Hi,
can you try to
cd $AMBERHOME/AmberTools/src
make parmed
and attach the output?
PS: or paste your output here: https://gist.github.com/
Hai
On Thu, Aug 11, 2016 at 10:55 AM, Abhilash J <md.scfbio.gmail.com> wrote:
> Hi everyone!
>
> I am trying to install amber tools 16 but am getting error in the "make
> install" step.
> I am trying a serial build with gnu (./compile gnu).
> I allowed the updates and other downloads that amber tools16 asked for.
> To best of my knowledge there was no previous error.
> I did source amber.sh (as we have bash) before install step.
> I tried searching but was unable to solve the issue. If i have missed
> some post which could be of help, please let me know.
> We already have amber14 working on the same machine.
> I am pasting the last few lines before the error.
> Please help.
>
> g++ -DHAVE_CONFIG_H -I. -I/home/abhilash/amber16/include -fPIC -c -o
> umbrella.o umbrella.cc
> g++ -DHAVE_CONFIG_H -I. -I/home/abhilash/amber16/include -fPIC -c -o
> dimension.o dimension.cc
> g++ -DHAVE_CONFIG_H -I. -I/home/abhilash/amber16/include -fPIC -c -o
> utils.o utils.cc
> g++ -DHAVE_CONFIG_H -I. -I/home/abhilash/amber16/include -fPIC -c -o
> main.o main.cc
> g++ -fPIC -o nfe-umbrella-slice umbrella.o dimension.o utils.o main.o
> /home/abhilash/amber16/lib/libnetcdf.a
> mv nfe-umbrella-slice /home/abhilash/amber16/bin
> make[2]: Leaving directory
> `/home/abhilash/amber16/AmberTools/src/nfe-umbrella-slice'
> (if [ "no" = "no" ]; then \
> make python_serial ;\
> fi;\
> )
> make[2]: Entering directory `/home/abhilash/amber16/AmberTools/src'
> (cd parmed && /home/abhilash/amber16/bin/amber.python setup.py install
> --no-setuptools -f --prefix=/home/abhilash/amber16
> --install-scripts=/home/abhilash/amber16/bin)
> /bin/sh: line 1: 15298 Segmentation fault (core dumped)
> /home/abhilash/amber16/bin/amber.python setup.py install --no-setuptools
> -f
> --prefix=/home/abhilash/amber16 --install-scripts=/home/
> abhilash/amber16/bin
> make[2]: *** [parmed] Error 139
> make[2]: Leaving directory `/home/abhilash/amber16/AmberTools/src'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory `/home/abhilash/amber16/AmberTools/src'
> make: *** [install] Error 2
>
> regards
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Aug 11 2016 - 12:00:04 PDT
