Re: [AMBER-Developers] pbsa amber compilation error

From: MengJuei Hsieh <>
Date: Sat, 31 Oct 2009 21:27:36 -0700


We haven't taken a serious look at the pbsa module in amber11 sander for mac
os x 10.6 just yet. However I did encounter exactly the same problem before.
The problem went away when I used some certain versions of gfortran.
Currently I don't have this exception fr my gfortran (gcc version 4.5.0
20091022 (experimental), Mac OS X 10.6.1, Macbook pro):
    cpp -traditional -P -DNO_SANDER_DIVCON pb_force.f > _pb_force.f
    gfortran -c -O3 -mtune=generic -mfpmath=sse -ffree-form -o pb_force.o
Works for me...

If this pb_force problem also happens to gfortran compilers on other
platform, we might need to change its optimization level in the Makefile.

Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of California Irvine.
> From: Jason Swails <>
> Reply-To: AMBER Developers Mailing List <>
> Date: Sat, 31 Oct 2009 20:54:27 -0400
> To: AMBER Developers Mailing List <>
> Subject: Re: [AMBER-Developers] pbsa amber compilation error
> Ben,
> You were right-- this is an optimization level.  Gfortran version 4.5.0
> Using built-in specs.
> Target: x86_64-apple-darwin10
> Configured with: ../gcc-4.5-20090910/configure --enable-languages=fortran
> --host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10
> Thread model: posix
> gcc version 4.5.0 20090910 (experimental) (GCC)
> Optimization level -O1 for this file by hand allowed the compilation to
> finish.
> Thanks!
> Jason
> On Sat, Oct 31, 2009 at 8:49 PM, Ben Roberts <> wrote:
>> Hi Jason,
>> I've seen this one before; in my case, I traced it down to a compiler
>> bug.
>> Have you tried to compile that file with less rigorous optimisation? I
>> managed to get it done with -O2 instead of -O3.
>> On the other hand, a more permanent solution is to download and build an
>> updated gfortran. What build of gfortran do you have (i.e., gfortran
>> -v)?
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Received on Sat Oct 31 2009 - 21:30:03 PDT
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