Hi Quentin,
OpenMP and OpenMPI are different technologies: OpenMP is a shared-memory
(threads) approach that is used only for some components of AmberTools,
while OpenMPI is an implementation of a distributed-memory approach that is
used in Sander and PMEMD.
If you want to actually use openmp (which only speeds up some parts of
cpptraj and NAB), you need to run ./configure with -openmp flag, make
clean, and then *make openmp *(see page 15 of AmberTools13 manual). The
make file in $AMBERHOME/src doesn't understand 'openmp' because there is
nothing in Amber that uses OpenMP and your error is innocuous (the build
should have finished with no other errors).
If you, on the other hand, wanted to build with OpenMPI support to use in
PMEMD, then you need to run ./configure with -mpi flag, make clean, and
then *make install*. This should build the parallel version of Amber. If
you have a built-in version of OpenMPI or MPICH then make sure that
mpicc/mpif77 are in your $PATH. If you want to use the Amber-provided
versions, they should already be installed by you running "./configure_openmpi
gnu".
The Amber installation steps are outlined in much greater detail in pages
12-15 of the AmberTools13 manual
<
http://ambermd.org/doc12/AmberTools13.pdf> and
on Jason's wiki<
http://jswails.wikidot.com/installing-amber12-and-ambertools-13>
.
Thank you,
Eugene Yedvabny
On Mon, Feb 17, 2014 at 9:09 PM, Quentin Kaas <q.kaas.imb.uq.edu.au> wrote:
>
> Hi all,
> I tried to re-install amber12 using openmp and the recent patches and
> the
> build failed with the message:
> ```
> make[1]: *** No rule to make target `openmp', needed by `install'.
> Stop.
> ```
> I followed the instructions in manual: changed directory to
> AmberTools/src,
> uncompressed openmpi-1.5.5.tar.bz2, run "./configure_openmpi gnu",
> changed
> directory to $AMBERHOME, run "./configure -openmp gnu" and then "make
> install".
> It seems that the configure script set the vaiable "INSTALLTYPE" to
> "openmp"
> which might be a problem as "openmp" is not recognised by the in the
> $AMBERHOME/src/MakeFile.
> Changing manually INSTALLTYPE to 'parallel' does not solve the problem
> as
> the config.h is not recognised as of a parallel type because it does not
> contain the DMPI keyword. Make returns the following error message
> ```
> Error: config.h is not of type parallel!
> Rerun ./configure and specify an MPI implementation.
> ```
> Which I already did as I ran it with the -openmp option...
> Could someone provide some help in compiling amber 12 with openmp using
> the
> last pacthes.
> Thank you
> Quentin
>
> --
> -------------------------------------
> Quentin Kaas, PhD
> Institute for Molecular Bioscience IMB (L2N)
> Laboratory of David Craik
> The University of Queensland, St Lucia campus
> Brisbane 4072, Queensland, Australia
> Tel: +61 7 3346 2021
> -------------------------------------
> _______________________________________________
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> AMBER.ambermd.org
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>
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Received on Mon Feb 17 2014 - 22:30:02 PST
