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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head> <link rel="canonical" href="http://www.mcs.anl.gov/petsc/petsc-current/docs/installation.html" />
<meta http-equiv="content-type" content="text/html;charset=utf-8">
<title>Documentation: Installation</title>
</head>
<body bgcolor="#ffffff">
<div id="version" align=right><b>petsc-3.14.5 2021-03-03</b></div>
<div id="bugreport" align=right><a href="mailto:petsc-maint@mcs.anl.gov?subject=Typo or Error in Documentation &body=Please describe the typo or error in the documentation: petsc-3.14.5 v3.14.5 docs/installation.html "><small>Report Typos and Errors</small></a></div>
<h1>Documentation: Installation</h1>
<style type="text/css">
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<div id="main">
<!-- This is here for the grepping between begin / end, weaksauce! -->
<h3>Quick Instructions:</h3>
<ul>
<li>
On systems where MPI and BLAS/LAPACK are installed.
<ul class="code">
<li>./configure</li>
<li>make all check</li>
</ul>
</li>
<li>
Or to specify compilers and have PETSc download and install MPI and BLAS/LAPACK (when they are not already on your machine)
<ul class="code">
<li>./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-fblaslapack</li>
<li>make all check</li>
</ul>
</li>
<li>
<a style="color: rgb(204,102,0);" href="#windows"><b>Microsoft Windows installation</b></a> and <a style="color: rgb(204,102,0);" href="#doemachines"><b>DOE large scale systems installation</b></a>
</li>
</ul>
Don't need Fortran, use --with-fortran-bindings=0 to reduce the build times. If you are not using external packages
that use Fortran (for example, MUMPS requires Fortran) you can use --with-fc=0 for even faster build times.
<h3>Encounter problems?</h3>
<ul>
<li><b>Read the error message from ./configure!</b></li>
<li>Read help <code>./configure --help</code></li>
<li>Refer to <a href="#exampleusage">example usages</a> (e.g., build PETSc without a Fortran compiler)</li>
<li><i><b>make</i></b> problems? Just copy/paste <i><b>make</i></b> command printed by configure including any PETSC_DIR and PETSC_ARCH options</li>
<li> Check the <a href="https://www.mcs.anl.gov/petsc/documentation/bugreporting.html">bug-reporting</a> section</li>
</ul>
<h3>Notes:</h3>
<ul>
<li>Please obtain PETSc via the <a href="../download/index.html">repository</a> or download the <b>latest</b> patched tarball
<li>To extract the sources use: <code>gunzip -c petsc-<version number>.tar.gz | tar -xof -</code></li>
<li>We highly recommend installing PETSc as a <b>regular/non-root user</b>, perhaps in <b>/home/username/soft</b></li>
</ul>
<h3>Table of Contents:</h3>
<ul>
<li><a href="#exampleusage">Example usages</a></li>
<li><a href="#compilers">Specify compilers and compiler options used to build PETSc [and perhaps external packages]</a></li>
<li><a href="#external">External packages</a></li>
<li><a href="#blaslapack">BLAS and LAPACK problems</a></li>
<li><a href="#mpi">MPI problems / I don't want MPI</a></li>
<li><a href="#root">Installation location: in-place or out-of-place.</li>
<li><a href="#envvars">Environmental variables PETSC_DIR and PETSC_ARCH</li>
<li><a href="#cross">Installing on machine requiring cross compiler or a job scheduler</a></li>
<li><a href="#windows">Microsoft Windows installation</a></li>
<li><a href="#usingtau">Installing with TAU instrumentation package</a></li>
<li><a href="#CUDA">Installing PETSc to use NVIDIA GPUs (aka CUDA)</a></li>
<li><a href="#Kokkos">Installing PETSc with Kokkos</a></li>
<li><a href="#OpenCL">Installing PETSc to use GPUs and accelerators via OpenCL (NVIDIA, AMD, and Intel)</a></li>
<li><a href="#pkgconfig">PETSc ./configure automatically generates Pkgconfig and module files for each install</a></li>
<li><a href="#doemachines">Installing on large scale DOE systems</a></li>
<li><a href="#iosandroid">Installing PETSc on an iOS or Android platform</a></li>
</ul>
</div>
<hr>
<div id="details">
<div>
<h3><a name="exampleusage">Example Usages:</a></h3>
<ul>
<li>
Examples are at <b>config/examples/*.py</b>. We use some of these scripts
locally for testing - for example one can update these files and run as:
<ul>
<li>./config/examples/arch-osx-10.6.py</li>
</ul>
</li>
<li>
Assuming BLAS, LAPACK, MPICH are not currently
installed <code>./configure</code> will download & install BLAS,
LAPACK, MPICH if they are not already installed on the system):
<ul>
<li>./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack --download-mpich</li>
</ul>
</li>
<li>
Same as above - but do not have a fortran compiler [and want to use PETSc from C only].
<ul>
<li>./configure --with-cc=gcc --with-cxx=0 --with-fc=0 --download-f2cblaslapack --download-mpich</li>
</ul>
</li>
<li>
Same as above - but install in a user specified (prefix) location.
<ul>
<li>./configure --prefix=/home/user/soft/petsc-install --with-cc=gcc --with-cxx=0 --with-fc=0 --download-f2cblaslapack --download-mpich</li>
</ul>
</li>
<li>
If BLAS, LAPACK, MPI sources (in "-devel" packages in most distros) are already installed in default system/compiler locations and mpicc,
mpif90, mpiexec are available via PATH - configure does not require any additional options.
<ul>
<li>./configure</li>
</ul>
</li>
<li>
If BLAS, LAPACK, MPI are already installed in known user location use:<br>
[Note: Do not specify --with-cc --with-fc etc when using --with-mpi-dir -
so that mpicc/mpif90 can be picked up from mpi-dir]
<ul>
<li>./configure --with-blaslapack-dir=/usr/local/blaslapack --with-mpi-dir=/usr/local/mpich</li>
</ul>
or
<ul>
<li>./configure --with-blaslapack-dir=/usr/local/blaslapack --with-cc=/usr/local/mpich/bin/mpicc --with-mpi-f90=/usr/local/mpich/bin/mpif90 --with-mpiexec=/usr/local/mpich/bin/mpiexec</li>
</ul>
</li>
<li>
Build Complex version of PETSc [using c++ compiler]:
<ul>
<li>./configure --with-cc=gcc --with-fc=gfortran --with-cxx=g++ --with-clanguage=cxx --download-fblaslapack --download-mpich --with-scalar-type=complex</li>
</ul>
</li>
<li>
Install 2 variants of PETSc, one with gnu, the other with Intel compilers. Specify different PETSC_ARCH for each build.
<ul>
<li>./configure PETSC_ARCH=linux-gnu --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich</li>
<li>make PETSC_ARCH=linux-gnu all test</li>
<li>./configure PETSC_ARCH=linux-gnu-intel --with-cc=icc --with-cxx=icpc --with-fc=ifort --download-mpich --with-blaslapack-dir=/usr/local/mkl</li>
<li>make PETSC_ARCH=linux-gnu-intel all test</li>
</ul>
</li>
</ul>
</div><!-- #exampleusage -->
<hr>
<div>
<h3><a name="compilers">Compilers:</a></h3>
<p>Specify compilers and compiler options used to build PETSc [and perhaps external packages]</p>
<ul>
<li>
Specify compilers using the options <code>--with-cc --with-cxx --with-fc</code> for c, c++, and fortran compilers
<ul>
<li>--with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90</li>
<li>--with-cc=gcc --with-cxx=g++ --with-fc=gfortran</li>
<li>--with-cc=gcc --with-cxx=g++ --with-fc=gfortran</li>
</ul>
</li>
<li>
If fortran compiler is not available or not needed - then disabling using fortran
<ul>
<li>--with-fc=0</li>
</ul>
</li>
<li>
If a C++ compiler is not available or not needed - disable configuring with it
<ul>
<li>--with-cxx=0</li>
</ul>
</li>
<li>
If no compilers are specified - configure will
automatically look for available MPI or regular
compilers in the user's PATH
<ul>
<li>mpicc/mpiCC/mpif90</li>
<li>gcc/g++/gfortran</li>
<li>cc/CC etc..</li>
</ul>
</li>
<li>
It's best to use MPI compilers
as this will avoid the situation where MPI is compiled
with one set of compilers [like gcc/gfortran] and user
specified incompatible compilers to PETSc [perhaps
icc/ifort]. This can be done by either specifying
--with-cc=mpicc or --with-mpi-dir [and not
--with-cc=gcc]
<ul>
<li>--with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90</li>
<li>--with-mpi-dir=/opt/mpich2-1.1 [but <b>*no*</b> --with-cc=gcc]</li>
</ul>
</li>
<li>
Configure defaults to building PETSc in debug mode.
One can switch to using optimzed mode with the configure
option --with-debugging=0 (We suggest using a different PETSC_ARCH for debug and optimized builds, for example arch-debug and arch-opt, this
way you can switch between debugging your code and running for performance by simply changing the value of PETSC_ARCH.
Additionally one can specify more suitable optimization
flags with the options COPTFLAGS, FOPTFLAGS,
CXXOPTFLAGS. For example when using gnu compilers with corresponding
optimization flags:
<ul>
<li>./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --with-debugging=0 COPTFLAGS='-O3 -march=native -mtune=native' CXXOPTFLAGS='-O3 -march=native -mtune=native' FOPTFLAGS='-O3 -march=native -mtune=native' --download-mpich</li>
</ul>
</li>
<li>
Configure cannot detect compiler libraries for certain
set of compilers. In this case one can specify
additional system/compiler libraries using the LIBS option
<ul>
<li>./configure --LIBS='-ldl /usr/lib/libm.a' </li>
</ul>
</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #compilers -->
<hr>
<div id="externalpackages">
<h3><a name="external">External Packages:</a></h3>
<p>
PETSc provides interfaces to various <a href="../miscellaneous/external.html">external packages</a>.
BLAS/LAPACK is a required package, MPI is not required if running sequentially. One can optionally use
<a href="linearsolvertable.html">external solvers</a> like Hypre, MUMPS, etc. from within PETSc applications.
</p>
<p>
PETSc configure has the ability to download and install these external packages. Alternatively if these packages
are already installed, then configure can detect and use them.
</p>
<p>
If you are behind a firewall and cannot use a proxy for the downloads or have a very slow network use the additional option <code>--with-packages-download-dir=/adirectory</code>.
This will trigger ./configure to print the URLs of all the packages you must download this directory (do not uncompress or untar the files) and then
use these copies of the packages instead of trying to download them directly from the internet.
</p>
<p>The following modes can be used to install/use external packages with configure.</p>
<ul>
<li>
<span class="def">--download-PACKAGENAME</span>: Download specified
package and install it and configure PETSc to use this package.
<ul>
<li>--download-fblaslapack --download-mpich</li>
<li>--download-scalapack --download-mumps</li>
</ul>
</li>
<li>
<span class="def">--download-PACKAGENAME=/PATH/TO/package.tar.gz</span>:
If ./configure cannot automatically download the package
[due to network/firewall issues], one can download the
package by alternative means [perhaps wget, curl, or scp via some
other machine]. Once the tarfile is downloaded, the path
to this file can be specified to configure with this
option. Configure will proceed to install this package and
then configure PETSc with it.
<ul>
<li>--download-mpich=/home/petsc/mpich2-1.0.4p1.tar.gz</li>
</ul>
</li>
<li>
<span class="def">--with-PACKAGENAME-dir=PATH</span>:
If the external package is already installed - specify
its location to configure [it will attempt to detect,
include, library files from this location.] Normally this
corresponds to the top-level installation dir for the
package.
<ul>
<li>--with-mpi-dir=/home/petsc/software/mpich2-1.0.4p1</li>
</ul>
Note that we hightly recommend you have PETSc download and install the external packages rather than you installing them separately first. The reason is
that this insures the packages are installed with the same compilers and compiler options etc as PETSc so that they can work together.
</li>
<li>
<span class="def">--with-PACKAGENAME-include=INCLUDEPATH --with-PACKAGENAME-lib=LIBRARYLIST</span>:
Usually a package is defined completely by its include file location -
and library list. [If the package is already installed] - then one can use
these two options to specify the package to configure. For example
<ul>
<li>
--with-superlu-include=/home/petsc/software/superlu/include
--with-superlu-lib=/home/petsc/software/superlu/lib/libsuperlu.a
</li>
<li>
--with-parmetis-include=/sandbox/balay/parmetis/include
--with-parmetis-lib="-L/sandbox/balay/parmetis/lib -lparmetis -lmetis"
</li>
<li>
--with-parmetis-include=/sandbox/balay/parmetis/include
--with-parmetis-lib=[/sandbox/balay/parmetis/lib/libparmetis.a,libmetis.a]
</li>
</ul>
</li>
</ul>
<b>Notes:</b>
<ul>
<li>
Run <code>./configure --help</code> to get the list of external
packages and corresponding additional options [for example
<code>--with-mpiexec</code> for MPICH]
</li>
<li>
Generally one would use either one of the above 4 modes for any given
package - and not mix these. [i.e mixing <code>--with-mpi-dir</code> and
<code>--with-mpi-include</code> etc.. should be avoided]
</li>
<li>
Some packages might not support certain options like
<code>--download-PACKAGENAME</code> or
<code>--with-PACKAGENAME-dir</code>. Architectures like Microsoft
Windows might have issues with these options. In these cases,
<code>--with-PACKAGENAME-include --with-PACKAGENAME-lib</code>
options should be preferred.
</li>
<li>
It's best to install some external packages like SuperLU_DIST, MUMPS,
Hypre, METIS, and ParMETIS with the option <code>--download-PACKAGENAME</code>. [the
correct options for these packages are <code>--download-superlu_dist
--download-mumps --download-hypre</code>]
<ul style="color: black">
<li>
This will install the COMPATIBLE version of the external package.
A generic install of this package might not be compatible with
PETSc [perhaps due to version differences - or perhaps due to the
requirement of additional patches for it to work with PETSc]
</li>
<li>
Some packages have bug fixes, portability patches, and upgrades
for dependent packages that have not yet been included in an
upstream release.
</li>
<li>
All packages will be installed with the same set of compilers
- this avoids problems [for example weird link time errors] with
mixing code compiled with multiple compilers [for example mixing
gfortran and ifort compiled code].
</li>
</ul>
</li>
<li>
If you want to download a compatible external package manually, then
the URL for this package is listed in configure source for this
package. For example, check
<code>config/BuildSystem/config/packages/SuperLU.py</code> for the url for
download this package.
</li>
</ul>
<b>Additional options</b>:
<ul>
<li>
<span class="def">--with-packages-build-dir=PATH</span>: By default,
external packages will be unpacked and the build process is run in <code>${PETSC_DIR}/${PETSC_ARCH}/externalpackages</code>.
However one can choose a different location where these packages are unpacked and the build process is run.
</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #externalpackages -->
<hr>
<div>
<h3><a name="blaslapack">BLAS/LAPACK</a></h3>
<p>These packages provide some basic numeric kernels used by PETSc.</p>
<ul>
<li>
Configure will automatically look for blas/lapack in certain standard
locations, on most systems you should not need to provide any
information about BLAS/LAPACK in the ./configure command.
</li>
<li>
One can use the following options to let configure download/install BLAS/LAPACK automatically.
<ul>
<li>--download-fblaslapack [when fortran compiler is present]</li>
<li>--download-f2cblaslapack [when configuring without a fortran compiler - i.e --with-fc=0]</li>
</ul>
</li>
<li>
Alternatively one can use other options like one of the following.
<ul>
<li>--with-blaslapack-lib=libsunperf.a</li>
<li>--with-blas-lib=libblas.a --with-lapack-lib=liblapack.a</li>
<li>--with-blaslapack-dir=/soft/com/packages/intel/13/079/mkl</li>
</ul>
</li>
</ul>
<b>Notes:</b>
<ul>
<li> <h4> Intel MKL</h4>
Intel provides BLAS/LAPACK via the <a href="https://software.intel.com/en-us/mkl">MKL</a> library.
It usually works from GNU/Intel compilers on Linux and Microsoft/Intel compilers on Microsoft Windows.
One can specify it to PETSc configure with for example: <code>--with-blaslapack-dir=$MKLROOT</code> or, for example,
<code>--with-blaslapack-dir=/soft/com/packages/intel/13/079/mkl</code>
<br>
If the above option does not work - one could determine the correct library list for your compilers using
<a href="https://software.intel.com/sites/products/mkl/">Intel MKL Link Line Advisor</a>
and specify with the configure option <code>--with-blaslapack-lib</code>
</li>
<li> <h4>IBM ESSL</h4>
Sadly, IBM's ESSL does not have all the routines of BLAS and LAPACK
that some packages, such as SuperLU expect; in particular slamch,
dlamch and xerbla. In this case instead of using ESSL we suggest
<code>--download-fblaslapack</code>. If you really want to use ESSL,
see <a href="https://www.pdc.kth.se/hpc-services">https://www.pdc.kth.se/hpc-services</a>.
</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #blas -->
<hr>
<div id="mpi">
<h3><a name="mpi">MPI</a></h3>
<p>This software provides the parallel functionality for PETSc.</p>
<ul>
<li>Configure will automatically look for MPI compilers mpicc/mpif90 etc and use them if found in your PATH.</li>
<li>
One can use the following options to let configure download/install MPI automatically
<ul>
<li>--download-mpich [install and use MPICH]</li>
<li>--download-openmpi [Install and use Open MPI]</li>
</ul>
</li>
<li>See <a href="installation.html#external">externalpackages</a> for other installation options.</li>
</ul>
<h4><a name="mpicompilers">Using MPI Compilers:</a></h4>
<ul>
<li>
It's best to install PETSc with MPI compiler wrappers (often called
mpicc, mpicxx, mpif90) - this way, the SAME compilers used to build
MPI are used to build PETSc [this avoids incompatibilities which
might crop up - when using libraries compiled with different c or
fortran compilers.]. This can be achieved with the following
modes.
<ul style="color: black">
<li>
Vendor provided MPI might already be installed. IBM, SGI, Cray etc provide their own:<br>
<code>./config/confiure.py --with-cc=mpcc --with-fc=mpf90</code>
</li>
<li>
If using MPICH which is already installed [perhaps using
myrinet/gm] then use [without specifying --with-cc=gcc etc.so
that configure picks up mpicc from mpi-dir]:<br>
<code>./configure --with-mpi-dir=/path-to-mpich-install</code>
</li>
</ul>
</li>
</ul>
<h4><a name="i-dont-want-to-use-mpi">Installing without MPI:</a></h4>
<ul>
<li>
You can build (sequential) PETSc without an MPI. This is useful for
quickly installing PETSc [if MPI is not available - for whatever
reason]. However - if there is any MPI code in user application, then
its best to install a full MPI - even if the usage is currently
limited to uniprocessor mode.
<ul>
<li>./configure --with-mpi=0</li>
</ul>
</li>
</ul>
<h4>Installing with Open MPI with shared MPI libraries:</h4>
<p>
OpenMPI defaults to building shared libraries for MPI. However, the
binaries generated by MPI wrappers mpicc/mpif90 etc require
LD_LIBRARY_PATH to be set to the location of these libraries.
</p>
<p>
Due to this OpenMPI restriction one has to set
<code>LD_LIBRARY_PATH</code> correctly [per OpenMPI installation
instructions], before running PETSc configure. If you do not set this
environmental variables you will get messages when running
<code>./configure</code> such as
</p>
<pre>
UNABLE to EXECUTE BINARIES for config/configure.py
-------------------------------------------------------------------------------
Cannot run executables created with C. If this machine uses a batch system
to submit jobs you will need to configure using/configure.py with the additional option --with-batch.
Otherwise there is problem with the compilers. Can you compile and run code with your C/C++ (and maybe Fortran) compilers?
</pre>
<p>or when running a code compiled with OpenMPI</p>
<p>
<code>
-bash-3.3$ ./conftest <br>
./conftest: error while loading shared libraries: libmpi.so.0: cannot open shared object file: No such file or directory
</code>
</p>
<h4>Notes:</h4>
<ul>
<li>
Avoid specifing compilers [with options <code>--with-cc</code> or
<code>--with-fc</code>] when using the option
<code>--with-mpi-dir</code>. [Option<code>--with-mpi-dir</code>
specifies using MPI compilers - so its best to use them - and not
overwride them with user specified <code>--with-cc</code>].
</li>
<li>
One can specify mpiexec or mpiexec with the options <code>--with-mpiexec</code>
</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #mpi -->
<hr>
<div>
<h3><a name="root">Installation location: In-place or out-of-place</a></h3>
By default, PETSc does an in-place installation, meaning the libraries are kept in the same directories used to compile PETSc. This is particularly useful for
those application developers who follow the PETSc git repository <code>master</code> or <code>release</code> branches since rebuilds for updates are very quick and painless,
see <a href="saws.html">easyrebuild</a>.
<h4>Out-of-place installation with --prefix</h4>
To install the libraries and include files in another location use the --prefix option
<ul class="code">
<li>./configure --prefix=/home/userid/petsc-3.14.0 [other configure options]</li>
</ul>
The libraries and include files needed by the users will be located in <code>/home/userid/petsc-3.14.0/lib</code> and <code>/home/userid/petsc-3.14.0/include</code>.</p>
<strong>Installs in root location (uncommon).</strong>
<p>
If one wants to install PETSc in a common system
location like /usr/local or /opt that requires root access we suggest creating a directory for
PETSc with user privileges, and then do the
PETSc install [as a <b>regular/non-root user</b>]. i.e.
</p>
<ul class="code">
<li>sudo mkdir /opt/petsc</li>
<li>sudo chown user:group /opt/petsc</li>
<li>cd /home/userid/petsc</li>
<li>./configure --prefix=/opt/petsc/petsc-3.14.0 [other configure options]</li>
<li>make</li>
<li>make install</li>
</ul>
If one prefers to use root access for the install they only need change the final line
<ul class="code">
<li>sudo make install</li>
</ul>
One should never run configure or make on any package using root access.</p>
<strong>Installs for package managers: using DESTDIR (very uncommon)</strong>
<ul class="code">
<li>./configure --prefix=/opt/petsc/petsc-3.14.0</li>
<li>make</li>
<li>make install DESTDIR=/tmp/petsc-pkg</li>
<li>[package up /tmp/petsc-pkg The package should then be installed at /opt/petsc/petsc-3.14.0]</li>
</ul>
<strong>Multiple installs using --prefix [and DESTDIR]:</strong></p>
Specify a different --prefix location for each configure of different options - at configure time. For example
<ul class="code">
<li>./configure --prefix=/opt/petsc/petsc-3.14.0-mpich --with-mpi-dir=/opt/mpich</li>
<li>make</li>
<li>make install [DESTDIR=/tmp/petsc-pkg]</li>
<li>./configure --prefix=/opt/petsc/petsc-3.14.0-openmpi --with-mpi-dir=/opt/openmpi</li>
<li>make</li>
<li>make install [DESTDIR=/tmp/petsc-pkg]</li>
</ul>
<h4>In-place installation</h4>
The PETSc libraries and generated included files are placed in the sub-directory off the current directory <code>$PETSC_ARCH</code> which is either provided by the user with, for example,
<ul class="code">
<li>export PETSC_ARCH=arch-debug</li>
<li>./configure </li>
<li>make</li>
<li>export PETSC_ARCH=arch-opt</li>
<li>./configure --with-debugging=0</li>
<li>make</li>
</ul>
or
<ul class="code">
<li> ./configure PETSC_ARCH=arch-debug</li>
<li>make</li>
<li> ./configure --with-debugging=0 PETSC_ARCH=arch-opt</li>
<li>make</li>
</ul>
If not provided <code>./configure</code> will generate a unique value automatically (for in-place non <code>--prefix</code> configurations only)
<ul class="code">
<li> ./configure </li>
<li>make</li>
<li> ./configure --with-debugging=0 </li>
<li>make</li>
</ul>
produces the directories (on an Apple MacOS machine) <code>arch-darwin-c-debug</code> and <code>arch-darwin-c-opt</code>.</p>
The libraries and include files needed by the users are located off the current directory in <code>$PETSC_ARCH/lib</code>, <code>include</code> and <code>$PETSC_ARCH/include</code></p>
<strong>Following master or release on Git</strong></p>
<a name="easyrebuild">If you follow the <code>master</code> or <code>release</code> branches off PETSc you can update your libraries with
<ul class="code">
<li> git pull</li>
<li>make libs</li>
</ul>
Most of the time this will work, if there are errors regarding compiling Fortran stubs you need to also do
<ul class="code">
<li>make allfortranstubs</li>
</ul>
If there are large changes in PETSc's configure code when you pull you may need to rerun the <code>./configure</code> which you can do with
<ul class="code">
<li>$PETSC_ARCH/lib/petsc/conf/reconfigure-$PETSC_ARCH.py</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div>
<hr>
<div>
<h3><a name="envvars">Environmental variables PETSC_DIR and PETSC_ARCH</h3>
Applications completely providing their own makefiles do not need to use <code>PETSC_DIR</code> or <code>PETSC_ARCH</code></p>
<code>PETSC_DIR</code> and <code>PETSC_ARCH</code> (in-place installs only)
are used by the PETSc <strong>makefiles</strong> to indicate which directory and configuration of PETSc to use when compiling examples or application code.
These variables can be set as
envirnment variables or specified on the command line
<ul>
<li>
specify enviornment variable for csh/tcsh [can be specified in ~/.cshrc]
<ul>
<li>setenv PETSC_DIR /home/balay/petsc-3.14.0</li>
<li>setenv PETSC_ARCH linux-gnu-c-debug</li>
</ul>
</li>
<li>
specify environment variable for bash [can be specified in ~/.bashrc]
<ul>
<li>export PETSC_DIR=/home/balay/petsc-3.14.0</li>
<li>export PETSC_ARCH=linux-gnu-c-debug</li>
</ul>
</li>
<li>
specify variable on commandline (bash) to build an example in src/ts/tutorials
<ul>
<li>PETSC_ARCH=linux-gnu-c-debug make PETSC_DIR=/home/balay/petsc-3.14.0 ex1</li>
</ul>
</li>
</ul>
<p>
<code>PETSC_DIR</code>
should point to the location of the PETSc
installation. For out-of-place installations this is the <code>--prefix</code> location. For in-place installations it is the directory where you ran configure PETSc.
</p>
<p>
<code>PETSC_ARCH</code>
is only needed for in-place installations.
</p>
<a href="#" target="_top">Return to Installation Instructions</a>
</div>
<hr>
<div>
<h3><a name="windows">Microsoft Windows Installation:</a></h3>
Are you sure you want to use Microsoft Windows? We recommend using Linux
if possible [and minimize troubleshooting Microsoft Windows related issues].
<h4>Installation With GNU gcc/g++/gfortran compilers:</h4>
The following configurations are much like regular Linux systems. Our regular [Linux] instructions
should work with them. Most externalpackages will also work. The configure option --download-mpich should work
for these systems. (These do not support Microsoft/Intel Windows compilers; nor can you use MS-MPI, Intel-MPI or MPICH2).
<ul>
<li>
<a href="http://www.cygwin.com">Cygwin</a> Unix emulator for Microsoft Windows. See the instructions below for
installing Cygwin for PETSc. Be sure to install the GNU compilers, do not use the win32fe script.
</li>
<li>
<a href="https://devblogs.microsoft.com/commandline/announcing-wsl-2/">Microsoft Windows Subsystem for Linux 2 (WLS2)</a>.
Untested, let us know your experience.
</li>
<li>
<a href="https://docs.docker.com/docker-for-windows/">Docker for Microsoft Windows</a>.
Untested, let us know your experience.
</li>
<li>
<a href="https://www.atlassian.com/git/tutorials/git-bash">Git bash</a>. You must
also install the GNU compilers via
<a href="https://yichaoou.github.io/tutorials/software/2016/06/28/git-bash-install-gcc">MinGW</a>.
Untested, let us know your experience.
</li>
<li>
Linux virtual machine via <a href="https://www.virtualbox.org/">VirtualBox</a>.
One sample tutorial is at
<a href="https://www.psychocats.net/ubuntu/virtualbox">https://www.psychocats.net/ubuntu/virtualbox</a>.
Google can provide more tutorials.
Untested, let us know your experience.
</li>
</ul>
<hr>
<h4>Installation With Microsoft/Intel Windows Compilers:</h4>
<p>
Microsoft Windows does not provide the same unix shell enviornment
as the other OSes. Also the default Microsoft/Intel compilers behave
differently than other unix compilers. So to install PETSc on Microsoft
Windows - one has to install <a href="http://www.cygwin.com">Cygwin</a>
[for the unix enviornment] and use <a href="#win32fe">win32fe</a> [part
of PETSc sources, to interface to Microsoft/Intel compilers].
</p>
<p>
<strong>Install Cygwin: </strong>Please download and install
Cygwin package from <a href="http://www.cygwin.com">http://www.cygwin.com</a>.
Make sure the following Cygwin components are installed.
</p>
<ul>
<li>python3</li>
<li>make</li>
<li>[default selection should already have <code>diff</code> and other tools]</li>
</ul>
<p>
Note: If installing PETSc with <strong>Cygwin/GNU</strong> compilers - install additional Cygwin components.
<ul>
<li>gcc-core gcc-g++ gcc-fortran</li>
<li>liblapack-devel</li>
<li>openmpi libopenmpi-devel</li>
</ul>
Additional cygwin components like <code>git cmake</code> can be useful for installing external packages.
</p>
<p>
<strong>Remove Cygwin link.exe: </strong>Cygwin link.exe can
conflict with Intel ifort compiler. If you are using ifort -
please do [from Cygwin terminal/bash-shell]:
</p>
<ul>
<li><code>mv /usr/bin/link.exe /usr/bin/link-cygwin.exe</code></li>
</ul>
<p>
<strong>Setup Cygwin terminal/bash-shell with Working Compilers:
</strong>We require the compilers to be setup properly in a Cygwin bash
command shell, so that "<code>cl foo.c</code>" or "<code>ifort
foo.f</code>" works from this shell. For example - if using VS2005
C and Intel 10 Fortran one can do:
</p>
<ul>
<li>
Start -> Programs -> Intel Software Development Tools ->
Intel Fortran Compiler 10 -> Visual Fortran Build Enviornment
[32bit or 64bit depending on your usage]. This should start a 'dos
cmd' shell.
</li>
<li>
Within this shell - run Cygwin terminal/bash-shell mintty.exe as:
<code>c:\cygwin\bin\mintty.exe</code>
</li>
<li>
Within mintty.exe - run:<code>/usr/bin/bash --login</code>
</li>
<li>verify if the compilers are useable [by running cl, ifort in this Cygwin terminal/bash-shell]</li>
<li>Now run configure with win32fe and then build the libraries with make [as per the usual instructions]</li>
</ul>
<strong>Example Configure usage with Microsoft Windows Compilers:</strong>
<p>
Use configure with VC2005 C and Intel Fortran 10 [Without MPI].
</p>
<ul>
<li><code>./configure --with-cc='win32fe cl' --with-fc='win32fe ifort' --with-cxx='win32fe cl' --with-mpi=0 --download-fblaslapack</code></li>
</ul>
<p>If fortran, c++ usage is not required, use:</p>
<ul>
<li><code>./configure --with-cc='win32fe cl' --with-fc=0 --with-cxx=0 --download-f2cblaslapack</code></li>
</ul>
<p> <strong>Using MPI:</strong>
We support both <a href="https://www.microsoft.com/en-us/download/details.aspx?id=57467">MS-MPI</a> [64-bit] and <a href="https://software.intel.com/en-us/mpi-library">Intel MPI</a> on Microsoft Windows (MPICH2 does not work, do not use it). For example usages, check <code>config/examples/arch-mswin*.py</code></p>
<p> <strong>Avoiding spaces in PATHs:</strong>
Its best to avoid spaces or similar special chars when specifying configure options. On Microsoft Windows - this usually affects specifying MPI or MKL. Microsoft Windows supports <b>dos short form</b> for dir names - so its best to use this notation. And cygwin tool <code>cygpath</code> can be used to get paths in this notation. For example
<code><br><br>
$ cygpath -u `cygpath -ms '/cygdrive/c/Program Files (x86)/Microsoft SDKs/MPI'`<br>
/cygdrive/c/PROGRA~2/MICROS~2/MPI<br>
$ cygpath -u `cygpath -ms '/cygdrive/c/Program Files (x86)/IntelSWTools/compilers_and_libraries/windows/mkl/lib/intel64'`<br>
/cygdrive/c/PROGRA~2/INTELS~1/COMPIL~2/windows/mkl/lib/intel64<br><br>
</code>
i.e use:
<ul>
<li><code>./configure --with-cc='win32fe cl' --with-fc='win32fe ifort' --with-cxx='win32fe cl' --with-shared-libraries=0 \<br>
--with-mpi-include='[/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include,/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/x64]' \<br>
--with-mpi-lib='-L/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64 msmpifec.lib msmpi.lib' \<br>
--with-mpiexec=/cygdrive/c/PROGRA~1/MICROS~2/Bin/mpiexec \<br>
--with-blaslapack-lib='-L/cygdrive/c/PROGRA~2/INTELS~1/COMPIL~2/windows/mkl/lib/intel64 mkl_intel_lp64_dll.lib mkl_sequential_dll.lib mkl_core_dll.lib'</code>
</ul>
<p>
<strong>ExternalPackages</strong>: The <code>--download-package
</code> option does not work with many external packages on Microsoft
Windows.
</p>
<p>
<strong>Project Files:</strong> We cannot provide Microsoft
Visual Studio project files for users as they are specific to the
configure options, location of external packages, compiler versions
etc. used for any given build of PETSc, so they are potentially
different for each build of PETSc. So if you need a project file for
use with PETSc - please do the following.
</p>
<ul>
<li>
create an empty project file with one of the examples say
<code>src/ksp/ksp/tutorials/ex2.c</code>
</li>
<li>
try compiling the example from Cygwin bash shell - using makefile - for example
<ul>
<li>cd src/ksp/ksp/tutorials</li>
<li>make ex2</li>
</ul>
</li>
<li>
if the above works - then make sure all the compiler/linker options
used by make are also present in the project file in the correct
notation.
</li>
<li>
if errors - redo the above step. [if all the options are correctly
specified - then the example should compile from MSDev.
</li>
</ul>
<p>
<strong>Debugger:</strong> Running PETSc probrams with
-start_in_debugger is not supported on this platform, so debuggers will
need to be initiated manually. Make sure your environment is properly
configured to use the appropriate debugger for your compiler. The
debuggers can be initiated using Microsoft Visual Studio 6: <code>msdev
ex1.exe</code>, Microsoft Visual Studio .NET: <code>devenv
ex1.exe</code>, Intel Enhanced Debugger: <code>edb ex1.exe</code>, or
GNU Debugger <code>gdb ex1.exe</code>.
</p>
<p>
<strong><a name="win32fe">PETSc win32 front end</a>:</strong>
This tool is used as a wrapper to Microsoft and Intel compilers
and associated tools - to enable building PETSc libraries using Cygwin
make and other UNIX tools. For additional info, run
<code>${PETSC_DIR}/lib/petsc/bin/win32/win32fe</code> without any options.
</p>
<h4>Using MinGW with Microsoft/Intel Windows Compilers:</h4>
Users report that it is possible to build to build PETSc using MinGW and link against them using the Microsoft/Intel Windows Compilers.
We have no experience with this, nor knowledge on how it can be accomplished. Let us know your experience.
<h4>Notes on using other systems besides Cygwin to compile with Microsoft and Intel compilers</h4>
For any alternate system, we would have to redo win32fe functionality for that system. This includes
<ul>
<li>
Marshal unix type compiler options to Cl (Microsoft compiler).
</li>
<li>
Convert paths in some of these options from this system (for example Cygwin paths) to Microsoft Windows paths.
</li>
<li>
Have python that works with system path notation.
</li>
<li>
Have the ability equivalent to Microsoft Windows process spawning; Cygwin process spawning produces Microsoft Windows processes. WSL1 lacked this.
</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #windows -->
<hr>
<div>
<h3><a name="pkgconfig">PETSc ./configure automatically generates Pkgconfig and module files for each install</a></h3>
These can be found in ${PETSC_DIR}/${PETSC_ARCH}/lib/pkgconfig/petsc.pc and ${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/modules/${PETSC_VERSION}-${PETSC_ARCH}.
The module file may need to be edited for your particular system. Note that if --prefix is used then $PETSC_ARCH is not included in the above directories
nor is -${PETSC_ARCH} included in the module file name.
</p>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #pkgconfig -->
<hr>
<div id="cross">
<h3><a name="SP">Installing packages that utilize OpenMP:</a></h3>
<p>
Some external packages include MKL BLAS/LAPACK, OpenBLAS, SuperLU_DIST, and Hypre support using OpenMP for
thread level parallelism in addition to the MPI parallelism in PETSc. To utilize this insure your compilers
support OpenMP and use the additional configure option <code>--with-openmp</code>
</p>
<p>
To control the number of OpenMP threads each MPI process utilizes you can set the environmental variable <code>OMP_NUM_THREADS n</code> or
the PETSc command line option <code>-omp_num_threads n</code>.
</p>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #cross -->
<hr>
<div id="module">
<h3><a name="module">Installing on machines that use the module command:</a></h3>
<p>
On systems where you can use modules to load packages such as HDF5, the locations of the include files and libraries are known
by the compiler. Hence you simply load the appropriate module for the package and run <code>./configure</code> with the option <code>--with-package</code>.
For example
<ul>
<li>
module load hdf5
</li>
<li>
./configure --with-hdf5
</li>
</p>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #module -->
<hr>
<div id="cross">
<h3><a name="cross">Installing on machine requiring cross compiler or a job scheduler (Batch systems):</a></h3>
<p>
On systems where you need to use a job scheduler or batch submission to run jobs
use the configure option <code>--with-batch</code>. On such systems the <code>make check</code> option will not work
</p>
<ul>
<li>
You must first insure you have loaded appropriate modules for the compilers etc that you
wish to use. Often the compilers are provided automatically for you and you do not need to provide <code>--with-cc=XXX</code> etc
Consult with the documentation and local support for such systems for information on these topics.
</li>
<li>
On such systems you generally should not provide <code>--with-blaslapack-dir</code> or <code>--download-fblaslapack</code> since the
systems provide those automatically (sometimes appropriate modules must be loaded first)
</li>
<li>
Some packages <code>--download-package</code> options do not work on these systems, for example HDF5. Thus you must use
modules to load those packages and <code>--with-package</code> to configure with the package.
</li>
<li>
Since building external packages on these systems is often troublesome and slow we recommend only installing PETSc with those
configuration packages that you need for your work, not extras.
</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #cross -->
<hr>
<div id="tau">
<h3><a name="usingtau">Installing with TAU Instrumentation package:</a></h3>
<p>
<a href="http://www.cs.uoregon.edu/research/paracomp/tau/tautools/">TAU</a>
package and the prerequisite <a href="http://www.cs.uoregon.edu/research/paracomp/pdtoolkit/">PDT</a>
packages need to be installed separately [perhaps with MPI].
Now use tau_cc.sh as compiler to PETSc configure.
</p>
<ul class="code">
<li>export TAU_MAKEFILE=/home/balay/soft/linux64/tau-2.20.3/x86_64/lib/Makefile.tau-mpi-pdt</li>
<li>./configure CC=/home/balay/soft/linux64/tau-2.20.3/x86_64/bin/tau_cc.sh --with-fc=0 PETSC_ARCH=arch-tau</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #tau -->
<hr>
<div>
<h3><a name="CUDA">Installing PETSc to use NVIDIA GPUs (aka CUDA)</a></h3>
<ul>
<li>
Requires <a href="https://developer.nvidia.com/cuda-downloads"> CUDA</a>,
</li>
<li>
On Linux - make sure you have compatible <a href="https://developer.nvidia.com/cuda-downloads"> NVIDIA driver</a>
installed.
</li>
<li>In most cases you need only pass the configure option --with-cuda; check <code>config/examples/arch-ci-linux-cuda-double.py</code> for example usage.</li>
</ul>
<p>
CUDA build of PETSc currently works on Mac OS X, Linux, Microsoft Windows.
</p>
<p>
Examples that use CUDA have the suffix .cu; see see src/snes/tutorials/ex47.cu
</p>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #CUDA -->
<hr>
<h3><a name="Kokkos">Installing PETSc with Kokkos</a></h3>
<p>
In most cases you need only pass the configure option --download-kokkos and one of --with-cuda --with-openmp --with-pthread (or nothing to use sequential Kokkos)
</p>
<p>
Examples that use Kokkos have the suffix .kokkos.cxx; see src/snes/tutorials/ex3k.kokkos.cxx
</p>
<a href="#" target="_top">Return to Installation Instructions</a>
</div>
<hr>
<div>
<h3><a name="OpenCL">Installing PETSc to use GPUs and accelerators via OpenCL (NVIDIA, AMD, Intel MIC)</a></h3>
<ul>
<li>
Requires the OpenCL shared library, which is shipped in the vendor graphics driver and the OpenCL headers; if needed you can download them
from the <a href="https://www.khronos.org/opencl/">Khronos Group</a> directly.
Package managers on Linux provide these headers through a package named 'opencl-headers' or similar.
On Apple systems the OpenCL drivers and headers are always available and do not need to be downloaded.
</li>
<li>
Always make sure you have the latest GPU driver installed. There are several known issues with older driver versions.
</li>
<li>Run configure with --download-viennacl; check <code>config/examples/arch-ci-linux-viennacl.py</code> for example usage.</li>
</ul>
<p>
OpenCL/ViennaCL builds of PETSc currently work on Mac OS X, Linux, and Microsoft Windows.
</p>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #OpenCL -->
<hr>
<div>
<h3><a name="doemachines">Installing on Large Scale DOE Systems</a></h3>
<ul>
<li>
NERSC - CORI machine.
<ul>
<li>
Project ID: m3353
</li>
<li>
PI: Richard Mills
</li>
<li>
Notes on usage:
</li>
</ul>
</li>
<li>
ALCF - Argonne National Laboratory - theta machine - Intel KNL based system
<ul>
<li>
Project ID:
</li>
<li>
PI:
</li>
<li>
Notes on usage:
<ul>
<li> Log into theta.alcf.anl.gov </li>
<li> There are three compiler suites <a href="https://www.alcf.anl.gov/user-guides/compiling-and-linking-xc40">Modules</a>
<ul>
<li> module load PrgEnv-intel intel </li>
<li> module load PrgEnv-gnu gcc/7.1.0/</li>
<li> module load PrgEnv-cray </li>
</ul>
<li> List currently loaded modules: module list </li>
<li> List all available modules: module avail </li>
<li> Blas/lapack will automatically be found so you do not need to provide it </li>
<ul>
<li> It is best not to use built-in modules for external packages (except blas/lapack) because they are often buggy.
Most external packages can be built using the --download option with the intel or Gnu environment but not cray </li>
<li> You can use config/examples/arch-cray-xc40-knl-opt.py as a template for running configure but it is outdated </li>
<li> When using the Intel module you may need to use --download-sowing-cc=icc --download-sowing-cxx=icpc -download-sowing-cpp="icc -E" --download-sowing-cxxpp="icpc -E" since the GNU compilers may not work as they access Intel files</li>
</li>
<li> To get an interactive node use qsub -A CSC250STMS07 -n 1 -t 60 -q debug-flat-quad -I </li>
<li> To run on interactive node using two MPI ranks use aprun -n 2 ./program options</li>
</ul>
</li>
</ul>
</ul> </ul>
<li>
OLCF - Oak Ridge National Laboratory - Summit machine - NVIDIA GPUs and IBM Power PC processors
<ul>
<li>
Project ID: CSC314
</li>
<li>
PI: Barry Smith
</li>
<li>
Apply at: https://docs.olcf.ornl.gov/accounts/accounts_and_projects.html#applying-for-a-user-account
</li>
<li>
Notes on usage:
<ul>
<li> <a href="https://www.olcf.ornl.gov/support/getting-started/olcf-user-account-application/">Getting Started</a> </li>
<li> Log into summit.olcf.ornl.gov </li>
<li> module load cmake hdf5 cuda</li>
<ul>
<li> module load pgi (for PGI compilers) </li>
<li> module load essl netlib-lapack xl (for IBM compilers) </li>
<li> module load gcc (for GNU compilers) </li>
</ul>
<li> Use config/examples/arch-olcf-opt.py as a template for running configure </li>
<li> You configure PETSc and build examples in your home directory, but launch them from your "work" directory. </li>
<li> Use the bsub command to submit jobs to the queue. See the "Batch Scripts" section here
<a href="https://www.olcf.ornl.gov/for-users/system-user-guides/summit/summit-user-guide/#running-jobs.">running jobs</a> </li>
<li> Tools for profiling </li>
<ul>
<li> -log_view that adds GPU communication and computation to the summary table </li>
<li> nvprof and nvvp from the CUDA toolkit </li>
</ul>
</ul>
</ul>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div>
<hr>
<div>
<h3><a name="iosandroid">Installing PETSc on an iOS or Android platform</a></h3>
<ul>
<li>
For iOS see systems/Apple/iOS/bin/makeall
</li>
<li>
A thorough discussion of the installation procedure is given <a href="https://www.researchgate.net/publication/308973080_Comparison_of_Migration_Techniques_for_High-Performance_Code_to_Android_and_iOS">here</a>.
</li>
<li>
For Android, you must have your standalone bin folder in the path, so that the compilers are visible.
</li>
<li>Check <code>config/examples/arch-arm64-opt.py</code> for iOS
and <code>config/examples/arch-armv7-opt.py</code> for example usage.</li>
</ul>
<a href="#" target="_top">Return to Installation Instructions</a>
</div> <!-- #iosandroid -->
<hr>
</div>
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