AMBER Archive (2009)

Subject: [AMBER] Script for parallel runs

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Mon May 04 2009 - 04:17:42 CDT

 Dear Sir/Madam

I do the following calculations (tutorial 1 test job) with the following command, the job finished without error.
 
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
[supercomputer]$ mpirun -np 2 /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 &
 
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
However, when I tried to specify the number of processors used (in power of 2, i.e. 2, 4, 8) with the scrips (pasted below ****), 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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