AMBER Archive (2006)

Subject: AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software

From: Muhammad Naim Mohmad Rouyan (m_naim_at_putra.upm.edu.my)
Date: Fri Dec 22 2006 - 01:40:32 CST

Dear Amber users,

I have been attempting to compile a parallel version of amber 8 (Sun HPC
ClusterTools 5) on a Sun Fire V1280 running on Solaris 9 using sparc as my
compiler. The serial version compiles with no problems but when i attempt
to compile the parallel version I don't know which one parallel flag to
use. I'm trying to use mpi native flag and the compilation is succeed but
when running a test run with make test.sender it get an error like this:

.
.
.
==============================================================
cd aspash; ./Run.aspash
This test not set up for parallel
 cannot run in parallel with #residues < #pes
cd circ_dna; ./Run.circdna
diffing mdout.circdna.save with mdout.circdna
PASSED
==============================================================
.
.
.
cd tgtmd/change_target.ntr; ./Run.tgtmd
SANDER: Targeted MD with changing target and restraints
Fatal error, aborting.
 Must have more residues than processors!
 Must have more residues than processors!
Fatal error, aborting.
Fatal error, aborting.
 Must have more residues than processors!
Fatal error, aborting.
 Must have more residues than processors!
Fatal error, aborting.
 Must have more residues than processors!
Fatal error, aborting.
 Must have more residues than processors!
Fatal error, aborting.
 Must have more residues than processors!
Fatal error, aborting.
Job cre.4202 on inspem1: received signal ABRT.
  ./Run.tgtmd: Program error
*** Error code 1
make: Fatal error: Command failed for target `test.sander.no_lmod'

The config.h was made using the following command.

./configure -mpi sparc

If anyone could advise me i would be most grateful.

Many regards

naim, UPM

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