AMBER Archive (2006)

Subject: RE: AMBER: AMBER9 compilation error on IBM Cluster

From: Ross Walker (
Date: Mon May 15 2006 - 22:28:12 CDT

Dear Amit,

> `.__qmmm_module_NMOD_deallocate_qmmm':
> : undefined reference to `.qm2_dftb_deallocate'
> dynlib.PIMD.o(.text+0x48): In function `.corpac':
> : undefined reference to `.__bintraj_NMOD_write_binary_traj'

These errors look like some kind of compatibility problem between the C and
Fortran compilers. At least they seem to originate from problems with the
binary trajectory support. I have attached the config.h files I used for
amber and pmemd on Datastar which consists of p690 and p655 nodes. You can
try this out on your machine. You may need to change the cpu type to pwr5 if
your p720 machine contains power 5 chips. Note, make sure you do a make
clean in the amber src tree and src/pmemd trees first. Or even better start
from a completely fresh untar of the distribution. Note you need to run
./configure -mpi xlf90_aix in $AMBERHOME/src/ first to get the autoconfigure
done for netcdf. You can then replace the config.h file in src and place
config.h.pmemd as config.h in src/pmemd/ and then you should be able to
build both in parallel.

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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