AMBER Archive (2006)

Subject: RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred

From: Maniopoulou, A \(Mina\) (
Date: Tue Oct 24 2006 - 08:59:26 CDT

Hi Ross,

"Can you just try one thing though.
Create a completely new directory and untar your original amber9.tgz file
into that directory so that you have a completely clean copy of amber9. Then
get apply the bugfix.all file that is attached to this email (this is the
one from the amber website with the divcon bugfix also added to it). Then do
a full serial compile and run the full test suite again. If the problem is
still showing up then it needs looking into."

Well, I did as you suggested but I get the same results. When I use the gcc and g++ compilers though (instead of the icc and icpc that I was replacing manually in the config.h) the differences in the TEST_DIFF files are only roundoff errors..So, I would guess that the problem is again the compiler, or not?

PS:At some point I thought that the problem might be caused because in the $AMBERHOME/src/netcdf/src there is are config files that use gcc, while in the $AMBERHOME/src configure file I had made the replacemnets from gcc to icc and g++ to icpc. So I made the replacements there (although there is a possibility I was not that accurate) but this didn't work either.

Thanks a lot,

Mina Maniopoulou


|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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