Sorry, it does not work.
The output is as follows:
make[3]: Leaving directory `/opt/amber12/AmberTools/src/ptraj/pdb'
cd ../arpack && make
make[3]: Entering directory `/opt/amber12/AmberTools/src/arpack'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/opt/amber12/AmberTools/src/arpack'
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
-DHASBZ2 \
-o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o io.o
trajectory.o netcdf_ptraj.o parallel_ptraj.o evec.o torsion.o mask.o rms.o
display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o
thermo.o pubfft.o cluster.o clusterLib.o -L/opt/amber12/lib -lpdb -larpack
-llapack -lblas -lgfortran -w -L/opt/amber12/lib -lnetcdf -lm
/usr/bin/ld: cannot find -lnetcdf
collect2: error: ld returned 1 exit status
make[2]: *** [rdparm] Error 1
make[2]: Leaving directory `/opt/amber12/AmberTools/src/ptraj'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/opt/amber12/AmberTools/src'
make: *** [install] Error 2
-- Joshi
On Thu, Oct 31, 2013 at 7:22 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Oct 31, 2013 at 7:07 AM, Dhananjay <dhananjay.c.joshi.gmail.com
> >wrote:
>
> > Thank you for the suggestions.
> > Unfortunately, I don't have Intel compiles right now, therefore, tried
> > installation with gnu.
> >
> > The argument I gave to configure is: ./configure gnu
> >
> > As per the David's suggestion, I make uninstall and then configured and
> > compiled again with the above argument.
> > Following is the error message I got:
> >
> > Warning: Type mismatch in argument 'c' at (1); passed COMPLEX(8) to
> REAL(8)
> > gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
> > -DHASBZ2 -I/opt/amber12/include -o cluster.o cluster.c
> > gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
> > -DHASBZ2 -I/opt/amber12/include -o clusterLib.o clusterLib.c
> > gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
> > -DHASBZ2 \
> > -o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o
> io.o
> > trajectory.o netcdf_ptraj.o parallel_ptraj.o evec.o torsion.o mask.o
> rms.o
> > display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o
> > thermo.o pubfft.o cluster.o clusterLib.o -L/opt/amber12/lib -lpdb
> -larpack
> > -llapack -lblas -lgfortran -w -L/opt/amber12/lib -lnetcdf -lm
> > /usr/bin/ld: cannot find -lnetcdf
> >
>
> Try deleting the netcdf.mod file and then recompiling.
>
> cd /opt/amber12
> rm include/netcdf.mod
> make install
>
> Does that work?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Oct 31 2013 - 05:00:03 PDT
