python on gacrc computing resources...python overview –scientific distributions • anaconda “a...

Georgia Advanced Computing Resource CenterEITS/University of GeorgiaZhuofei Hou, [email protected]

Python on GACRC Computing Resources

110/26/2016 PYTHON ON GACRC COMPUTING RESOURCES

mailto:[email protected]

Outline

• GACRC

• Python Overview

• Python on Clusters

• Python Packages on Clusters

• Run Python Interactively on Clusters

• Run Python Batch Job on Clusters


GACRCWho Are We? Georgia Advanced Computing Resource Center Collaboration between the Office of Vice President for Research (OVPR) and

the Office of the Vice President for Information Technology (OVPIT) Guided by a faculty advisory committee (GACRC-AC)

Why Are We Here? To provide computing hardware and network infrastructure in support of high-

performance computing (HPC) at UGA

Where Are We? http://gacrc.uga.edu (Web) http://wiki.gacrc.uga.edu (Wiki) http://gacrc.uga.edu/help/ (Web Help) https://wiki.gacrc.uga.edu/wiki/Getting_Help (Wiki Help)


http://gacrc.uga.edu/

http://wiki.gacrc.uga.edu/

http://gacrc.uga.edu/help/

https://wiki.gacrc.uga.edu/wiki/Getting_Help

Python Overview – Language

• Open source general-purpose scripting language (https://www.python.org/)

• Working with procedural, object-oriented, and functional programming

• Glue language with Interfaces to C/C++ (via SWIG), Object-C (via PyObjC),

Java (Jython), and Fortran (via F2PY) , etc.

(https://wiki.python.org/moin/IntegratingPythonWithOtherLanguages)

• Mainstream version is 2.7.x; new version is 3.5.x (as to March 2016)


https://www.python.org/

https://wiki.python.org/moin/IntegratingPythonWithOtherLanguages

Python Overview – Modules

• Python has a large collection of built-in modules included in standard distributions:

https://docs.python.org/2/py-modindex.html


• Many third-party packages for scientific modules:

5

NumPy

Sympy

SciPy

Biopy

Matplotlib




Python Overview – Scientific Modules

NumPy: Matlab-ish capabilities, fast N-D array operations, linear algebra, etc.

(http://www.numpy.org/)

SciPy: Fundamental library for scientific computing (http://www.scipy.org/)

Sympy: Symbolic mathematics (http://www.sympy.org/en/index.html)

matplotlib: High quality plotting (http://matplotlib.org/)

Biopy: Phylogenetic exploration (https://code.google.com/archive/p/biopy/)

6

A scientific Python distribution may include all those packages for you!


http://www.numpy.org/

http://www.scipy.org/

http://www.sympy.org/en/index.html

http://matplotlib.org/

https://code.google.com/archive/p/biopy/

Python Overview – Scientific Distributions

• Anaconda

“A Python distribution including ~200 of the most popular Python packages for science, math, engineering, and data analysis.”

Supports Linux, Mac and Windows (https://www.continuum.io/)

• Python(x,y)

Windows only (http://python-xy.github.io/)

• WinPython

Windows only (http://winpython.github.io/)


https://www.continuum.io/

http://python-xy.github.io/

http://winpython.github.io/

Python on Clusters

• Python

https://wiki.gacrc.uga.edu/wiki/Python

https://wiki.gacrc.uga.edu/wiki/Python-Sapelo

• Anaconda Python

https://wiki.gacrc.uga.edu/wiki/Anaconda

https://wiki.gacrc.uga.edu/wiki/Anaconda-Sapelo






Python on zcluster

9

Version Installation Path Invoke Command

2.4.3 (default) /usr/bin python

2.7.2* /usr/local/python/2.7.2 python2.7

2.7.8 /usr/local/python/2.7.8 python2.7.8

3.3.0 /usr/local/python/3.3.0 python3

3.4.0 /usr/local/python/3.4.0 python3.4


* Most Python site-packages GACRC installed are for the version of 2.7.2 on zcluster

Python on Sapelo

10

Version Installation Path Module Load Invoke Command

2.6.6 (default) /usr/bin

python

2.7.8 /usr/local/apps/python/2.7.8 module load python/2.7.8

3.4.3 /usr/local/apps/python/3.4.3 module load python/3.4.3 python3


Anaconda Python on zcluster

11

Version Installation PathPython Version

ExportsInvoke

Command

2.3.0 /usr/local/anaconda/2.3.0 2.7.11export

PATH=/usr/local/anaconda/2.3.0/bin:$PATH

python

3-2.2.0 /usr/local/anaconda/3-2.2.0 3.4.3export

PATH=/usr/local/anaconda/3-2.2.0/bin:$PATH


Anaconda Python on Sapelo

12

Version Installation PathPythonVersion

Module LoadInvoke

Command

2.2.0 /usr/local/apps/anaconda/2.2.0 2.7.12 module load anaconda/2.2.0

python2.5.0 /usr/local/apps/anaconda/2.5.0 2.7.11 module load anaconda/2.5.0

3-2.2.0 /usr/local/apps/anaconda/3-2.2.0 3.4.3 module load anaconda/3-2.2.0


Python Packages on Clusters

• Python Packages



• Anaconda Python Packages









How to know if the package you need is already installed on clusters?

1. python –c ‘import pkgName; print pkgName__version__’

2. conda list pkgName

3. python -m pip list | grep pkgName

Examples: Next page!




zcluster

1. python2.7 –c ‘import numpy; print numpy.__version__’

2. python2.7.8 –m pip list | grep numpy

3. export PATH=/usr/local/anaconda/2.3.0/bin:$PATH

conda list numpy

Sapelo

1. module load python/2.7.8

python –c ‘import numpy; print numpy.__version__’

2. python -m pip list | grep numpy

3. module load anaconda/3-2.2.0

conda list numpy

Common Python Packages on zcluster


Packagepython2.7

(python2.7.2)python2.7.8

(python2.7.8)python3.4

(python3.4.0)Anaconda2.3.0(python2.7.11)

Anaconda3-2.2.0(python3.4.3)

Numpy 1.11.0 1.10.1 1.9.1 1.10.2 1.10.2

Scipy 0.10.1 0.14.1 n/a 0.15.1 0.15.1

Biopython 1.65 1.67 n/a 1.66 1.66

Matplotlib 1.3.1 1.3.1 1.3.1 1.4.3 1.5.0

Cython 0.16 0.19.1 0.19.1 0.23.2 0.23.4

Pandas 0.17.0 n/a n/a 0.17.1 0.15.2

Scikit-image n/a 0.10.1 n/a 0.11.3 0.11.2

Scikit-learn 0.15.2 0.17 n/a 0.16.1 0.15.2

Networkx 2.0.dev 1.11 1.11 1.9.1 1.9.1

Requests 2.5.1 2.8.0 n/a 2.9.0 2.9.0

Common Python Packages on Sapelo


Packagepython

(python2.7.8)python3

(python3.4.3)Anaconda2.5.0(python2.7.11)

Anaconda3-2.2.0(python3.4.3)

Numpy 1.9.2 1.9.2 1.10.4 1.9.2

Scipy 0.16.1 n/a 0.17.0 0.15.1

Biopython 1.66 n/a 1.66 1.66

Matplotlib 1.4.3 1.5.1 1.5.1 1.4.3

Cython 0.24.1 0.22 0.23.4 0.22

Pandas 0.17.1 0.17.1 0.17.1 0.15.2

Scikit-image n/a n/a 0.11.3 0.11.2

Scikit-learn 0.17.1 n/a 0.17 0.15.2

Networkx n/a n/a 1.11 1.9.1

Requests 2.5.1 n/a 2.9.1 2.6.0

Python Package Paths on zcluster

18

Version Python Package Path Python Shared Library Path

2.7.2/usr/local/python/2.7.2/lib/python2.7/usr/local/python/2.7.2/lib/python2.7/site-packages

N/A


/usr/local/python/2.7.8/lib


N/A


N/A


python can find those packages automatically! To be exported in LD_LIBRARY_PATH

Python Package Paths on Sapelo

19

Version Python Package Path Python Shared Library Path

2.7.8/usr/local/apps/python/2.7.8/lib/python2.7

/usr/local/apps/python/2.7.8/lib/python2.7/site-packages/usr/local/apps/python/2.7.8/lib

3.4.3/usr/local/apps/python/3.4.3/lib/python2.7

/usr/local/apps/python/3.4.3/lib/python3.4/site-package/usr/local/apps/python/3.4.3/lib


python can find those packages automatically! To be exported in LD_LIBRARY_PATH

Anaconda Python Package Paths on zcluster

20

Version Installation PathPython Version

Python Package Path

2.3.0 /usr/local/anaconda/2.3.0 2.7.11

/usr/local/anaconda/2.3.0/lib/python2.7

/usr/local/anaconda/2.3.0/lib/python2.7/site-

packages

3-2.2.0 /usr/local/anaconda/3-2.2.0 3.4.3

/usr/local/anaconda/3-2.2.0/lib/python3.4

/usr/local/anaconda/3-2.2.0/lib/python3.4/site-

packages


python can find those packages automatically!Python Shared Libraries were built for all versions in lib

Anaconda Python Package Paths on Sapelo

21

Version Installation PathPythonVersion

Python Package Path

2.2.0 /usr/local/apps/anaconda/2.2.0 2.7.12/usr/local/apps/anaconda/2.2.0/lib/python2.7/usr/local/apps/anaconda/2.2.0/lib/python2.7/site-packages

2.5.0 /usr/local/apps/anaconda/2.5.0 2.7.11/usr/local/apps/anaconda/2.5.0/lib/python2.7/usr/local/apps/anaconda/2.5.0/lib/python2.7/site-packages

3-2.2.0 /usr/local/apps/anaconda/3-2.2.0 3.4.3/usr/local/apps/anaconda/3-2.2.0/lib/python3.4/usr/local/apps/anaconda/3-2.2.0/lib/python3.4/site-packages


python can find those packages automatically!Python Shared Libraries were built for all versions in lib

Run Python Interactively on Clusters

• Run Python Interactively

• Run Anaconda Python Interactively


DO NOT run jobs from login node; Run interactive tasks from interactive node:

zcluster.rcc.uga.edu (zcluster)

sapelo1.gacrc.uga.edu (Sapelo)

https://wiki.gacrc.uga.edu/wiki/Training - Download

qlogin

interactive node

https://wiki.gacrc.uga.edu/wiki/Training#Download


23

zhuofei@compute-18-16:~$ python

Python 2.4.3 (#1, Oct 23 2012, 22:02:41)

[GCC 4.1.2 20080704 (Red Hat 4.1.2-54)] on linux2

Type "help", "copyright", "credits" or "license" for

more information.

>>> a = 7

>>> e = 2

>>> a**e

49

>>>

[zhuofei@n15 ~]$ python

Python 2.6.6 (r266:84292, Jan 22 2014, 09:42:36)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2

Type "help", "copyright", "credits" or "license" for

more information.

>>> a = 7

>>> e = 2

>>> a**e

49

>>>


Running on zcluster interactive node: Running on Sapelo interactive node:


24

zhuofei@compute-18-16:~$ /usr/local/python/2.7.8/bin/python myScript.py

2.7.8 (default, Jan 7 2015, 15:33:35)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]

49

[zhuofei@n15 ~]$ module load python/2.7.8

[zhuofei@n15 ~]$ python myScript.py

2.7.8 (default, Sep 26 2014, 07:26:46)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]

49

import sysprint sys.version

a = 7e = 2print a**e



25

zhuofei@compute-18-16:~$ chmod u+x myScript.py

zhuofei@compute-18-16:~$ ./myScript.py

2.7.8 (default, Jan 7 2015, 15:33:35)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]

49

[zhuofei@n15 ~]$ chmod u+x myScript.py

[zhuofei@n15 ~]$ ./myScript.py

2.7.8 (default, Sep 26 2014, 07:26:46)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]

49

#!/usr/local/python/2.7.8/bin/python


a = 7; e = 2print a**e

tells exec where python is on zcluster


#!/usr/local/apps/python/2.7.8/bin/python2.7



tells exec where python is on Sapelo


26

zhuofei@compute-18-16:~$ chmod u+x myScript.py

zhuofei@compute-18-16:~$ export PATH=/usr/local/python/2.7.8/bin:$PATH

zhuofei@compute-18-16:~$ ./myScript.py

2.7.8 (default, Jan 7 2015, 15:33:35)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]

49


[zhuofei@n15 ~]$ module load python/2.7.8


2.7.8 (default, Sep 26 2014, 07:26:46)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]

49

#!/usr/bin/env python



env tells exec where python is by searching PATH



[zhuofei@n15 ~]$ module load anaconda/2.5.0


2.7.11 |Anaconda 2.5.0 (64-bit)| (default, Dec 6 2015, 18:08:32)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]

49

Run Anaconda Python Interactively on Clusters

27

zhuofei@compute-18-16:$ chmod u+x myScript.py

zhuofei@compute-18-16:$ export PATH=/usr/local/anaconda/2.3.0/bin:$PATH

zhuofei@compute-18-16:$ ./myScript.py

2.7.11 |Anaconda 2.3.0 (64-bit)| (default, Dec 6 2015, 18:08:32)

[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]

49

#!/usr/bin/env python




Run Python Batch Job on Clusters

• Run Python Batch Job on zcluster

• Run Python Bach Job on Sapelo


Note: zcluster Job Working Space: /escratch4/username/

Sapelo Job Working Space: /lustre1/username/

https://wiki.gacrc.uga.edu/wiki/Training - Download

https://wiki.gacrc.uga.edu/wiki/Training#Download

Run Python Batch Job on zcluster


#!/bin/bash

cd working_directory

export PATH=/usr/local/python/2.7.8/bin:$PATH

export PYTHONPATH=/usr/local/python/2.7.8/lib/python2.7:/usr/local/python/2.7.8/lib/python2.7/site-\

packages:$PYTHONPATH

time python myScript.py [options]

qsub -q rcc-30d sub.sh optional qsub options, e.g., -pe threads 4 -l mem_total=20g

Run Anaconda Python Batch Job on zcluster


#!/bin/bash

cd working_directory

export PATH=/usr/local/anaconda/2.3.0/bin:$PATH

export PYTHONPATH=/usr/local/anaconda/2.3.0/bin:/usr/local/anaconda/2.3.0/lib/python2.7:$PYTHONPATH


qsub -q rcc-30d sub.sh optional qsub options, e.g., -pe threads 4 -l mem_total=20g

Run (Anaconda) Python Batch Job on Sapelo


#PBS -S /bin/bash

#PBS -q batch

#PBS -N PythonJob1

#PBS -l nodes=1:ppn=4:AMD

#PBS -l walltime=48:00:00

#PBS -l mem=10gb

cd $PBS_O_WORKDIR

module load python/3.4.3

time python3 myScript.py [options]

qsub sub.sh #PBS -S /bin/bash

#PBS -q batch

#PBS -N PythonJob1

#PBS -l nodes=1:ppn=4:AMD

#PBS -l walltime=48:00:00

#PBS -l mem=10gb

cd $PBS_O_WORKDIR

module load anaconda/3-2.2.0


Thank You!


python on gacrc computing resources...python overview –scientific distributions • anaconda “a...

Documents