Jason,
many thanks for suggestions. Indeed I've used "sudo make install" because
"make install" results in the
/usr/bin/ld: cannot find -lstdc++
collect2: error: ld returned 1 exit status
(this error have been fixed on another debian machine during amber
installation by using sudo make install)
James
2014-05-06 16:05 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Tue, 2014-05-06 at 11:09 +0400, James Starlight wrote:
> > Dear Amber Users!
> >
> > I've faced with the problem during compilation of amber tools-14 on one
> of
> > my debian machine (I've do such task both from regular and root user)
>
> I strongly recommend you never use root to install Amber... ever (that
> includes using "sudo"). If you get "Permission denied" errors when you
> try to build Amber, use "sudo chown -R <user>:<group> /path/to/amber14"
> to change the ownership to you (<user> should be your username and
> <group> should be the group you want that directory assigned to --
> possibly also your username).
>
> > export AMBERHOME=/home/own/amber14/
> > ./configure gnu
> > source amber.sh
> > make install
> >
> >
> > results in the
> >
> > make[2]: Leaving directory `/home/own/amber14/AmberTools/src/rism'
> > (cd nab && make install )
> > make[2]: Entering directory `/home/own/amber14/AmberTools/src/nab'
> > gcc -DCC='"gcc"' -DCPP='"ucpp -l"' -DFLIBS='"-lsff -lpbsa -lrism -lfftw3
> > -larpack -llapack -lblas -lnetcdf -lgfortran -w "' \
> > -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
> > -DHASGZ -DHASBZ2 \
> > -o /home/own/amber14/bin/nab nab.c
> > /home/own/amber14/bin/nab -c allatom_to_dna3.nab
> > AMBERHOME is not set!
> > make[2]: *** [allatom_to_dna3.o] Error 1
> > make[2]: Leaving directory `/home/own/amber14/AmberTools/src/nab'
> > make[1]: *** [serial] Error 2
> > make[1]: Leaving directory `/home/own/amber14/AmberTools/src'
> >
> >
> > Also I've defined AMBERHOME In .bashrc and checked it
> >
> > own.arrakis ~ $ cd $AMBERHOME
> > own.arrakis ~/amber14
> >
> > How it could be fixed?
>
> Are you using "sudo" when you install? The only two ways I've seen this
> problem occur is either
>
> a) You used "sudo make install" instead of just "make install", and the
> "sudo" command basically trashes your environment (unsetting environment
> variables).
>
> b) You did not make AMBERHOME part of the environment; the command "set
> AMBERHOME=/home/own/amber" will make it seem like AMBERHOME is an
> environment variable. i.e., "cd $AMBERHOME" and "echo $AMBERHOME" will
> both appear to work correctly, but "printenv | grep AMBERHOME" will not
> indicate that AMBERHOME is set.
>
> My suspicion is that (a) is happening.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 06 2014 - 07:30:05 PDT
