Hello,
We are trying to compile Amber9 (well, we do not have yet Amber10).
Sander has been compiled successfully both in serial and in parallel.
Pmemd has been successfully compiled only in serial. Parallel
compilation appears to be successful, but when we try to run in
parallel, there is no speed up with respect to a single processor run.
When I look at the job status in the queue, I see that it runs on
multiple processors, but the speed is the same as a single processor
run. Also, in the output file the number of processors used is not
written (I guess, for parallel pmemd, it should be written somewhere
near the beginning of the output file). So although there is no
apparent error in the compilation, it seems that the parallel pmemd
compilation has failed.
The configure command has been used as follows:
./configure linux_em64t ifort mpi fftw bintraj
The compilers and libraries listed below have been used:
Intel C/C++ compiler: 11.1.056
Intel Fortran compiler: 11.1.056
Intel MPI library: 3.1
Intel MKL library: 10.1.1.019
FFTW library: 3.2
The operating system is RHEL 5.1. Kernel patched for Lustre.
Infiniband network is used for MPI.
Can anybody help us for the parallel compilation of pmemd please?...
Thanks in advance...
Bülent Balta
Istanbul Technical University
Department of Mol. Biology and Genetics
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 25 2010 - 08:00:02 PST
