ok I am not quite sure where to add it
so if I compile with -static I get the following error
Configuring netcdf; (may be time-consuming)
configure: WARNING: No F90 compiler found. F90 API will not be built.
configure: error: Could not link conftestf.o and conftest.o
netcdf configure returned 1
NETCDF configure failed! Check the netcdf_config.log file
On Wed, Jan 25, 2012 at 8:23 PM, Jason Swails <jason.swails.gmail.com> wrote:
> Hmm... can you try adding the "-static" flag to the end of the "mpif90"
> lines in the config.h file (which will hopefully force static linking).
> The shared library libgfortran.so.1 is not available (at least not in the
> standard library paths or anywhere specified by LD_LIBRARY_PATH) wherever
> you are trying to run, but it was linked into the executable (which is why
> you are getting this error message). You'll have to recompile if you
> choose this route.
>
> Alternatively, if you can find this library file (libgfortran.so.1), you
> can add that directory to your LD_LIBRARY_PATH like so:
>
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH\:/folder/containing/lib/
>
> This shouldn't happen in general if "gfortran" is the same on the node that
> you compiled it on as it is on the node that you're trying to run on.
>
> HTH,
> Jason
>
> On Wed, Jan 25, 2012 at 2:09 PM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
>
>> it returns the following
>>
>> opt/SUNWhpc/HPC8.2.1c/gnu/bin/mpif90 -show
>> gfortran -I/opt/SUNWhpc/HPC8.2.1c/gnu/include/64
>> -I/opt/SUNWhpc/HPC8.2.1c/gnu/lib/lib64 -Wl,--enable-new-dtags
>> -Wl,-rpath,/opt/mx/lib/lib64
>> -Wl,-rpath,/opt/SUNWhpc/HPC8.2.1c/gnu/lib/lib64
>> -I/opt/SUNWhpc/HPC8.2.1c/gnu/lib/lib64
>> -J/opt/SUNWhpc/HPC8.2.1c/gnu/lib/lib64
>> -L/opt/SUNWhpc/HPC8.2.1c/gnu/lib/lib64 -lmpi -lopen-rte -lopen-pal
>> -lnsl -lrt -lm -ldl -lutil -lpthread -lmpi_f77 -lmpi_f90
>>
>> On Wed, Jan 25, 2012 at 6:56 PM, Jason Swails <jason.swails.gmail.com>
>> wrote:
>> > What does
>> >
>> > /opt/SUNWhpc/HPC8.2.1c/gnu/bin/mpif90 -show
>> >
>> > return?
>> >
>> > All the best,
>> > Jason
>> >
>> > On Wed, Jan 25, 2012 at 12:18 PM, Jorgen Simonsen <jorgen589.gmail.com
>> >wrote:
>> >
>> >> hi all
>> >>
>> >> I have compiled amber10 with the following settings
>> >>
>> >> ./configure_amber -intelmpi -static gfortran
>> >>
>> >> and it compiles fine but when I try to test it I get the following error
>> >>
>> >> export DO_PARALLEL='mpirun -np 2'
>> >> make test.parallel
>> >>
>> >> sander.MPI: error while loading shared libraries: libgfortran.so.1:
>> >> cannot open shared object file: No such file or directory
>> >> ./Run.cytosine: Program error
>> >> make[1]: *** [test.sander.BASIC] Error 1
>> >>
>> >> my config_amber is like this
>> >>
>> >> # C compiler
>> >>
>> >>
>> #------------------------------------------------------------------------------
>> >> CC= gcc
>> >> CPLUSPLUS=g++
>> >> CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m64
>> >> $(AMBERBUILDFLAGS)
>> >> CPPFLAGS= -DBINTRAJ -I../netcdf/include $(AMBERBUILDFLAGS)
>> >>
>> >>
>> >>
>> #------------------------------------------------------------------------------
>> >> # Fortran preprocessing and compiler.
>> >> # FPPFLAGS holds the main Fortran options, such as whether MPI is used.
>> >>
>> >>
>> #------------------------------------------------------------------------------
>> >> FPPFLAGS= -I/opt/SUNWhpc/HPC8.2.1c/gnu/include/ -P -DBINTRAJ -DMPI
>> >> $(AMBERBUILDFLAGS)
>> >> FPP= cpp -traditional $(FPPFLAGS)
>> >> FC= /opt/SUNWhpc/HPC8.2.1c/gnu/bin/mpif90
>> >> FFLAGS= -O0 -fno-range-check -fno-second-underscore $(LOCALFLAGS)
>> >> $(AMBERBUILDFLAGS)
>> >> FOPTFLAGS= -O3 -fno-range-check -fno-second-underscore $(LOCALFLAGS)
>> >> $(AMBERBUILDFLAGS)
>> >> FREEFORMAT_FLAG= -ffree-form
>> >>
>> >>
>> >>
>> #------------------------------------------------------------------------------
>> >> # Loader:
>> >>
>> >>
>> #------------------------------------------------------------------------------
>> >> LOAD= /opt/SUNWhpc/HPC8.2.1c/gnu/bin/mpif90 $(LOCALFLAGS)
>> >> $(AMBERBUILDFLAGS)
>> >> LOADCC= gcc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
>> >> LOADLIB=
>> >> LM= -lm
>> >> XHOME= /usr/X11R6
>> >> XLIBS= -L/usr/X11R6/lib64 -L/usr/X11R6/lib
>> >>
>> >>
>> >>
>> #------------------------------------------------------------------------------
>> >> :
>> >>
>> >> _______________________________________________
>> >> 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 Wed Jan 25 2012 - 12:30:03 PST
