[gmx-users] Reducing Standard Error output

Jack Shultz js at drugdiscoveryathome.com
Sat Dec 5 19:36:55 CET 2009

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
2) modify the code so it reports progress regardless of verbose flag

On Thu, Dec 3, 2009 at 7:39 PM, Jack Shultz <js at 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.Abraham at 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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