gromacs.grompp output in my Jupyter nootbook
frchalaoux opened this issue · comments
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.
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 ??
Thanks, I will investigate these tracks but there is already a problem with the ipythonkernel=4.3.1.
To be continued ...
FR.
Closing, no further comments. Please re-open if necessary.