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

From: M. L. Dodson <>
Date: Thu, 17 Feb 2005 20:21:29 -0600

On Thursday 17 February 2005 06:23 pm, Greg Recine wrote:
> 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.
> Thanks!!
> - greg

Hi Greg,

I run FreeBSD on my nodes. I agree with your decision. The
FreeBSD people have identified most of the issues already. If you
look at the FreeBSD "ports" collection (pkgsrc to you), you will
find a port to run the Linux x86 ifort compiler on FreeBSD
(lang/ifc). It will generate FreeBSD executables (but the compiler
runs under Linux emulation). The FBSD port should give you a good
idea of what the issues are. Look at in the lang section. If you are
familiar with Berkeley makefile conventions, the Makefile should
be fairly easily readable (the macro names are mostly obvious). If
you need more help, look at

Good luck,
Bud Dodson

M. L. Dodson                      
409-772-2178                                FAX: 409-772-1790
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Received on Fri Feb 18 2005 - 02:53:00 PST
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