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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Received on Tue May 06 2014 - 05:30:02 PDT
