Re: help with running namd-cuda for the tutorials

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 20 2009 - 11:25:14 CST

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.

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