[gmx-users] Parallel running problem

[Alan Dodd]

For completeness, this is the configure command I'm
using for installing fftw:
./configure --prefix=/home/ad0303/fftw --enable-float
--enable-type-prefix --enable-mpi
And this is the result:

checking for mpicc... mpicc
checking for MPI_Init... no
checking for MPI_Init in -lmpi... no
configure: error: couldn't find mpi library for
--enable-mpi

I'm certain there's some critical command I'm not
specifying here - what did you mean by "I also linked
FFTW against MPICH"?

--- "Peter C. Lai" <sirmoo at cowbert.2y.net> wrote:

> On Fri, Sep 16, 2005 at 03:23:07AM -0700, Alan Dodd
> wrote:
> > Thanks for all your help, I thought I had compiled
> > with MPI but from trying to reinstall, it appears
> not.
> > The system I'm trying to install on is using
> mpich,
> > rather than lammpi.  I wouldn't have thought this
> > would be a problem, but installing fftw locally
> > doesn't work - it can't find the mpi libraries. 
> Both
> > using the rpms and compiling from source seem to
> > produce similar errors.  I'm pretty sure others
> have
> > used mpich, so have any of you come across a
> similar
> > problem (and, ideally, a solution?)
> > Thanks,
> > Alan
> > 
> 
> I dunno, I recently (a few months ago, really)
> compiled 3.2.1 against
> mpich1.2.5.2 initially and then against mpich1.2.6
> on a dual-socket p3 
> with gcc3.4.2 and ran all the test suites with no
> problems (I was actually 
> running gromacs-mpich to debug the new FreeBSD
> kernel scheduler while getting 
> some side work out of the otherwise idle cpus), so I
> really don't know what 
> your problem is either [i.e. WORKSFORME albeit on a
> different platform] :(
> 
> Note that I also linked FFTW against MPICH - I think
> this is a critical step
> (and everything was built as single precision, but I
> vaguely remember running
> double over mpich without any problems either).
> 
> > --- David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
> > 
> > > On Wed, 2005-09-07 at 05:18 -0700, Alan Dodd
> wrote:
> > > > Hello Gromacs users,
> > > > I gather this problem is similar to many
> previous,
> > > but
> > > > can't see an obvious solution in the replies
> to
> > > any of
> > > > them.  I've been trying to get GROMACS to run
> on
> > > this
> > > > sample dual-core, dual-socket opteron box that
> we
> > > have
> > > > on loan.  Despite my best efforts, I seem
> unable
> > > to
> > > > get mdrun to understand that it's supposed to
> run
> > > on
> > > > more than one node.  I'm telling it to do so,
> and
> > > it
> > > > even appreciates it's supposed to in the
> output
> > > (see
> > > > below), but then decides I've told it to run
> on
> > > just
> > > > the one and dies.  Has anyone any idea what's
> > > going
> > > > wrong?  Is it just some kind of
> incompatibility
> > > with
> > > > mpich/the hardware?
> > > Have you compiled with MPI?
> > > 
> > > you can check by typing
> > > ldd `which mdrun`
> > > It should show some MPI libraries.
> > > 
> > > Dual core opterons run fine by the way. We have
> a
> > > brand new cluster
> > > humming along at 85 decibel.
> > > > 
> > > > Input: 
> > > > mpirun -np 4 -machinefile machines mdrun -np 4
> 
> > > > 
> > > > mdrun output:
> > > > for all file options
> > > >          -np    int      4  Number of nodes,
> must
> > > be
> > > > the same as used for
> > > >                             grompp
> > > >          -nt    int      1  Number of threads
> to
> > > start
> > > > on each node
> > > >       -[no]v   bool     no  Be loud and noisy
> > > > -[no]compact   bool    yes  Write a compact
> log
> > > file
> > > >   -[no]multi   bool     no  Do multiple
> > > simulations in
> > > > parallel (only with
> > > >                             -np > 1)
> > > >    -[no]glas   bool     no  Do glass
> simulation
> > > with
> > > > special long range
> > > >                             corrections
> > > >  -[no]ionize   bool     no  Do a simulation
> > > including
> > > > the effect of an X-Ray
> > > >                             bombardment on
> your
> > > system
> > > > 
> > > > 
> > > > Back Off! I just backed up md.log to
> ./#md.log.5#
> > > > Reading file short.tpr, VERSION 3.2.1 (single
> > > > precision)
> > > > Fatal error: run input file short.tpr was made
> for
> > > 4
> > > > nodes,
> > > >              while mdrun expected it to be for
> 1
> > > > nodes.
> > > > 
> > > > 
> > > > Alan Dodd (University of Bristol)
> > > > 
> > > > 
> > > > 	
> > > > 		
> > > >
> > > _
> > > _______________________________________________
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> > >
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> > 
> > 
> > 
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> -- 
> Peter C. Lai
> Cesium Hyperfine Enterprises
> http://cowbert.2y.net/
> 
> 



		
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