uhm, very weird. I have never got this. I think the segmentation fault is
from somewhere else.
Can you continue to try
cd $AMBERHOME/AmberTools/src
make python_serial
# successful or not?
# if successful, try
make pysander
# successful or not?
Hopefully someone else knows better about this issue.
Hai
On Thu, Aug 11, 2016 at 3:18 PM, Abhilash J <md.scfbio.gmail.com> wrote:
> 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
> > > > >
> > > > _______________________________________________
> > > > 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 - 13:00:02 PDT
