Building PETSc¶

Quickstart¶

This tutorial walks you through installing the PETSc library on a local, UNIX-style machine for the first time using MPICH and BLAS/LAPACK.

Commands

./configure --download-mpich --download-fblaslapack

or if MPI and BLAS/LAPACK is installed and in $PATH

./configure

Prerequisites¶

Important

This tutorial assumes basic knowledge on the part of the user on how to navigate your system using the Command-Line Interface (CLI), a.k.a. “from the terminal”. Being a library-based solver suite, PETSc does not have a front-end Graphical User Interface, so all tutorial examples here will heavily use the CLI.

While this tutorial will provide all commands necessary, it will not explain the usage or syntax of commands not directly written by PETSc. If you find the commands confusing, consider reviewing tutorials on basic UNIX and shell usage.

Before beginning, make sure you have the following necessary pre-requisites installed and up to date:

It is important to make sure that your compilers are correctly installed (i.e. functional and in your $PATH). To test the compilers, run the following commands:

printf '#include<stdio.h>\nint main(){printf("cc OK!\\n");}' > t.c && cc t.c && ./a.out && rm -f t.c a.out

Note

While it is recommended that you have functional C++ and Fortran compilers installed, they are not directly required to run PETSc in its default state. If they are functioning, PETSc will automatically find them during the configure stage, however it is always useful to test them on your own.

printf '#include<iostream>\nint main(){std::cout<<"c++ OK!"<<std::endl;}' > t.cpp && cc++ t.cpp && ./a.out && rm -f t.cpp a.out
printf 'program t\nprint"(a)","gfortran OK!"\nend program' > t.f90 && gfortran t.f90 && ./a.out && rm -f t.f90 a.out

If compilers are working, each command should print out <compiler_name> OK! on the command line.

Should you be missing any of these dependencies or would like to update them, either download and install the latest versions from their respective websites, or use your preferred package manager to update them. For example on macOS using homebrew to install Python:

brew update
brew list    # Show all packages installed through brew
brew upgrade # If they are already installed through brew!
brew install python

Downloading Source¶

With all dependencies installed, navigate to a suitable directory on your machine and pull the latest version of the PETSc library to your machine with git. This will create a directory “petsc” inside the current directory and retrieve the latest master branch of the repository.

mkdir -p ~/my/petsc/dir/
cd ~/my/petsc/dir/
git clone -b maint https://gitlab.com/petsc/petsc
cd petsc

Warning

It is IMPERATIVE to install PETSc in a directory whose path does not contain any of the following special characters:

~ ! @ # $ % ^ & * ( ) ` ; < > ? , [ ] { } ‘ ” | (including spaces!)

While PETSc is equipped to handle these errors, other installed dependencies may not be so well protected.

The download process may take a few minutes to complete. Successfully running this command should yield a similar output:

git clone -b maint https://gitlab.com/petsc/petsc.git petsc

Cloning into 'petsc'...
remote: Enumerating objects: 862597, done.
remote: Counting objects: 100% (862597/862597), done.
remote: Compressing objects: 100% (197622/197622), done.
remote: Total 862597 (delta 660708), reused 862285 (delta 660444)
Receiving objects: 100% (862597/862597), 205.11 MiB | 3.17 MiB/s, done.
Resolving deltas: 100% (660708/660708), done.
Updating files: 100% (7748/7748), done.

cd petsc
git pull

Already up to date.

At this stage we will refer to ~/my/petsc/dir/petsc as $PETSC_DIR to avoid clutter.

Configuration¶

Next, PETSc needs to be configured using ./configure for your system with your specific options. This is the stage where users can specify the exact parameters to customize their PETSc installation. Common configuration options are:

Specifying different compilers
Specifying different MPI implementations
Enabling CUDA/OpenCL/ViennaCL support
Specifying options for BLAS/LAPACK
Specifying external packages to use or download automatically. PETSc can automatically download and install a wide range of other software, such as direct solvers.
Setting various known machine quantities for PETSc to use such as additional compiler flags

Important

You MUST specify all of your configuration options at this stage. In order to enable additional options or packages in the future, you will have to reconfigure your PETSc installation in a similar manner with these options enabled.

For a full list of available options call ./configure --help from $PETSC_DIR

All PETSc options and flags follow the standard CLI formats --option-string=<value> or --option-string, where <value> is typically either 1 (for true) or 0 (for false) or a directory path. Directory paths must be absolute (i.e. full path from the root directory of your machine), but do accept environment variables as input.

From $PETSC_DIR call the following ./configure command to configure PETSc as well as download and install MPICH on your system.

./configure --download-mpich --download-fblaslapack

PETSc will begin configuring and printing its progress. A successful configure will have the following general structure as its output:

===============================================================================
          Configuring PETSc to compile on your system
===============================================================================
TESTING: configureSomething from PETSc.something(config/PETSc/configurescript.py:lineNUM)
===============================================================================
          Trying to download MPICH_DOWNLOAD_URL for MPICH
===============================================================================
===============================================================================
          Running configure on MPICH; this may take several minutes
===============================================================================
===============================================================================
          Running make on MPICH; this may take several minutes
===============================================================================
===============================================================================
          Running make install on MPICH; this may take several minutes
===============================================================================
===============================================================================
          Trying to download FBLASLAPACK_URL for FBLASLAPACK
===============================================================================
===============================================================================
          Compiling FBLASLAPACK; this may take several minutes
===============================================================================
===============================================================================
          Trying to download SOWING_DOWNLOAD_URL for SOWING
===============================================================================
===============================================================================
          Running configure on SOWING; this may take several minutes
===============================================================================
===============================================================================
          Running make on SOWING; this may take several minutes
===============================================================================
===============================================================================
          Running make install on SOWING; this may take several minutes
===============================================================================
Compilers:
  C Compiler:   Location information and flags
C++ Compiler: Location information and flags
.
.
.
MPI:
     Includes:     Include path
Other Installed Packages:
.
.
.
PETSc:
     PETSC_ARCH: {YOUR_PETSC_ARCH}
PETSC_DIR:  {YOUR_PETSC_DIR}
.
.
.
.

xxx=========================================================================xxx
Configure stage complete. Now build PETSc libraries with (gnumake build):
make PETSC_DIR=/your/petsc/dir PETSC_ARCH=your-petsc-arch  all
xxx=========================================================================xxx

Warning

At this stage it is useful to make a note of the $PETSC_DIR and $PETSC_ARCH variables, and set them as environment variables. Copy the values directly from your configure output:

export PETSC_DIR=/your/petsc/dir
export PETSC_ARCH=your-petsc-arch

You should set them in a login file (e.g. ~/.bash_profile) to avoid having to reset them every time you open a fresh terminal.

echo "export PETSC_DIR=/your/petsc/dir" >> ~/.bash_profile
echo "export PETSC_ARCH=your-petsc-arch" >> ~/.bash_profile

Compilation¶

After successfully configuring, build the binaries from source using the make command. This stage may take a few minutes, and will consume a great deal of system resources as the binaries are compiled in parallel.

If $PETSC_DIR and $PETSC_ARCH are defined as environment variables:

make all check

If $PETSC_DIR and $PETSC_ARCH are not defined as environment variables, or you have another installation of PETSc on the machine:

make PETSC_DIR=/your/petsc/dir PETSC_ARCH=your-petsc-arch all check

A successful make will provide an output of the following structure:

-----------------------------------------
PETSC_VERSION_RELEASE
.
.
.
-----------------------------------------
#define SOME_PETSC_VARIABLE
.
.
.
-----------------------------------------
Installed Compiler, Package, and Library Information
.
.
.
=========================================
       FC arch-darwin-c-debug/obj/sys/f90-mod/petscsysmod.o
       FC arch-darwin-c-debug/obj/sys/fsrc/somefort.o
       FC arch-darwin-c-debug/obj/sys/f90-src/fsrc/f90_fwrap.o
       CC arch-darwin-c-debug/obj/sys/info/verboseinfo.o
       CC arch-darwin-c-debug/obj/sys/info/ftn-auto/verboseinfof.o
       CC arch-darwin-c-debug/obj/sys/info/ftn-custom/zverboseinfof.o
       .
       .
       .
       FC arch-darwin-c-debug/obj/snes/f90-mod/petscsnesmod.o
       FC arch-darwin-c-debug/obj/ts/f90-mod/petsctsmod.o
       FC arch-darwin-c-debug/obj/tao/f90-mod/petsctaomod.o
  CLINKER arch-darwin-c-debug/lib/libpetsc.3.11.3.dylib
 DSYMUTIL arch-darwin-c-debug/lib/libpetsc.3.11.3.dylib
gmake[2]: Leaving directory '/your/petsc/dir'
gmake[1]: Leaving directory '/your/petsc/dir'
=========================================
Running test examples to verify correct installation
Using PETSC_DIR=/your/petsc/dir and PETSC_ARCH=your-petsc-arch
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI process
C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 MPI processes
Fortran example src/snes/examples/tutorials/ex5f run successfully with 1 MPI process
Completed test examples

Congratulations!¶

You now have a working PETSc installation and are ready to start using the library.

The next tutorial will demonstrate how to run your first program using PETSc.

Table of Contents

Previous topic

Next topic

This Page