Re: [gmx-users] Restarting crashed simulation

2017-11-18 Thread Mark Abraham 
Hi,

Looks like you made a typo with state.cpt and that you perhaps have
multiple mdrun processes running such that the actual output file is in one
of the backup files labelled with # characters.

Mark

On Fri, 17 Nov 2017 19:37 Ali Ahmed  wrote:

> Hello GROMACS users
> My MD simulation was crashed then I restarted the simulation from the point
> when the point was written using this command on 64 processors: mpirun -np
> 64  mdrun_mpi -s md.tpr -cpi stat.cpt
>
> After few days I got nothing in the folder usch as output.gro and I got the
> following
> ___
> Command line:
>   mdrun_mpi -s md.tpr -cpi stat.cpt
>
> Warning: No checkpoint file found with -cpi option. Assuming this is a new
> run.
>
>
> Back Off! I just backed up md.log to ./#md.log.2#
>
> Running on 4 nodes with total 64 cores, 64 logical cores
>   Cores per node:   16
>   Logical cores per node:   16
> Hardware detected on host compute-2-27.local (the node of MPI rank 0):
>   CPU info:
> Vendor: Intel
> Brand:  Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
> SIMD instructions most likely to fit this hardware: AVX_256
> SIMD instructions selected at GROMACS compile time: AVX_256
>
>   Hardware topology: Basic
>
> Reading file md.tpr, VERSION 2016.3 (single precision)
> Changing nstlist from 10 to 40, rlist from 1 to 1.003
>
> Will use 48 particle-particle and 16 PME only ranks
> This is a guess, check the performance at the end of the log file
> Using 64 MPI processes
> Using 1 OpenMP thread per MPI process
>
> Non-default thread affinity set probably by the OpenMP library,
> disabling internal thread affinity
> WARNING: This run will generate roughly 50657 Mb of data
>
> starting mdrun 'Molecular Dynamics'
> 2500 steps,  5.0 ps.
>
> step 888000 Turning on dynamic load balancing, because the performance loss
> due to load imbalance is 8.7 %.
> step 930400 Turning off dynamic load balancing, because it is degrading
> performance.
> step 1328000 Turning on dynamic load balancing, because the performance
> loss due to load imbalance is 3.4 %.
> step 1328800 Turning off dynamic load balancing, because it is degrading
> performance.
> step 1336000 Turning on dynamic load balancing, because the performance
> loss due to load imbalance is 3.4 %.
> step 1338400 Turning off dynamic load balancing, because it is degrading
> performance.
> step 134 Will no longer try dynamic load balancing, as it degraded
> performance.
> Writing final coordinates.
>  Average load imbalance: 13.2 %
>  Part of the total run time spent waiting due to load imbalance: 7.5 %
>  Average PME mesh/force load: 1.077
>  Part of the total run time spent waiting due to PP/PME imbalance: 4.1 %
>
> NOTE: 7.5 % of the available CPU time was lost due to load imbalance
>   in the domain decomposition.
>   You might want to use dynamic load balancing (option -dlb.)
>
>
>Core t (s)   Wall t (s)(%)
>Time: 26331875.601   411435.556 6400.0
>  4d18h17:15
>  (ns/day)(hour/ns)
> Performance:   10.5002.286
> _
>
> Any advise or suggestion will be helpful.
>
> Thanks in advance
> --
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[gmx-users] Restarting crashed simulation

2017-11-17 Thread Ali Ahmed 
Hello GROMACS users
My MD simulation was crashed then I restarted the simulation from the point
when the point was written using this command on 64 processors: mpirun -np
64  mdrun_mpi -s md.tpr -cpi stat.cpt

After few days I got nothing in the folder usch as output.gro and I got the
following
___
Command line:
  mdrun_mpi -s md.tpr -cpi stat.cpt

Warning: No checkpoint file found with -cpi option. Assuming this is a new
run.


Back Off! I just backed up md.log to ./#md.log.2#

Running on 4 nodes with total 64 cores, 64 logical cores
  Cores per node:   16
  Logical cores per node:   16
Hardware detected on host compute-2-27.local (the node of MPI rank 0):
  CPU info:
Vendor: Intel
Brand:  Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: AVX_256

  Hardware topology: Basic

Reading file md.tpr, VERSION 2016.3 (single precision)
Changing nstlist from 10 to 40, rlist from 1 to 1.003

Will use 48 particle-particle and 16 PME only ranks
This is a guess, check the performance at the end of the log file
Using 64 MPI processes
Using 1 OpenMP thread per MPI process

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
WARNING: This run will generate roughly 50657 Mb of data

starting mdrun 'Molecular Dynamics'
2500 steps,  5.0 ps.

step 888000 Turning on dynamic load balancing, because the performance loss
due to load imbalance is 8.7 %.
step 930400 Turning off dynamic load balancing, because it is degrading
performance.
step 1328000 Turning on dynamic load balancing, because the performance
loss due to load imbalance is 3.4 %.
step 1328800 Turning off dynamic load balancing, because it is degrading
performance.
step 1336000 Turning on dynamic load balancing, because the performance
loss due to load imbalance is 3.4 %.
step 1338400 Turning off dynamic load balancing, because it is degrading
performance.
step 134 Will no longer try dynamic load balancing, as it degraded
performance.
Writing final coordinates.
 Average load imbalance: 13.2 %
 Part of the total run time spent waiting due to load imbalance: 7.5 %
 Average PME mesh/force load: 1.077
 Part of the total run time spent waiting due to PP/PME imbalance: 4.1 %

NOTE: 7.5 % of the available CPU time was lost due to load imbalance
  in the domain decomposition.
  You might want to use dynamic load balancing (option -dlb.)


   Core t (s)   Wall t (s)(%)
   Time: 26331875.601   411435.556 6400.0
 4d18h17:15
 (ns/day)(hour/ns)
Performance:   10.5002.286
_

Any advise or suggestion will be helpful.

Thanks in advance
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Re: [gmx-users] Restarting crashed simulation

2015-01-01 Thread bharat gupta 
Hi,

My simulation stopped because of power outage and I restarted it using the
command:

mpirun -np 32 mdrun_mpi -cpi mdrun.cpt -s mdrun.cpt

It shows correctly the restarting time point, however the mdrun.log is not
getting updated and I don't know how to verify whether the simulation is
being continued or not ?


-- 
*Best Regards*
Bharat
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