From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Wed Sep 13 2006 - 07:54:48 CDT
Hi Leandro,
For how long does your simulation run until it halts? I have been
running NAMD 2.6 for more than 2 days now without any problem. Perhaps
your problem might be related to a bug or some incompatibility in your
libraries.
Have you tried running the Linux Test Project on your machines?
http://ltp.sourceforge.net/. It is a large set of test developed to
validate the reliability, robustness, and stability of Linux.
Cesar
Leandro Martínez escribió:
>
> Hi all,
> I'm still having problems in running namd2 in our Athlon 64 Dual Core
> machines. The problem is that the simulation runs well to a point where
> all processes, except for one, stop, and I get a single process in a
> single cpu running. The simulation does not crash, but it does not
> continues as well, and this single process appears to last forever
> doing something I don't know what it is.
>
> Now, as Jim suggested, I have attached gdb to this process. I have
> never used it, but I could get the information bellow. Any help is
> appreciated. I believe the bolded output bellow is the one referring
> to the namd2 process.
>
> ------------ OUTPUT FROM GDB: --------------------------
>
> Attaching to program: /usr/bin/namd2, process 19438
> Reading symbols from /lib64/libdl.so.2...(no debugging symbols
> found)...done.
> Loaded symbols for /lib64/libdl.so.2
> Reading symbols from /lib64/libm.so.6...(no debugging symbols
> found)...done.
> Loaded symbols for /lib64/libm.so.6
> Reading symbols from /usr/lib64/libstdc++.so.6...(no debugging symbols
> found)...done.
> Loaded symbols for /usr/lib64/libstdc++.so.6
> Reading symbols from /lib64/libc.so.6...
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libc.so.6
> Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging
> symbols found)...done.
> Loaded symbols for /lib64/ld-linux-x86-64.so.2
> Reading symbols from /lib64/libgcc_s.so.1...(no debugging symbols
> found)...done.
> Loaded symbols for /lib64/libgcc_s.so.1
> Reading symbols from /lib64/libnss_files.so.2...
> (no debugging symbols found)...done.
> Loaded symbols for /lib64/libnss_files.so.2
> 0x0000000000714caa in Set::find ()
> (gdb) next
> Single stepping until exit from function _ZN3Set4findEP10InfoRecord,
> which has no line number information.
> 0x00000000006f407f in Rebalancer::numAvailable ()
> (gdb) next
> Single stepping until exit from function
> _ZN10Rebalancer12numAvailableEP11computeInfoP13processorInfoPiS4_S4_,
> which has no line number information.
> 0x00000000006f3f34 in Rebalancer::refine_togrid ()
> (gdb) next
> Single stepping until exit from function
> _ZN10Rebalancer13refine_togridERA3_A3_A2_NS_6pcpairEdP13processorInfoP11computeInfo,
>
> which has no line number information.
> 0x00000000006f23b5 in Rebalancer::refine ()
> (gdb) next
> Single stepping until exit from function _ZN10Rebalancer6refineEv,
> which has no line number information.
> -----------------------------------------------------------------------
> From this point on nothing happens.
>
> Thank you very much,
> Leandro.
>
>
>
>
> --------------------------------------------------------------------
> Leandro Martinez
> Institute of Chemistry
> State University of Campinas, Brazil
> http://www.ime.unicamp.br/~martinez/packmol
> <http://www.ime.unicamp.br/%7Emartinez/packmol>
> --------------------------------------------------------------------
>
>
>
>
>
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