AMBER Archive (2004)

Subject: Re: AMBER: Error message while testing

From: Scott Brozell (
Date: Mon Apr 12 2004 - 20:10:30 CDT


On Wed, 7 Apr 2004, [iso-8859-1] Alessio Comisso wrote:

> I'm tryng to install Amber 8 on a p4 with fedora core 1
> and Intel Ifort 8 and Mkl 6.1. Installation is
> successfull, but when I try to test it i get the
> following error message:
> cd qmmm/divcon; ./Run.crambin
> ../../../exe/sander.QMMM: relocation error:
> ../../../exe/sander.QMMM: symbol mkstemp, version
> GLIBC_2.0 not defined in file with link time
> reference
> ./Run.crambin: Program error
> make: *** [test.sander.QMMM] Error 1
> All other tests performed before this were PASSED.

You may have out of sync system libraries on your machine:
and others from google ...
Fixing this can get ugly; talk to your computer support people.

On the other hand sander.QMMM has a big memory footprint;
for example, it won't execute on an old SGI octane with 128M:
cd qmmm/divcon; ./Run.crambin
  ./Run.crambin: Program error

It may be that your machine doesn't have enough free memory or
that your resource limits are too restrictive.

3. General notice: Beware of resource limits with Amber8
The conversion of some executables to Fortran 90 in Amber 8
has been known to cause strange failures which we believe are due
to automatic array usage.
Apparently, some compilers do not create code to detect stack overruns,
and a stack overrun may cause a segmentation violation, etc.

One can try to increase ones limits with unlimit or limit:

 Sets your user limits to the maximums.

limit datasize unlimited
limit stacksize unlimited
limit memoryuse unlimited
 Increases the individual limits.

Scott Brozell

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