AMBER Archive (2008)

Subject: RE: AMBER: help to install AMBER9

From: Ross Walker (
Date: Fri May 09 2008 - 11:12:53 CDT

Hi Jeffrey,

> ../lmod/lmod.a .../lapack/lapack.a ../blas/blas.a \
> ../lib/nxtsec.o ../lib/sys.a .../netcdf/lib/libnetcdf.a
-L/home/user/tk/opt/mpich-gm-1.2.6/lib ->lmpichf90 -lmpich -L/opt/gm/lib/
>/usr/bin/ld: skipping incompatible
/home/user/tk/opt/mpich-gm-1.2.6/lib/libmpichf90.a when searching for
>/usr/bin/ld: cannot find -lmpichf90
>make[1]: *** [sander.MPI] Error 2
>make[1]: Leaving directory
>make: *** [parallel] Error 2
What has happened here is that your mpich library was built as a 64 bit
library. However, amber9's configure script for Portland group compilers
manually forces a 32 bit amber build. The reason for this is that the
compilers at release time were notoriously buggy - and still are as you saw
from the compiler segfaulting while trying to build leap.

You have two options. I would start by editing the config.h file and
removing all occurances of '-tp p7'

Then make clean and then build again. This will build a 64 bit version of
amber and it should link successfully against the mpi libraries. However,
you will need to run ALL THE TEST CASES and very very carefully check those
that don't pass. The reason we forced 32 bit compilation was that in 64 bit
mode the Portland group compilers were leading to completely incorrect

If you find the 64 bit bugs have not gone away then your next step is to go
and compile a 32 bit version of mpich-gm (with the -tp p7 flag forced) and
then build a 32 bit version of amber and link against the 32 bit mpich

Or alternatively you could just get the Intel compiler and use that - works
well on Opterons in my experience.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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