AMBER Archive (2007)

Subject: Re: AMBER: Amber 9 - bugfix.40 fails

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed Dec 05 2007 - 11:56:23 CST

Dear Kevin,

I am looking into this. I need to provide a new bugfix.40

Best regards

Holger

Am Mittwoch, 5. Dezember 2007 18:27 schrieb Kevin Davies:
> Hello all - I'm quite new to both compiling in general, and Amber
> specifically, so don't spare the obvious... My configuration, in
> brief: p4 processor, OS="Scientific Linux" (a redhat descendant, I
> believe), latest Intel compilers installed, Amber installed in
> /usr/local/amber9/, directory added to PATH via /root/.bash_profile,
> and all work done in Root account.
>
> Every time I attempt to run the patch bugfix.all onto Amber 9 (patch
> -p0 -N -r patch-rejects < bugfix.all) I get an error in bugfix.40 -
> this time it was:
> ...
> patching file src/sander/runmd.f
> Hunk #1 FAILED at 814.
> Hunk #2 succeeded at 837 with fuzz 2 (offset 4 lines).
> 1 out of 2 hunks FAILED -- saving rejects to file patch-rejects
>
> patch-rejects shows the following:
> ***************
> *** 814,820 ****
> iprint = 0
> if( nstep == 0 .or. nstep+1 == nstlim ) iprint = 1
> ! TIME_force is started and stopped inside force
> !
> call force(xx,ix,ih,ipairs,x,f,ener(23),vir, &
> xx(l96),xx(l97),xx(l98),xx(l99), qsetup,qpsander, &
> do_list_update)
> --- 814,825 ----
> iprint = 0
> if( nstep == 0 .or. nstep+1 == nstlim ) iprint = 1
> ! TIME_force is started and stopped inside force
> ! #ifdef MPI
> ! if( initremd ) then
> ! irespa = 0
> ! end if
> ! #endif
> !
> call force(xx,ix,ih,ipairs,x,f,ener(23),vir, &
> xx(l96),xx(l97),xx(l98),xx(l99), qsetup,qpsander, &
> do_list_update)
>
> I've 'sucessfully' compiled Amber once by ignoring this issue, but
> while running the "make test.serial" test, the test associated with
> the line "cd qmmm2/pure_QM_MD; ./Run.nma" ran for ~18 hours (p4
> processor), so I decided to abort the test and recompile from scratch
> (completely removed Amber directory tree, re-unpacked files from CD).
> Since this is a Sander test (I think), and bugfix.40 acts on the
> sander/runmd.f file, I'm under the impression these issues are all
> related.
>
> So in short, my questions are:
> - am I doing something obviously incorrect in applying the bugfix? (I
> googled around, but didn't find anything which seemed relevant)
> - is the bugfix error related to the long time spent on the Run.nma test?
>
> Thanks for any ideas!
> Kevin Davies
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Juniorprofessor fuer Molekulare Bioinformatik

J.W. Goethe-Universitaet
Fachbereich Biowissenschaften
Institut fuer Zellbiologie und Neurowissenschaft
Max-von-Laue-Str. 9
60438 Frankfurt/Main
Germany

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29527
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://mbilab.uni-frankfurt.de
++++++++++++++++++++++++++++++++++++++++++++++++++
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