Hi!
I tried "make install" the output is:
byte-compiling
/home/abhilash/amber16/lib/python2.7/site-packages/parmed/gromacs/_gromacsfile.py
to _gromacsfile.pyc
byte-compiling
/home/abhilash/amber16/lib/python2.7/site-packages/parmed/gromacs/__init__.py
to __init__.pyc
running install_scripts
copying build/scripts-2.7/parmed -> /home/abhilash/amber16/bin
copying build/scripts-2.7/xparmed -> /home/abhilash/amber16/bin
changing mode of /home/abhilash/amber16/bin/parmed to 775
changing mode of /home/abhilash/amber16/bin/xparmed to 775
running install_egg_info
Removing
/home/abhilash/amber16/lib/python2.7/site-packages/ParmEd-2.4.0-py2.7.egg-info
Writing
/home/abhilash/amber16/lib/python2.7/site-packages/ParmEd-2.4.0-py2.7.egg-info
/bin/sh: line 1: 12865 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
On Fri, Aug 12, 2016 at 12:42 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> > 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
> > > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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Received on Thu Aug 11 2016 - 12:30:04 PDT
