On Thu, Oct 31, 2013 at 7:33 AM, Dhananjay <dhananjay.c.joshi.gmail.com>wrote:
> 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
>
Is there a libnetcdf.a in /opt/amber12/lib?
> 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
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 31 2013 - 05:00:03 PDT
