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