[Beowulf] Really efficient MPIs??

Donald Shillady quantummechanicsllc at msn.com
Sat Dec 1 13:25:09 PST 2007

Please pardon my naive questions but this is surely the place to get an expert answer.  I am enthused by the recent micrWulf built by Prof. Adoms and his student at Calvin College.  That device approached a "homogeneous" parallel system with all the same core frequencies and achieved over 26 GFLOPS for about $1200.  With private funds and a curious 3 yo grandson I prefer to enclose the "System" into four PC cases and an external Ethernet switch.  I also want to maintain the performance I now have with a 3 GHz Toshiba Pentium 4 laptop so I prefer an "asymmetric" system with a fast Master node with a lot of frills and three slower dual core satellite PCs.  About ten years ago I was able to link an HP 9000/720 running HP-UX in one building with three other SGI nodes running IRIX in another building connected by TCP/IP Ethernet.  Sadly I do not recall the name of that message passing system but the link was a pretty bad mismatch between the slower HP9000/720 and the faster SGI CPUs at that time but it was something with "Theoretical Chemists ......".  Was that TCP/IP?  Anyway I know it is possible to link CPU/cores with different speeds and different memory-bus speeds so my question is whether "Open MPI" can handle this situation?  Specifically, suppose I set up:
1. a Master box with an AMD X2 5800+ overclocked to 3.0 GHz with DDR2 800 memory (at least 4GB, maybe 8GB), 1 300 GB SATA drive; there would also be other creature comfort frills on the Master box like CD R/W, floppy drive, graphics card etc.
2. three cheaper AMD X2 4000+ (2.1 GHz) and running cheaper DDR2 667 memory; bare bones, no drives just CPU, memory and gigE switch.
3. connected by a Trendware TEG-S80TXE 8-port Gigabit Ethernet switch with associated NIC switches.
If all the CPU/nodes/cores were AMD X2 4000+ units this should be similar to the Calvin College microWulf and run at about 27 GFLOPS (LINPAK) due to the slightly faster 2.1 GHz AMD 4000+ CPUs compared to the microWulf AMD 3800+ 2.0 GHz units.  I do not seek the  ultimate (GFLOP/$) minimum, just an inexpensive system to run GAMESS for molecular calculations and a chance to learn about parallel software late in my career.
So, can "Open MPI" handle different CPU/core frequencies and different memory bus frequencies over gigE.  I note that the writer of GAMESS (Mike Schmidt) recommends TCP/IP for GAMESS rather than OPEN MPI and GAMESS is the overwhelming goal for my use but using UBUNTU I would like to be able to access the Internet as well from the Master box.  While I have your attention, could you comment on whether Open MPI will run under LINSPIRE?  I have messed around with LINSPIRE more than UBUNTU (although I have both source disks) and I like LINSPIRE because it looks more like WINDOWS.
1. Can Open MPI handle different clock speeds across several node/cores?
2. Can Open MPI handle different memory bus clock speeds across several node/cores?
3. Why not LINSPIRE instead of UBUNTU?
Sorry about the dumb questions but I seem to recall that the Duke Beowulf managed to run using many different X86 PCs so what I want to do should be possible, but is Open MPI the best choice or what else?
Don Shillady
Emeritus Professor of Chemistry, VCU
Ashland VA (working at home)

Date: Wed, 28 Nov 2007 10:37:45 -0500From: peter.st.john at gmail.comTo: charliep at cs.earlham.eduSubject: Re: [Beowulf] Really efficient MPIs??CC: beowulf at beowulf.org
For the sake of others as easily confused as myself, I note (now, thanks!) that OpenMP and OpenMPI are two different things:
OpenMP (an alternative to the MPI method) is http://en.wikipedia.org/wiki/OpenMP
OpenMPI (an implementation of MPI) is http://en.wikipedia.org/wiki/OpenMPI
On Nov 28, 2007 8:49 AM, Charlie Peck <charliep at cs.earlham.edu> wrote:

On Nov 28, 2007, at 8:04 AM, Jeffrey B. Layton wrote:> If you don't want to pay money for an MPI, then go with Open-MPI.> It too can run on various networks without recompiling. Plus it's > open-source.Unless you are using a gigabit ethernet, Open-MPI is noticeably lessefficient that LAM-MPI over that fabric.I suspect at some point in the future gige will catch-up but for now my (limited) understanding is that the Open-MPI folks are focusingtheir time on higher bandwidth/lower latency fabrics than gige.charlie

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