Re: [AMBER] Problem with Configuring NetCDF

From: Alaa Mohye El-din Soliman <alaa.mohye.aucegypt.edu>
Date: Mon, 11 May 2015 02:05:22 +0300

Thanks for your time and suggestions!
I have fixed the past errors, and finally the configuration completed
successfully. However, after I typed "make install" I get stuck on fixing
the following error, which I got in the middle of the installation process.


>
> gcc -c -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
> -DHASGZ -DHASBZ2 -I/home/alaa/amber12/include -o clusterLib.o
> clusterLib.c

gcc -DSYSV -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/home/alaa/amber12/lib -lpdb
> -larpack -llapack -lblas -lgfortran -w /home/alaa/amber12/lib/libnetcdf.a
> -lm

gcc: error: /home/alaa/amber12/lib/libnetcdf.a: No such file or directory

make[2]: *** [rdparm] Error 1

make[2]: Leaving directory `/home/alaa/amber12/AmberTools/src/ptraj'

make[1]: *** [serial] Error 2

make[1]: Leaving directory `/home/alaa/amber12/AmberTools/src'

make: *** [install] Error 2

alaa.alaa-HP-Pavilion-dv5-Notebook-PC ~/amber12 $


By the way, I checked the path *home/alaa/amber12/lib/* to see whether the
file *libnetcdf.a* is exist, and I found it
I don't know what does this error mean.


On Sat, May 9, 2015 at 10:43 PM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Sat, May 9, 2015 at 3:19 PM, Alaa Mohye El-din Soliman <
> alaa.mohye.aucegypt.edu> wrote:
>
> > The file named "netcdf_config.log" contains the following
> >
> > ./configure2: 1945: ./configure2: ./configure: Permission denied5
> >
>
> ‚ÄčIt looks like something weird happened with your permissions. Make sure
> that the files $AMBERHOME/AmberTools/src/configure2 and
> $AMBERHOME/AmberTools/src/netcdf/src/configure have execute permissions.
>
> HTH,
> Jason
>
> --
> 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 Sun May 10 2015 - 16:30:02 PDT
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