AMBER Archive (2006)

Subject: Re: AMBER: SGI compiler problems

From: Atro Tossavainen (
Date: Wed Jun 21 2006 - 06:30:00 CDT


The question has been posed previously by Justin Sanders from Salem
Int'l Uni on this mailing list. There hasn't been much of an answer
so far so I'll try to pipe in:

> f90 -c -n32 -mips4 -r10000 -O0 -o new2oldparm.o
> _new2oldparm.f
> f90: Error: -32 compilation not supported for ucode

What does "f90 -v", or "versions ftn90_dev" say?

I have a hunch that you might be overdue for a compiler update. The
current release is, if I'm not mistaken, 7.4.4.

On a side note, to S. Sundar Raman,

> We would like to install AMBER9 in SGI FUEL system which has IRIX 6.5. We
> would like to know the exact requirements (i.e. compiler with version and
> hardware) to install amber9 in that system. Hence it will be easy for us
> to order the required features from SGI.

There is no reason to order anything else but the current versions of
the compilers. You will need FORTRAN 90 to get AMBER anything to compile,
and you will want the C/C++ compiler as well. There are no hardware
specific packages in the software, it's the same software across the
entire range of IRIX-compatible hardware. There are additional
licensing options that allow you to benefit from autoparallelisation
options, but for a single CPU machine such as the Fuel, you're not
going to be interested in those. Just get the whole deal.

Back to Pete:

> So, what is the problem. I guess it does not care for the -n32 option
> but I guess I've a couple of questions. First, why doesn't the
> configure routine select the correct option (OK, so in a perfect world
> it would and it doesn't so what can I do to help configure out).

As you can see, the command is "-n32" but the error message says some-
thing about "-32". "-32" would indicate attempting to compile for the
old 32-bit ISA (pre IRIX 6.0), which is rather surprising given that
the instructions all are asking for "-n32" which is the new 32-bit
ISA introduced in IRIX 6.0 if I remember correctly. If there is a bug
with the FORTRAN compiler environment, the first thing you need to check
is the version you are currently using.

> Second, how do I need to modify either the config.h file (reproduced
> below) so I can compile amber 9.

The config.h file looks all right.

> Third, what is ucode.

"man uopt" refers to "man ucode" which does not exist. I have filed
a bug report with our local SGI office on this one...

Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
Systems Analyst, Techno-Amish &     / the University of Helsinki, Finland,
+358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are my own.
< URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE ATTACHMENTS
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to