Installing scikit.sparse on CentOS or Fedora

Step 1: install the METIS library:

1 ) Install cmake as described here:,

For the lazy:

– Dowload the latest atrpms-repo rpm from

– Install atrpms-repo rpm as an admin:

# sudo rpm -Uvh atrpms-repo*rpm

– Install cmake rpm package:

# yum --enablerepo=atrpms-testing install cmake

2) Install either the GNU make with

# yum install make

or the whole Development tools with

# yum groupinstall "Development Tools"

3) Download METIS from and follow the instructions in the “install.txt” to actually install it:

– adjust the include.metix.h to adjust the length of ints and floats to better correspond to your architecture and wanted precision (32 or 64 bits)


$ make config 
$ make 
# make install

Step 2: Install SuiteSparse:

1) Download the latest version from, untar it and cd into it

2) Modify the INSTALL_INCLUDE variable :

INSTALL_INCLUDE = /usr/local/include

3) Build and install it

$ make 
# make install

Step 3: Install the scikit.sparse:

1) Download the latest scikit.sparse from PiPy:

2) in edit the last statement so that it looks like this:


Step 4:

Well, the scikit.sparse imports well at this point, but if we try to import scikits.sparse.cholmod, we have an Import error, where our egg/scikits/sparse/ fails to recognize the amd_printf symbol….

Hmmm. Looks like there is still work to be done to get it all working correctly…

Scipy Sparse Matrixes and Linear Algebra

If you need to do a LU decomposition of a Scipy Sparse Matrix (pretty useful for solving systems of differential equations), keep in mind that Cholesky decomposition is generally more stable and rapid for the Hermitian Symmetric positive definite matrixes. In my case, the default LU decompsition method from scipy.sparse.linalg was failing because of the procedural problems.

However you cannot just apply Numpy.linalg.cholesky because the a scipy.sparse.lil_matrix is seen as a linked list and is not a 2D matrix. A solution for this is to use the cholesky decomposition from the scikit.sparse module