH=/home/anands/Documents/CODE_SATURNE/Code_Saturne/6.0.0/code_saturne-6.0.0/arch/Linux_x86_64/bin:$PATH

# Run command:
\code_saturne run --param MiddleStove.xml --threads-per-task 8
Of the outputs by CS for a typical case, I have attached the 'summary' file output by CS; there is no error file and the listing is not a valid file.

Am I missing some dependencies? Please suggest.

Regards
Anand
Attachments
summary.txt
(5.27 KiB) Downloaded 134 times
install_saturne.log
(2.13 MiB) Downloaded 156 times
setup.txt
(4.35 KiB) Downloaded 148 times
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: "Preprocessing stage required but no mesh is given"

Post by Yvan Fournier »

Hello,

Could you post the xml file, and (if present in DATA), the cs_user_scripts.py file ?

Regards,

Yvan
senartcon
Posts: 37
Joined: Wed May 08, 2013 6:46 pm

Re: "Preprocessing stage required but no mesh is given"

Post by senartcon »

Hello Yvan,

thanks for your reply. Please find attached files you have asked.

I should note that this case was generated and run successfully in CS 5.0.7. Now the xml file has been modified because of saving the case in CS 6.0.0.

Anand
Attachments
cs_user_scripts.py
(8.27 KiB) Downloaded 152 times
MiddleStove.xml
(10.4 KiB) Downloaded 149 times
senartcon
Posts: 37
Joined: Wed May 08, 2013 6:46 pm

Re: "Preprocessing stage required but no mesh is given"

Post by senartcon »

Hello Yvan,

attached herewith are xml and cs_user_scripts.py for case created using CS 6.0.

Anand
Attachments
cs_user_scripts.py
(6.45 KiB) Downloaded 151 times
middle_stove.xml
(4.63 KiB) Downloaded 162 times
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: "Preprocessing stage required but no mesh is given"

Post by Yvan Fournier »

Hello,

I do not reproduce your issue using these same files (running on Arch Linux) so I do not really understand where this is coming from. In your case, it seems the cs_user_scripts.py is not useful (it does not contain any additional option) so you can remove it. Can you test again without it ? Also did you vist the mesh page in the GUI before running the case ?

The xml file in your example log (MiddleStove.xml) is different from the one you posted (middle_stove.xml).
Are you sure both have the mesh info ?

Regards,

Yvan
senartcon
Posts: 37
Joined: Wed May 08, 2013 6:46 pm

Re: "Preprocessing stage required but no mesh is given"

Post by senartcon »

Hello Yvan,

I removed cs_user_scripts.py but to no avail.

Yes I visited the mesh page in GUI, cleaned the directory listing and populated the meshes again many times, but to no avail.

I have attached mesh files and the latest xml file, if that would help you reproduce any error.
It can be seen that the xml file does have the mesh file names and the path.


I am posting the error Traceback I am getting on the terminal:

Code: Select all

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

 Single processor Code_Saturne simulation.


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

Traceback (most recent call last):
  File "/home/anands/Documents/CODE_SATURNE/Code_Saturne/6.0.0/code_saturne-6.0.0/arch/Linux_x86_64/bin/code_saturne", line 76, in <module>
    retcode = cs.execute()
  File "/home/anands/Documents/CODE_SATURNE/Code_Saturne/6.0.0/code_saturne-6.0.0/arch/Linux_x86_64/lib/python3.6/site-packages/code_saturne/cs_script.py", line 93, in execute
    return self.commands[command](options)
  File "/home/anands/Documents/CODE_SATURNE/Code_Saturne/6.0.0/code_saturne-6.0.0/arch/Linux_x86_64/lib/python3.6/site-packages/code_saturne/cs_script.py", line 170, in run
    return cs_run.main(options, self.package)
  File "/home/anands/Documents/CODE_SATURNE/Code_Saturne/6.0.0/code_saturne-6.0.0/arch/Linux_x86_64/lib/python3.6/site-packages/code_saturne/cs_run.py", line 329, in main
    return run(argv, pkg)[0]
  File "/home/anands/Documents/CODE_SATURNE/Code_Saturne/6.0.0/code_saturne-6.0.0/arch/Linux_x86_64/lib/python3.6/site-packages/code_saturne/cs_run.py", line 317, in run
    stages=stages)
  File "/home/anands/Documents/CODE_SATURNE/Code_Saturne/6.0.0/code_saturne-6.0.0/arch/Linux_x86_64/lib/python3.6/site-packages/code_saturne/cs_case.py", line 2042, in run
    mpiexec_options)
  File "/home/anands/Documents/CODE_SATURNE/Code_Saturne/6.0.0/code_saturne-6.0.0/arch/Linux_x86_64/lib/python3.6/site-packages/code_saturne/cs_case.py", line 1738, in preprocess
    d.preprocess()
  File "/home/anands/Documents/CODE_SATURNE/Code_Saturne/6.0.0/code_saturne-6.0.0/arch/Linux_x86_64/lib/python3.6/site-packages/code_saturne/cs_case_domain.py", line 896, in preprocess
    raise RunCaseError(err_str)
Attachments
MiddleStove.zip
(66.27 KiB) Downloaded 147 times
middle_stove.xml
(4.86 KiB) Downloaded 150 times
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: "Preprocessing stage required but no mesh is given"

Post by Yvan Fournier »

Hello,

You files work fine on my system, so I would suspect some installation issue.

One last thing you may try on your current install is to uncheck the "preprocessing only" option in the mesh settings, or switch to "import only", which would produce a "mesh_input" file usable for another run.

Otherwise do you have references to a previous install somewhere in you environment (in PATH, LD_LIBRARY_PATH, PYTHONPATH)... ? or Ubuntu packages of another version of Code_Saturne installed ? This might cause issues. Doing a fresh install in another directory may help.

Best regards,

Yvan
senartcon
Posts: 37
Joined: Wed May 08, 2013 6:46 pm

Re: "Preprocessing stage required but no mesh is given"

Post by senartcon »

Hello Yvan,

it is unfortunate that the following recommendations did not work
One last thing you may try on your current install is to uncheck the "preprocessing only" option in the mesh settings, or switch to "import only", which would produce a "mesh_input" file usable for another run.
And i went for a fresh ubuntu 18.04 install today and the error still persists!
Otherwise do you have references to a previous install somewhere in you environment (in PATH, LD_LIBRARY_PATH, PYTHONPATH)... ? or Ubuntu packages of another version of Code_Saturne installed ? This might cause issues. Doing a fresh install in another directory may help.
Yvan Fournier
Posts: 4070
Joined: Mon Feb 20, 2012 3:25 pm

Re: "Preprocessing stage required but no mesh is given"

Post by Yvan Fournier »

Hello,

Are you sure you do not have another code_saturne install in Ubuntu (such as packaged install, installed through Synaptic / apt-get) ?

Otherwise, I will send you some slightly modified version of the Python scripts, with additional instrumentation/logging, so as to understand what is going wrong....

Best regards,

Yvan
senartcon
Posts: 37
Joined: Wed May 08, 2013 6:46 pm

Re: "Preprocessing stage required but no mesh is given"

Post by senartcon »

Hello Yvan,

yes, I am sure there is no other code_saturne install.
I am trying to install CS on a fresh Ubuntu installation.

Please send the required files. I shall execute as you suggest.

Anand
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