Hi All,
It looks like this problem also extends to issues with connectivity - e.g. turn off my internet (or have a firewall) - working on a plane etc.
Rosss-MacBook:amber_master rcw$ ./configure -cuda gnu
Checking for updates...
Checking for available patches online. This may take a few seconds...
NoInternetAccess: Cannot connect to http://ambermd.org
Check for updates failed.
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 Mac OS X operating system. Downloading the Mac installer
Downloading the latest Miniconda distribution
curl: (6) Could not resolve host: repo.continuum.io
Installing Miniconda Python.
Updating and installing required and optional packages...
./configure_python: line 152: /Users/rcw/Desktop/amber_master/miniconda/bin/conda: No such file or directory
Error occurred during Python install:
Updating existing packages
Problem installing Miniconda... see error above.
Configure failed due to the errors above!
/fail....
Can we fix this please.
ps. is this going to work on things like a Cray - or IBM Power 8 system? I am concerned how fragile this is going to be and it looks lie the failures are fatal which is not good.
All the best
Ross
> On Jan 28, 2016, at 15:59, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> Hi All,
>
> I just pulled the latest AMBER git tree and I run ./configure -cuda gnu and the following happens
>
> Rosss-MacBook:amber_master rcw$ ./configure -cuda gnu
> Checking for updates...
> Checking for available patches online. This may take a few seconds...
>
> Available AmberTools 16 patches:
>
> No patches available
>
> Available Amber 16 patches:
>
> No patches available
> 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 Mac OS X operating system. Downloading the Mac installer
> Downloading the latest Miniconda distribution
> ######################################################################## 100.0%
> Installing Miniconda Python.
> PREFIX=/Users/rcw/Desktop/amber_master/miniconda
> installing: _cache-0.0-py27_x0 ...
> installing: python-2.7.11-0 ...
> installing: conda-env-2.4.5-py27_0 ...
> installing: openssl-1.0.2d-0 ...
> installing: pycosat-0.6.1-py27_0 ...
> installing: pyyaml-3.11-py27_1 ...
> installing: readline-6.2-2 ...
> installing: requests-2.9.0-py27_0 ...
> installing: sqlite-3.8.4.1-1 ...
> installing: tk-8.5.18-0 ...
> installing: yaml-0.1.6-0 ...
> installing: zlib-1.2.8-0 ...
> installing: conda-3.19.0-py27_0 ...
> installing: pycrypto-2.6.1-py27_0 ...
> installing: pip-7.1.2-py27_0 ...
> installing: wheel-0.26.0-py27_1 ...
> installing: setuptools-18.8.1-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 /Users/rcw/Desktop/amber_master/miniconda:
>
> The following packages will be downloaded:
>
> package | build
> ---------------------------|-----------------
> openssl-1.0.2e | 0 3.0 MB
> sqlite-3.9.2 | 0 1.2 MB
> requests-2.9.1 | py27_0 604 KB
> setuptools-19.4 | py27_0 365 KB
> pip-8.0.1 | py27_0 1.5 MB
> ------------------------------------------------------------
> Total: 6.7 MB
>
> The following packages will be UPDATED:
>
> openssl: 1.0.2d-0 --> 1.0.2e-0
> pip: 7.1.2-py27_0 --> 8.0.1-py27_0
> requests: 2.9.0-py27_0 --> 2.9.1-py27_0
> setuptools: 18.8.1-py27_0 --> 19.4-py27_0
> sqlite: 3.8.4.1-1 --> 3.9.2-0
>
> Fetching packages ...
> openssl-1.0.2e 100% |############################################################################################| Time: 0:00:04 769.87 kB/s
> sqlite-3.9.2-0 100% |############################################################################################| Time: 0:00:04 273.01 kB/s
> requests-2.9.1 100% |############################################################################################| Time: 0:00:03 189.55 kB/s
> setuptools-19. 100% |############################################################################################| Time: 0:00:01 312.14 kB/s
> pip-8.0.1-py27 100% |############################################################################################| Time: 0:00:06 244.15 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 /Users/rcw/Desktop/amber_master/miniconda:
>
> The following packages will be downloaded:
>
> package | build
> ---------------------------|-----------------
> libpng-1.6.17 | 0 184 KB
> freetype-2.5.5 | 0 732 KB
> appnope-0.1.0 | py27_0 4 KB
> backports_abc-0.4 | py27_0 5 KB
> cython-0.23.4 | py27_1 2.2 MB
> decorator-4.0.6 | py27_0 11 KB
> ipython_genutils-0.1.0 | py27_0 32 KB
> jsonschema-2.4.0 | py27_0 51 KB
> markupsafe-0.23 | py27_0 22 KB
> mistune-0.7.1 | py27_0 173 KB
> numpy-1.10.2 | py27_0 3.0 MB
> path.py-8.1.2 | py27_1 45 KB
> pexpect-3.3 | py27_0 60 KB
> ptyprocess-0.5 | py27_0 19 KB
> pygments-2.0.2 | py27_0 1.0 MB
> pyparsing-2.0.3 | py27_0 63 KB
> python.app-1.2 | py27_4 7 KB
> pytz-2015.7 | py27_0 174 KB
> pyzmq-15.2.0 | py27_0 650 KB
> qt-4.8.7 | 1 39.0 MB
> simplegeneric-0.8.1 | py27_0 6 KB
> sip-4.16.9 | py27_0 234 KB
> six-1.10.0 | py27_0 16 KB
> ssl_match_hostname-3.4.0.2 | py27_0 6 KB
> cycler-0.9.0 | py27_0 6 KB
> jinja2-2.8 | py27_0 263 KB
> pickleshare-0.5 | py27_0 8 KB
> pyqt-4.11.4 | py27_1 4.0 MB
> python-dateutil-2.4.2 | py27_0 219 KB
> scipy-0.16.1 | np110py27_0 11.8 MB
> singledispatch-3.4.0.3 | py27_0 12 KB
> traitlets-4.1.0 | py27_0 104 KB
> ipython-4.0.3 | py27_0 917 KB
> jupyter_core-4.0.6 | py27_0 48 KB
> matplotlib-1.5.1 | np110py27_0 5.9 MB
> pandas-0.17.1 | np110py27_0 6.3 MB
> tornado-4.3 | py27_0 542 KB
> jupyter_client-4.1.1 | py27_0 89 KB
> nbformat-4.0.1 | py27_0 112 KB
> terminado-0.5 | py27_1 17 KB
> ipykernel-4.2.2 | py27_0 113 KB
> nbconvert-4.1.0 | py27_0 273 KB
> notebook-4.1.0 | py27_0 4.4 MB
> ------------------------------------------------------------
> Total: 82.8 MB
>
> The following NEW packages will be INSTALLED:
>
> appnope: 0.1.0-py27_0
> backports_abc: 0.4-py27_0
> cycler: 0.9.0-py27_0
> cython: 0.23.4-py27_1
> decorator: 4.0.6-py27_0
> freetype: 2.5.5-0
> ipykernel: 4.2.2-py27_0
> ipython: 4.0.3-py27_0
> ipython_genutils: 0.1.0-py27_0
> jinja2: 2.8-py27_0
> jsonschema: 2.4.0-py27_0
> jupyter_client: 4.1.1-py27_0
> jupyter_core: 4.0.6-py27_0
> libpng: 1.6.17-0
> markupsafe: 0.23-py27_0
> matplotlib: 1.5.1-np110py27_0
> mistune: 0.7.1-py27_0
> nbconvert: 4.1.0-py27_0
> nbformat: 4.0.1-py27_0
> notebook: 4.1.0-py27_0
> numpy: 1.10.2-py27_0
> pandas: 0.17.1-np110py27_0
> path.py: 8.1.2-py27_1
> pexpect: 3.3-py27_0
> pickleshare: 0.5-py27_0
> ptyprocess: 0.5-py27_0
> pygments: 2.0.2-py27_0
> pyparsing: 2.0.3-py27_0
> pyqt: 4.11.4-py27_1
> python-dateutil: 2.4.2-py27_0
> python.app: 1.2-py27_4
> pytz: 2015.7-py27_0
> pyzmq: 15.2.0-py27_0
> qt: 4.8.7-1
> scipy: 0.16.1-np110py27_0
> simplegeneric: 0.8.1-py27_0
> singledispatch: 3.4.0.3-py27_0
> sip: 4.16.9-py27_0
> six: 1.10.0-py27_0
> ssl_match_hostname: 3.4.0.2-py27_0
> terminado: 0.5-py27_1
> tornado: 4.3-py27_0
> traitlets: 4.1.0-py27_0
>
> Fetching packages ...
> libpng-1.6.17- 100% |############################################################################################| Time: 0:00:01 114.11 kB/s
> freetype-2.5.5 100% |############################################################################################| Time: 0:00:01 417.08 kB/s
> appnope-0.1.0- 100% |############################################################################################| Time: 0:00:00 2.89 MB/s
> backports_abc- 100% |############################################################################################| Time: 0:00:00 1.18 MB/s
> cython-0.23.4- 100% |############################################################################################| Time: 0:00:08 279.05 kB/s
> decorator-4.0. 100% |############################################################################################| Time: 0:00:00 822.65 kB/s
> ipython_genuti 100% |############################################################################################| Time: 0:00:00 61.72 kB/s
> jsonschema-2.4 100% |############################################################################################| Time: 0:00:00 181.55 kB/s
> markupsafe-0.2 100% |############################################################################################| Time: 0:00:00 3.77 MB/s
> mistune-0.7.1- 100% |############################################################################################| Time: 0:00:01 159.75 kB/s
> numpy-1.10.2-p 100% |############################################################################################| Time: 0:00:15 202.20 kB/s
> path.py-8.1.2- 100% |############################################################################################| Time: 0:00:00 65.80 kB/s
> pexpect-3.3-py 100% |############################################################################################| Time: 0:00:00 84.27 kB/s
> ptyprocess-0.5 100% |############################################################################################| Time: 0:00:00 271.97 kB/s
> pygments-2.0.2 100% |############################################################################################| Time: 0:00:02 385.77 kB/s
> pyparsing-2.0. 100% |############################################################################################| Time: 0:00:00 109.67 kB/s
> python.app-1.2 100% |######################################################################################
>
> etc etc -- I aborted it at this point...
>
> What is going on here? Should we downloading all this stuff and installing it? It seems like this could be a serious security concern for some people and also extremely fragile.
>
> It also polutes the git tree and a make clean / make dist clean does not clear this up.
>
> In my opinion we really really really should not be depending on tons of external libraries and the configure script in AMBER should definitely NOT be connecting to any external sites EXCEPT ambermd.org.
>
> It also should not be doing this for a configure that does not involve an AMBERTools build.
>
> Comments?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Associate Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Associate Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.
>
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Received on Thu Jan 28 2016 - 06:30:03 PST
