AMBER Archive (2003)

Subject: RE: AMBER: tru64 alpha

From: Mu Yuguang (Dr) (YGMu_at_ntu.edu.sg)
Date: Wed Oct 15 2003 - 21:59:29 CDT

Dear Robert,

I try quadrics, because the switch -lelan also used here for other
parallel jobs.

The compilation looks fine.

When I use prun to submit the job, the errors appeared as I showed in
the last mail.

The machine here is called AlphaServer SC45 having 42*4 processors.

 

Maybe the problem is from the prun. What kind of tools you have used
fro submitting jobs there ?

Rgds

yuguang

 

-----Original Message-----
From: Robert Duke [mailto:rduke_at_email.unc.edu]
Sent: Thursday, October 16, 2003 10:51 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: tru64 alpha

 

Mu -

All the Machine files that contain "axp" somewhere in their name are for
the Tru64 OS running on Compaq or HP alphaservers. The generic mpi one
is src.pmemd/Machines/Machine.axp_f90_mpi. I have used the
Machine.axp_f90_mpi.ev7 file for the salk servers at PSC, and the first
file (Machine.axp_f90_mpi) is just a generalization of this one that you
can't use on the jonas front-end at PSC because it has a different chip
architecture (ie., you can use the generic one if your target machine
and build machine have the same chip). There are also axp files with a
"quadrics" extension, which you can use if you have a quadrics mpi
interconnect between the nodes, as is the case for lemieux.psc.edu, the
"terascale computer" at PSC. You should not have any problems with
dynamic memory allocation in pmemd. Sorry for the late reply; the UNC
email server was dead for 2 days, which kind of backed things up. If
you have problems, let me know more about your machine config.

Regards - Bob Duke

 

        ----- Original Message -----

        From: Mu Yuguang (Dr) <mailto:YGMu_at_ntu.edu.sg>

        To: amber_at_scripps.edu

        Sent: Tuesday, October 14, 2003 9:19 PM

        Subject: AMBER: tru64 alpha

         

        Dear All,

        Do you have experiences in install PMEMD in tru64 alpha machine
?

        Thanks in advance

        yuguang

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