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=$PATH:/opt/intel/bin
export MPI_HOME=/share/apps/amber12
mpcc
-bash: mpcc: command not found
which mpcc
/usr/bin/which: no mpcc in
(/opt/intel/composer_xe_2011_sp1.9.293/bin/intel64:/opt/intel/composer_xe_2011_sp1.9.293/bin/intel64:/opt/intel/composer_xe_2011_sp1.9.293/bin/intel64:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/openmpi/bin/:/opt/maui/bin:/opt/torque/bin:/opt/torque/sbin:/opt/rocks/bin:/opt/rocks/sbin:/opt/sun-ct/bin:/opt/intel/composer_xe_2011_sp1.9.293/mpirt/bin/intel64://share/apps/amber12/bin:/opt/intel/bin:/root/bin:/opt/intel/composer_xe_2011_sp1.9.293/mpirt/bin/intel64:/share/apps/amber12/bin:/opt/intel/bin:/opt/intel/composer_xe_2011_sp1.9.293/mpirt/bin/intel64://share/apps/amber12/bin:/opt/intel/bin)
mpif90
gfortran: no input files
which mpif90
/opt/openmpi/bin/mpif90
"it" is bash or configure? as I pasted above mpif90 calls gfortran.
whatever I did to bashrc killed mpcc, as it is no longer around. before
mpcc would give gcc: no input files.
in the above error I noticed that it's looking in
//share/apps/amber12/bin
//share/apps/amber12/bin
is the // the problem? If so where is it finding that? if not... i'm lost
again.. sorry.
On Mon, Jun 4, 2012 at 2:54 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Jun 04, 2012, Jonathan Gough wrote:
> >
> > I compiled mpich2 in the Ambertools directory with no errors (as far as I
> > could tell)
>
> Did you use the configure_mpich2 script? What arguments did you give it?
> >
> > placed the following in .bashrc
> >
> > source /opt/intel/bin/compilervars.sh intel64
> > # User specific aliases and functions
> > export AMBERHOME=/share/apps/amber12
> > export MKL_HOME=/opt/intel/mkl
> > export PATH=$PATH:/opt/intel/bin
> > export MPI_HOME=/share/apps/amber12/AmberTools/src
> > export PATH=$PATH:/$MPI_HOME/mpich2-1.4.1p1/bin
>
> Your PATH variable should include $AMBERHOME/bin near the beginning.
> Typing
> "which mpicc" should return $AMBERHOME/bin/mpicc.
>
> > the issue is it is using gcc and gfortran (which are installed)
>
> What is "it" that is using gcc?
>
> >
> > any insights on how to properly call the proper mpicc and mpif90 in
> > AmberTools?
>
> See instructions about the $PATH, above. Also, $MPI_HOME should point to
> the
> same place as $AMBERHOME, not to the subdirectory you have above. (Not
> sure
> that this makes any real difference.)
>
> ....dac
>
> >
> > p.s. - i tried placing the full path (to mpicc and mpif90) in the
> config.h,
> > which allowed it to compile, but then all the tests failed.
>
> Tests assume that the mpirun that you want is the first one in your $PATH.
>
>
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>
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Received on Mon Jun 04 2012 - 12:30:03 PDT
