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
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Received on Mon Jun 04 2012 - 13:30:03 PDT
