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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Received on Thu Apr 23 2015 - 04:00:03 PDT
