[gmx-users] timestep fraction complete

[Jack Shultz]

Ah of course!
 fc = (int)dt / ir->nstlist;
I should cast these as data types that support decimals right?

On Thu, Sep 24, 2009 at 6:44 PM, Jack Shultz <js at drugdiscoveryathome.com>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);
> 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>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
>



-- 
Jack

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