AMBER Archive (2006)

Subject: Re: AMBER: compiler error for Amber9

From: David A. Case (case_at_scripps.edu)
Date: Wed Jun 07 2006 - 10:52:14 CDT

On Wed, Jun 07, 2006, Weihua Li wrote:

> /usr/bin/ld: skipping incompatible
> /home/ytang/gdata/whli/openmpi/lib/libmpi_f90.a when searching for -lmpi_f90
> /usr/bin/ld: cannot find -lmpi_f90

Basically, this message is saying that the mpi library files don't match the
object files from sander.

You can use the "file" command on both the libmpi_f90.a library and the object
files in the sander directory to try to track down how they are different. It
is probably a 32-bit vs. 64-bit incompatibility. Note the comment in the
configure script:

#################### Portland Compiler #####################
pgf90)

    # (Note that we are forcing 32-bit compilation even on x86_64 machines;
    # More testing may find a good 64-bit configuration, but we don't have
    # one available at the time of the Amber 9 release.)

So, for sander, you will probably have to compile openmpi in 32-bit mode
(I think it's the "-tp p7" flag).

It's probably best to work on PMEMD first, since it *can* be compiled in
64-bit mode. (Aside: the parts of sander that are roughly equivalent to pmemd
do work in 64-bit mode with pgf90; it's the extra stuff, like QM/MM, that
fails). Make sure you really need a parallel sander before spending time
trying to compile one: if pmemd meets your needs, that's the code to use.

...good luck....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu