AMBER Archive (2009)

Subject: [AMBER] Script for parallel runs 2

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Mon May 04 2009 - 04:41:58 CDT

Dear Sir/Madam,
 

I tried to specify the number of processors used (in power of 1, 2, i.e. 2, 4, 8) with the scrips (pasted below under ****).

 

When I used one node only "#PBS -l nodes=1:ppn=1" in the following scripps, the jobs finished without error. However, when I use 2, 4, 8 nodes in the following scripps, i.e. "#PBS -l nodes=1:ppn=2 or 4 or 8". , the jobs stopped in the following section:

 =============================================================================================
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
> vdwmeth = 1, eedmeth = 1, netfrc = 1
> Box X = 53.071 Box Y = 53.071 Box Z = 53.071
> Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> NFFT1 = 54 NFFT2 = 54 NFFT3 = 54
> Cutoff= 10.000 Tol =0.100E-04
> Ewald Coefficient = 0.27511
> Interpolation order = 4
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
> Keep DNA fixed with weak restraints
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
> GRP 1 RES 1 TO 20
> Number of atoms in this group = 638
> ----- END OF GROUP READ -----
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
>
> begin time read from input coords = 0.000 ps
>
> Number of triangulated 3-point waters found: 2968
> ===========================================================================================
 
 
 This is the script that I used, please kindly instruct if we should modify the scripts so that the calculations can be done accoridingly to use the parallel nodes in the supercomputer system.
 
 
 ********************************************************************************************
>
> #!/bin/sh
> ### Job name
> #PBS -N test-amber
> ### Declare job non-rerunable
> #PBS -r n
>
> ### Queue name (qprod or qdev)
>
> ### qprod is the queue for running production jobs.
> ### 22 nodes can run jobs in this queue.
> ### Each job in this queue can use 1-8 nodes.
> ### Parallel jobs will be favoured by the system.
>
> ### qdev is the queue for program testing.
> ### 2 nodes can run jobs in this queue.
> ### Each job in this queue can use 1 nodes.
>
> #####PBS -q qprod
> #PBS -q parallel
>
> ### Wall time required. This example is 30 min
> #PBS -l walltime=04:10:00
>
> ### Number of nodes
>
> ### The following means 1 node and 1 core.
> ### Clearly, this is for serial job
> ###PBS -l nodes=1:ppn=1
>
> ### The following means 1 nodes required. Processor Per Node=8,
> ### i.e., total 8 CPUs needed to be allocated.
> ### ppn (Processor Per Node) can be either 1 or 2 or 4 or 8.
> #PBS -l nodes=1:ppn=2
>
> ### Another example
> ### 2 nodes required. Processor per node=8, total 16 cores
> ### need to be allocated.
> ###PBS -l nodes=2:ppn=8
>
>
> #The following stuff will be executed in the first allocated node.
> #Please don't modify it
>
> echo $PBS_JOBID : `wc -l < $PBS_NODEFILE` CPUs allocated: `cat $PBS_NODEFILE`
> cd $PBS_O_WORKDIR
> # Define number of processors
> NPROCS=`wc -l < $PBS_NODEFILE`
>
> echo ===========================================================
> echo "Job Start Time is `date "+%Y/%m/%d -- %H:%M:%S"`"
>
>
> # Run the parallel MPI executable "a.out"
> #time mpirun -np $NPROCS ./a.out -machinefile $PBS_NODEFILE > ${PBS_JOBNAME}.`echo ${PBS_JOBID} | sed "s/.supercomputer.u//" `
>
> PGMSTR="/share1/amber8/exe/sander -O -i polyAT_wat_md1.in -o polyAT_wat_md1.out -p polyAT_wat.prmtop -c polyAT_wat_min2.rst -r polyAT_wat_md1.rst -x polyAT_wat_md1.mdcrd -ref polyAT_wat_min2.rst "
>
> echo ${PGMSTR}
> mpirun -np $NPROCS -machinefile $PBS_NODEFILE \
> ${PGMSTR} > ${PBS_JOBNAME}.`echo ${PBS_JOBID} | sed "s/.supercomputer.u//" `
>
>
> echo "Job Finish Time is `date "+%Y/%m/%d -- %H:%M:%S"`"
>
> *********************************************************************************************
>
>
>
> Best regards and many thanks,
>
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