[gmx-users] possible compatibility issue

[Luciane Vieira de Mello]

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?

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          |
> > +-------------------------------------------------------------------------+
> >
> >
> >
> > _______________________________________________
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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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