Thanks David, Bill and Rob for your helpful reply.
Now I try to complie PMEMD with little changed machine file, using
mpif90 and mpicc, and then submit with corresponding mpirun.
It works well in one node with 4 cpus with scaling up to 92%, but the
scaling drops to 25% using 2 nodes with 8 cpus.
My system is 18er duplex DNA with total 56999 atoms using PME.
The inter-node connections should be a little better than Myrinet, and
here the MPI is mpich-1.2.5.
I am not sure that the scaling failure is due to the mpich or something
else.
-----Original Message-----
From: Bill Ross [mailto:ross.cgl.ucsf.edu]
Sent: Wednesday, October 15, 2003 10:39 PM
To: amber.scripps.edu
Subject: RE: AMBER: tru64 alpha
> FATAL dynamic memory allocation error in subroutine alloc_ew_dat_mem
> Could not allocate ipairs array!
In unix,
% man ulimit
Bill Ross
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Received on Fri Oct 17 2003 - 01:53:01 PDT
