[gmx-users] timestep fraction complete

Jack Shultz js at drugdiscoveryathome.com
Fri Sep 25 02:29:09 CEST 2009 

Thanks a bunch for the help Mark!
I made some additional changes that seem to work the way I need it.

src/mdlib/sim_util.c:122:      fprintf(stderr, "Fraction complete: %g\n",
(step - ir->init_step) / (float) ir->nsteps);
src/mdlib/sim_util.c-123-
src/mdlib/sim_util.c-124-      f = fopen("progress.txt", "w");
src/mdlib/sim_util.c-125-      if (!f) return;
src/mdlib/sim_util.c-126-      fprintf(f, "%g", (step - ir->init_step) /
(float) ir->nsteps);
src/mdlib/sim_util.c-127-      fclose(f);
src/mdlib/sim_util.c-128-  }


On Thu, Sep 24, 2009 at 6:58 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  Jack Shultz wrote:
>
>> I am hoping for an update every 10 minutes just to satisfy the anxieties
>> of volunteers crunching on my project, but every hour may be satisfactory.
>> And if I can do this without requiring any shell scripts it would be better
>> in my environment. So I started making some code modifications which
>> apparently did not work
>>  src/mdlib/sim_util.c:93:void print_time(FILE *out,time_t start,int
>> step,t_inputrec *ir)
>> src/mdlib/sim_util.c-94-{
>> src/mdlib/sim_util.c-95-  static real time_per_step;
>> src/mdlib/sim_util.c-96-  static time_t end;
>> src/mdlib/sim_util.c-97-  time_t finish;
>> src/mdlib/sim_util.c-98-  double dt, fc;
>> src/mdlib/sim_util.c-99-  char buf[48];
>> src/mdlib/sim_util.c-100-  FILE *progress="progress.txt";
>> src/mdlib/sim_util.c-101-
>> src/mdlib/sim_util.c-102-  if (!gmx_parallel_env)
>> src/mdlib/sim_util.c-103-    fprintf(out,"\r");
>> src/mdlib/sim_util.c-104-  fprintf(out,"step %d",step);
>> src/mdlib/sim_util.c-105-  if ((step >= ir->nstlist)) {
>> src/mdlib/sim_util.c-106-    if ((ir->nstlist == 0) || ((step %
>> ir->nstlist) == 0)) {
>> src/mdlib/sim_util.c-107-      /* We have done a full cycle let's update
>> time_per_step */
>> src/mdlib/sim_util.c-108-      end=time(NULL);
>> src/mdlib/sim_util.c-109-      dt=difftime(end,start);
>> src/mdlib/sim_util.c-110-      time_per_step=dt/(step - ir->init_step +
>> 1);
>> src/mdlib/sim_util.c-111-    }
>> src/mdlib/sim_util.c-112-    dt=(ir->nsteps + ir->init_step -
>> step)*time_per_step;
>> src/mdlib/sim_util.c-113-
>> src/mdlib/sim_util.c-114-    if (dt >= 300) {   src/mdlib/sim_util.c-115-
>>      finish = end+(time_t)dt;
>> src/mdlib/sim_util.c-116-      sprintf(buf,"%s",ctime(&finish));
>> src/mdlib/sim_util.c-117-      buf[strlen(buf)-1]='\0';
>> src/mdlib/sim_util.c-118-      fprintf(out,", will finish %s",buf);
>> src/mdlib/sim_util.c-119-    }
>> src/mdlib/sim_util.c-120-    else
>> src/mdlib/sim_util.c-121-      fprintf(out,", remaining runtime: %5d s
>>      ",(int)dt);
>> src/mdlib/sim_util.c-122-      fc = (int)dt / ir->nstlist;
>> src/mdlib/sim_util.c-123-      fprintf(stderr, "Fraction complete: %d \n",
>> fc);
>>
>
> You're doing integer division and writing an integer. That won't get you
> fraction complete, even if the ratio of dt (the remaining runtime in
> seconds) and ir->nstlist (the number of steps between neighboursearches)
> meant anything! Use
>
> fprintf(stderr, "Fraction complete: %g\n", (step - ir->init_step) / (float)
> ir->nsteps);
>
> Mark
>
>  src/mdlib/sim_util.c-124-  }
>> src/mdlib/sim_util.c-125-  if (gmx_parallel_env)
>> src/mdlib/sim_util.c-126-    fprintf(out,"\n");
>> src/mdlib/sim_util.c-127-
>> src/mdlib/sim_util.c-128-  fflush(out);
>> src/mdlib/sim_util.c-129-}
>>  Back Off! I just backed up md.edr to ./#md.edr.4#
>> starting mdrun 'Protein in water'
>> 500 steps,      1.0 ps.
>> step 100, remaining runtime:   122 s          Fraction complete: 0
>> step 200, remaining runtime:    92 s          Fraction complete: 0
>>
>>
>> On Thu, Sep 24, 2009 at 6:34 PM, Mark Abraham <Mark.Abraham at anu.edu.au<mailto:
>> Mark.Abraham at anu.edu.au>> wrote:
>>
>>    Jack Shultz wrote:
>>
>>        I figured out another way to update the progress of my
>>        simulation, but I need to report the fraction of completion at
>>        the certain intervals of mdrun. Possibly at every time step or
>>        if that does not make sense every 100 timesteps. I don't think
>>        this is a feature currently supported, so I will have to make
>>        some source code chages. I am looking for the variables related
>>        to total number of time steps and where it controls the the
>>        current time step so I can calculate the fraction of complete
>>        where current-timestep / total-timestep
>>
>>
>>    Under at least some circumstances GROMACS writes the expected
>>    runtime remaining to stderr, but I don't recall what/when. Piping
>>    that to some useful script has to be a good start. You certainly
>>    don't need this data every time step, and don't want to be
>>    perturbing mdrun to get it.
>>
>>    Even if the above was unsuitable, surely progress would only need to
>>    be moderately accurate and for simulations that last many hours. If
>>    so, you'll get good enough data by grepping a gmxdump of the .tpr to
>>    get the expected frequencies of output and length of run, and then
>>    watching the growth of whichever of .log/.trr/.edr is written most
>>    frequently. I/O buffering will affect the numbers somewhat.
>>
>>    Mark
>>
>>    _______________________________________________
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>>
>>
>>
>>
>> --
>> Jack
>>
>> http://drugdiscoveryathome.com
>> http://hydrogenathome.org
>>
>>
>> ------------------------------------------------------------------------
>>
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-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org
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