Dear All,
I am trying run a REMD simulation according to tutorial A7 using the exact same input files, but on a 35 aa peptide. The calculations using sander.MPI went perfectly well, however, when I changed from sander.MPI to pmemd.MPI, I got the error message in the subject line:
MPI version of PMEMD must be used with 2 or more processors!
The job was submitted to a CPU cluster for 1 node with 28 cores for 8 temperatures, therefore there were more than 2 processors available for each replica. By studying the AMBER mailing list, I have seen this error message several times, but I could not identify the relevant information how I could switch to pmemd.MPI instead of sander.MPI. The runscript and the input files are described below. Please, help me with this problem.
Bes regards,Kris
jobscript:
#!/bin/bash
#
###########################################################################
#
#PBS -N remd-pmemd
#PBS -o remd-pmemd.out
#PBS -e remd-pmemd.err
#PBS -q q72h
#PBS -m be
ulimit -s unlimited
module purge
module load Amber/14-intel2016a
cd /scratch/leuven/405/vsc40565/8Tpmemd
cd 1_min
$AMBERHOME/bin/pmemd -O -i min.in -o min.out -p wAnTx_gb.prmtop -c wAnTx_gb.inpcrd -r wAnTx_gb_min.rst
cd ..
cd 2_eq
pwd
./setup_equilibrate_input.x > setup_equilibrate_input.x.out
cp ../1_min/wAnTx_gb_min.rst .
mpirun -np 8 $AMBERHOME/bin/pmemd.MPI -ng 8 -groupfile equilibrate.groupfile
cd ..
cd 3_remd
pwd
./setup_remd_input.x > setup_remd_input.x.out
cp ../2_eq/equilibrate.rst.* .
mpirun -np 8 $AMBERHOME/bin/pmemd.MPI -ng 8 -groupfile remd.groupfile
cd ..
echo "ALL DONE"
error message:: vsc40565.login1 /scratch/leuven/405/vsc40565/8Tpmemd2 17:31 $ more remd-pmemd.out
time: 259200
nodes: 1
procs: 28
account string: lt1_2016-57
queue: q72h
========================================================================
/scratch/leuven/405/vsc40565/8Tpmemd/2_eq
Running multipmemd version of pmemd Amber12
Total processors = 8
Number of groups = 8
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
/scratch/leuven/405/vsc40565/8Tpmemd/3_remd
Running multipmemd version of pmemd Amber12
Total processors = 8
Number of groups = 8
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
MPI version of PMEMD must be used with 2 or more processors!
ALL DONE
========================================================================
Epilogue args:
Date: Tue Apr 11 16:56:06 CEST 2017
Allocated nodes:
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
r01i24n1
Job ID: 40097547.tier1-p-moab-1.tier1.hpc.kuleuven.be
User ID: vsc40565
Group ID: vsc40565
Job Name: remd-pmemd
Session ID: 17971
Resource List: neednodes=1:ppn=28,nodes=1:ppn=28,pmem=4gb,walltime=72:00:00
Resources Used: cput=00:00:00,energy_used=0,mem=0kb,vmem=0kb,walltime=00:00:03
Queue Name: q72h
Account String: lt1_2016-57
-------------------------------------------------------------------------
time: 3
nodes: 1
procs: 28
account: lt1_2016-57
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Received on Wed Apr 12 2017 - 10:00:02 PDT
