wow, congrats. cheers.
Hai
On Thu, Aug 11, 2016 at 5:00 PM, Abhilash J <md.scfbio.gmail.com> wrote:
> Hi!
>
> I got this message after make clean followed by make install. (I do not
> have amber16 license)
>
> 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
> make[2]: Leaving directory `/home/abhilash/amber16/AmberTools/src'
>
> Installation of AmberTools16 serial is complete at Fri Aug 12 01:03:08 IST
> 2016.
>
> make[1]: Leaving directory `/home/abhilash/amber16/AmberTools/src'
> ==============================================================
> /home/abhilash/amber16/src/Makefile not found, or -noamber was set.
> This is expected if you do not have Amber16.
> ==============================================================
>
> Regards
>
> On Fri, Aug 12, 2016 at 2:14 AM, Abhilash J <md.scfbio.gmail.com> wrote:
>
> > 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/amb
> >> er.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
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Received on Thu Aug 11 2016 - 14:30:03 PDT
