Dear all,
(forgive me for my ignorance regarding compilation in advance...)
I have downloaded and installed Amber12. I would like to install parallel
versions of the executables now (sander.MPI, pmemd.MPI).
I was hoping to use the easy script
provided: $AMBERHOME/AmberTools/src/configure_openmpi
This is what I did:
cd $AMBERHOME/AmberTools/src
wget
http://www.open-mpi.org/software/ompi/v1.5/downloads/openmpi-1.5.4.tar.bz2
tar xvfj openmpi-1.5.4.tar.bz2
./configure_openmpi gnu
I seem to get to the 'make install' stage (final lines of the
configure_openmpi script), as these are the final lines from running the
above command:
rm -f *.o *.obj *.mod pmemd.MPI pmemd pmemd.cuda pmemd.cuda.MPI *.d work.pc*
make -C ./cuda clean
make[3]: Entering directory
`/export/users/chmwvdk/amber12/src/pmemd/src/cuda'
rm -f *.o *.linkinfo cuda.a *.mod
make[3]: Leaving directory
`/export/users/chmwvdk/amber12/src/pmemd/src/cuda'
make[2]: Leaving directory `/export/users/chmwvdk/amber12/src/pmemd/src'
make[1]: Leaving directory `/export/users/chmwvdk/amber12/src/pmemd'
(cd pmemd.amoeba && make clean)
make[1]: Entering directory `/export/users/chmwvdk/amber12/src/pmemd.amoeba'
make -C src/ clean
make[2]: Entering directory
`/export/users/chmwvdk/amber12/src/pmemd.amoeba/src'
rm -f *.o *.obj *.mod pmemd.amoeba.MPI pmemd.amoeba *.d work.pc*
make[2]: Leaving directory
`/export/users/chmwvdk/amber12/src/pmemd.amoeba/src'
make[1]: Leaving directory `/export/users/chmwvdk/amber12/src/pmemd.amoeba'
However, I don't have any .MPI executables in $AMBERHOME/bin/ afterwards.
AmberTools12.pdf section 1.2 point 7 says: "Follow the instructions of
these scripts, then return to step 6."
(But step 6 is "make test")
What am I suppose to do after this to get the .MPI executables?
I tried "make install" and "make parallel" in $AMBERHOME and
$AMBERHOME/AmberTools/src, to no avail (apart from reinstalling serial
executables).
Many thanks in advance,
Marc
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Received on Fri Apr 13 2012 - 08:00:06 PDT
