AMBER Archive (2008)

Subject: AMBER: PKa calculation

From: Wang, Xuelin (Xuelin.Wang_at_stjude.org)
Date: Tue Feb 12 2008 - 10:45:16 CST

Dear amber users,

I am trying to run a PKa calculation. I followed the steps in tutorial. However, when I submit my script to cluster, I met the below error message. Any idea about it?

The group file 1 and script are attached.

Thanks
Xuelin

My group file:

-O -i mdin1_HIP -p d2c_hip.prmtop -c d2c_mm1_hip.rst -o d2c_md1_hip.out -inf hip.mdinfo -x d2c_md1_hip.mdcrd -r d2c_md1_hip.rst
-O -i mdin1_HIE -p d2c_hie.prmtop -c d2c_mm1_hie.rst -o d2c_md1_hie.out -inf hie.mdinfo -x d2c_md1_hie.mdcrd -r d2c_md1_hie.rst

My script file:
------------------------------------------------------------
# LSBATCH: User input
#!/bin/csh
#BSUB -n 16
#BSUB -q normal

set MPIRUN="pam -g 1 mpichp4_wrapper"
set AMBER9=/nfs_exports/apps/intel-apps/amber9-8.1-mpi2-1.0.4p1-mkl7.2.1/exe/sander.MPI

set path= ($path $AMBER9)

cd ~/lchen1/PKa/d2c

$MPIRUN $AMBER9 -ng 2 -groupfile d2c_groupfile.1

#$MPIRUN $AMBER9 -ng 2 -groupfile d2c_groupfile.2

#$MPIRUN $AMBER9 -ng 2 -groupfile d2c_groupfile.3

#$MPIRUN $AMBER9 -ng 2 -groupfile d2c_groupfile.4

#$MPIRUN $AMBER9 -ng 2 -groupfile d2c_groupfile.5

Error message:
------------------------------------------------------------

Exited with exit code 1.

Resource usage summary:

    CPU time : 0.27 sec.
    Max Memory : 2 MB
    Max Swap : 4 MB

    Max Processes : 1

The output (if any) follows:

 Error: specified more groups ( 2 ) than the number of processors (
           1 ) !
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
P4 procgroup file is /home/xuelin/.lsf_674339_genmpi_pifile.
PAM: Time expired waiting for tasks to register.
PAM: An error occurred starting the PJL.
pWaitRtask(): ls_rwait() failed: Communication time out
pWaitAll: NIOS is dead

TID HOST_NAME COMMAND_LINE STATUS TERMINATION_TIME
==== ========== ================ ======================= ===================
0001 node175 mpichp4_wrapper Exit (1) 02/11/2008 17:44:48
0002 node175 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0003 node187 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0004 node187 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0005 node165 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0006 node165 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0007 node192 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0008 node192 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0009 node205 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0010 node205 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0011 node162 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0012 node162 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0013 node157 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0014 node157 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0015 node199 mpichp4_wrapper Undefined 12/31/1969 17:59:59
0016 node199 mpichp4_wrapper Undefined 12/31/1969 17:59:59

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