Re: [AMBER-Developers] 31 March release candidates for Amber

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 2 Apr 2010 17:05:01 -0400

Sorry, just remembered about the patch to look for executables in
AMBERHOME rather than depending on PATH.

This patch will make MMPBSA.py look through AMBERHOME/exe for the
executables if they cannot be found in PATH. It should be applied
from $AMBERHOME.

Thanks!
Jason

On Fri, Apr 2, 2010 at 4:03 PM, case <case.biomaps.rutgers.edu> wrote:
> On Fri, Apr 02, 2010, Volodymyr Babin wrote:
>
>> FreeBSD 8.0 on Intel em64t (Xeon) gcc 4.4.2
>
> Great -- it's a good portablity test to go with BSD, and we do have users
> there.
>
>> 0. configure -noX11 gnu -- OK (but there was a minor annoyance: 4.4.2
>>    binaries are named gcc44/gfortran44/g++44 contrary to what is expected)
>
> Not sure what to do here--same things pops up on RedHat, etc.  Personally,
> I set links (e.g. ln -s /usr/bin/gcc44 gcc) in ~/bin, and put that first
> in my path.  Not sure what there is that is better.
>
>> 1. 'make install' stops with
>>
>> (cd leap && make install )
>> "Makefile", line 14: Missing dependency operator
>
> grrr....I was going to try to remove all dependencies on gmake, but I think
> they actually exist in netcdf (for which we need to track external code).
> So for now, I think we just have to say the Amber requires gmake.  [sleap
> has always required gmake, as well, so we may be stuck.  I have a feeling
> that BSD folks are used to this.
>
>> -----------------------------------------------------------------------------
>>
>> added "#include <stdio.h> to sff/sff.h and it went through
>>
>> #ifdef getchar
>> #  undef getchar
>> #endif
>>
>> before "virtual getchar()" in mortsrc/guilib/console.hpp to make it
>> through
>>
>> had to add "#include <cstdio>" to strmain and strbuf to make it happier
>
>> added "#include <sys/types.h>" to pmemd/src/pmemd_clib.c (as suggested
>> by "man getrlimit")
>
> all of the above changed are staged for commits; I'll test first on Linux,Mac
>
>> there is no /bin/bash; bash is in /usr/local/bin instead; PASSED
>> with correct path; re-running the tests (hours)
>
> Also fixed....not sure why things are so slow....suggests some other errors.
> I suppose we should time the test suites and put that info in the log...
>
> ...thanks for the inputs....dave
>
>
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-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032



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Received on Fri Apr 02 2010 - 14:30:02 PDT
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