AMBER: Compilation problem at dual processor linux !

From: Pradipta Bandyopadhyay <>
Date: Wed, 2 Feb 2005 18:02:52 +0530 (IST)

Apologies if this is a FAQ.

I am trying to compile AMBER7 in a dual processor Linux machine

The operating system is GNU/LINUX

The hardware platform is i386

I have done the following steps:

 Installed MPICH-1.2.6

 Compiled AMBER7 after defining $AMBERHOME and $MPICH_HOME

Compilation was done without problem. But when I start to run the
sander test job (I defined
DO_PARALLEL="/home1/fac/pradipta/MPI/mpich-1.2.6/bin/mpirun -np 2")

I got the following error
cd dmp; ./Run.dmp
This test not set up for parallel
 cannot run in parallel with #residues < #pes
cd adenine; ./Run.adenine
This test not set up for parallel
 cannot run in parallel with #residues < #pes
cd cytosine; ./Run.cytosine
quantum: Connection refused
p0_14945: p4_error: Child process exited while making connection to
remote process on quantum: 0
/home1/fac/pradipta/MPI/mpich-1.2.6/bin/mpirun: line 1: 14945 Broken pipe
"-O" "-i" "" "-c" "" "-o" "cytosine.out" -p4pg
/home1/fac/pradipta/AMBER/amber7/test/cytosine/PI14861 -p4wd
  Program error
make: *** [test.sander] Error 1

quantum is the name of the network node hostname - somehow two processors
can not communicate.

Can somebody please help me with this?



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Received on Wed Feb 02 2005 - 12:53:02 PST
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