[gmx-users] Problems using mdrun_d

[David van der Spoel]

Arneh Babakhani wrote:
> sure, here you go,
> 
> [ababakha at chemcca50 ~]$ ldd 
> /u1/ababakha/gromacs-3.3.1_double_precision_mpi/bin/mdrun_d
>        libnsl.so.1 => /lib/libnsl.so.1 (0x006e4000)
>        libm.so.6 => /lib/tls/libm.so.6 (0x00ae3000)
>        libXm.so.3 => /usr/X11R6/lib/libXm.so.3 (0x0020c000)
>        libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x00111000)
>        libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x00b1e000)
>        libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x00b32000)
>        libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x00b0e000)
>        libXp.so.6 => /usr/X11R6/lib/libXp.so.6 (0x00443000)
>        libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x03237000)
>        liblamf77mpi.so.0 => /usr/lib/lam/liblamf77mpi.so.0 (0x00540000)
>        libmpi.so.0 => /usr/lib/lam/libmpi.so.0 (0x00b5f000)
>        liblam.so.0 => /usr/lib/lam/liblam.so.0 (0x00162000)
>        libaio.so.1 => /usr/lib/libaio.so.1 (0x009b1000)
>        libutil.so.1 => /lib/libutil.so.1 (0x005f1000)
>        libdl.so.2 => /lib/libdl.so.2 (0x00b08000)
>        libpthread.so.0 => /lib/tls/libpthread.so.0 (0x00c25000)
>        libc.so.6 => /lib/tls/libc.so.6 (0x009b5000)
>        libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00dc8000)
>        /lib/ld-linux.so.2 (0x00997000)
>        libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x006ff000)
> [ababakha at chemcca50 ~]$
> 
so what typically happens is you compile on one node anr run on another 
node which has different libraries. so you'd have to compare the ldd 
output for both.

otherwise I  wouldn't know.
> 
> Yang Ye wrote:
>> this is mostly likely due to mismatched version between runtime 
>> library and compile library. Could you run
>> ldd full/path/to/mdrun_d
>>
>> and paste the output here for us to continue our help?
>>
>> On 9/6/2007 5:43 AM, Arneh Babakhani wrote:
>>> Hi,
>>>
>>> I've compiled a mpi double-precision version of mdrun_d.  I'm trying 
>>> to use it, but I get the following error.  Any ideas what the 'symbol 
>>> lookup error' is?
>>> ----------------------
>>>
>>> [ababakha at chemcca50 Window-1]$ mpirun -np 4 mdrun_d -np 4 -s 
>>> UmbrellaMD.tpr -o UmbrellaMD -c AfterUmbrellaMD -e UmbrellaMD -g 
>>> UmbrellaMD -pi Window-$number.ppa -pn ../CommonFiles/Pull.ndx
>>> . . .
>>> Reading file UmbrellaMD.tpr, VERSION 3.3.1 (double precision)
>>> mdrun_d: symbol lookup error: mdrun_d: undefined symbol: 
>>> _intel_fast_memset
>>> ----------------------------------------------------------------------------- 
>>>
>>> One of the processes started by mpirun has exited with a nonzero exit
>>> code.  This typically indicates that the process finished in error.
>>> If your process did not finish in error, be sure to include a "return
>>> 0" or "exit(0)" in your C code before exiting the application.
>>>
>>> PID 10814 failed on node n0 (127.0.0.1) with exit status 127.
>>> ----------------------------------------------------------------------------- 
>>>
>>> [ababakha at chemcca50 Window-1]$ which mdrun_d
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se