[gmx-users] possible compatibility issue

David van der Spoel spoel at xray.bmc.uu.se
Fri Feb 28 20:04:33 CET 2003


On Fri, 2003-02-28 at 13:53, Luciane Vieira de Mello wrote:
> 
> hi David,
> 
> I checked the libraries, and I got:
> 
> machine where mdrun_mpi is working fine:
> 
> [mello at bemtevi mello]$  ldd `which mdrun`
>         libmd.so.2 => /usr/local/lib/libmd.so.2 (0x40018000)
>         libgmx.so.2 => /usr/local/lib/libgmx.so.2 (0x40084000)
>         libnsl.so.1 => /lib/libnsl.so.1 (0x401c1000)
>         libsrfftw.so.2 => /usr/local/lib/libsrfftw.so.2 (0x401d7000)
>         libsfftw.so.2 => /usr/local/lib/libsfftw.so.2 (0x40208000)
>         libm.so.6 => /lib/i686/libm.so.6 (0x4023e000)
>         libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x40261000)
>         libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x4026b000)
>         libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x40282000)
>         libc.so.6 => /lib/i686/libc.so.6 (0x40360000)
>         /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000)
> 
> machine where mdrun_mpi does not work fine:
> 
> [mello at acgt phospho_iPGM]$ ldd `which mdrun`
>         libmd.so.2 => /usr/local/lib/libmd.so.2 (0x40013000)
>         libgmx.so.2 => /usr/local/lib/libgmx.so.2 (0x40080000)
>         libnsl.so.1 => /lib/libnsl.so.1 (0x401bd000)
>         libsrfftw.so.2 => /usr/local/lib/libsrfftw.so.2 (0x401d2000)
>         libsfftw.so.2 => /usr/local/lib/libsfftw.so.2 (0x40203000)
>         libm.so.6 => /lib/i686/libm.so.6 (0x40239000)
>         libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x4025b000)
>         libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x40265000)
>         libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x4027c000)
>         libc.so.6 => /lib/i686/libc.so.6 (0x42000000)
>         libdl.so.2 => /lib/libdl.so.2 (0x4035a000)
>         /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000)
> 
> 
> so:
> 
> there is one extra labrary in the second one: libdl.so.2 =>
> /lib/libdl.so.2 (0x4035a000)
> 
> and there are difference in the numbers (0x40013000) for basically all of
> them.
> what should I do?
recompile everything...
sorry about that.
> 
> thanks a lot.
> 
> Luciane
> 
> 
> +-------------------------------------------------------------------------+
> |                  Dra. Luciane Vieira de Mello Rigden                    |
> | e-mail: mello at cenargen.embrapa.br                                       |
> | Embrapa Recursos Geneticos e Biotecnologia                              |
> | Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
> | PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
> | 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
> +-------------------------------------------------------------------------+
> 
> 
> 
> On 28 Feb 2003, David van der Spoel wrote:
> 
> > On Fri, 2003-02-28 at 13:15, Luciane Vieira de Mello wrote:
> > >
> > > Dear all,
> > >
> > > I've been using gmx 3.14 happily on RedHat7.2.  Now, after upgrading to
> > > RH8.0 I find that while editconf and tpbconv still work, I can;t do the
> > > dynamics.  I give the usual command
> > >
> > > /usr/bin/mpirun C /usr/local/bin/mdrun_mpi -s restart1.tpr -v >&
> > > restart1.lis
> > probably different libraries for either LAM or FFTW check by running:
> > ldd `which mdrun`
> >
> > >
> > > And get the following
> > >
> > > -rw-r--r--    1 mello    desenv          0 Feb 28 09:05 restart1.lis
> > > -rw-------    1 mello    desenv     364544 Feb 28 09:05 core.13715
> > >
> > > i.e. a binary core file and an empty lis file.
> > >
> > > This does seem to be related to the version of RedHat since I get the same
> > > on two different machines, server and workstation, that run 8.0.  Machines
> > > with 7.2 continue fine.
> > >
> > > Can anyone help?
> > >
> > > Thanks in advance
> > >
> > > Luciane
> > >
> > >
> > > +-------------------------------------------------------------------------+
> > > |                  Dra. Luciane Vieira de Mello Rigden                    |
> > > | e-mail: mello at cenargen.embrapa.br                                       |
> > > | Embrapa Recursos Geneticos e Biotecnologia                              |
> > > | Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
> > > | PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
> > > | 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
> > > +-------------------------------------------------------------------------+
> > >
> > >
> > >
> > > _______________________________________________
> > > gmx-users mailing list
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> > > http://www.gromacs.org/mailman/listinfo/gmx-users
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> > >
> > --
> > Groeten, David.
> > ________________________________________________________________________
> > Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
> > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > phone:	46 18 471 4205		fax: 46 18 511 755
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > _______________________________________________
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> >
> 
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> 
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



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