AMBER Archive (2006)

Subject: RE: AMBER: compiling amber9

From: Ross Walker (
Date: Mon Jul 03 2006 - 05:48:10 CDT

Hi Nadia,

> I have successfully compiled amber 9 on Red-hat linux machine
> in 32-bit,
> however compiling amber9 on opterons in 64-bit has not been
> successful. We
> have the latest version of pgf90 6.1-6 and tried the p7 flag
> or p7-64 and
> neither work. Compiling with no optimisation flags doesn't
> work either.

You don't define what "doesn't work" actually means so it is a little hard
to help you out here. Although I will offer some advice. Testing of the
Portland group compilers prior to the release of Amber 9 showed up a number
of bugs in Portland's compiler when one selected 64 bit compilation on EM64T
machines. This resulted in a number of the test cases failing with incorrect
answers. The only workaround we could find for this was to force 32 bit
compilation with the Portland group compilers. Thus if you start editing the
config.h file to turn 64 bit compilation back on you should make sure you do
this with the caveat that you know what you are doing and rigorously test
the Amber installation. We are hoping that Portland group will fix the bugs
in their compiler and so if you have the very latest compiler you could try
it in 64 bit mode but I wouldn't hold out much hope.

My advice on 64 bit machines is to obtain Intel Fortran Compiler v9.0.033
(note the 033) this version I have tested on Intel P4-EM64T, AMD64 and
Opteron and it works flawlessly and the executables pass all the tests. It
also give code that is at least as fast as the Portland group or Pathscale
compilers even on AMD Opteron chips ;-). The only thing to note is that for
some strange reason Intel don't give you .033 by default, they only give you
.031 which contains some compiler bugs. Hence after registering you need to
go to and download v9.0.033.

If you can provide me with more error messages with regards to using PGF90
above I can try and help some more.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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