[gmx-users] problem to restart REMD
leila salimi
leilasalimi at gmail.com
Thu Jun 25 16:23:13 CEST 2015
Thanks very much. Ok I will check again, it seems that they are at the same
step!
only the thing that comes to my mind is that I used different number of
cpus when I tried to update few steps for some replicas, and then I used
the primary numbers of cpu that I used.
Also I got this error when I update it the some state.cpt
Fatal error:
Checksum wrong for 'md0.log'. The file has been replaced or its contents
have been modified. Cannot do appending because of this condition.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
and also this!
#nodes mismatch,
current program: 2
checkpoint file: 128
#PME-nodes mismatch,
current program: -1
checkpoint file: 32
I hope to figure out this problem, otherwise I have to run it from
beginning!
Thanks!
Leila
On Thu, Jun 25, 2015 at 4:15 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> I can't tell either. Please run gmxcheck on all your input files, to check
> the simulation part, time and step number are all what you think they are
> (and that they match across the simulations) and try again.
>
> Mark
>
> On Thu, Jun 25, 2015 at 4:12 PM leila salimi <leilasalimi at gmail.com>
> wrote:
>
> > Dear Mark,
> >
> > When I tried with new update of the state.cpt files, I got this error.
> >
> > Abort(1) on node 896 (rank 896 in comm 1140850688): Fatal error in
> > MPI_Allreduce: Message truncated, error stack:
> > MPI_Allreduce(912).......: MPI_Allreduce(sbuf=MPI_IN_PLACE,
> > rbuf=0x7ffc783af760, count=4, MPI_DOUBLE, MPI_SUM, comm=0x84000002)
> failed
> > MPIR_Allreduce_impl(769).:
> > MPIR_Allreduce_intra(419):
> > MPIC_Sendrecv(467).......:
> > MPIDI_Buffer_copy(73)....: Message truncated; 64 bytes received but
> buffer
> > size is 32
> > Abort(1) on node 768 (rank 768 in comm 1140850688): Fatal error in
> > MPI_Allreduce: Message truncated, error stack:
> > MPI_Allreduce(912).......: MPI_Allreduce(sbuf=MPI_IN_PLACE,
> > rbuf=0x7ffdba5176a0, count=4, MPI_DOUBLE, MPI_SUM, comm=0x84000002)
> failed
> > MPIR_Allreduce_impl(769).:
> > MPIR_Allreduce_intra(419):
> > MPIC_Sendrecv(467).......:
> > MPIDI_Buffer_copy(73)....: Message truncated; 64 bytes received but
> buffer
> > size is 32
> > ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in
> > task 896
> > "job.err.1011016.out" 399L, 17608C
> >
> > Actually I don't know what is the problem!
> >
> > Regards,
> > Leila
> >
> >
> > On Thu, Jun 18, 2015 at 12:00 AM, leila salimi <leilasalimi at gmail.com>
> > wrote:
> >
> > > I understand what you meant, I run only few steps for the other
> replicas
> > > and then continue with the whole replicas.
> > > I hope every thing is going well.
> > >
> > > Thanks very much.
> > >
> > > On Wed, Jun 17, 2015 at 11:43 PM, leila salimi <leilasalimi at gmail.com>
> > > wrote:
> > >
> > >> Thanks Mark for your suggestion.
> > >> Actually I don't understand the new two state6.cpt and state7,cpt
> files,
> > >> because the time that it shows is 127670.062 !
> > >> That is strange! because my time step is 2 fs and I saved the output
> > >> every 250 steps, means every 500 fs. I expect the time should be like
> > >> 127670.000 or 127670.500 .
> > >>
> > >> By the way you mean with mdrun_mpi ... -nsteps ... , I can get the
> steps
> > >> that I need for the old state.cpt files?
> > >>
> > >> Regards,
> > >> Leila
> > >>
> > >> On Wed, Jun 17, 2015 at 11:22 PM, Mark Abraham <
> > mark.j.abraham at gmail.com>
> > >> wrote:
> > >>
> > >>> Hi,
> > >>>
> > >>> That's all extremely strange. Given that you aren't going to exchange
> > in
> > >>> that short period of time, you can probably do some arithmetic and
> work
> > >>> out
> > >>> how many steps you'd need to advance whichever set of files is behind
> > the
> > >>> other. Then mdrun_mpi ... -nsteps y can write a set of checkpoint
> files
> > >>> that will be all at the same time!
> > >>>
> > >>> Mark
> > >>>
> > >>> On Wed, Jun 17, 2015 at 10:18 PM leila salimi <leilasalimi at gmail.com
> >
> > >>> wrote:
> > >>>
> > >>> > Hi Mark,
> > >>> >
> > >>> > Thanks very much. Unfortunately both the state6.cpt,
> state6_prev,cpt
> > >>> and
> > >>> > state7.cpt and state7_prev.cpt updated and their time are different
> > >>> from
> > >>> > other replicas file (also with *_prev.cpt )!
> > >>> >
> > >>> > I am thinking maybe I can use init-step in mdp file, and start from
> > the
> > >>> > time that I have, because all trr files have the same time! I
> checked
> > >>> with
> > >>> > gmxcheck. But I am not sure that I will get correct results!
> > >>> > Actually I got confused that with the mentioned Note, only two
> > replicas
> > >>> > were running and the state file is changed and the others not!
> > >>> >
> > >>> > regards,
> > >>> > Leila
> > >>> > --
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