Re: [AMBER-Developers] make serial compile error

From: Jason Swails <>
Date: Sat, 4 Dec 2010 14:59:50 -0500


My comments are below:

On Sat, Dec 4, 2010 at 2:21 PM, B. Lachele Foley <> wrote:

> If the installation instructions have changed, just say and sorry I missed
> it. I'll run again. I pulled just now (4 Dec., 13:30h EST). It looks like
> it might be an environment settings error. Or not...
> On that note, can there be a file for the developers that contains the most
> recent installation instructions? Even to have a file that says "no changes
> from last release" would be great. I always worry I missed something on
> the list.
> I did:
> export AMBERHOME=/path/to/amber
> export PATH=$AMBERHOME/bin:$PATH
> cd AmberTools/src
> ./configure gnu
> make install
> cd ../../src
> make serial
> AmberTools (serial) compiled fine, but Amber serial fails with:
> gfortran -O0 -ffree-form -c -o rmsgrd.o rmsgrd.f

The above is wrong. cpp should first preprocess the file, and _rmsgrd.f
should actually be compiled. That is the cause of the warnings below (the
fortran preprocessor doesn't recognize the #include directive, just

> Warning: rmsgrd.f:2: Illegal preprocessor directive
> Warning: rmsgrd.f:3: Illegal preprocessor directive
> Warning: rmsgrd.f:4: Illegal preprocessor directive
> Warning: rmsgrd.f:19: Illegal preprocessor directive
> Warning: rmsgrd.f:20: Illegal preprocessor directive
> Warning: rmsgrd.f:21: Illegal preprocessor directive

This is indicative of an outdated depend file. Run "make depend" in the
sander directory to update it. I'm in the process of testing now, and I'll
check in the updated depend file if that is all that is required to fix the
error below as well. Once the depend script is updated, there is no change
to the installation procedure.

All the best,

> use poisson_boltzmann, only : outwat, oution
> 1
> Fatal Error: Can't open module file 'poisson_boltzmann.mod' for reading at
> (1): No such file or directory
> make[1]: *** [rmsgrd.o] Error 1
> make[1]: Leaving directory `/e14/programs/amber.git_20101203/src/sander'
> make: *** [serial] Error 2
> The file is present in: ./AmberTools/src/pbsa/poisson_boltzmann.mod
> I suspect the complaints about the include lines are the more important
> error, but I don't have enough experience using fortran in a C world to
> diagnose.
> I only two systems with a pull last night, both Intel-based. One RHEL
> using gcc 4.4.0 and the other Slackware using gcc 4.2.4. They did the same.
> :-) Lachele
> Dr. B. Lachele Foley
> Complex Carbohydrate Research Center
> The University of Georgia
> Athens, GA USA
> _______________________________________________
> AMBER-Developers mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Sat Dec 04 2010 - 12:00:13 PST
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