On Thu, Oct 31, 2013 at 7:41 AM, Dhananjay <dhananjay.c.joshi.gmail.com>wrote:
> not found in /opt/amber12/lib but it is in /opt/amber12/lib64
>
Ah. This would be a problem. Copy all of the files from
/opt/amber12/lib64 into /opt/amber12/lib and it should work:
cp /opt/amber12/lib64/* /opt/amber12/lib
These should probably be simlinked to each other...
Thanks for the report,
Jason
>
>
>
>
> On Thu, Oct 31, 2013 at 7:36 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > 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
> > _______________________________________________
> > 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 - 06:30:04 PDT
