Running Amber on Sun OS

This page is outdated (circa 2005). If you are an Amber user planning to run on SunOS then contact Scott Brozell via the AMBER Mail Reflector: amber@ambermd.org.

All of Amber (except for pmemd, which might be easily ported?) will compile and run on SunOS. Note that a Fortran 90 compiler is distributed with SunOS. The Sun Performance Library is a viable replacement for source compiled BLAS and LAPACK routines; support for the Sun Performance Library is included in Amber's configure.

Known Problems

• In Amber 8 the -q option of grep (which designates Quiet and produces no output) is used in src/Makefile, benchmarks/Makefile, and test/sugarlp/Run.sugarlp. Unfortunately, SunOS has several greps, and the grep that supports -q may not be first in ones PATH. /usr/xpg4/bin/grep does support -q, and the recommendation is that users ensure that this grep is executed by the command grep. Alternatively, one could remove the -q option from the grep commands and ignore the spurious output (or with a little more UNIX savvy redirect the grep output to the null device).

• The /usr/ccs/bin/m4 macro processor has a push-back buffer of default size 4096. This is too small to build xleap:
  m4:xaLeap.rm4:993 pushed back more than 4096 chars
  This is Amber8 bugfix.39.

• The archive utility should be in ones PATH. There are a couple:
  /usr/xpg4/bin/ar
/usr/ccs/bin/ar

• The archive utility command invocation by make may be missing whitespace:
  ar rvsys.a sys.o wallclock.o
  It should be
  ar rv sys.a sys.o wallclock.o
  This is related to the version of make. I'm investigating this; for now:

  On Tuesday 22 February 2005 06:52 pm, David A. Case wrote:
  > On Tue, Feb 22, 2005, Joe Nolan wrote:
  > > ar rvsys.a sys.o wallclock.o
  >
  > You could do a couple of things here:
  >
  > 1. read more carefully the answer I sent to you last Friday on this
  > issue:
  >
  >      http://amber.ch.ic.ac.uk/archive/200409/0039.html
  >
  > 2. put "rvsys.a" into the Google search bar, and search the e-mail
  > archives.
  >
  > ...dac
  >
  
  Here's the way I do it.  I think this works with all flavors of
  make, and you only need to change one file.  In config.h, do the
  following where AR is defined:
  
  ANEMPTYMACRO=
  AR=ar rv $(ANEMPTYMACRO)
  
  Bud Dodson