From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Fri Jan 06 2012 - 12:58:08 CST
The testing that I did was several months ago. My notes and show that the ibverbs on qlogic made it through compilation and the charmm tests worked but that namd2.8 didn't run, but hung with no error to go on.
From: Chris Harrison [charris5_at_gmail.com]
Sent: Friday, January 06, 2012 10:52 AM
To: Bennion, Brian
Cc: Thomas Bishop; namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: IB fabrics
When you say it "doesn't do it very well then," could you elaborate?
Are crashes more frequent, and if so are they reproducible and what is
the error message? Or is a difference in performance speed compared to
We'd appreciate anything more quantitative you could send our way on the
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 773-570-0329 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 "Bennion, Brian" <Bennion1_at_llnl.gov> writes: > Date: Fri, 6 Jan 2012 10:39:04 -0800 > From: "Bennion, Brian" <Bennion1_at_llnl.gov> > To: Thomas Bishop <bishop_at_latech.edu> > CC: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu> > Subject: RE: namd-l: IB fabrics > > The only concern that I have seen is the implementation of charm++ on the two IB layers when using IBVERBS instead of the mpi versions. > > at our institution we have qlogic and mellanox ib hardware. qlogic in our implementation will only run ibverbs in a software mode and it doesn't do it very well even then. > > Brian > > > > ________________________________________ > From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of Axel Kohlmeyer [akohlmey_at_gmail.com] > Sent: Friday, January 06, 2012 9:58 AM > To: Thomas Bishop > Cc: namd-l_at_ks.uiuc.edu > Subject: Re: namd-l: IB fabrics > > On Fri, Jan 6, 2012 at 12:42 PM, Thomas Bishop <bishop_at_latech.edu> wrote: > > Is namd very sensitive to which vendor is used for a 40Gbps IB fabric. > > Specifically I'm interested in Qlogic vs. Mellanox. > > don't think so, why should it be? > > i can think of at least 10 other things that > i would worry about more before worrying > about ib vendor impact on NAMD speed. > > . and the things w.r.t. IB vendors that i *would* > worry about are independent of the application. > > cheers, > axel. > > > Any comments greatly appreciated. > > Thanks > > TOm > > > > > > -- > > ******************************* > > Thomas C. Bishop > > Tel: 318-257-5209 > > Fax: 318-257-3823 > > http://dna.engr.latech.edu > > ******************************** > > > > > > -- > Dr. Axel Kohlmeyer > akohlmey_at_gmail.com http://goo.gl/1wk0 > > College of Science and Technology > Temple University, Philadelphia PA, USA. > >
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