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Becksteinlab / GromacsWrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
https://gromacswrapper.readthedocs.org
GNU General Public License v3.0
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gromacs.grompp output in my Jupyter nootbook #108

Closed frchalaoux closed 7 years ago

frchalaoux commented 7 years ago

Hi all,

I use gromacswrapper 0.6.2. and gromacs 2016-1

Neither, gromacs.grompp('v', f="ions.mdp", c="solvate_clean.gro", p="topol.top", o="ions.tpr") or gromppy = Grompp(v=True, f="ions.mdp", c="solvate_clean.gro", p="topol.top", o="ions.tpr") gromppy.run(v=True)

writes into the output of my Jupyter nootbook ('v', or v=True).

By cons, It writes in an ipython session.

Did I forgot something ?

FR.

orbeckst commented 7 years ago

Have a look at the options for stdout and stderr under Input/Output – maybe that is going to help.

By default we do write to stderr and stdout (unless you changed some of the flags – Input/Output) so maybe the notebook is doing its own thing with these filedescriptors? – maybe http://stackoverflow.com/questions/35936086/jupyter-notebook-does-not-print-logs-to-the-output-cell ??

frchalaoux commented 7 years ago

Thanks, I will investigate these tracks but there is already a problem with the ipythonkernel=4.3.1. To be continued ... FR.

orbeckst commented 7 years ago

Closing, no further comments. Please re-open if necessary.