Links OK

docs.it4i/software/numerical-libraries/fftw.md

@@ -68,6 +68,9 @@ $ ml fftw3-mpi
 $ mpicc testfftw3mpi.c -o testfftw3mpi.x -Wl,-rpath=$LIBRARY_PATH -lfftw3_mpi
 ```
 
-Run the example as [Intel MPI program](software/mpi/running-mpich2/).
+Run the example as [Intel MPI program][1].
 
-Read more on FFTW usage on the [FFTW website.](http://www.fftw.org/fftw3_doc/)
+Read more on FFTW usage on the [FFTW website][a].
+
+[1]: ../mpi/running-mpich2.md
+[a]: http://www.fftw.org/fftw3_doc/

docs.it4i/software/numerical-libraries/gsl.md

@@ -8,39 +8,39 @@ The GNU Scientific Library (GSL) provides a wide range of mathematical routines
 
 The library covers a wide range of topics in numerical computing. Routines are available for the following areas:
 
-                           Complex Numbers              Roots of Polynomials
+Complex Numbers              Roots of Polynomials
 
-                           Special Functions            Vectors and Matrices
+Special Functions            Vectors and Matrices
 
-                           Permutations                 Combinations
+Permutations                 Combinations
 
-                           Sorting                      BLAS Support
+Sorting                      BLAS Support
 
-                           Linear Algebra               CBLAS Library
+Linear Algebra               CBLAS Library
 
-                           Fast Fourier Transforms      Eigensystems
+Fast Fourier Transforms      Eigensystems
 
-                           Random Numbers               Quadrature
+Random Numbers               Quadrature
 
-                           Random Distributions         Quasi-Random Sequences
+Random Distributions         Quasi-Random Sequences
 
-                           Histograms                   Statistics
+Histograms                   Statistics
 
-                           Monte Carlo Integration      N-Tuples
+Monte Carlo Integration      N-Tuples
 
-                           Differential Equations       Simulated Annealing
+Differential Equations       Simulated Annealing
 
-                           Numerical Differentiation    Interpolation
+Numerical Differentiation    Interpolation
 
-                           Series Acceleration          Chebyshev Approximations
+Series Acceleration          Chebyshev Approximations
 
-                           Root-Finding                 Discrete Hankel Transforms
+Root-Finding                 Discrete Hankel Transforms
 
-                           Least-Squares Fitting        Minimization
+Least-Squares Fitting        Minimization
 
-                           IEEE Floating-Point          Physical Constants
+IEEE Floating-Point          Physical Constants
 
-                           Basis Splines                Wavelets
+Basis Splines                Wavelets
 
 ## Modules
 

docs.it4i/software/numerical-libraries/hdf5.md

@@ -2,7 +2,7 @@
 
 Hierarchical Data Format library. Serial and MPI parallel version.
 
-[HDF5 (Hierarchical Data Format)](http://www.hdfgroup.org/HDF5/) is a general purpose library and file format for storing scientific data. HDF5 can store two primary objects: datasets and groups. A dataset is essentially a multidimensional array of data elements, and a group is a structure for organizing objects in an HDF5 file. Using these two basic objects, one can create and store almost any kind of scientific data structure, such as images, arrays of vectors, and structured and unstructured grids. You can also mix and match them in HDF5 files according to your needs.
+[HDF5 (Hierarchical Data Format)][a] is a general purpose library and file format for storing scientific data. HDF5 can store two primary objects: datasets and groups. A dataset is essentially a multidimensional array of data elements, and a group is a structure for organizing objects in an HDF5 file. Using these two basic objects, one can create and store almost any kind of scientific data structure, such as images, arrays of vectors, and structured and unstructured grids. You can also mix and match them in HDF5 files according to your needs.
 
 Versions **1.8.11** and **1.8.13** of HDF5 library are available on Anselm, compiled for **Intel MPI** and **OpenMPI** using **Intel** and **gnu** compilers. These are available via modules:
 
@@ -84,6 +84,10 @@ $ ml hdf5-parallel
 $ mpicc hdf5test.c -o hdf5test.x -Wl,-rpath=$LIBRARY_PATH $HDF5_INC $HDF5_SHLIB
 ```
 
-Run the example as [Intel MPI program](software/mpi/running-mpich2/).
+Run the example as [Intel MPI program][1].
 
-For further information, see the website: [http://www.hdfgroup.org/HDF5/](http://www.hdfgroup.org/HDF5/)
+For further information, see the [website][a].
+
+[1]: ../mpi/running-mpich2.md
+
+[a]: http://www.hdfgroup.org/HDF5/

docs.it4i/software/numerical-libraries/intel-numerical-libraries.md

@@ -10,7 +10,7 @@ Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, e
 $ ml mkl **or** ml imkl
 ```
 
-Read more at the [Intel MKL](software/intel/intel-suite/intel-mkl/) page.
+Read more at the [Intel MKL][1].
 
 ## Intel Integrated Performance Primitives
 
@@ -20,7 +20,7 @@ Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is avai
 $ ml ipp
 ```
 
-Read more at the [Intel IPP](software/intel/intel-suite/intel-integrated-performance-primitives/) page.
+Read more at the [Intel IPP][2].
 
 ## Intel Threading Building Blocks
 
@@ -30,4 +30,8 @@ Intel Threading Building Blocks (Intel TBB) is a library that supports scalable
 $ ml tbb
 ```
 
-Read more at the [Intel TBB](software/intel/intel-suite/intel-tbb/) page.
+Read more at the [Intel TBB][3].
+
+[1]: ../intel/intel-suite/intel-mkl.md
+[2]: ../intel/intel-suite/intel-integrated-performance-primitives.md
+[3]: ../intel/intel-suite/intel-tbb.md

docs.it4i/software/numerical-libraries/magma-for-intel-xeon-phi.md

@@ -69,8 +69,12 @@ To test if the MAGMA server runs properly we can run one of examples that are pa
 !!! note
     MAGMA relies on the performance of all CPU cores as well as on the performance of the accelerator. Therefore on Anselm number of CPU OpenMP threads has to be set to 16 with `export OMP_NUM_THREADS=16`.
 
-See more details at [MAGMA home page](http://icl.cs.utk.edu/magma/).
+See more details at [MAGMA home page][a].
 
 ## References
 
-[1] MAGMA MIC: Linear Algebra Library for Intel Xeon Phi Coprocessors, Jack Dongarra et. al, [http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf](http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf)
+[1] [MAGMA MIC: Linear Algebra Library for Intel Xeon Phi Coprocessors][1], Jack Dongarra et. al
+
+[1]: http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf
+
+[a]: http://icl.cs.utk.edu/magma/

docs.it4i/software/numerical-libraries/petsc.md

@@ -8,11 +8,11 @@ PETSc (Portable, Extensible Toolkit for Scientific Computation) is a suite of bu
 
 ## Resources
 
-* [project webpage](http://www.mcs.anl.gov/petsc/)
-* [documentation](http://www.mcs.anl.gov/petsc/documentation/)
-  * [PETSc Users Manual (PDF)](http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf)
-  * [index of all manual pages](http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/singleindex.html)
-* PRACE Video Tutorial [part1](http://www.youtube.com/watch?v=asVaFg1NDqY), [part2](http://www.youtube.com/watch?v=ubp_cSibb9I), [part3](http://www.youtube.com/watch?v=vJAAAQv-aaw), [part4](http://www.youtube.com/watch?v=BKVlqWNh8jY), [part5](http://www.youtube.com/watch?v=iXkbLEBFjlM)
+* [project webpage][a]
+* [documentation][b]
+  * [PETSc Users Manual (PDF)][c]
+  * [index of all manual pages][d]
+* PRACE Video Tutorial [part1][e], [part2][f], [part3][g], [part4][h], [part5][i]
 
 ## Modules
 
@@ -23,35 +23,63 @@ $# ml petsc/version-compiler-mpi-blas-variant, e.g.
 $ ml petsc/3.4.4-icc-impi-mkl-opt
 ```
 
-where `variant` is replaced by one of `{dbg, opt, threads-dbg, threads-opt}`. The `opt` variant is compiled without debugging information (no `-g` option) and with aggressive compiler optimizations (`-O3 -xAVX`). This variant is suitable for performance measurements and production runs. In all other cases use the debug (`dbg`) variant, because it contains debugging information, performs validations and self-checks, and provides a clear stack trace and message in case of an error. The other two variants `threads-dbg` and `threads-opt` are `dbg` and `opt`, respectively, built with [OpenMP and pthreads threading support](https://www.mcs.anl.gov/petsc/miscellaneous/petscthreads.html).
+where `variant` is replaced by one of `{dbg, opt, threads-dbg, threads-opt}`. The `opt` variant is compiled without debugging information (no `-g` option) and with aggressive compiler optimizations (`-O3 -xAVX`). This variant is suitable for performance measurements and production runs. In all other cases use the debug (`dbg`) variant, because it contains debugging information, performs validations and self-checks, and provides a clear stack trace and message in case of an error. The other two variants `threads-dbg` and `threads-opt` are `dbg` and `opt`, respectively, built with [OpenMP and pthreads threading support][j].
 
 ## External Libraries
 
 PETSc needs at least MPI, BLAS and LAPACK. These dependencies are currently satisfied with Intel MPI and Intel MKL in Anselm `petsc` modules.
 
-PETSc can be linked with a plethora of [external numerical libraries](http://www.mcs.anl.gov/petsc/miscellaneous/external.html), extending PETSc functionality, e.g. direct linear system solvers, preconditioners or partitioners. See below a list of libraries currently included in Anselm `petsc` modules.
+PETSc can be linked with a plethora of [external numerical libraries][k], extending PETSc functionality, e.g. direct linear system solvers, preconditioners or partitioners. See below a list of libraries currently included in Anselm `petsc` modules.
 
 All these libraries can be used also alone, without PETSc. Their static or shared program libraries are available in
 `$PETSC_DIR/$PETSC_ARCH/lib` and header files in `$PETSC_DIR/$PETSC_ARCH/include`. `PETSC_DIR` and `PETSC_ARCH` are environment variables pointing to a specific PETSc instance based on the PETSc module loaded.
 
 * dense linear algebra
-  * [Elemental](http://libelemental.org/)
+  * [Elemental][l]
 * sparse linear system solvers
-  * [Intel MKL Pardiso](https://software.intel.com/en-us/node/470282)
-  * [MUMPS](http://mumps.enseeiht.fr/)
-  * [PaStiX](http://pastix.gforge.inria.fr/)
-  * [SuiteSparse](http://faculty.cse.tamu.edu/davis/suitesparse.html)
-  * [SuperLU](http://crd.lbl.gov/~xiaoye/SuperLU/#superlu)
-  * [SuperLU_Dist](http://crd.lbl.gov/~xiaoye/SuperLU/#superlu_dist)
+  * [Intel MKL Pardiso][m]
+  * [MUMPS][n]
+  * [PaStiX][o]
+  * [SuiteSparse][p]
+  * [SuperLU][q]
+  * [SuperLU_Dist][r]
 * input/output
-  * [ExodusII](http://sourceforge.net/projects/exodusii/)
-  * [HDF5](http://www.hdfgroup.org/HDF5/)
-  * [NetCDF](http://www.unidata.ucar.edu/software/netcdf/)
+  * [ExodusII][s]
+  * [HDF5][t]
+  * [NetCDF][u]
 * partitioning
-  * [Chaco](http://www.cs.sandia.gov/CRF/chac.html)
-  * [METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/overview)
-  * [ParMETIS](http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview)
-  * [PT-Scotch](http://www.labri.fr/perso/pelegrin/scotch/)
+  * [Chaco][v]
+  * [METIS][w]
+  * [ParMETIS][x]
+  * [PT-Scotch][y]
 * preconditioners & multigrid
-  * [Hypre](http://www.nersc.gov/users/software/programming-libraries/math-libraries/petsc/)
-  * [SPAI - Sparse Approximate Inverse](https://bitbucket.org/petsc/pkg-spai)
+  * [Hypre][z]
+  * [SPAI - Sparse Approximate Inverse][aa]
+
+[a]: http://www.mcs.anl.gov/petsc/
+[b]: http://www.mcs.anl.gov/petsc/documentation/
+[c]: http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf
+[d]: http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/singleindex.html
+[e]: http://www.youtube.com/watch?v=asVaFg1NDqY
+[f]: http://www.youtube.com/watch?v=ubp_cSibb9I
+[g]: http://www.youtube.com/watch?v=vJAAAQv-aaw
+[h]: http://www.youtube.com/watch?v=BKVlqWNh8jY
+[i]: http://www.youtube.com/watch?v=iXkbLEBFjlM
+[j]: https://www.mcs.anl.gov/petsc/miscellaneous/petscthreads.html
+[k]: http://www.mcs.anl.gov/petsc/miscellaneous/external.html
+[l]: http://libelemental.org/
+[m]: https://software.intel.com/en-us/node/470282
+[n]: http://mumps.enseeiht.fr/
+[o]: http://pastix.gforge.inria.fr/
+[p]: http://faculty.cse.tamu.edu/davis/suitesparse.html
+[q]: http://crd.lbl.gov/~xiaoye/SuperLU/#superlu
+[r]: http://crd.lbl.gov/~xiaoye/SuperLU/#superlu_dist
+[s]: http://sourceforge.net/projects/exodusii/
+[t]: http://www.hdfgroup.org/HDF5/
+[u]: http://www.unidata.ucar.edu/software/netcdf/
+[v]: http://www.cs.sandia.gov/CRF/chac.html
+[w]: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
+[x]: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview
+[y]: http://www.labri.fr/perso/pelegrin/scotch/
+[z]: http://www.nersc.gov/users/software/programming-libraries/math-libraries/petsc/
+[aa]: https://bitbucket.org/petsc/pkg-spai

docs.it4i/software/numerical-libraries/trilinos.md

@@ -18,7 +18,7 @@ Current Trilinos installation on ANSELM contains (among others) the following ma
 * **IFPACK** - distributed algebraic preconditioner (includes e.g. incomplete LU factorization)
 * **Teuchos** - common tools packages. This package contains classes for memory management, output, performance monitoring, BLAS and LAPACK wrappers etc.
 
-For the full list of Trilinos packages, descriptions of their capabilities, and user manuals see [http://trilinos.sandia.gov.](http://trilinos.sandia.gov)
+For the full list of Trilinos packages, descriptions of their capabilities, and user manuals [see][a].
 
 ## Installed Version
 
@@ -47,3 +47,5 @@ include Makefile.export.<package>
 ```
 
 if you are interested only in a specific Trilinos package. This will give you access to the variables such as Trilinos_CXX_COMPILER, Trilinos_INCLUDE_DIRS, Trilinos_LIBRARY_DIRS etc.
+
+[a]: http://www.mcs.anl.gov/petsc/miscellaneous/external.html