Error in MOD compilation with a Slurm script
Posted: Thu Feb 15, 2018 4:20 pm
Hi.
On a cluster I have a custom installation of NEURON 7.5 (October build) compiled with a Python 2.7.12 module, installed on the machine.
The problem arise in the way I try to compile the MOD files:
1) if I manually load the python module, the path to NEURON and start the virtual environment, containing numpy, scipy, etc, than I can compile the MOD files without problems. In this case i remain on the login node.
2) if I do the same module load, path and virtualenv, with a sbatch script, when the compute node try to compile the MOD files, it does all of them but then it stops with:
/usr/bin/ld: cannot find -lreadline
collect2: error: ld returned 1 exit status
make: *** [libnrnmech.la] Error 1
What can cause this error?
Best regards
Stefano Masoli PhD
On a cluster I have a custom installation of NEURON 7.5 (October build) compiled with a Python 2.7.12 module, installed on the machine.
The problem arise in the way I try to compile the MOD files:
1) if I manually load the python module, the path to NEURON and start the virtual environment, containing numpy, scipy, etc, than I can compile the MOD files without problems. In this case i remain on the login node.
2) if I do the same module load, path and virtualenv, with a sbatch script, when the compute node try to compile the MOD files, it does all of them but then it stops with:
/usr/bin/ld: cannot find -lreadline
collect2: error: ld returned 1 exit status
make: *** [libnrnmech.la] Error 1
What can cause this error?
Best regards
Stefano Masoli PhD