AMBER Archive (2006)

Subject: AMBER: Probelm with running Amber 9 parallelly

From: Rafi Ahmad (Rafi.Ahmad_at_fagmed.uit.no)
Date: Fri Oct 20 2006 - 09:29:14 CDT

Hi Amber users,

 

for amber 9.

when using the serial-version of sander it works on both i386 and ia64
running CentOS linux.

 

when using a parallel version of sander (sander.MPI ) on ia64 it crashes
in the middle of the run.

on i386 it runs to the end, but hangs for several minutes before it
crashes with an mpi-write eror.

 

when I use the MPICH library the job

run runs for about 18 minutes before it crashes, with this error:

 

steinar_at_compute-0-0 % time mpirun -np

4 --all-local /home/steinar/src/amber9/amber9/exe/sander.MPI -i heat.in
-p VSA_DNA_min_wat.prmtop -c VSA_DNA_min_all.rst -r VSA_DNA_heat.rst -x
VSA_DNA_heat.mdcrd -o heat.out.1 -ref VSA_DNA_min_all.rst

p0_31185: p4_error: interrupt SIGx: 15

Killed by signal 2.

Killed by signal 2.

Killed by signal 2.

forrtl: error (69): process interrupted (SIGINT)

p0_31185: (1090.372580) net_send: could not write to fd=4, errno = 32

 

real 18m10.854s

user 16m38.686s

sys 0m32.270s

 

when I try to use another MPI library namly scampi, I get an similar
error:

 

steinar_at_compute-0-0 % time

mpimon /home/steinar/src/amber9/amber9/exe/sander.MPI -i heat.in -p

VSA_DNA_min_wat.prmtop -c VSA_DNA_min_all.rst -r VSA_DNA_heat.rst -x
VSA_DNA_heat.mdcrd -o heat.out.1 -ref VSA_DNA_min_all.rst -- compute-0-0
4

forrtl: error (78): process killed (SIGTERM)

forrtl: error (78): process killed (SIGTERM)

forrtl: error (78): process killed (SIGTERM)

forrtl: error (78): process killed (SIGTERM)

--- mpimon --- Aborting run after process-1 terminated abnormally
Childprocess 2874 exited with exitcode 1 ---

 

real 57m51.757s

user 0m0.002s

sys 0m0.005s

 

when using pmemd

it crashes in the middle of the run on both

i386 and ia64.

 

I am attaching the output and input files.

 

Thanks in advance for the reply.

 

Regards

 

Rafi

 

 



  • application/octet-stream attachment: heat.in

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