[gmx-users] Replica exchange shell script

[Sukit Leekumjorn]

Thank you very much Mark

I got REMD to run now but I ended up having the same problem as the 
other users had in the past.  Below is the error message.  I got this to 
run for 2 nodes.  For 4, 6, and 8 nodes, the below error shows up in the 
log files.  I did try several suggestions from the mailing list, but I 
could not get  it to runs more than 2 nodes.  Any suggestion in fixing 
this problem would be greatly appreciated.  Here is the executable 
command line I used:

export EXEC="$FF/mdrun_3.3_gcc_mpi -multi -np 8 -replex 200 -s dpp.tpr 
-deffnm dpp"

I did try removing -multi but did not work.  I also "grompp" the .mdp in 
the double precision mode (floating problem), but still did not work.

Thanks you very much,
Sukit



Multi-checking the number of atoms ... OK
Multi-checking the integrator ... OK
Multi-checking nsteps ... OK
Multi-checking init_step ... OK
Multi-checking the temperature coupling ... OK
Multi-checking the number of temperature coupling groups ... OK
Multi-checking the pressure coupling ... OK
Repl  There are 8 replicas:
Repl      0     1     2     3     4     5     6     7 
Repl  T 340.0 345.0 350.0 355.0 360.0 365.0 370.0 375.0
Repl  p  1.00  1.00  1.00  1.00  1.00  1.00  1.00  
1.00-------------------------------------------------------
Program mdrun_3.3_gcc_mpi, VERSION 3.3
Source code file: repl_ex.c, line: 142

Fatal error:
The reference pressure decreases with increasing temperature
-------------------------------------------------------



Mark Abraham wrote:
> Sukit Leekumjorn wrote:
>> Dear GMX users;
>>
>> I have a question about running replica exchange MD on parallel 
>> machines.  Current, I am able to run a single job in parallel using 
>> Gromacs 3.3 official version.  To submitted and run this job I have 
>> to have a shell script.  My question is  how to write a shell script 
>> to submitted a job in parallel using REMD.  Below is the shell script 
>> that I use to submitted a job running with 12 nodes.  I have seen 
>> several emails on replica exchange but none had mentioned using a 
>> shell script.  I have four md#.tpr files "grompp" at different 
>> temperatures (did not use -np option) and I want to run using 4 
>> nodes.  I tried to modify the line "export EXEC=" line to match what 
>> others have posted on mailing list but it does not seem to work.  If 
>> anyone had experience with this, please give me some insight on how 
>> to summited REMD job in parallel using a shell script.
>
> Your script looks basically fine. I use a perl script called by a PBS 
> shell script to do both system setup and MD. The actual mdrun command 
> I use is
>
> ${mdrun} -multi -np $ENV{'PBS_NCPUS'} -v -replex ${exchange_frequency} 
> -s ${tpr_filename} -o ${tpr_filename} -c ${tpr_filename} -g 
> ${tpr_filename} -e ${tpr_filename} -stepout 500
>
> where ${xxx} are sensible variable contents. Obviously ${tpr_filename} 
> does not have the file type suffix, or the integer suffix.
>
> You'll need to actually tell us what you were trying that you found 
> didn't work if you want more help than this :-)
>
> Mark
>
>
>> #!/bin/bash
>>
>> ## The time limit for the job.  If it runs over this it will be killed.
>> ## -lwalltime=0:05:0 would be five minutes.
>> #PBS -lwalltime=150:00:00
>>
>> #PBS -W group_list=heroes
>> #PBS -q production_q
>> #PBS -lnodes=6:ppn=2
>>
>> #$ -notify
>>
>> #PBS -A jobx
>>
>> #PBS -N pe128_330
>>
>> NUM_NODES=`cat $PBS_NODEFILE | wc -l | sed "s/ //g"`
>>
>> ## Get in to the directory qsub was run from
>> cd $PBS_O_WORKDIR
>>
>> export PATH=/nfs/software/bin:$PATH
>>
>> export FF=/nfs/storage1/users/gromacs3.3_022006/bin
>> export EXEC="$FF/mdrun_3.3_gcc_mpi -s 1pe330_2.tpr -np 12 -deffnm 
>> 1pe330_2"
>>
>> echo starting
>>
>> date
>> echo "/// Running on:"
>> cat $PBS_NODEFILE
>> echo "///"
>> echo
>> jmdrun -printhostname -np $NUM_NODES -hostfile $PBS_NODEFILE $EXEC
>> echo
>> date
>>
>> echo ending
>>
>> exit;
>>
>>
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