Jack Shultz wrote:
Even though I can sucessfully run this when I remove the verbose flag,
it causes another problem. We keep trac of the progress of indivual
simulations using a code modfication in sim_util.c
124: f = fopen("progress.txt", "w");
125- if (!f) return;
126- fprintf(f, "%g", (step - ir->init_step) / (float) ir->nsteps);
127- fclose(f);
Apparently this code is only used if the app is in verbose mode. So I
guess we have two choices:
1) either find the cause of the lincs warnings
That is always necessary if you don't want an expensive random number
generator. Your simulation system is ill conditioned, and the lincs
warnings will exist and be reported in at least the .log file regardless
of the verbosity.
2) modify the code so it reports progress regardless of verbose flag
Sure, but that's independent of the former. You should consider other
modifications too - opening and closing a file every integration step
might be prohibitively expensive. Since from previous threads you're
monitoring this progress file with some other process to report to the
user, you should consider more efficient means of such communication,
such as an inter-process socket.
Mark
On Thu, Dec 3, 2009 at 7:39 PM, Jack Shultz <j...@drugdiscoveryathome.com>
wrote:
yes the environment I was running in was the boinc wrapper and its
supposed to somehow return the standard error output. It probably got
overloaded. It is curious why I only had the problem on windows 64 but
I'm not going to worry about it.
On Thu, Dec 3, 2009 at 6:33 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote:
Jack Shultz wrote:
Thanks,
I just figured out removing the -v will reduce output. Interestingly I
only have this problem with 64-bit Windows hosts. I have not observed
it in any others and I have a fairly diverse environment on this
project. For now I can say removing the -v gets the app to finish the
run.
mdrun -v will have no effect on correct completion, unless the use of -v is
causing some I/O buffer external to GROMACS to over-run. I suspect your
observation indicates you were comparing apples and oranges.
Mark
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Jack
http://drugdiscoveryathome.com
http://hydrogenathome.org
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