AMBER Archive (2006)

Subject: RE: AMBER: Amber 8 QMMM tests fail on AIX

From: Ross Walker (
Date: Thu Jun 01 2006 - 11:27:24 CDT

Hi Shan,

> I have compiled Amber8 on an IBM power4 cluster running
> AIX 5.2, using XLF 8.1.1 and the following steps:

> cd qmmm/standard; ./Run.lysine
> STOP 0
> diffing with lysine.out
> possible FAILURE: check lysine.out.dif
> ==============================================================
> cd qmmm/divcon; ./Run.crambin
> Segmentation fault

I can't reproduce this problem exactly but everytime I try and run
sander.QMMM from Amber 8 on AIX I get the following error:

exec(): 0509-036 Cannot load program ./sander.QMMM because of the following
        0509-026 System error: There is not enough memory available now.

This is really weird as hpmcount returns that the resident size of the code
is only 824KB. Plus the stack and memory limits are set to unlimited...

To be totally honest I wouldn't bother with QMMM in Amber 8. If you want to
do QMMM calculations you should seriously consider using amber 9. I would
just delete the sander.QMMM executable from the exe directory to stop
anybody 'accidentally' using it and then edit $AMBERHOME/test/Makefile and
change the serial: line from:

serial: test.sander test.sander.LES test.sander.QMMM \
        test.nmode test.anal test.ptraj test.leap test.resp \
        test.antechamber test.pbsa


serial: test.sander test.sander.LES \
        test.nmode test.anal test.ptraj test.leap test.resp \
        test.antechamber test.pbsa

Then you can re-run the tests. Everything else should work okay so it will
just be the QMMM functionality that you are missing.

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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