sorry for all troubles you got. I am running out of solutions now.
try:
make clean
make install
I forget to ask about you version info (gcc, gfortran, ... + which Linux
version you are using.)
Hai
On Thu, Aug 11, 2016 at 4:27 PM, Abhilash J <md.scfbio.gmail.com> wrote:
> 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
> > 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 - 14:00:02 PDT
