Error during compilation via CMake or via Python

[qduez]

Hello,

As I indicated in another thread (#4), I am facing "Segmentation fault" issues when running the cluster module of gmx_clusterByFeatures compiled via Pip3. The compilation is performed without any error with Pip3.

So, I tried to compile gmx_clusterByFeatures via Python or via Cmake. However, the compilation fails in both cases and I obtain the following error:
error.txt
(here for the Python compilation)

For info, I am working on a Linux machine with Python 3.7.4 and GROMACS 1.8.3 without MPI or GPU support.

Thanks for any help.

[stephaneabel]

Hello
What is the OS ?
For Ubuntu did you use "exactly" the how to mentioned here
https://gmx-clusterbyfeatures.reathedocs.io/en/latest/install.html
And in particular the sections "Installation from source-code" and "Updating gmx_clusterByFeatrues"
Stéphane

[qduez]

Hello,

Thanks for your answer, Stéphane!

The compilation via Pip3 was done both on a Windows Subsystem for Linux (machine 1) and on a Linux Mint OS (machine 2).

Yesterday, I tried both compilations on machine 1. Today, I'm trying on machine 2. The python compilation (sudo pip3 install numpy scipy sklearn matplotlib / export GMX_PATH=/path/to/installed/gromacs
sudo GMX_PATH=$GMX_PATH python3 setup.py install) which failed
Error_Python_LinuxMint.txt.

The C++ installation worked on machine 2! But when I'm using the cluster module of gmx_clusterByFeatures I still get the "Segmentation fault (core dumped)"...

[rjdkmr]

Hi,

Presently compilation only work with Gromacs-2016 version. Therefore, compilation is ending with error. I will try to update it for Gromacs-2020 version, however, it might take time depending on the internal changes in Gromacs.

With pip, when segmentation fault occurs. All commands resulted to this error? Try running help of a command, e.g. gmx_clusterByFeatures cluster -h. If this command ends with segmentation fault then you will need to compile.

[qduez]

Hi,

Thanks for your answer.

I reinstalled Gromacs 2016.5 on my machine 1 and performed the compilation with pip and Python. This time, I did not encounter any problems for the compilation.

However, when I run gmx_clusterByFeatures, I still get the segmentation fault. When I type gmx_clusterByFeatures cluster -h as you suggested, I get the help as expected.