.Vaibhav: it's likely that the updates were not successfully downloaded
(may be because your Python version is quite old (v2.6)).
AMBER then offered to install python2.7 for you. However, you need to
explicit apply the update by yourself in this case
Can you try
*amber.python ./update_amber --update*
*make install* # like Ross said
(do not use "./update_amber" in your case since that script will look for
the old python2.6 existing in your env)
Let us know if there is any issue.
Hai
On Fri, Aug 12, 2016 at 12:32 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Vaibhav,
>
> I don't see anything highlighted in bold here but I also don't see any
> error. It is complaining that your don't have python installed but then you
> say yes to download one which should fix it - does configure finish? If yes
> you should then be good do type 'make'.
>
> All the best
> Ross
>
> > On Aug 11, 2016, at 8:44 PM, Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
> >
> > Dear All,
> > I am trying to install AMBERTOOLS16 on my Linux PC.
> > While following the standard procedure I am getting the following
> message,
> > but I am not sure is it is an error (in bold) which might cause problems
> > later.
> >
> > Is it that an update failed to patch?
> > Please suggest.
> > Thank you.
> >
> >
> > [root.localhost Downloads]# cd amber16/
> > [root.localhost amber16]# ls -arlt
> > total 44
> > -rwxrwxr-x. 1 501 games 1336 Apr 15 05:55 update_amber
> > -rw-rw-r--. 1 501 games 1452 Apr 15 17:57 README
> > -rwxrwxr-x. 1 501 games 2509 Apr 15 17:57 configure
> > drwxrwxr-x. 2 501 games 4096 Apr 15 17:57 updateutils
> > -rw-rw-r--. 1 501 games 3033 Apr 27 21:41 Makefile
> > drwxr-xr-x. 14 vaibhav vaibhav 4096 Aug 11 16:31 ..
> > drwxr-xr-x. 6 root root 4096 Aug 11 16:33 AmberTools
> > drwxrwxr-x. 143 501 games 4096 Aug 11 16:33 test
> > drwxr-xr-x. 13 root root 4096 Aug 11 16:33 dat
> > drwxr-xr-x. 2 root root 4096 Aug 11 16:33 doc
> > drwxr-xr-x. 7 root root 4096 Aug 11 16:33 .
> > [root.localhost amber16]# export AMBERHOME=`pwd`
> > [root.localhost amber16]# ./configure gnu
> > Checking for updates...
> > Checking for available patches online. This may take a few seconds...
> > Checking for available patches online. This may take a few seconds...
> > Traceback (most recent call last):
> > File "./update_amber", line 23, in <module>
> > app.mainloop()
> > File "/home/vaibhav/Downloads/amber16/updateutils/main.py", line 479,
> in
> > mainloop
> > self.check_updates()
> > File "/home/vaibhav/Downloads/amber16/updateutils/main.py", line 171,
> in
> > check_updates
> > self.verbose) + '\n')
> > File "/home/vaibhav/Downloads/amber16/updateutils/repos.py", line 184,
> in
> > patch_details
> > self.fill_list()
> > File "/home/vaibhav/Downloads/amber16/updateutils/downloader.py", line
> > 104, in new_fcn
> > return fcn(*args, **kwargs)
> > File "/home/vaibhav/Downloads/amber16/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 timed out>Check for updates
> > failed.*
> > require Python version 2.7 or >= 3.4
> >
> > No compatible Python installation found. I can download one from
> Continuum
> > via Miniconda with all prerequisites. This will only need to be done
> once.
> > This may take several minutes and will require Internet access.
> > (You can also install missing packages by yourself)
> >
> > Should I do that? [y/n] y
> > Downloading an Amber-compatible Python version 2.7 via Miniconda
> > and installing it. This may take several minutes.
> >
> > ============================================================
> > ====================
> > This script will download and install a version of Python compatible
> > with every component of AmberTools and install all required and optional
> > prerequisites. The Python distribution is downloaded for your operating
> > system from Miniconda.
> >
> > Downloading Python 2.7 Miniconda
> > Detected Linux kernel. Downloading the Linux installer
> > Downloading the latest Miniconda distribution
> > Detected 64-bit Linux
> > --2016-08-11 16:34:32-- https://repo.continuum.io/
> > miniconda/Miniconda-latest-Linux-x86_64.sh
> > Resolving repo.continuum.io... 54.225.68.13, 50.16.198.140,
> 54.225.146.221,
> > ...
> > Connecting to repo.continuum.io|54.225.68.13|:443... connected.
> > HTTP request sent, awaiting response... 200 OK
> > Length: 27208383 (26M) [application/octet-stream]
> > Saving to: “miniconda.sh”
> >
> > 100%[=======================================================
> > ======================================================================>]
> > 27,208,383 199K/s in 2m 14s
> >
> > 2016-08-11 16:36:48 (198 KB/s) - “miniconda.sh” saved [27208383/27208383]
> >
> > Installing Miniconda Python.
> > PREFIX=/home/vaibhav/Downloads/amber16/miniconda
> > installing: _cache-0.0-py27_x0 ...
> > installing: python-2.7.11-0 ...
> > installing: conda-env-2.4.5-py27_0 ...
> > installing: openssl-1.0.2g-0 ...
> > installing: pycosat-0.6.1-py27_0 ...
> > installing: pyyaml-3.11-py27_1 ...
> > installing: readline-6.2-2 ...
> > installing: requests-2.9.1-py27_0 ...
> > installing: sqlite-3.9.2-0 ...
> > installing: tk-8.5.18-0 ...
> > installing: yaml-0.1.6-0 ...
> > installing: zlib-1.2.8-0 ...
> > installing: conda-4.0.5-py27_0 ...
> > installing: pycrypto-2.6.1-py27_0 ...
> > installing: pip-8.1.1-py27_1 ...
> > installing: wheel-0.29.0-py27_0 ...
> > installing: setuptools-20.3-py27_0 ...
> > Python 2.7.11 :: Continuum Analytics, Inc.
> > creating default environment...
> > installation finished.
> > Updating and installing required and optional packages...
> > Fetching package metadata: ....
> > Solving package specifications: .........
> >
> > Package plan for installation in environment /home/vaibhav/Downloads/
> > amber16/miniconda:
> >
> > The following packages will be downloaded:
> >
> > package | build
> > ---------------------------|-----------------
> > nomkl-1.0 | 0 402 B
> > sqlite-3.13.0 | 0 4.0 MB
> > python-2.7.12 | 1 12.1 MB
> > conda-env-2.5.1 | py27_0 26 KB
> > ruamel_yaml-0.11.14 | py27_0 352 KB
> > conda-4.1.11 | py27_0 201 KB
> > ------------------------------------------------------------
> > Total: 16.6 MB
> >
> > The following NEW packages will be INSTALLED:
> >
> > nomkl: 1.0-0
> > ruamel_yaml: 0.11.14-py27_0
> >
> > The following packages will be UPDATED:
> >
> > conda: 4.0.5-py27_0 --> 4.1.11-py27_0
> > conda-env: 2.4.5-py27_0 --> 2.5.1-py27_0
> > python: 2.7.11-0 --> 2.7.12-1
> > sqlite: 3.9.2-0 --> 3.13.0-0
> >
> > Fetching packages ...
> > nomkl-1.0-0.ta 100% |#############################
> > ############################################################
> > ##############################| Time: 0:00:00 351.71 kB/s
> > sqlite-3.13.0- 100% |#############################
> > ############################################################
> > ##############################| Time: 0:00:40 101.75 kB/s
> > python-2.7.12- 100% |#############################
> > ############################################################
> > ##############################| Time: 0:01:14 170.23 kB/s
> > conda-env-2.5. 100% |#############################
> > ############################################################
> > ##############################| Time: 0:00:00 63.07 kB/s
> > ruamel_yaml-0. 100% |#############################
> > ############################################################
> > ##############################| Time: 0:00:03 101.73 kB/s
> > conda-4.1.11-p 100% |#############################
> > ############################################################
> > ##############################| Time: 0:00:01 140.04 kB/s
> > Extracting packages ...
> > [ COMPLETE ]|############################
> > ############################################################
> > ##################################################| 100%
> > Unlinking packages ...
> > [ COMPLETE ]|############################
> > ############################################################
> > ##################################################| 100%
> > Linking packages ...
> > [ COMPLETE ]|############################
> > ############################################################
> > ##################################################| 100%
> > Fetching package metadata .......
> > Solving package specifications: ..........
> >
> > Package plan for installation in environment /home/vaibhav/Downloads/
> > amber16/miniconda:
> >
> > The following packages will be downloaded:
> >
> > package | build
> > ---------------------------|-----------------
> > libgfortran-3.0.0 | 1 281 KB
> > libsodium-1.0.10 | 0 1.2 MB
> > openblas-0.2.14 | 4 3.6 MB
> > zeromq-4.1.4 | 0 4.1 MB
> > backports-1.0 | py27_0 1 KB
> > backports_abc-0.4 | py27_0 5 KB
> > conda-env-2.5.2 | py27_0 26 KB
> > cython-0.24.1 | py27_0 5.3 MB
> > decorator-4.0.10 | py27_0 12 KB
> > functools32-3.2.3.2 | py27_0 15 KB
> > ipython_genutils-0.1.0 | py27_0 32 KB
> > markupsafe-0.23 | py27_2 31 KB
> > mistune-0.7.2 | py27_0 570 KB
> > numpy-1.11.1 | py27_nomkl_0 6.2 MB
> > path.py-8.2.1 | py27_0 45 KB
> > ptyprocess-0.5.1 | py27_0 19 KB
> > pygments-2.1.3 | py27_0 1.2 MB
> > pyzmq-15.4.0 | py27_0 705 KB
> > simplegeneric-0.8.1 | py27_1 7 KB
> > six-1.10.0 | py27_0 16 KB
> > wcwidth-0.1.7 | py27_0 21 KB
> > configparser-3.5.0 | py27_0 31 KB
> > get_terminal_size-1.0.0 | py27_0 4 KB
> > jinja2-2.8 | py27_1 264 KB
> > jsonschema-2.5.1 | py27_0 55 KB
> > pathlib2-2.1.0 | py27_0 26 KB
> > pexpect-4.0.1 | py27_0 63 KB
> > prompt_toolkit-1.0.3 | py27_0 295 KB
> > scipy-0.18.0 |np111py27_nomkl_0 31.0 MB
> > singledispatch-3.4.0.3 | py27_0 12 KB
> > ssl_match_hostname-3.4.0.2 | py27_1 6 KB
> > traitlets-4.2.2 | py27_0 108 KB
> > entrypoints-0.2.2 | py27_0 6 KB
> > jupyter_core-4.1.0 | py27_0 51 KB
> > pickleshare-0.7.3 | py27_0 8 KB
> > tornado-4.4.1 | py27_0 552 KB
> > ipython-5.0.0 | py27_0 933 KB
> > jupyter_client-4.3.0 | py27_0 96 KB
> > nbformat-4.0.1 | py27_0 112 KB
> > terminado-0.6 | py27_0 18 KB
> > ipykernel-4.3.1 | py27_0 117 KB
> > nbconvert-4.2.0 | py27_0 310 KB
> > notebook-4.2.2 | py27_0 5.0 MB
> > ------------------------------------------------------------
> > Total: 62.3 MB
> >
> > The following NEW packages will be INSTALLED:
> >
> > backports: 1.0-py27_0
> > backports_abc: 0.4-py27_0
> > configparser: 3.5.0-py27_0
> > cython: 0.24.1-py27_0
> > decorator: 4.0.10-py27_0
> > entrypoints: 0.2.2-py27_0
> > functools32: 3.2.3.2-py27_0
> > get_terminal_size: 1.0.0-py27_0
> > ipykernel: 4.3.1-py27_0
> > ipython: 5.0.0-py27_0
> > ipython_genutils: 0.1.0-py27_0
> > jinja2: 2.8-py27_1
> > jsonschema: 2.5.1-py27_0
> > jupyter_client: 4.3.0-py27_0
> > jupyter_core: 4.1.0-py27_0
> > libgfortran: 3.0.0-1
> > libsodium: 1.0.10-0
> > markupsafe: 0.23-py27_2
> > mistune: 0.7.2-py27_0
> > nbconvert: 4.2.0-py27_0
> > nbformat: 4.0.1-py27_0
> > notebook: 4.2.2-py27_0
> > numpy: 1.11.1-py27_nomkl_0 [nomkl]
> > openblas: 0.2.14-4
> > path.py: 8.2.1-py27_0
> > pathlib2: 2.1.0-py27_0
> > pexpect: 4.0.1-py27_0
> > pickleshare: 0.7.3-py27_0
> > prompt_toolkit: 1.0.3-py27_0
> > ptyprocess: 0.5.1-py27_0
> > pygments: 2.1.3-py27_0
> > pyzmq: 15.4.0-py27_0
> > scipy: 0.18.0-np111py27_nomkl_0 [nomkl]
> > simplegeneric: 0.8.1-py27_1
> > singledispatch: 3.4.0.3-py27_0
> > six: 1.10.0-py27_0
> > ssl_match_hostname: 3.4.0.2-py27_1
> > terminado: 0.6-py27_0
> > tornado: 4.4.1-py27_0
> > traitlets: 4.2.2-py27_0
> > wcwidth: 0.1.7-py27_0
> > zeromq: 4.1.4-0
> >
> > The following packages will be UPDATED:
> >
> > conda-env: 2.5.1-py27_0 --> 2.5.2-py27_0
> >
> > Fetching packages ...
> > libgfortran-3. 100% |#############################
> > ############################################################
> > ##############################| Time: 0:00:03 93.87 kB/s
> > libsodium-1.0. 100% |#############################
> > ############################################################
> > ##############################| Time: 0:00:15 79.69 kB/s
> > openblas-0.2.1 100% |#############################
> > ############################################################
> > ##############################| Time: 0:00:23 161.98 kB/s
> >
> > --
> > With Regards.
> >
> > Dr. Vaibhav A. Dixit, (M.S. and Ph.D.: NIPER, Postdoc: AstraZeneca, UK
> and
> > IISc, Bangalore)
> > Associate Professor,
> > Department of Pharmaceutical Chemistry,
> > School of Pharmacy & Technology Management,
> > SVKM's NMIMS,
> > Mukesh Patel Technology Park
> > Babulde, Bank of Tapi River,
> > Mumbai-Agra Road,
> > Shirpur, Dist. Dhule -425405
> > India.
> > Email: vaibhav.dixit.nmims.edu
> > www.nmims.edu
> >
> > http://pharmacy-shirpur.nmims.edu/faculty-and-research/
> > faculty/dr-vaibhav-dixit/
> >
> >
> > +91-7709129400.
> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> >
> > Please consider the environment before printing this e-mail
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Aug 11 2016 - 22:30:03 PDT
