Download AmberTools 12 and install it, along with mpich2 using
configure_mpich2. Then, prepend the AmberTools12 directory to your path
before trying to build Amber 10 in parallel so you end up using the
AmberTools12-compiled-mpich2 instead of the system MPI.
Maybe...
On Wed, Jul 25, 2012 at 1:35 PM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> Hi again,
>
> I fixed the former error but I think there might be an issue with
> libnuma on the cluster
>
> ompi_info | grep libnuma
>
> I get nothing is there a simple workaround here ?
>
> On Wed, Jul 25, 2012 at 10:15 AM, Jorgen Simonsen <jorgen589.gmail.com>
> wrote:
> > Hi
> >
> > I have restarted which gives me new error
> >
> > make clean
> >
> > I load the libraries used
> >
> > module load gcc-openmpi
> >
> > ./configure -mpi gfortran
> >
> > and I change the gfortran variable to mpif90 and I include the path to
> > the mpif.h in the config_amber.h file.
> >
> > the version of mpif90 is mpif90 -v
> >
> > Using built-in specs.
> > Target: x86_64-redhat-linux
> > Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
> > --infodir=/usr/share/info --enable-shared --enable-threads=posix
> > --enable-checking=release --with-system-zlib --enable-__cxa_atexit
> > --disable-libunwind-exceptions --enable-libgcj-multifile
> > --enable-languages=c,c++,objc,obj-c++,java,fortran,ada
> > --enable-java-awt=gtk --disable-dssi --disable-plugin
> > --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre
> > --with-cpu=generic --host=x86_64-redhat-linux
> > Thread model: posix
> > gcc version 4.1.2 20080704 (Red Hat 4.1.2-52)
> >
> >
> > and now I get the following error
> >
> > cd ../netcdf/src; make install
> > make[2]: Entering directory `/home/pgreisen/amber10/src/netcdf/src'
> > Making install in f90
> > make[3]: Entering directory `/home/pgreisen/amber10/src/netcdf/src/f90'
> > /bin/sh ../libtool --mode=compile gfortran -I../libsrc -I. -g -O2 -c
> > -o typeSizes.lo typeSizes.f90
> > libtool: compile: unable to infer tagged configuration
> > libtool: compile: specify a tag with `--tag'
> > make[3]: *** [typeSizes.lo] Error 1
> > make[3]: Leaving directory `/home/pgreisen/amber10/src/netcdf/src/f90'
> > make[2]: *** [install-recursive] Error 1
> > make[2]: Leaving directory `/home/pgreisen/amber10/src/netcdf/src'
> > make[1]: *** [netcdf.mod] Error 2
> > make[1]: Leaving directory `/home/pgreisen/amber10/src/sander'
> > make: *** [parallel] Error 2
> >
> >
> >
> > On Wed, Jul 25, 2012 at 9:30 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >> Hi,
> >>
> >> What compilers (type/version) are you using, and what was your exact
> >> input to configure?
> >>
> >> On Wed, Jul 25, 2012 at 10:18 AM, Jorgen Simonsen <jorgen589.gmail.com>
> wrote:
> >>> /usr/bin/ld: cannot find -lnuma
> >>
> >> I don't think this is an Amber issue - it sounds like a problem with
> >> your MPI compilers. Either the NUMA library is not installed or it's
> >> not in your LD_LIBRARY_PATH. Check your package manager for libnuma.
> >>
> >> -Dan
> >>
> >>> collect2: ld returned 1 exit status
> >>> make[1]: *** [sander.MPI] Error 1
> >>>
> >>> Thanks
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Lab Specialist
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 201
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-9119 (Fax)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jul 25 2012 - 12:30:04 PDT
