AMBER Archive (2008)

Subject: Re: AMBER: AmberTools on OS X Leopard with Intel compilers

From: Mike Summers (summers_at_hhmi.umbc.edu)
Date: Tue Apr 22 2008 - 07:22:18 CDT

I've compiled amber10 (serial and parallel) on my Apple Macbook Pro
(OSX 10.5.2) using the latest compilers downloaded with Fink. Everthing
works fine.

I also have problems with the AmberTools test script. It first
fails when running Run.c60. It does NOT fail if I comment out
the last two parts of the test, as shown below.

Mike

#!/bin/csh -f

../../../exe/antechamber -i buckyball.pdb -fi pdb -o buckyball.mol2 -fo mol2 \
>& antechamber.out || goto error

../../../exe/antechamber -i buckyball.pdb -fi pdb -o buckyball.gzmat -fo gzmat \
>& antechamber.out || goto error

../../../exe/antechamber -i buckyball.pdb -fi pdb -o buckyball.jcrt -fo jcrt \
>& antechamber.out || goto error

#../../../exe/antechamber -i buckyball.gzmat -fi gzmat -o buckyball.prepi \
# -fo prepi >& antechamber.out || goto error

#../../../exe/antechamber -i buckyball.jcrt -fi jcrt -o buckyball.ac -fo ac \
# >& antechamber.out || goto error

../../dacdif buckyball.mol2.save buckyball.mol2
../../dacdif buckyball.gzmat.save buckyball.gzmat
../../dacdif buckyball.jcrt.save buckyball.jcrt
#../../dacdif buckyball.prepi.save buckyball.prepi
#../../dacdif buckyball.ac.save buckyball.ac

On Mon, Apr 21, 2008 at 11:21:34PM -0400, Yu Chen wrote:
> >>
> >>Now the test part, lots of them passed, althought quite few of them failed
> >>too. They failed with "Bus error" messages. Like antechamber/c60, and
> >>everything in sleap/ directory. No output file had been generated.
> >
> >The c60 failure has been seen before. We have not had reports of sleap
> >failing. But the problem is that very few Amberites use Macs. I am
> >suppposed
> >to get a login on your machine (or one like it) soon, and I will look into
> >this at this point.
>
> After Dr. Zhang Wei's patch for the gleap, everything except c60
> passed! Maybe we could ignore c60 for now. I will check with Dr. Summers.
>
> >
> >It might be good if you could post the results of "icc -V" and "gcc
> >--version". That way, we will know whether we are testing something
> >relevant
> >to your environment.
>
> icc -V:
> Intel(R) C Compiler for applications running on Intel(R) 64, Version 10.1
> Build 20080312 Package ID: m_cc_p_10.1.014
>
> gcc --version:
> gcc (GCC) 4.3.0
>
> Thank you,
> Best regards,
>
> Chen
>
> >
> >Also, lots of people are downloading AmberTools, so other Mac users will
> >probably be able to chime in soon.
> >
> >...regards...dac
> >
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>
>
> ===========================================
> Yu Chen
> Howard Hughes Medical Institute
> Chemistry Building, Rm 182
> University of Maryland at Baltimore County
> 1000 Hilltop Circle
> Baltimore, MD 21250
>
> phone: (410)455-1728 (primary)
> (410)455-6347 (secondary)
> fax: (410)455-1174
> email: chen_at_hhmi.umbc.edu
> ===========================================
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
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-- 

*********************************
Michael F. Summers
Department of Chemistry and Biochemistry
  and Howard Hughes Medical Institute
University of Maryland Baltimore County
1000 Hilltop Circle 
Baltimore, MD 21250

Phone: (410)-455-2527  
FAX:   (410)-455-1174
Email: summers_at_hhmi.umbc.edu
Web:   www.hhmi.umbc.edu
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