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)
>> >>
>> >> _______________________________________________
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>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
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>> 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
