Re: [AMBER] Amber16 installation error.

From: Abhilash J <md.scfbio.gmail.com>
Date: Fri, 12 Aug 2016 00:36:33 +0530

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/AmberTools/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
>


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Received on Thu Aug 11 2016 - 12:30:02 PDT
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