HPC clusters: Vilje and Kongull
Scipy and Numpy are part of the Python module on Vilje and Kongull. Odespy is not impemented yet. How to load the Python module:
Available modules: $ module avail Default versions: Vilje 2.7.2, Kongull 2.7.1 $ module load python Vilje -----------------------------: Python v.2.7.3: $ module load intelcomp/13.0.1 $ module load mpt/2.06 $ module load python/2.7.3 Python v.2.7.6: $ module load intelcomp/14.0.1 $ module load mpt/2.09 $ module load python/2.7.6 Kongull ---------------------------: Python 2.7.3 $ module load python/2.7.3 Python 2.7.6 $ module load intelcomp/13.0.1 $ module load openmpi/1.6.5 $ module load python/2.7.6-intel
CalcFarm
Scipy, Numpy and Odespy are implemented in Python on the CalcFarm.
1.Start Remote Desktop Connection on your Laptop/PC/Smartphone/Tablet.
a. Windows: Remote Desktop Connection
b. Android App: "RD Client"
c. iPhone/iPad App: "Microsoft Remote Desktop"
d. Linux: eg. "Remmina Remote Desktop Client"
2. Login: Computer: calcfarm.ntnu.no, Username: win-ntnu-no\my-ntnu-username and Ntnu-password. For Linux: Domene: win-ntnu-no, Username: my-ntnu-username.
3. Click on Connect.
4. Click on "Startmeny" in the CalcFarm desktop.
5. Use one of the Python Apps: IPython (Qt), IPython (sh) or Python interpreter
Scipy/Numpy
NumPy is the fundamental package for scientific computing with Python (http://www.numpy.org/)
SciPy (pronounced “Sigh Pie”) is a Python-based ecosystem of open-source software for mathematics, science, and engineering (http://scipy.org/).
How to install Scipy/Numpy on a Laptop or PC
Linux.
You need Python installed (Python is normaly installed on every linux distro).
Installation of Scipy/Numpy see: http://scipy.org/install.html
(Note that you can install linux on Windows PC with VMWare player. See http://www.vmware.com/)
Windows
Install python for Windows (32bit), the recommended version is 2.7.6 because of numpy: See http://www.python.org/download/releases/2.7.6/ and Windows x86 MSI Installer (2.7.6).
Install numpy for Windows (32bit), the recommended version is "numpy-1.8.0-win32-superpack-python2.7.exe". See http://sourceforge.net/projects/numpy/files/NumPy/1.7.2/
Install scipy for Windows (32bit), the recommended version is "scipy-0.13.2-win32-superpack-python2.7.exe". See http://sourceforge.net/projects/scipy/files/scipy/0.13.2/
The installation is on path c:\python2.7\ (by default)
Set the path to python in System Properties -> Advanced Tab -> Enviroment Varilables; Add the directory to python under "System variables" and "path".
To install matplotlib
https://github.com/matplotlib/matplotlib/downloads and download "matplotlib-1.2.0.win32-py2.7.exe".
Mac
Install python: sudo port install python27
Install numpy and scipy; see http://www.scipy.org/install.html
Test the installation
Start python (Windows: Start->Programs->Python 2.7):
>>>import numpy
>>>import scipy
>>>
OK, if none error messages.
Example codes
See reference: http://docs.scipy.org/doc/scipy/reference/linalg.html
See also http://wiki.scipy.org/Numpy_Example_List
Sample code (numpy and scipy is equal for the examples below. Use import numpy instead of import scipy):
import scipy from scipy import linalg n=100; a=scipy.random.rand(n,n); b=scipy.ones((n,n)); c=scipy.zeros((n,n)); A=scipy.mat((a)); B=scipy.mat((b)); C=scipy.mat((c)); # Matrix multiplication with operator C = A * B; # Matrix determinant d = scipy.linalg.det(A); # Inv matrix B2 = A.I * C; # FFT (only scipy) F = scipy.fft(A);
Odespy
Odespy (ODE Software in Python) offers a unified interface to a a large collection of software for solving systems of ordinary differential equations (ODEs). There is also some support for Differential Algebraic Equations (DAEs)
(see http://hplgit.github.io/odespy/doc/web/index.html and https://github.com/hplgit/odespy).
Note! Odespy is not installed on our HPC clusters Vilje and Kongull.
How to install Odespy
For linux
Download and install odespy: (See git://github.com/hplgit/odespy)
$ git clone git://github.com/hplgit/odespy
$ cd odespy
$ python setup.py install
(If you don't have git installed then install git with "sudo yum install git" or "sudo apt-get install git".)
(Note that you can install linux on Windows PC with VMWare player. See http://www.vmware.com/)
For Windows and Mac
Download zip file file (hplgit-odespy-1081789.zip) from http://hplgit.github.io/odespy/doc/web/index.html and Download.
Unzip the file and in the command prompt:
python setup.py install --no-fortran
(If you have a fortran compiler installed; you can write: python setup.py install)
Windows: Copy the odespy folder to c:\pythonxx\LIb\site-packages\. Ex: ..\hplgit-odespy-1081789\odespy to c:\python27\LIb\site-packages\
Test the installation
Start python:
>>>import odespy
>>>
OK, If none error messages.
Example
def f(u, t):
"""2x2 system for a van der Pool oscillator."""
return [u[1], 3.*(1. - u[0]*u[0])*u[1] - u[0]]
import odespy, numpy
solver = odespy.Vode(f, rtol=0.0, atol=1e-6,
adams_or_bdf='adams', order=10)
solver.set_initial_condition([2.0, 0.0])
t_points = numpy.linspace(0, 30, 150)
u, t = solver.solve(t_points)
u0 = u[:,0]
from matplotlib.pyplot import *
plot(t, u0)
show()