Hi amber people,
My IT guy has sander serial installed ok, and he say he just installed
parallel amber11.
Serial sander runs fine at the command line with the input files shown
below.
My input script for pmemd.MPI is:
_______________________________
#!/bin/bash
# qsub -cwd -pe am.mpi 16 -l pn=compute test.sh
mpirun -np $NSLOTS -hostfile $TMPDIR/machines /var/amber11/bin/pmemd.MPI
-O \
-i test.in \
-o test1.out -p ben57mp2.top -c test.crd \
-r test1.rst -x test1.mdcrd
___________________________________
I submit the job on the command line as follows:
> qsub -cwd -pe am.mpi 16 -l pn=compute test.sh
The command line says the job was submitted.
Standard error and output files are created with the job not having run:
_________________________________________________
-catch_rsh
/opt/gridengine/default/spool/hal9000-274-3/active_jobs/11.1/pe_hostfile
hal9000-274-3
hal9000-274-3
hal9000-274-3
hal9000-274-3
hal9000-274-4
hal9000-274-4
hal9000-274-4
hal9000-274-4
hal9000-274-5
hal9000-274-5
hal9000-274-5
hal9000-274-5
hal9000-274-6
hal9000-274-6
hal9000-274-6
hal9000-274-6
_______________________________________________
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
___________________________________________________________
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-3 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=2 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-4 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=5 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-6 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=13 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-5 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=10 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-4 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=6 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-6 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=15 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-4 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=4 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-4 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=7 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-6 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=12 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-3 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=1 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-5 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=8 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-6 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=14 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-3 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=0 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-5 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=9 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-3 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=3 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
/opt/gridengine/bin/lx26-amd64/qrsh -inherit hal9000-274-5 cd
/home/dcuebas/Documents/Amber; /usr/bin/env MPIRUN_HOST=hal9000-274-3
MPIRUN_PORT=39164 MPIRUN_RANK=11 MPIRUN_NPROCS=16 MPIRUN_ID=6107
RAIDEV_DEVICE=/dev/rai_hbx0 /var/amber11/bin/pmemd.MPI "-O" "-i" "test.in"
"-o" "test1.out" "-p" "ben57mp2.top" "-c" "test.crd" "-r" "test1.rst" "-x"
"test1.mdcrd"
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!
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!
_______________________________________________________________
Interestingly, running serial pmemd (NOT pmemd.MPI) on the command line:
>var/amber11/bin/pmemd -O \
-i test.in \
-o test1.out -p ben57mp2.top -c test.crd \
-r test1.rst -x test1.mdcrd
Gives the following .out file
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 10/25/2011 at 07:11:12
[-O]verwriting output
File Assignments:
| MDIN: test.in
| MDOUT: test1.out
| INPCRD: test.crd
| PARM: ben57mp2.top
| RESTRT: test1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: test1.mdcrd
| MDINFO: mdinfo
Here is the input file:
Vacuum simulation at 300šC, weak coupling
&cntrl
imin = 0, ntb = 0, ig=-1,
igb = 0, ntpr = 10, ntwx = 10,
ntt = 1, tautp=0.5, gamma_ln = 0,
tempi = 300.0, temp0 = 300.0
nstlim = 1000000, dt = 0.0001,
cut = 999
/
| ERROR: nfft1 must be in the range of 6 to 512!
| ERROR: nfft2 must be in the range of 6 to 512!
| ERROR: nfft3 must be in the range of 6 to 512!
| ERROR: a must be in the range of 0.10000E+01 to 0.10000E+04!
| ERROR: b must be in the range of 0.10000E+01 to 0.10000E+04!
| ERROR: c must be in the range of 0.10000E+01 to 0.10000E+04!
Input errors occurred. Terminating execution.
_____________________________________________________________
Does anyone have any suggestions? I would greatly appreciate it!!!!!
Thanks a million in advance.
Dean
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Received on Tue Oct 25 2011 - 12:00:02 PDT
