Re: Difference between Linux-x86_64-TCP and Linux-x86_64

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Nov 24 2009 - 07:53:57 CST

On Mon, 2009-11-23 at 14:33 -0800, Lee Wei Yang wrote:
> Dear NAMD users,
>
> I am confused. what is the difference between Linux-x86_64-TCP and Linux-x86_64 version? Do both support MPI ?

neither is compiled with MPI. the difference is one binary uses UDP,
the other TCP to transfer data. to support MPI, one has to compile
a binary that matches the local MPI installation. those are as a general
rule not binary compatible, so any pre-compiled binaries would not
be very portable (unlike TCP/UPD).

cheers,
    axel.

> Lee
> ________________________________________
> 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, November 20, 2009 9:25 AM
> To: paul.rigor_at_uci.edu
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: help with running namd-cuda for the tutorials
>
> On Fri, Nov 20, 2009 at 11:24 AM, Paul Rigor (uci) <paul.rigor_at_uci.edu> wrote:
> > Hi,
>
> hi paul,
>
>
> > I receive a fatal error when attempting to run the cuda-enabled version of
> > namd2 even on the simple tutorials. Below are my system config, error
> > message and ldd output (which verifies that my system has all the requisite
> > libraries).
> >
> > I'd really appreciate any help!
>
> just read the error message and add +idlepoll to your namd command line.
>
> cheers,
> axel.
>
> >
> > Thanks,
> > Paul
> >
> > ==System==
> > Fedora Core 11, x64, NVidia GTX260
> >
> > ==Error==
> > [prigor_at_localhost 1-3-box]$ ~/Download/NAMD_CVS_Linux-x86_64-CUDA/namd2
> > ubq_wb_eq.conf
> > Charm++: standalone mode (not using charmrun)
> > FATAL ERROR: Please add +idlepoll to command line for proper performance.
> > ------------- Processor 0 Exiting: Called CmiAbort ------------
> > Reason: FATAL ERROR: Please add +idlepoll to command line for proper
> > performance.
> >
> > [0] Stack Traceback:
> > [0] CmiAbort+0x7f [0x9cd929]
> > [1] _Z8NAMD_diePKc+0x62 [0x509d02]
> > [2] _ZN7BackEnd4initEiPPc+0x84 [0x512994]
> > [3] main+0x2f [0x50e237]
> > [4] __libc_start_main+0xfd [0x3fbe81ea2d]
> > [5] _ZNSt8ios_base4InitD1Ev+0x6a [0x50966a]
> > Charm++ fatal error:
> > FATAL ERROR: Please add +idlepoll to command line for proper performance.
> >
> > Aborted
> >
> > ==ldd output==
> > [prigor_at_localhost 1-3-box]$ ldd ~/Download/NAMD_CVS_Linux-x86_64-CUDA/namd2
> > linux-vdso.so.1 => (0x00007fff937ff000)
> > libdl.so.2 => /lib64/libdl.so.2 (0x0000003fbf000000)
> > libcudart.so.2 => /usr/local/cuda/lib64/libcudart.so.2
> > (0x00007f53381d4000)
> > libm.so.6 => /lib64/libm.so.6 (0x0000003fbec00000)
> > libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003d90800000)
> > libc.so.6 => /lib64/libc.so.6 (0x0000003fbe800000)
> > libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003fbf400000)
> > /lib64/ld-linux-x86-64.so.2 (0x0000003fbe200000)
> > librt.so.1 => /lib64/librt.so.1 (0x0000003fc0400000)
> > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003fcd000000)
> >
> > --
> > Paul Rigor
> > Pre-doctoral BIT Fellow and Graduate Student
> > Institute for Genomics and Bioinformatics
> > Donald Bren School of Information and Computer Sciences
> > University of California, Irvine
> > http://www.ics.uci.edu/~prigor
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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