Install.md

INSTALL.md

@@ -0,0 +1,178 @@
+# Installation Guide
+
+## Basic install
+
+Most users will be fine using the binary bundled in the default `pip` install:
+
+```shell
+pip install mfem
+```
+The above installation will download and install a *serial* version of `MFEM`.
+
+##  Building from source
+PyMFEM has many options for installation, when building from source, including:
+ - Serial and parallel (MPI) wrappers
+ - Using pre-built local dependencies
+ - Installing additional dependencies such as
+   - `hypre`
+   - `gslib`
+   - `libceed`
+   - `metis`
+
+Most of the options for PyMFEM can be used directly when installing via `python setup.py install`, e.g.
+```shell
+git clone git@github:mfem/PyMFEM.git
+cd PyMFEM
+python setup.py install --user
+```
+For example, parallel (MPI) support is built with  the `--with-parallel` flag:
+```shell
+python setup.py install --with-parallel
+```
+
+Note: this option turns on building `metis` and `Hypre`
+
+## Commonly used flags
+
+| Flag | Description |
+|------|-------------|
+| `--with-parallel` | Install both serial and parallel versions of `MFEM` and the wrapper<br>(note: this option turns on building `metis` and `hypre`) |
+| `--mfem-branch=<reference>` | Download/install MFEM using a specific reference (`git` `branch`, `hash`, or `tag`) |
+| `--user` | Install in user's site-package |
+
+In order to see the full list of options, use
+
+```shell
+python setup.py install --help
+```
+
+## Advanced options
+
+### Suitesparse
+`--with-suitesparse` : build MFEM with `suitesparse`. `suitesparse` needs to be installed separately.
+Point to the location of `suitesparse` using the flag `--suitesparse-prefix=<location>`
+
+Note: this option turns on building `metis` in serial
+
+### CUDA
+`--with-cuda` : build MFEM with CUDA. Hypre cuda build is also supported using
+`--with-cuda-hypre`. `--cuda-arch` can be used to specify cuda compute capablility.
+(See table in https://en.wikipedia.org/wiki/CUDA#Supported_GPUs)
+
+CUDA needs to be installed separately and nvcc must be found in PATH ([Example](https://github.com/mfem/PyMFEM/blob/e1466a6a/.github/workflows/build-and-test-callable.yml#L111-L122)).
+
+(examples)
+```shell
+python setup.py install --with-cuda
+
+python setup.py install --with-cuda --with-cuda-hypre
+
+python setup.py install --with-cuda --with-cuda-hypre --cuda-arch=80 (A100)
+
+python setup.py install --with-cuda --with-cuda-hypre --cuda-arch=75 (Turing)
+```
+
+### gslib
+`--with-gslib` : build MFEM with [GSlib](https://github.com/Nek5000/gslib)
+
+Note: this option downloads and builds GSlib
+
+### libCEED
+`--with-libceed` : build MFEM with [libCEED](https://github.com/CEED/libCEED)
+
+Note: this option downloads and builds libCEED
+
+### Specifying compilers
+| Flag | Description |
+|------|--------|
+| `--CC` | c compiler |
+| `--CXX` | c++ compiler |
+| `--MPICC` | mpic compiler |
+| `--MPICXX` | mpic++ compiler |
+
+(example)
+Using Intel compiler
+```shell
+python setup.py install --with-parallel --CC=icc, --CXX=icpc, --MPICC=mpiicc, --MPICXX=mpiicpc
+```
+
+### Building MFEM with specific version
+By default, setup.py build MFEM with specific SHA (which is usually the released latest version).
+In order to use the latest MFEM in Github. One can specify the branch name or SHA using mfem-branch
+option.
+
+`--mfem-branch = <branch name or SHA>`
+
+(example)
+```shell
+python setup.py install --mfem-branch=master
+```
+
+### Using MFEM build externally.
+These options are used to link PyMFEM wrapper with existing MFEM library. We need `--mfem-source`
+and `--mfem-prefix`
+
+| Flag                       | Description                                                       |
+|----------------------------|-------------------------------------------------------------------|
+| `--mfem-source <location>` | The location of MFEM source used to build MFEM |
+| `--mfem-prefix <location>` | The location of the MFEM library. `libmfem.so` needs to be found in `<location>/lib` |
+| `--mfems-prefix <location>`| (optional) Specify serial MFEM location separately |
+| `--mfemp-prefix <location>`| (optional) Specify parallel MFEM location separately |
+
+
+### Blas and Lapack
+--with-lapack : build MFEM with lapack
+
+`<location>` is used for CMAKE call to buid MFEM
+`--blas-libraries=<location>`
+`--lapack-libraries=<location>`
+
+### Options for development and testing
+| Flag | Description |
+|------|--------|
+| `--swig` | run swig only |
+| `--skip-swig` | build without running swig` |
+| `--skip-ext` | skip building external libraries.|
+| `--ext-only` | build exteranl libraries and exit.|
+
+During the development, often we update depenencies (such as MFEM) and edit `*.i` file.
+
+
+First clean everything.
+
+```shell
+python setup.py clean --all
+```
+
+Then, build externals alone
+```shell
+python setup.py install --with-parallel --ext-only --mfem-branch=master
+```
+
+Then, genrate swig wrappers.
+```shell
+python setup.py install --with-parallel --swig --mfem-branch=master
+```
+
+If you are not happy with the wrapper (`*.cxx` and `*.py`), you edit `*.i` and redo
+the same. When you are happy, build the wrapper. `--swig` does not clean the
+existing wrapper. So, it will only update wrapper for updated `*.i`
+
+When building a wrapper, you can use `--skip-ext` option. By default, it will re-run
+swig to generate entire wrapper codes.
+```shell
+python setup.py install --with-parallel --skip-ext --mfem-branch=master
+```
+
+If you are sure, you could use `--skip-swig` option, so that it compiles the wrapper
+codes without re-generating it.
+```shell
+python setup.py install --with-parallel --skip-ext --skip-swig --mfem-branch=master
+```
+
+### Other options
+`--unverifiedSSL` :
+   This addresses error relating SSL certificate. Typical error message is
+   `<urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:xxx)>`
+
+

README.md

@@ -11,7 +11,7 @@ By default, "pip install mfem" downloads and builds the serial version of MFEM a
 Additionally, the installer supports building MFEM with specific options together with other external libraries, including MPI version.
 
 ## Install
-```bash
+```shell
 pip install mfem                    # binary install is available only on linux platforms (Py36-310)
 pip install mfem --no-binary mfem   # install serial MFEM + wrapper from source
 
@@ -24,12 +24,12 @@ and build parallel version of MFEM library (linked with Metis and Hypre)
 and installs under <prefix>/mfem. See also, docs/install.txt
 
 ### Using pip
-```bash
-$ pip install mfem --install-option="--with-parallel" 
+```shell
+pip install mfem --install-option="--with-parallel"
 ```
 
 ### Build from local source file
-```python
+```shell
 # Download source and build
 $ pip download mfem --no-binary mfem (expand tar.gz file and move to the downloaded directory)
 or clone this repository
@@ -59,75 +59,80 @@ $ python setup.py install --help
 ```
 
 ## Usage
-Here is an example to solve div(alpha grad(u)) = f in a square and to plot the result
-with matplotlib (modified from ex1.cpp). Use the badge above to open this in Binder.
+This example (modified from `ex1.cpp`) solves the Poisson equation,
+$$\nabla \cdot (\alpha \nabla u) = f$$
+in a square and plots the result using matplotlib.
+Use the badge above to open this in Binder.
+
 ```python
 import mfem.ser as mfem
 
-# create sample mesh for square shape
+# Create a square mesh
 mesh = mfem.Mesh(10, 10, "TRIANGLE")
 
-# create finite element function space
+# Define the finite element function space
 fec = mfem.H1_FECollection(1, mesh.Dimension())   # H1 order=1
 fespace = mfem.FiniteElementSpace(mesh, fec)
 
-#
+# Define the essential dofs
 ess_tdof_list = mfem.intArray()
 ess_bdr = mfem.intArray([1]*mesh.bdr_attributes.Size())
 fespace.GetEssentialTrueDofs(ess_bdr, ess_tdof_list)
 
-# constant coefficient (diffusion coefficient and RHS)
+# Define constants for alpha (diffusion coefficient) and f (RHS)
 alpha = mfem.ConstantCoefficient(1.0)
 rhs = mfem.ConstantCoefficient(1.0)
 
-# Note:
-#    Diffusion coefficient can be variable. To use numba-JIT compiled
-#    functio. Use the following, where x is numpy-like array.
-# @mfem.jit.scalar
-# def alpha(x):
-#     return x+1.0
-#
+"""
+Note
+-----
+In order to represent a variable diffusion coefficient, you
+must use a numba-JIT compiled function. For example:
 
-# define Bilinear and Linear operator
+>>> @mfem.jit.scalar
+>>> def alpha(x):
+>>>     return x+1.0
+"""
+
+# Define the bilinear and linear operators
 a = mfem.BilinearForm(fespace)
 a.AddDomainIntegrator(mfem.DiffusionIntegrator(alpha))
 a.Assemble()
 b = mfem.LinearForm(fespace)
 b.AddDomainIntegrator(mfem.DomainLFIntegrator(rhs))
 b.Assemble()
 
-# create gridfunction, which is where the solution vector is stored
-x = mfem.GridFunction(fespace);
+# Initialize a gridfunction to store the solution vector
+x = mfem.GridFunction(fespace)
 x.Assign(0.0)
 
-# form linear equation (AX=B)
+# Form the linear system of equations (AX=B)
 A = mfem.OperatorPtr()
 B = mfem.Vector()
 X = mfem.Vector()
-a.FormLinearSystem(ess_tdof_list, x, b, A, X, B);
+a.FormLinearSystem(ess_tdof_list, x, b, A, X, B)
 print("Size of linear system: " + str(A.Height()))
 
-# solve it using PCG solver and store the solution to x
+# Solve the linear system using PCG and store the solution in x
 AA = mfem.OperatorHandle2SparseMatrix(A)
 M = mfem.GSSmoother(AA)
 mfem.PCG(AA, M, B, X, 1, 200, 1e-12, 0.0)
 a.RecoverFEMSolution(X, b, x)
 
-# extract vertices and solution as numpy array
+# Extract vertices and solution as numpy arrays
 verts = mesh.GetVertexArray()
 sol = x.GetDataArray()
 
-# plot solution using Matplotlib
-
+# Plot the solution using matplotlib
 import matplotlib.pyplot as plt
 import matplotlib.tri as tri
 
 triang = tri.Triangulation(verts[:,0], verts[:,1])
 
-fig1, ax1 = plt.subplots()
-ax1.set_aspect('equal')
-tpc = ax1.tripcolor(triang, sol, shading='gouraud')
-fig1.colorbar(tpc)
+fig, ax = plt.subplots()
+ax.set_aspect('equal')
+tpc = ax.tripcolor(triang, sol, shading='gouraud')
+fig.colorbar(tpc)
 plt.show()
 ```
 ![](https://raw.githubusercontent.com/mfem/PyMFEM/master/docs/example_image.png)