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Research Express is on its way! Today's topic: Python
Transcript of Research Express is on its way! Today's topic: Python
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Research Expressis on its way!
● The demonstration will start at 12:30 pm.● To use the Live Chat:
● Maximize your browser window so you can see the postings.● If you refresh the browser page, you'll need to log in again.● After the demonstration, staff will remain available in the
chat for a few minutes to answer additional questions.
Today's topic: Python
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Python (NumPy, SciPy and mpi4py) on Mills
Information Technologies
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Objectives● Use VALET to automate your
environment-setup for Python (Numpy, SciPy and mpi4py)
● Modify queue submission scripts to work with Grid Engine on Mills
Python (Cornell Virtual Workshop) at http://www.udel.edu/001278 NumPy Tutorial (SciPy.org) at http://www.udel.edu/001279
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Python packages on Mills
● vpkg_list | grep py
mpi4py numpy python python-nose scipy
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● vpkg_versions python
Available versions in package (* = default version):
python Python Programming Language
3.2 Version 3.2
* 3 Version 3
2.7 Version 2.7
2 Version 2
module list python
Python versions on Mills
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● vpkg_versions numpy
Available versions in package (* = default version):
numpy Python NumPy
* 1.6.1-2.7.2 Version 1.6.1 for Python 2.7.2
NumPy versions on Mills
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● vpkg_versions scipy
Available versions in package (* = default version):
scipy Python SciPy - Scientific Tools for Python
* 0.10.0-2.7.2 Version 1.6.1 for Python 2.7.2
SciPy versions on Mills
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● vpkg_versions mpi4py
Available versions in package (* = default version):
mpi4py mpi4py - MPI for Python
* 1.3-2.7.2 Version 1.3 for Python 2.7.2
1.3-3.2.2 Version 1.3 for Python 3.2.2
mpi4py versions on Mills
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● vpkg_require python
Adding package `python/3` to your environment
module add python
● vpkg_rollback all● vpkg_require python/2.7
Adding dependency `mkl/10.3.8-64bit` to your environment
Adding package `python/2.7` to your environment
Using Python on Mills
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● NumPy and SciPy: Python 2.7.2mpi4py: Python 2.7.2 and 3.2.2
● Important to use the built in dependencies by VALET
● An incorrect version of Python added will generate a conflict when we try to add a library
ERROR: unable to add versioned package: python/2.7 conflicts with version: python/3
vpkg_rollback all
NumPy, SciPy and mpi4py
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● vpkg_require numpy
Adding dependency `mkl/10.3.8-64bit` to your environment
Adding dependency `python/2.7` to your environment
Adding dependency `python-nose/1.1.2-2.7.2` to your environment
Adding package `numpy/1.6.1-2.7.2` to your environment
NumPy
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● vpkg_require scipy
Adding dependency `mkl/10.3.8-64bit` to your environment
Adding dependency `python/2.7` to your environment
Adding dependency `python-nose/1.1.2-2.7.2` to your environment
Adding dependency `numpy/1.6.1-2.7.2` to your environment
Adding package `scipy/0.10.0-2.7.2` to your environment
SciPy
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● vpkg_require mpi4py
Adding dependency `openmpi/1.4.4-gcc` to your environment
Adding dependency `mkl/10.3.8-64bit` to your environment
Adding dependency `python/2.7` to your environment
Adding package `mpi4py/1.3-2.7.2` to your environment
● vpkg_require mpi4py/1.3-3.2.2
Adding dependency `openmpi/1.4.4-gcc` to your environment
Adding dependency `python/3` to your environment
Adding package `mpi4py/1.3-3.2.2` to your environment
mpi4py
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● vpkg_require mpi4py numpy
Adding dependency `openmpi/1.4.4-gcc` to your environment
Adding dependency `mkl/10.3.8-64bit` to your environment
Adding dependency `python/2.7` to your environment
Adding package `mpi4py/1.3-2.7.2` to your environment
Adding dependency `python-nose/1.1.2-2.7.2` to your environment
Adding package `numpy/1.6.1-2.7.2` to your environment
mpi4py and NumPy
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● vpkg_require mpi4py scipy
Adding dependency `openmpi/1.4.4-gcc` to your environment
Adding dependency `mkl/10.3.8-64bit` to your environment
Adding dependency `python/2.7` to your environment
Adding package `mpi4py/1.3-2.7.2` to your environment
Adding dependency `python-nose/1.1.2-2.7.2` to your environment
Adding dependency `numpy/1.6.1-2.7.2` to your environment
Adding package `scipy/0.10.0-2.7.2` to your environment
mpi4py and SciPy
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● vpkg_require mpi4py numpy
Adding dependency `openmpi/1.4.4-gcc` to your environment
Adding dependency `mkl/10.3.8-64bit` to your environment
Adding dependency `python/2.7` to your environment
Adding package `mpi4py/1.3-2.7.2` to your environment
Adding dependency `python-nose/1.1.2-2.7.2` to your environment
Adding package `numpy/1.6.1-2.7.2` to your environment
● vpkg_require scipy
Adding package `scipy/0.10.0-2.7.2` to your environment
mpi4py, NumPy and SciPy
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Interactive example$ vpkg_require numpy mpi4py Adding dependency `mkl/10.3.8-64bit` to your environmentAdding dependency `python/2.7` to your environmentAdding dependency `python-nose/1.1.2-2.7.2` to your environmentAdding package `numpy/1.6.1-2.7.2` to your environmentAdding dependency `openmpi/1.4.4-gcc` to your environmentAdding package `mpi4py/1.3-2.7.2` to your environment$ pythonPython 2.7.2 (default, Dec 27 2011, 15:05:10)[GCC 4.4.5 20110214 (Red Hat 4.4.5-6)] on linux2Type "help", "copyright", "credits" or "license" for more information.>>> from numpy import *>>> a = arange(10).reshape(2,5)>>> aarray([[0, 1, 2, 3, 4], [5, 6, 7, 8, 9]])>>> a.shape(2, 5)>>> a.ndim2>>> a.dtype.name'int64'>>> a.itemsize8>>>
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Interactive example>>> from scipy import *Traceback (most recent call last): File "<stdin>", line 1, in <module>ImportError: No module named scipy>>>$ vpkg_require scipyAdding package `scipy/0.10.0-2.7.2` to your environment$ pythonPython 2.7.2 (default, Dec 27 2011, 15:05:10)[GCC 4.4.5 20110214 (Red Hat 4.4.5-6)] on linux2Type "help", "copyright", "credits" or "license" for more information.>>> from scipy import *>>> x = r_[-2:3]>>> xarray([-2, -1, 0, 1, 2])>>> select([x > 3, x >= 0],[0,x+2])array([0, 0, 2, 3, 4])>>> r_[3,[0]*5,-1:1:10j]array([ 3. , 0. , 0. , 0. , 0. , 0. , -1. , -0.77777778, -0.55555556, -0.33333333, -0.11111111, 0.11111111, 0.33333333, 0.55555556, 0.77777778, 1. ])>>>
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Batch script (batch.qs)#!/bin/bash#$ -q development#$ -A TG-STA060015N#$ -V#$ -cwd#$ -N mpi4py-demo#$ -j y#$ -o $JOB_NAME.o$JOB_ID#$ -pe 12way 12#$ -l h_rt=00:05:00#$ -M [email protected]#$ -m be # Prohibit writing core files on error.ulimit -c 0 set -x python receiver.py& ibrun python sample.py --loghost `hostname` --level debug pkill python
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Grid Engine script (batch.qs)#$ -N mpi4py-demo#$ -o $JOB_NAME.o$JOB_ID#$ -pe openmpi 12#$ -l h_rt=00:05:00#$ -M [email protected]#$ -m be #source /opt/shared/valet/docs/valet.shvpkg_require mpi4py numpy # Prohibit writing core files on error.ulimit -c 0 set -x python receiver.py& mpirun python sample.py --loghost `hostname` --level debug pkill python
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● Take advantage of the power of VALET to do the work for you to automate your environment-setup.
● Use the Mills User Guide to help with modifications of Grid Engine scripts that may be different from other HPC sites.
Summary
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Upcoming Python Training
HPC Python Training Webcast in 011 Smith Hall on Mon, Apr 23 10am-5pm Register at:http://webapps.css.udel.edu/calendar/detail.php?classid=3711
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More information● IT Research Computinghttp://www.it.udel.edu/research-computing
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Contact the IT Support Center● Email: [email protected]
If you make the first line of the e-mail
message
Type=Cluster-Mills
your question will be routed more quickly.
● Phone: (302) 831-6000
● Text: (302) 722-6820