Problem with matlab compilator mcc on bamboo

HPC Support HPC issues
1

Primary informations

Username: cuny
Cluster: bamboo

I try to compile a matlab code in an executable with mcc on bamboo but get the following error:

mclCopyDir failed: Failed copying '/home/users/c/cuny/.matlab/R2022a/matlab.prf' to '/tmp/mcc1340-7eef-fa78-08e6.tmp/user/matlab.prf':  reason 'fl:filesystem:SystemError'
Failed to copy user-level MATLAB settings from "/home/users/c/cuny/.matlab/R2022a" into temporary directory "/tmp/mcc1340-7eef-fa78-08e6.tmp/user". Cannot continue without risk of corrupting MATLAB settings.

Here is the command I use:

mcc -m -v -R '-nojvm, -nodisplay' -I functions_dynamics/ -o epithelia_closed Epithelia_Dynamics.m
2

Dear @Nicolas.Cuny

on which server do you issue this command? login1 or a compute node?

3

I did try it both on login1 and on compute node and did get the same result.

4

I was able to reproduce the error. I tried like that and I went a little bit futher:

(bamboo)-[cuny@login1 TestYS]$ mkdir my_pref
(bamboo)-[cuny@login1 TestYS]$ MATLAB_PREFDIR=$PWD/my_pref mcc -m -v -R '-nojvm, -nodisplay' -I functions_dynamics/ -o epithelia_closed Epithelia_Dynamics.m
Opening log file:  /home/users/c/cuny/java.log.2348
Compiler version: 8.4 (R2022a)
Analyzing file dependencies.
Parsing file "/home/users/c/cuny/EpithelialShell/TestYS/Epithelia_Dynamics.m"
        (referenced from command line).
Failed to build CTF file: 'epithelia_closed.ctf'. Details: Error in closing CTF file 'epithelia_closed.ctf'. Details: 'Could not commit changes:  copy failed: fl:filesystem:SystemError: /tmp/.f1e3-1657-7cd0-11d3.tmp Invalid cross-device link'

Then, I tried again overriding $TMP. You have to empty the my_pref directory first.

(bamboo)-[cuny@login1 TestYS]$ rm my_pref/*
(bamboo)-[cuny@login1 TestYS]$ TMP=$PWD/my_tmp MATLAB_PREFDIR=$PWD/my_pref mcc -m -v -R '-nojvm, -nodisplay' -I functions_dynamics/ -o epithelia_closed Epithelia_Dynamics.m
Opening log file:  /home/users/c/cuny/java.log.23732
Compiler version: 8.4 (R2022a)
Analyzing file dependencies.
Parsing file "/home/users/c/cuny/EpithelialShell/TestYS/Epithelia_Dynamics.m"
        (referenced from command line).
Generating file "/home/users/c/cuny/EpithelialShell/TestYS/readme.txt".
Generating file "run_epithelia_closed.sh".

Seems to work?!