> make[2]: *** [parmed] Error 139
from this original error, I thought the installation had trouble with
ParmEd (which suprised me since ParmEd is pure Python).
Looking at you output.txt, you were able to install ParmEd without any
error.
Can you try
cd $AMBERHOME
make install
again to see what happens next.
Hai
On Thu, Aug 11, 2016 at 3:06 PM, Abhilash J <md.scfbio.gmail.com> wrote:
> Hi!
>
> I tried https://gist.github.com/ but i am new to it. I will try to get
> a
> hang of it. Till then i am attaching it to this mail as output.
> The output of ParmEd-2.4.0-py2.7.egg-info is:
>
> Metadata-Version: 1.0
> Name: ParmEd
> Version: 2.4.0
> Summary: Amber parameter file editor
> Home-page: http://jswails.wikidot.com/parmed
> Author: Jason Swails
> Author-email: jason.swails -at- gmail.com
> License: LGPL (or GPL if released with AmberTools)
> Description: UNKNOWN
> Platform: UNKNOWN
>
> Let me know if some other info is also required.
> In the meanwhile i will go and understand how https://gist.github.com/
> works. Hopefully it will be helpful in future.
> Thanks for help.
>
>
> Regards
>
>
> On Fri, Aug 12, 2016 at 12:24 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > 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
> > > _______________________________________________
> > > 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
> >
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Aug 11 2016 - 12:30:03 PDT
