Hi!
i commented out
# $(PYTHON)
AmberTools/src/fix_conda_fortran.py
# $(PYTHON) fix_conda_fortran.py
In the files you pointed to
and re-ran make install
It still gives error:
make[1]: Leaving directory
`/home/abhilash/amber16/AmberTools/src/nfe-umbrella-slice'
(if [ "no" = "no" ]; then \
make python_serial ;\
fi;\
)
make[1]: 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: 22224 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[1]: *** [parmed] Error 139
make[1]: Leaving directory `/home/abhilash/amber16/AmberTools/src'
make: *** [serial] Error 2
Regards
On Fri, Aug 12, 2016 at 1:46 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> probably you also need to turn it off in $AMBERHOME/Makefile too (search
> for "fix_conda_fortran.py")
>
> Hai
>
> On Thu, Aug 11, 2016 at 4:13 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > I think you're good to go to 'make install' again.
> >
> > Hai
> >
> >
> > On Thu, Aug 11, 2016 at 4:04 PM, Abhilash J <md.scfbio.gmail.com> wrote:
> >
> >> Hi!
> >>
> >> I commented out $(PYTHON) fix_conda_fortran.py and re-ran make
> >> python_seria the last few lines of output were:
> >>
> >> running install
> >> running build
> >> running build_py
> >> copying pytraj/version.py -> build/lib.linux-x86_64-2.7/pytraj
> >> running build_ext
> >> running install_lib
> >> copying build/lib.linux-x86_64-2.7/pytraj/version.py ->
> >> /home/abhilash/amber16/lib/python2.7/site-packages/pytraj
> >> byte-compiling
> >> /home/abhilash/amber16/lib/python2.7/site-packages/pytraj/version.py to
> >> version.pyc
> >> running install_egg_info
> >> Removing
> >> /home/abhilash/amber16/lib/python2.7/site-packages/pytraj-1.
> >> 0.4-py2.7.egg-info
> >> Writing
> >> /home/abhilash/amber16/lib/python2.7/site-packages/pytraj-1.
> >> 0.4-py2.7.egg-info
> >>
> >>
> >> Regards
> >>
> >>
> >>
> >> On Fri, Aug 12, 2016 at 1:22 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >>
> >> > I see now. May be due to "fix_conda_fortran.py".
> >> >
> >> > Can you try to turn if off by changing:
> >> >
> >> > $(PYTHON) fix_conda_fortran.py
> >> >
> >> > to
> >> >
> >> > # $(PYTHON) fix_conda_fortran.py
> >> >
> >> > in "./AmberTools/src/Makefile
> >> >
> >> > and try make python_serial again?
> >> >
> >> > Hai
> >> >
> >> > On Thu, Aug 11, 2016 at 3:45 PM, Abhilash J <md.scfbio.gmail.com>
> >> wrote:
> >> >
> >> > > Hi!
> >> > >
> >> > > Firstly thanks for the patience and prompt replies.
> >> > > I think make python_serial failed.
> >> > > Last few lines of the output were:
> >> > >
> >> > > byte-compiling
> >> > > /home/abhilash/amber16/lib/python2.7/site-packages/pytraj/compat.py
> >> to
> >> > > compat.pyc
> >> > > byte-compiling
> >> > > /home/abhilash/amber16/lib/python2.7/site-packages/pytraj/view.py
> to
> >> > > view.pyc
> >> > > running install_egg_info
> >> > > Writing
> >> > > /home/abhilash/amber16/lib/python2.7/site-packages/
> >> > > pytraj-1.0.4-py2.7.egg-info
> >> > > /home/abhilash/amber16/bin/amber.python fix_conda_fortran.py
> >> > > make: *** [python_serial] Segmentation fault (core dumped)
> >> > >
> >> > > Regards
> >> > >
> >> > >
> >> > >
> >> > > On Fri, Aug 12, 2016 at 1:11 AM, Hai Nguyen <nhai.qn.gmail.com>
> >> wrote:
> >> > >
> >> > > > 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/AmberT
> >> ools/src'
> >> > > > > make[1]: *** [serial] Error 2
> >> > > > > make[1]: Leaving directory `/home/abhilash/amber16/AmberT
> >> ools/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/AmberT
> >> ools/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
> >> > > > > > 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
> >> > > 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 - 13:30:03 PDT
