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 <[email protected]
<mailto:[email protected]>> 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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