cheers - after it was installed everything compiled smoothly - I made
the tests and I keep on getting the warning
warning:regcache incompatible with malloc
warning:regcache incompatible with malloc
warning:regcache incompatible with malloc
warning:regcache incompatible with malloc
all the tests pass though but how serious is this?
On Wed, Jul 25, 2012 at 8:27 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Jul 26 2012 - 19:00:04 PDT
