AMBER Archive (2004)

Subject: Re: AMBER: recompiling amber8

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Aug 03 2004 - 11:30:41 CDT

Carsten -
You should point to the directory that directly contains a lib directory,
which in turn has in it the mpich libraries built with the same compiler.
You may have different "devices" supporting mpich, which is what all the
ch_p4, ch_p4mpd stuff is about, and you probably actually need to be setting
MPICH_HOME to point inside one of these. You have to be sure that you have
the correct stuff built with the correct compiler, pointing to the correct
actual hardware, and that you access the correct mpirun command when you
execute the code. The MKL does NOT come with the intel compiler; you have
to purchase it separately.
Regards - Bob

----- Original Message -----
From: "Carsten Detering" <detering_at_u.washington.edu>
To: <amber_at_scripps.edu>
Sent: Tuesday, August 03, 2004 11:55 AM
Subject: Re: AMBER: recompiling amber8

> Dear David and Robert,
>
> I didnt imply a connection between the bugfix of pbsa and the
> unsuccessful recompilation. Sorry if it sounded that way.
>
> I had actually used the setenv command, I guess I wanted to say that I
> had set the variable, and then wanted to write the command, apologies
> for the confusion.
>
> Meanwhile I solved the problem by pointing to the correct mpich dir.
> Thanks for pointing that out. One question here: is it necessary to
> point to the .../mpich/ch_p4 respectively the .../mpich/ch_p4mpd dir, so
> that it finds the libraries there? Or is .../mpich sufficient?
>
> Do the MKL libraries come with the intel compiler? I dont have the mkl61
> dir in my /opt/intel/ directory.
>
> Thanks a lot again for your help.
>
> Carsten
>
> David A. Case wrote:
>
> > On Mon, Aug 02, 2004, Carsten Detering wrote:
> >
> >>after fixing a bug in pbsa (#4 in amber8) I needed to recompile amber,
> >>which worked ok for the serial version. For parallel however, the
> >>compilation interrupted with an error:
> >
> >
> > First: the fix to pbsa has nothing to do with problems you may have
compiling
> > sander. The two codes are unrelated, and sander does not use any of the
> > files in $AMBERHOME/src/pbsa.
> >
> >
> >>ew_dipole_recip.o: In function `do_pmesh_dipole_kspace_':
> >>ew_dipole_recip.o(.text+0x5c8): undefined reference to `mpi_barrier_'
> >>ew_dipole_recip.o(.text+0x74e): undefined reference to `mpi_barrier_'
> >>ew_dipole_recip.o(.text+0xa64): undefined reference to `mpi_barrier_'
> >
> >
> > You should check your $LOADLIB variable in config.h: is it actually
pointing
> > to the correct place to find the mpich libraries? Have you previously
> > compiled a parallel sander?
> >
> > There are detailed instructions for setting up mpich here:
> >
> > http://amber.scripps.edu/cluster_info/index.html
> >
> >
> >>set AMBERHOME /usr/local/amber8
> >>set MPICH_HOME /usr/local/mpich
> >
> >
> > I suspect that each of the above should use "setenv" rather than "set".
It
> > may be that AMBERHOME and MPICH_HOME are not really in your environment,
so
> > that the Makefile may not see them.
> >
> >
> >>Also, I am missing the MKL libraries. When I configure, I get
> >>
> >># ./configure -mpich ifc7
> >>AMBERHOME is set to /usr/local/amber8
> >>Setting up Amber configuration file for architecture: ifc7
> >>Using parallel communications library: mpich
> >>MPICH_HOME is set to /usr/local/mpich
> >>The MKL_HOME environment variable is not defined.
> >
> >
> > Again, you need to "setenv" (not just "set") MKL_HOME to point to the
> > location of the MKL libraries on your machine. This is typically (but
not
> > always) in a place like /opt/intel/mkl61.
> >
> > ...good luck...dac
> >
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