[gmx-users] possible compatibility issue
Luciane Vieira de Mello
mello at cenargen.embrapa.br
Fri Feb 28 14:08:40 CET 2003
hi David,
Thanks for the quick reply. I have always worked with rpms. This time
it's a question of compilation proper, right? No work-around?
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 13:53, 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
> > > > gmx-users at gromacs.org
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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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