AMBER Archive (2003)

Subject: RE: AMBER: tru64 alpha

From: Yong Duan (yduan_at_udel.edu)
Date: Thu Oct 16 2003 - 21:00:04 CDT

Dear Yuguang,

I am a bit curious. What was the interconnect?

yong

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Mu Yuguang (Dr)
> Sent: Thursday, October 16, 2003 8:41 PM
> To: amber_at_scripps.edu
> Subject: RE: AMBER: tru64 alpha
>
>
> 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_at_cgl.ucsf.edu]
> Sent: Wednesday, October 15, 2003 10:39 PM
> To: amber_at_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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