AMBER: Amber 9 - bugfix.40 fails

From: Kevin Davies <>
Date: Wed, 5 Dec 2007 12:27:27 -0500

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, &
--- 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, &

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

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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Received on Sun Dec 09 2007 - 06:07:11 PST
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