Mark's easier procedure probably worked for debian Linux amd64
as "make parallel" ended with
Installation of Amber9 (parallel) is complete at Wed Jul 25 22:23:48 CEST 2007
(it finished a couple of minutes before Wagner's Nuernberger .. from Bayreuth)
Just to avoid mistakes, is a correct procedure now (bash):
export DO_PARALLEL mpirun -np 4
before running the tests?
If test OK, is the compilation of PMEND to be folled (for my system) as
described at sect 8.6 of the manual)
Thanks
francesco pietra
--- "David A. Case" <case.scripps.edu> wrote:
> On Wed, Jul 25, 2007, Mark Williamson wrote:
>
>
> >
> > I'm desperately trying not cloud the waters here, but here's my take on
> > it :)
> >
> > When AMBER's configure script is run with the openmpi flag, the
> > following section of code within this script is visited:
> >
> >
> >
> > ...blah....
> >
> > openmpi)
> > if [ -z "$MPI_HOME" ]; then
> > PAR="OPENMPI"
> > FILES="mpif.h and libmpi.a, liblam.a or liblamf77mpi.a"
> > EXAMPLE="/usr/local/openmpi-1.0"
> > par_error
> > fi
> > echo "MPI_HOME is set to $MPI_HOME"
> > loadlib=`$MPI_HOME/bin/mpif90 -showme | perl -p -e
> > 's/(-[lLW]\S+\s)|\S+\s/$1/g'`
> > fppflags="-I$MPI_HOME/include $fppflags -DMPI"
> > ;;
> >
> > ...blah....
> >
> >
> >
> > Hence, I suggest trying:
> >
> >
> > cd $AMBERHOME/src
> > make clean
> >
> > export MPI_HOME=/usr/local
> > ./configure -openmpi ifort_x86_64
> >
> > make parallel
> >
>
> I'll defer to Mark here, because I guess this works for him. But here's the
> problem I have, and I don't quite understand why he doesn't have it as well:
>
> If config.h has FC=ifort, then the following happens when I try to compile
> a parallel code foo.f:
>
> 1. The preprocessor sees the "#include mpif.h" and correctly finds
> $MPI_HOME/include/mpif.h and puts it into the _foo.f file
>
> 2. However, $MPI_HOME/include/mpif.h has inside it a fortran90 include
> line "include 'mpif-common.h'". And when ifort sees this line,
> it doesn't know where to find mpif-common.h, and fails. If FC in
> config.h is set to mpif90, then there is no problem, since mpif90
> is smart enough to know where to find this second include file.
>
> It was after Amber9 was released that the openMPI folks changed their header
> file, to use the fortran90 include mechanism to get mpif-common.h.
> Previously, $MPI_HOME/include/mpif.h had been a simple file that could just
> be included at the cpp pre-processing step. So, the configure script above
> worked at release time, but stopped working later on (at least for me!).
>
> The simple question for Mark is this: what version of openMPI are you using?
> Can you check on what is inside your $MPI_HOME/include/mpif.h file?
>
> Somewhat of an aside: we've found that relying on the "showme" command is
> not always that reliable. This has been more a problem with lam than
> openmpi,if I remember correctly. But the general consensus among Amber
> developers is that we are better off setting FC=mpif90 (or mpif77 for lam)
> and relying on mpif90 to do the right thing, both for compiling and loading.
> (After all, that is its purpose in life.)
>
> Bottom line: it's a real pain that we have to rely on a outside MPI
> installation, which might be one of several flavors. For amber10, I am
> seriously considering including an MPI installation with Amber, along with
> instructions that we know(!?!) will work. This will at least get people
> going; more advanced users can then substitute a local MPI library in place
> of the one we supply, if they need that for efficiency. Comments and
> suggestions would be welcome here.
>
> ...regards...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
____________________________________________________________________________________
Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center.
http://autos.yahoo.com/green_center/
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jul 29 2007 - 06:07:16 PDT
