Segmentation fault loading Python/3.5.2

HPC Technical
1

Hello,

I try to load the version python 3.5.2.

I run the following commend:

module load GCC/5.4.0-2.26 OpenMPI/1.10.3 icc/2016.3.210-GCC-5.4.0-2.26 impi/5.1.3.181 ifort/2016.3.210-GCC-5.4.0-2.26 impi/5.1.3.181 Python/3.5.2

and when I try to check the version, I have

python3 --version

Segmentation fault

Best,

2

Hi,
Do you need icc, impi/5.13 (twice?), and ifort ? Otherwise, I tried and it works with GCC/5.4.0 and OMPI/1.10.3.

[boulmier@login2 ~]$ ml purge
[boulmier@login2 ~]$ ml
No modules loaded
[boulmier@login2 ~]$ ml GCC/5.4.0-2.26 OpenMPI/1.10.3 Python/3.5.2
[boulmier@login2 ~]$ python3 --version
Python 3.5.2

When you check module spider <something>, each line tells you a set of dependency (i.e., you need to load only one line of dependency).

Example:

module spider Python/3.5.2

Python: Python/3.5.2

Description:
  Python is a programming language that lets you work more quickly and integrate your systems more effectively. 


You will need to load all module(s) on any one of the lines below before the "Python/3.5.2" module is available to load.

  GCC/5.4.0-2.26  OpenMPI/1.10.3 
  icc/2016.3.210-GCC-5.4.0-2.26  impi/5.1.3.181
  ifort/2016.3.210-GCC-5.4.0-2.26  impi/5.1.3.181

You need to load any of these lines.

Hope this helps,

Best,

Anthony

3

Thanks for your answer.

I know how to find the dependency of a package, but the problem comes form the info given by module spider Python/3.5.2.

In this case of Python/3.5.2 if you try to load python using the second or the third line, there is no error message, but when you try to load python3, there is a segmentation fault.

It’s not a problem for me, because, I use an other version of Python, but I think that it can be a problem for other people that should be fixed, or the text given by module spider Python/3.5.2 should be modified.

4

Indeed, using the dependencies of the second or third line cause python3 to segfault.

It wasn’t clear to me due to the strange set of modules to load.

I also suggest to check why 2nd or 3rd line cause this behavior.

Best,

Anthony

5

Dear @Raphael.Conradin, dear @Anthony.Boulmier,

This version of Python was installed when we still had the cluster in CentOS6 and we didn’t rebuilt it (this is the same for a majority of the legacy software we provide on Baobab).

I’ve corrected the module, i.e. I’ve erase the lines with the broken dependencies. If needed I can re install this exact same version for the same compiler.

If you don’t need this particular version, I suggest you to use one of the other versions:

 Description:
      Python is a programming language that lets you work more quickly and integrate your systems more effectively.

     Versions:
        Python/2.7.9
        Python/2.7.11
        Python/2.7.12
        Python/2.7.13
        Python/2.7.14-bare
        Python/2.7.14
        Python/2.7.15-bare
        Python/2.7.15
        Python/2.7.16
        Python/3.5.2
        Python/3.6.1
        Python/3.6.3
        Python/3.6.4
        Python/3.6.6
        Python/3.7.2
        Python/3.7.4

Best