Error in MOD compilation with a Slurm script

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bremen
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Error in MOD compilation with a Slurm script

Post by bremen » 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

ted
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Re: Error in MOD compilation with a Slurm script

Post by ted » Fri Feb 16, 2018 9:39 am

nrnivmodl is a standalone executable, independent of NEURON's computational engine which is used to execute simulations. I'd expect that compilation of mod files should just work, period, unless your sbatch script does something to PATH that prevents nrnivmodl from finding a library that it needs.

hines
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Re: Error in MOD compilation with a Slurm script

Post by hines » Fri Feb 16, 2018 11:14 am

Just as you built nrniv and all the NEURON libraries on the login node. So should you translate mod files and build the libnrnmech.so file on the
login node (with nrnivmodl). In your case, it sounds like compute nodes are the same architecture as the login node and most of the development
environment is available on them. The question then is why libreadline is available on the login node but not (one of) the compute nodes.

bremen
Posts: 26
Joined: Mon Apr 24, 2017 8:15 am
Location: Italy

Re: Error in MOD compilation with a Slurm script

Post by bremen » Tue Feb 20, 2018 2:23 pm

Hi.
The question then is why libreadline is available on the login node but not (one of) the compute nodes.
That was the cause of the issue.
The admin of the cluster installed libreadline, on the compute nodes, and i was able to compile the MODs and run the simulations.

Thank you
Stefano

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