Hello Jason,
Thank you. Thank you very much. Now it is working.
Sanjib
On Thu, Apr 23, 2015 at 4:20 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, Apr 23, 2015 at 1:49 AM, Sanjib Paul <sanjib88paul.gmail.com>
> wrote:
>
> > Dear all,
> > I am going to install AMBER14 following the page
> > *swails.wikidot.com/installing-amber14-and-ambertools14
> > <http://swails.wikidot.com/installing-amber14-and-ambertools14>.*
> >
> > When I am trying to configure by the command *./configure gnu, *my
> machine
> > could not connect to http://ambermd.org for available patches. But, no
> > other error message has come. And 'the configuration file, config.h, was
> > successfully created'. But to get available patches I set the
> environment
> > variable http_proxy.
> >
> > *export http_proxy="http://username:password@proxyserver:port"*
> >
> > And then I tried to reconfigure by the same command, *./configure gnu.
> > *This
> > time
> > configuration stopped after showing few messages. I could understand most
> > of them. So I am copying those messages here.
> >
> > *Checking for updates...*
> > *Checking for available patches online. This may take a few seconds...*
> >
> > *Available AmberTools 14 patches:*
> >
> > *update.1.bz2, update.2, update.3, update.4, update.5, update.6,
> update.7,
> > update.8, update.9, update.10,*
> > *update.11, update.12, update.13, update.14.bz2, update.15, update.16,
> > update.17, update.18, update.19, update.20,*
> > *update.21, update.22, update.23, update.24, update.25, update.26 *
> >
> > *Available Amber 14 patches:*
> >
> > *update.1, update.2, update.3, update.4, update.5, update.6, update.7,
> > update.8, update.9, update.10,*
> > *update.11 *
> > *There are patches available. Do you want to apply them now? [y/N]
> > (Recommended Y) *
> > *Y*
> > *Preparing to apply updates... please wait.*
> > *Traceback (most recent call last):*
> > * File "./update_amber", line 23, in <module>*
> > * app.mainloop()*
> > * File "/home/software/AMBER14/amber14/updateutils/main.py", line 489,
> in
> > mainloop*
> > * self.update()*
> > * File "/home/software/AMBER14/amber14/updateutils/main.py", line 43, in
> > newfcn*
> > *fcn(self, *args, **kwargs)*
> > * File "/home/software/AMBER14/amber14/updateutils/main.py", line 317,
> in
> > update*
> > * self._update_ambertools()*
> > * File "/home/software/AMBER14/amber14/updateutils/main.py", line 43, in
> > newfcn*
> > * fcn(self, *args, **kwargs)*
> > * File "/home/software/AMBER14/amber14/updateutils/main.py", line 212,
> in
> > _update_ambertools*
> > * last)*
> > * File "/home/software/AMBER14/amber14/updateutils/main.py", line 43, in
> > newfcn*
> > * fcn(self, *args, **kwargs)*
> > * File "/home/software/AMBER14/amber14/updateutils/main.py", line 187,
> in
> > _update_tree*
> > *last = remote.last()*
> > * File "/home/software/AMBER14/amber14/updateutils/repos.py", line 289,
> in
> > last*
> > * self.fill_list()*
> > * File "/home/software/AMBER14/amber14/updateutils/downloader.py", line
> > 104, in new_fcn*
> > * return fcn(*args, **kwargs)*
> > * File "/home/software/AMBER14/amber14/updateutils/repos.py", line 204,
> in
> > fill_list*
> > * p = urlopen(url)*
> > * File "/usr/lib64/python2.6/urllib2.py", line 126, in urlopen*
> > * return _opener.open(url, data, timeout)*
> > * File "/usr/lib64/python2.6/urllib2.py", line 391, in open*
> > * response = self._open(req, data)*
> > * File "/usr/lib64/python2.6/urllib2.py", line 409, in _open*
> > * '_open', req)*
> > * File "/usr/lib64/python2.6/urllib2.py", line 369, in _call_chain*
> > * result = func(*args)*
> > *File "/usr/lib64/python2.6/urllib2.py", line 1190, in http_open*
> > * return self.do_open(httplib.HTTPConnection, req)*
> > * File "/usr/lib64/python2.6/urllib2.py", line 1165, in do_open*
> > * raise URLError(err)*
> > *urllib2.URLError: <urlopen error [Errno 104] Connection reset by peer>*
> > *Automatic patching failed! Check the errors before re-configuring*
> >
>
> The internet connection was interrupted somehow. Try running update_amber
> again:
>
> ./update_amber --update
>
> Try it a couple of times to see if some of the requests get through.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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>
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Received on Thu Apr 23 2015 - 06:30:03 PDT
