Dear All: I am trying to do trajectory analysis on-the-fly and encountered some difficulty.
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. The problem: 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. Questions: 1. I speculate that the segmentation fault is caused by thread conflict, i.e., I somehow break parallelization in Gromacs - is this right? 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. Best regards, Peng -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
