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/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
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> > > > > > > > >
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> > > > > > >
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> > > > > > >
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Received on Thu Aug 11 2016 - 13:30:02 PDT
