AMBER Archive (2009)

Subject: [AMBER] reg.error in parallel run

From: balaji nagarajan (
Date: Fri Jan 23 2009 - 04:05:21 CST

Dear Amber ,

I am trying parallel using LAM

I have installed it in two nodes with different IP # .
and they are having 2cores each

I have created .rhosts file for remote login with out password
when i give rsh with IP# it works

when I give lamboot

lamboot -v nodes
it gives the error
[balaji_at_ACTINIDE ~/mddna]$ lamboot -v nodes

LAM 7.1.3/MPI 2 C++/ROMIO - Indiana University

n-1<12069> ssi:boot:base:linear: booting n0 (
n-1<12069> ssi:boot:base:linear: booting n1 (
ERROR: LAM/MPI unexpectedly received the following on stderr:
connect to address port 544: Connection refused
connect to address port 544: Connection refused
trying normal rsh (/usr/bin/rsh)
LAM attempted to execute a process on the remote node "",
but received some output on the standard error. This heuristic
assumes that any output on the standard error indicates a fatal error,
and therefore aborts. You can disable this behavior (i.e., have LAM
ignore output on standard error) in the rsh boot module by setting the
SSI parameter boot_rsh_ignore_stderr to 1.
II) when i give
lamboot -v -ssi boot_rsh_ignore_stderr nodes

it works

 lamboot -v -ssi boot_rsh_ignore_stderr nodes

LAM 7.1.3/MPI 2 C++/ROMIO - Indiana University

n-1<12113> ssi:boot:base:linear: booting n0 (localhost)
n-1<12113> ssi:boot:base:linear: finished


but when i give the run from the directory
mpirun -np 2 $AMBERHOME/amber9/exe/sander -O -i -o polyAT_wat_min1.out -p polyAT_wat.prmtop -c polyAT_wat.inpcrd -r polyAT_wat_min1.rst -ref polyAT_wat.inpcrd

its not picking up the second machine
but in the first machine it takes the two processor

could some one help me to solve the problem
thanks in advance

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