On Wed, Jan 25, 2012 at 2:48 PM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> 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
>
What do you mean "compile with -static"? What I had meant was to replace
all instances of "mpif90" and "mpicc" with "mpif90 -static" and "mpicc
-static", respectively. Sorry for not making that clear. What happens if
you do that?
>
>
>
> 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
>
> _______________________________________________
> 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 Jan 25 2012 - 12:30:05 PST
