Hi!
I do am in trouble but I deeply appreciate the efforts you made to solve
this issue.
Without your help i would not have known what i know now of this issue.
Thanks for that.
The OS specifications are:
gcc version 4.4.6 20110731 (Red Hat 4.4.6-3) (GCC)
CentOS release 6.2 (Final)
I have run make clean. and i am running make install now.
I will post as soon as it is done.
Regards
On Fri, Aug 12, 2016 at 2:06 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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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>
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Received on Thu Aug 11 2016 - 14:00:03 PDT
