gfortran -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info
--with-bugurl=
http://bugzilla.redhat.com/bugzilla --enable-bootstrap
--enable-shared --enable-threads=posix --enable-checking=release
--with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-gnu-unique-object
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada
--enable-java-awt=gtk --disable-dssi
--with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre
--enable-libgcj-multifile --enable-java-maintainer-mode
--with-ecj-jar=/usr/share/java/eclipse-ecj.jar
--disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic
--with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.5 20110214 (Red Hat 4.4.5-6) (GCC)
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info
--with-bugurl=
http://bugzilla.redhat.com/bugzilla --enable-bootstrap
--enable-shared --enable-threads=posix --enable-checking=release
--with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-gnu-unique-object
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada
--enable-java-awt=gtk --disable-dssi
--with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre
--enable-libgcj-multifile --enable-java-maintainer-mode
--with-ecj-jar=/usr/share/java/eclipse-ecj.jar
--disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic
--with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.5 20110214 (Red Hat 4.4.5-6) (GCC)
I added the -static to the mpif90 in the config.h file but this adds a
new error
../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
../lib/nxtsec.o ../lib/sys.a mt19937.o ncsu-abmd-hooks.o
ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o ncsu-colvar-math.o
ncsu-colvar-type.o ncsu-colvar-utils.o ncsu-colvar.o ncsu-constants.o
ncsu-cv-ANGLE.o ncsu-cv-DISTANCE.o ncsu-cv-HANDEDNESS.o
ncsu-cv-MULTI_RMSD.o ncsu-cv-N_OF_BONDS.o ncsu-cv-N_OF_STRUCTURES.o
ncsu-cv-R_OF_GYRATION.o ncsu-cv-TORSION.o ncsu-lexer.o ncsu-parser.o
ncsu-pmd-hooks.o ncsu-rmsd.o ncsu-sander-hooks.o ncsu-sander-proxy.o
ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o
../netcdf/lib/libnetcdf.a -L/opt/SUNWhpc/HPC8.2.1c/gnu/include/lib64
/usr/bin/ld: cannot find -lmpi
collect2: ld returned 1 exit status
make[1]: *** [sander.MPI] Error 1
Thanks
On Wed, Jan 25, 2012 at 9:04 PM, Jason Swails <jason.swails.gmail.com> wrote:
> Do you have gfortran? If so, what version is it? (And what version is gcc
> and g++, also?)
>
> 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
>>
>>
>>
>> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
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Received on Wed Jan 25 2012 - 12:30:06 PST
