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
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Received on Wed Jul 25 2012 - 11:00:02 PDT
