[gmx-users] problem to restart REMD

[leila salimi]

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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>>
>