sorry for the typo.
which mpicc
/opt/openmpi/bin/mpicc
I did do the mpich2 install in AmberTools with the intel compiler.
You were correct, it was the syntax in .bashrc.
I now get:
which mpicc
/share/apps/amber12/bin/mpicc
[root.pople amber12]# which mpif90
/share/apps/amber12/bin/mpif90
Once again, thank you everyone!
I know this might be bad form but, is there a good resource that explains
the common sytax used? (maybe something to add to your wiki jason?)
warm regards,
Jonathan
On Mon, Jun 4, 2012 at 4:20 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Jun 4, 2012 at 3:17 PM, Jonathan Gough
> <jonathan.d.gough.gmail.com>wrote:
>
> > Thanks David,
> >
> > bashrc now looks like this
> >
> >
> > # .bashrc
> > source /opt/intel/bin/compilervars.sh intel64
> > # User specific aliases and functions
> > export AMBERHOME=/share/apps/amber12
> > export PATH=$PATH:/$AMBERHOME/bin
> > export MKL_HOME=/opt/intel/mkl
> > export PATH=$PATH:/opt/intel/bin
> > export MPI_HOME=/share/apps/amber12
> >
> > mpcc
> > -bash: mpcc: command not found
> >
> > which mpcc
> > /usr/bin/which: no mpcc in
> >
> >
> (/opt/intel/composer_xe_2011_sp1.9.293/bin/intel64:/opt/intel/composer_xe_2011_sp1.9.293/bin/intel64:/opt/intel/composer_xe_2011_sp1.9.293/bin/intel64:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/openmpi/bin/:/opt/maui/bin:/opt/torque/bin:/opt/torque/sbin:/opt/rocks/bin:/opt/rocks/sbin:/opt/sun-ct/bin:/opt/intel/composer_xe_2011_sp1.9.293/mpirt/bin/intel64://share/apps/amber12/bin:/opt/intel/bin:/root/bin:/opt/intel/composer_xe_2011_sp1.9.293/mpirt/bin/intel64:/share/apps/amber12/bin:/opt/intel/bin:/opt/intel/composer_xe_2011_sp1.9.293/mpirt/bin/intel64://share/apps/amber12/bin:/opt/intel/bin)
> >
>
> mpicc, not mpcc.
>
> My suggestion: unpack mpich2 in $AMBERHOME/AmberTools/src and use the
> configure_mpich2 script in that directory to make sure that you build an
> MPI that is compatible with Amber. Then, make sure that $AMBERHOME/bin
> comes in your PATH first when you build Amber so that the Amber
> installation uses the MPI built in AMBERHOME rather than another one on
> your system (i.e., put the line
>
> export PATH=$AMBERHOME/bin\:$PATH
>
> in your ~/.bashrc).
>
>
> > is the // the problem? If so where is it finding that? if not... i'm
> lost
> > again.. sorry.
> >
>
> // is no problem.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 04 2012 - 14:00:04 PDT
