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
Received on Thu Aug 11 2016 - 13:30:03 PDT
