AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD)

From: Greg Recine <>
Date: Thu, 17 Feb 2005 19:23:01 -0500

We have a netBSD cluster and would like to run Amber8 on it. Not
surprisingly, I've hit a few snags :)

(1) Fortran 90: I can't find any native F90 BSD compilers (not counting
xlf90 for Mac OS X)

(2) On my Linux boxes, I used Intel Fortran to compile Amber8 (using MPI
as well). I then tried to use BSD's Linux emulation (after copying all
the needed libs onto the netBSD machine), which looked promising for the
serial programs. However, when using mpirun, I get:

$ mpirun -np 1 /usr/local/amber8/exe/sander [...]
p0_12520: p4_error: create_procgroup: getpwuid failed: 0

Which indicated to me we need to either modify our mpich setup (the
linux mpich can do the same getpuid calls in netBSD since /etc/passwd
and friends are different) or try and cross-compile (yuck).

As I see it, I can either:

(1) find a F90 compiler for netBSD so I can skip all these emulations (a
good thing).

(2) get ifort running on BSD using emulation to compile Amber

(3) use gfortran to compile Amber. This would be great for both my
netBSD and Linux boxes.

(4) Fix the emulation of the linux/ifort/mpich binaries

I think the easiest/quickest right now would be (2), seeing as some
people have the intel compiler running on freeBSD using emulation. I
would greatly appreciate any advice. Has anyone ever come across any of
these issues? I searched the mailing list archive and couldn't find any
mention of these problems.


        - greg

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Greg Recine <>
Terahertz Spectroscopy Group
Department of Electrical & Computer Engineering
University of Virginia
Charlottesville, VA 22904
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Received on Fri Feb 18 2005 - 00:53:00 PST
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