[gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with multi-threading enabled?
gerogewu8 at gmail.com
Mon Oct 4 18:23:22 CEST 2010
I am trying to do trajectory analysis on-the-fly and encountered some
What did I do:
I inserted a small piece of code into "md.c" to READ the position of
atoms and do some simple analysis. In the GMX3.2, my code works fine.
In GMX4.5.1, my code works only if I set mdrun -nt to 1, i.e. force GMX
to use one thread. Otherwise, mdrun reports segmentation fault.
1. I speculate that the segmentation fault is caused by thread
conflict, i.e., I somehow break parallelization in Gromacs - is this
2. Is it possible to perform on-fly analysis or other types of
customization of Gromacs when multi-threading is enabled?
3. If answer to 2 is yes, where can I find the documentations for
doing so, and how difficult is it to write multi-threading code using
Gromacs's own library?
Thank you very much for your time.
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