On Thu, Apr 7, 2011 at 7:26 PM, David Case <dacase.rci.rutgers.edu> wrote:
>
>
> On Apr 7, 2011, at 5:48 PM, Thomas Cheatham III <tec3.utah.edu> wrote:
> >
> > Ah, the problem is likely that the *tar.bz has the memory of previous
> > Intel compiles in there; prior to tar'ing it up for release perhaps "make
> > uninstall" should likely be run? What I did was simply extract and do
> > ./configure followed by make install...
>
> Not true: I always make the tarball from a pristine tree, and,anyway, the
> "lib" directories are never present in the distribution anyway. in your
> earlier post, you indicated that you did
> more than "simply extract and ./configure ...."
>
> (Do a "tar tfj" on the tarball to double check that libfftw3.a, etc is not
> present.)
>
> If you are really seeing a reproducible error, we need exact details.
>
> > The at15-05apr11 tarball still has that python issue, as does an
> > updated compile out of my at15-with-patches git tree... I did
> > make uninstall; make clean; configure intel; make parallel
>
>
> > make[1]: Entering directory `/uufs/
> chpc.utah.edu/common/home/u0181375/AMBER/git/amber/AmberTools/src/mmpbsa_py
> '
> > /bin/bash setup.sh
> > Using system python
> > Error importing MMPBSA python modules! MMPBSA.py will not work.
>
> Can you give more details? Did you first configure and compile a serial
> version? What options did you give at that time? It's not clear why it
> says "using system python".
>
If you don't use -nopython (or another option that's incompatible with
Python, like -mpi, -cuda, or -crayxt5), then it will not build Python.
Otherwise, it will build and any Python build error will kill the install
process, so the install MUST be building python. All checks for the
existence of Amber's python are done via relative paths in configure, and
AMBERHOME is reset there locally, anyway. setup.sh, on the other hand,
checks for an Amber python using an absolute PATH:
# Find the proper python
if [ -x $AMBERHOME/bin/python ]; then
echo " Using AmberTools' python"
pythonexe=$AMBERHOME/bin/python
pythonstring="\$AMBERHOME/bin/python"
amberpy='yes'
else
echo " Using system python"
pythonexe=`which python`
pythonstring=`which python`
amberpy='no'
fi
So what I'm guessing here is that AMBERHOME wasn't manually set to the new
trial version, and the place where it WAS set (it had to be set, or the
setup script fails earlier) points to a location with no python installed,
which will be an old version. Since there is no python there, the setup
script decides to use the system python. To make sure it can find the
chemistry package, it adds AMBERHOME/AmberTools/src/etc to the PYTHONPATH;
but since AMBERHOME references an old tree with no chemistry/ package
located there, it can't be found and that's the error we get.
It could also explain some of the other errors, if there's a mix of
AMBERHOME and relative paths that are used.
At least I HOPE that's what happened here.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 07 2011 - 20:30:02 PDT
