AMBER Archive (2006)

Subject: RE: AMBER: amber9: SA Bomb in sa_arc

From: Ross Walker (
Date: Thu Oct 26 2006 - 11:35:19 CDT

Dear Giulio

> Amber9 was compiled with pgi 6.1
> the configure script for the serial compilation contained
> -opteron pgf90
> as options. That of the parallel executables contained -mpi
> -opteron pgf90
> Based on this, should I change these options or should I go back to
> intel (we have intel 9.0)

The issue here is likely to be a 32 bit limit. The pgf90 compiler at the
time of Amber 9's release was buggy in 64 bit mode causing numerous failures
of the test suite. For this reason we modified the configure script to force
32 bit compilation even on x86_64 machines. You could try 'undoing' this and
see if it works. Although you should run the test suite fully to check
things are working.

Edit the config.h file and remove the occurances of -tp p7. This will result
in the Portland group compiler compiling for your current cpu which is an
Opteron and so you should get x86-64 code. The allocation should then not
fail. Alternatively you can use the Intel compiler which (assuming you have
applied all the bugfixes) is known to work correctly in 64 bit mode on
x86-64 architectures.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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