Re: [AMBER] Workaround for gfortran-4.1.2?

From: Mark Williamson <>
Date: Tue, 20 Jul 2010 16:51:43 -0700

Marc Moreau wrote:
> Hello all,
> I am trying to compile against gcc-4.1.2 which includes the buggy
> gfortran-4.1.2.
> I'm trying to compile with -O2 instead of the default -O3. Does anyone
> know of any other things to try, or specific compiler flags that allow
> a work-around of the buggy section in fortran?
> I am aware that 4.3.2 and 4.4.x are out, but my system is old ( Centos
> 4.3 ) which doesn't have RPMS for those compilers. Further, if I
> upgrade the compiler ( more specifically the libraries ) I need to go
> back and recompile && regression test all the other MD suites in use.
> It's a non-trivial number so I really don't want to do that. We
> expect that we will be getting new Hardware soon which will allow for
> an upgrade of OS and such, then I can roll the old hardware to the new
> system. But that is later. For now, upgrade is not an option.
> -- Marc

Hi Marc,

I've hit this frustrating issue in the past with RHEL4 (which
essentially is what CentOS4 cloned). There is a RPM based solution
within RHEL5 and CentOS5, but I also had upgrade constraints here.

My solution for RHEL4 was to compile the 4.4 gcc compiler from scratch
and then use it to build AMBER. I've written a howto on this and you can
find it at:

It works rather well for me.

Mark Williamson, Post Doc
Walker Molecular Dynamics Group
Room 395E
San Diego Supercomputer Center
9500 Gilman Drive
La Jolla, CA 92093-0505
Email:  mjw at
Office: 858-246-0827
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Received on Tue Jul 20 2010 - 17:00:03 PDT
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