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
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> _______________________________________________
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>>
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Received on Thu Aug 11 2016 - 14:30:02 PDT
