[gmx-users] timestep fraction complete

Jack Shultz js at drugdiscoveryathome.com
Fri Sep 25 00:44:14 CEST 2009

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-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-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 -
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",
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-128-  fflush(out);

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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