AMBER Archive (2006)

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

From: Ross Walker (
Date: Thu Oct 26 2006 - 10:38:05 CDT

Dear Giulio

> >> Number of SA srf points exposed 52227
> >> SA Bomb in sa_arc(): Allocation aborted 0 0
> >> 1 0 0

If you check the source code you can see that this error message is a little
ambiguous since there are two places that could correspond to this error
message. Both are in sa_driver.f on lines 866 and 889. The first one
corresponds to allocating 5 1-D arrays of size natom so I doubt this is
where the problem is. The second one however is allocating larger arrays and
as you can see from the error message it was the 3rd allocation out of the 5
that failed:

  allocate( sphcrd1(3,maxarcdot*natom), stat = alloc_err(3) )

I don't know how big maxarcdot and natom are in your case but it is possible
that this is very large. You could try adding a print statement here to see
how big 3*maxarcdot*natom is. It looks like it is right on the limit of
memory as the subsequent 2 allocations of just maxarcdot*natom work.

It is probably unlikely that the code wants all 32GB of memory that you
have. I suspect it is more likely that the code was compiled in 32 bit mode
which means the maximum addressible memory is 2GB, regardless of how much
you have in the machine. What compiler and version did you use to compile
the code? What options did you pass to Amber's configure script?

My advice would be on an Opteron system to download Intel's (yes Intel's)
ifort compiler. Get the full version that includes the x86_64 version. This
will be installed in /opt/intel/fce/9.1.039. Source
/opt/intel/fce/9.1.039/bin/ (or .csh) and then run Amber's
configure script. make clean, make. This will get you a 64 bit executable
that can address all your memory. Then see if the problem remains.

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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