You can try to find it (by using locate or find or something) and add the
containing directory to LD_LIBRARY_PATH. Other than that, there's no help
we can give.
Do you have a sysadmin you can ask about this? They will be able to help
with this better than we can.
HTH,
Jason
On Wed, Jul 25, 2012 at 11:00 PM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> that gives me even more trouble - is there a way to include the
> missing library into the amber10 installation instead ?
>
> On Wed, Jul 25, 2012 at 12:09 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > 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
> > _______________________________________________
> > 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 - 20:30:02 PDT
