Closed felipeZ closed 6 years ago
Same behavior in python 2.7 and 3.5
That's weird, it's a Python error, but Gromacs is entirely C++. Maybe gromit uses Python to calculate something, and only works with Python 2.7; I'm using Python 3 on the cluster because cwltiny requires it. I'll be back to Cerise and this project on Monday, I'll have a look at it then.
I have found that the error is trigger by the following line in my .bashrc:
export PATH="/home/user/miniconda3/bin:$PATH"
If I comment that line everything goes well.
Ah, yes, gromit does use Python as a fancy calculator, and those Python statements won't work in Python 3, because the print statement is missing parenthesis. And the default Python on the DAS-5 is Python 2.7, so I guess when gromit is called it uses that. That line in your .bashrc probably changes the default to Python 3, which then makes it not work.
I think the correct solution is to add a module load python/2.7.13 line to mdstudio/gromit/call_gromit.sh so that it always gets Python 2. Oh and of course the correct correct solution is to replace gromit, but we'll get to that :).
I have been using the following python script to run jobs with Cerise-client:
Suddenly, The following error is trown:
Due to the following error in
gromit
:Any idea of what's going on?