User Tools

Site Tools


python

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
python [2017/04/25 17:43]
root
python [2017/06/07 21:40] (current)
root
Line 2: Line 2:
 AHPCC maintains Python versionsf rom source 2.7.5, 2.7.11, and 3.5.2. 2.7.11 is most used. AHPCC maintains Python versionsf rom source 2.7.5, 2.7.11, and 3.5.2. 2.7.11 is most used.
 [[https://​www.continuum.io/?​|Anaconda Python]] 2.7.13 is installed on razor. [[https://​www.continuum.io/?​|Anaconda Python]] 2.7.13 is installed on razor.
-[[https://​software.intel.com/​en-us/​intel-distribution-for-python|Intel Python]] is being tested.+[[https://​software.intel.com/​en-us/​intel-distribution-for-python|Intel Python]] ​2.7.13 ​is installed on razor.
  
 "​python"​ at the prompt (with no python enviroment modules loaded) defaults to /​usr/​bin/​python,​ which is the centos rpm installation of Python 2.6 with very few Python modules (installable code used with "​import"​ from Python source). ​ Use environment modules ("​module"​ command from Linux) to load the compiled version of Python 2.7 or Python 3.  Please contact hpc-support to request install/​upgrade of Python modules, or you can install a private library with PYTHONUSERBASE,​ virtualenv, or anaconda (see below). You can also install a full version of Python in your user space, but it is quite large and takes a long time to compile. "​python"​ at the prompt (with no python enviroment modules loaded) defaults to /​usr/​bin/​python,​ which is the centos rpm installation of Python 2.6 with very few Python modules (installable code used with "​import"​ from Python source). ​ Use environment modules ("​module"​ command from Linux) to load the compiled version of Python 2.7 or Python 3.  Please contact hpc-support to request install/​upgrade of Python modules, or you can install a private library with PYTHONUSERBASE,​ virtualenv, or anaconda (see below). You can also install a full version of Python in your user space, but it is quite large and takes a long time to compile.
Line 298: Line 298:
 </​code>​ </​code>​
  
-==Anaconda Python== 
-see [[https://​conda.io/​docs/​using/​cheatsheet.html]] 
-<​code>​ 
-$ module load python/​2.7.13-anaconda (or python/​3.6.0-anaconda ) 
-$ python -V 
-Python 2.7.13 :: Anaconda 4.3.1 (64-bit) 
-$ conda list 
-# packages in environment at /​share/​apps/​python/​Anaconda2:​ 
-# 
-_license ​                 1.1                      py27_1  ​ 
-alabaster ​                ​0.7.9 ​                   py27_0  ​ 
-anaconda ​                 4.3.1               ​np111py27_0  ​ 
-etc. 
-$ conda create --prefix ~/bio-env biopython 
-Fetching package metadata ......... 
-Solving package specifications:​ . 
  
-Package plan for installation in environment /​home/​rfeynman/​bio-env:​ 
- 
-The following NEW packages will be INSTALLED: 
- 
-    biopython: ​ 1.68-np112py27_0 
-    mkl:        2017.0.1-0 ​     ​ 
-    numpy: ​     1.12.1-py27_0 ​   
-    openssl: ​   1.0.2k-1 ​       ​ 
-    pip:        9.0.1-py27_1 ​   ​ 
-    python: ​    ​2.7.13-0 ​       ​ 
-    readline: ​  ​6.2-2 ​           
-    setuptools: 27.2.0-py27_0 ​   
-    sqlite: ​    ​3.13.0-0 ​       ​ 
-    tk:         ​8.5.18-0 ​       ​ 
-    wheel: ​     0.29.0-py27_0 ​   
-    zlib:       ​1.2.8-3 ​         
- 
-Proceed ([y]/n)? y 
- 
-...etc... 
-$ source activate /​home/​rfeynman/​bio-env 
-</​code>​ 
  
 ==PYTHONUSERBASE== ==PYTHONUSERBASE==
Line 364: Line 326:
 peppercorn (0.5) peppercorn (0.5)
 </​code>​ </​code>​
 +
  
 ==virtualenv== ==virtualenv==
Line 388: Line 351:
 six (1.10.0) six (1.10.0)
 wheel (0.29.0) wheel (0.29.0)
 +</​code>​
 +
 +==Anaconda Python==
 +Anaconda is a prepackaged distribution of Python. Private installations can be made through conda environments similar to virtualenv environments. ​  ​Anaconda and Intel python can also use pip --user, but all python2.7 versions will install to the same user directory /​home/​$USER/​python2.7 . 
 +
 +see [[https://​conda.io/​docs/​using/​cheatsheet.html]]
 +<​code>​
 +$ module load python/​2.7.13-anaconda (or python/​3.6.0-anaconda )
 +$ python -V
 +Python 2.7.13 :: Anaconda 4.3.1 (64-bit)
 +$ conda list
 +# packages in environment at /​share/​apps/​python/​Anaconda2:​
 +#
 +_license ​                 1.1                      py27_1  ​
 +alabaster ​                ​0.7.9 ​                   py27_0  ​
 +anaconda ​                 4.3.1               ​np111py27_0  ​
 +etc.
 +$ conda create --prefix ~/bio-env biopython
 +Fetching package metadata .........
 +Solving package specifications:​ .
 +
 +Package plan for installation in environment /​home/​rfeynman/​bio-env:​
 +
 +The following NEW packages will be INSTALLED:
 +
 +    biopython: ​ 1.68-np112py27_0
 +    mkl:        2017.0.1-0 ​     ​
 +    numpy: ​     1.12.1-py27_0 ​  
 +    openssl: ​   1.0.2k-1 ​       ​
 +    pip:        9.0.1-py27_1 ​   ​
 +    python: ​    ​2.7.13-0 ​       ​
 +    readline: ​  ​6.2-2 ​          
 +    setuptools: 27.2.0-py27_0 ​  
 +    sqlite: ​    ​3.13.0-0 ​       ​
 +    tk:         ​8.5.18-0 ​       ​
 +    wheel: ​     0.29.0-py27_0 ​  
 +    zlib:       ​1.2.8-3 ​        
 +
 +Proceed ([y]/n)? y
 +
 +...etc...
 +$ source activate /​home/​rfeynman/​bio-env
 +</​code>​
 +
 +==Intel Python==
 +Intel supplies another version of Anaconda python, supposedly optimized for runtime speed on Intel processors. It has about 130 conda modules installed.
 +<​code>​
 +$ module load python/​2.7.13-intel
 +$ source activate root
 +(root) $ conda list
 +# packages in environment at /​share/​apps/​intelpython2:​
 +#
 +backports ​                ​1.0 ​               py27_intel_6 ​ [intel] ​ intel
 +backports_abc ​            ​0.5 ​               py27_intel_0 ​ [intel] ​ intel
 +bleach ​                   1.5.0              py27_intel_0 ​ [intel] ​ intel
 +boost                     ​1.61.0 ​            ​py27_intel_3 ​ [intel] ​ intel
 +bzip2                     ​1.0.6 ​                 intel_10 ​ [intel] ​ intel
 +caffe                     ​1.0.0rc3 ​          ​py27_intel_4 ​ [intel] ​ intel
 +etc.
 </​code>​ </​code>​
  
python.txt · Last modified: 2017/06/07 21:40 by root