Documentation: Installation

Example Usages:

• Examples are at config/examples/*.py. We use some of these scripts locally for testing - for example one can update these files and run as:
  • ./config/examples/arch-osx-10.6.py
• Assuming BLAS, LAPACK, MPICH are not currently installed ./configure will download & install BLAS, LAPACK, MPICH if they are not already installed on the system):
  • ./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack --download-mpich
• Same as above - but do not have a fortran compiler [and want to use PETSc from C only].
  • ./configure --with-cc=gcc --with-cxx=0 --with-fc=0 --download-f2cblaslapack --download-mpich
• Same as above - but install in a user specified (prefix) location.
  • ./configure --prefix=/home/user/soft/petsc-install --with-cc=gcc --with-cxx=0 --with-fc=0 --download-f2cblaslapack --download-mpich
• 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.
  • ./configure
• If BLAS, LAPACK, MPI are already installed in known user location use:
  [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]
  • ./configure --with-blaslapack-dir=/usr/local/blaslapack --with-mpi-dir=/usr/local/mpich
  or
  • ./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
• Build Complex version of PETSc [using c++ compiler]:
  • ./configure --with-cc=gcc --with-fc=gfortran --with-cxx=g++ --with-clanguage=cxx --download-fblaslapack --download-mpich --with-scalar-type=complex
• Install 2 variants of PETSc, one with gnu, the other with Intel compilers. Specify different PETSC_ARCH for each build.
  • ./configure PETSC_ARCH=linux-gnu --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich
  • make PETSC_ARCH=linux-gnu all test
  • ./configure PETSC_ARCH=linux-gnu-intel --with-cc=icc --with-cxx=icpc --with-fc=ifort --download-mpich --with-blaslapack-dir=/usr/local/mkl
  • make PETSC_ARCH=linux-gnu-intel all test

Compilers:

Specify compilers and compiler options used to build PETSc [and perhaps external packages]

• Specify compilers using the options --with-cc --with-cxx --with-fc for c, c++, and fortran compilers
  • --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90
  • --with-cc=gcc --with-cxx=g++ --with-fc=gfortran
  • --with-cc=gcc --with-cxx=g++ --with-fc=gfortran
• If fortran compiler is not available or not needed - then disabling using fortran
  • --with-fc=0
• If a C++ compiler is not available or not needed - disable configuring with it
  • --with-cxx=0
• If no compilers are specified - configure will automatically look for available MPI or regular compilers in the user's PATH
  • mpicc/mpiCC/mpif90
  • gcc/g++/gfortran
  • cc/CC etc..
• 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]
  • --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90
  • --with-mpi-dir=/opt/mpich2-1.1 [but *no* --with-cc=gcc]
• 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:
  • ./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
• Configure cannot detect compiler libraries for certain set of compilers. In this case one can specify additional system/compiler libraries using the LIBS option
  • ./configure --LIBS='-ldl /usr/lib/libm.a'

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External Packages:

PETSc provides interfaces to various external packages. BLAS/LAPACK is a required package, MPI is not required if running sequentially. One can optionally use external solvers like Hypre, MUMPS, etc. from within PETSc applications.

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.

If you are behind a firewall and cannot use a proxy for the downloads or have a very slow network use the additional option --with-packages-download-dir=/adirectory. 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.

The following modes can be used to install/use external packages with configure.

• --download-PACKAGENAME: Download specified package and install it and configure PETSc to use this package.
  • --download-fblaslapack --download-mpich
  • --download-scalapack --download-mumps
• --download-PACKAGENAME=/PATH/TO/package.tar.gz: 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.
  • --download-mpich=/home/petsc/mpich2-1.0.4p1.tar.gz
• --with-PACKAGENAME-dir=PATH: 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.
  • --with-mpi-dir=/home/petsc/software/mpich2-1.0.4p1
  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.
• --with-PACKAGENAME-include=INCLUDEPATH --with-PACKAGENAME-lib=LIBRARYLIST: 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
  • --with-superlu-include=/home/petsc/software/superlu/include --with-superlu-lib=/home/petsc/software/superlu/lib/libsuperlu.a
  • --with-parmetis-include=/sandbox/balay/parmetis/include --with-parmetis-lib="-L/sandbox/balay/parmetis/lib -lparmetis -lmetis"
  • --with-parmetis-include=/sandbox/balay/parmetis/include --with-parmetis-lib=[/sandbox/balay/parmetis/lib/libparmetis.a,libmetis.a]

Notes:

• Run ./configure --help to get the list of external packages and corresponding additional options [for example --with-mpiexec for MPICH]
• Generally one would use either one of the above 4 modes for any given package - and not mix these. [i.e mixing --with-mpi-dir and --with-mpi-include etc.. should be avoided]
• Some packages might not support certain options like --download-PACKAGENAME or --with-PACKAGENAME-dir. Architectures like Microsoft Windows might have issues with these options. In these cases, --with-PACKAGENAME-include --with-PACKAGENAME-lib options should be preferred.
• It's best to install some external packages like SuperLU_DIST, MUMPS, Hypre, METIS, and ParMETIS with the option --download-PACKAGENAME. [the correct options for these packages are --download-superlu_dist --download-mumps --download-hypre]
  • 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]
  • Some packages have bug fixes, portability patches, and upgrades for dependent packages that have not yet been included in an upstream release.
  • 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].
• 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 config/BuildSystem/config/packages/SuperLU.py for the url for download this package.

Additional options:

• --with-packages-build-dir=PATH: By default, external packages will be unpacked and the build process is run in ${PETSC_DIR}/${PETSC_ARCH}/externalpackages. However one can choose a different location where these packages are unpacked and the build process is run.

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BLAS/LAPACK

These packages provide some basic numeric kernels used by PETSc.

• 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.
• One can use the following options to let configure download/install BLAS/LAPACK automatically.
  • --download-fblaslapack [when fortran compiler is present]
  • --download-f2cblaslapack [when configuring without a fortran compiler - i.e --with-fc=0]
• Alternatively one can use other options like one of the following.
  • --with-blaslapack-lib=libsunperf.a
  • --with-blas-lib=libblas.a --with-lapack-lib=liblapack.a
  • --with-blaslapack-dir=/soft/com/packages/intel/13/079/mkl

Notes:

• Intel MKL

  Intel provides BLAS/LAPACK via the MKL 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: --with-blaslapack-dir=$MKLROOT or, for example, --with-blaslapack-dir=/soft/com/packages/intel/13/079/mkl
  If the above option does not work - one could determine the correct library list for your compilers using Intel MKL Link Line Advisor and specify with the configure option --with-blaslapack-lib

• IBM ESSL

  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 --download-fblaslapack. If you really want to use ESSL, see https://www.pdc.kth.se/hpc-services.

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MPI

This software provides the parallel functionality for PETSc.

• Configure will automatically look for MPI compilers mpicc/mpif90 etc and use them if found in your PATH.
• One can use the following options to let configure download/install MPI automatically
  • --download-mpich [install and use MPICH]
  • --download-openmpi [Install and use Open MPI]
• See externalpackages for other installation options.

Using MPI Compilers:

• 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.
  • Vendor provided MPI might already be installed. IBM, SGI, Cray etc provide their own:
    ./config/confiure.py --with-cc=mpcc --with-fc=mpf90
  • 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]:
    ./configure --with-mpi-dir=/path-to-mpich-install

Installing without MPI:

• 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.
  • ./configure --with-mpi=0

Installing with Open MPI with shared MPI libraries:

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.

Due to this OpenMPI restriction one has to set LD_LIBRARY_PATH correctly [per OpenMPI installation instructions], before running PETSc configure. If you do not set this environmental variables you will get messages when running ./configure such as

            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?
        

or when running a code compiled with OpenMPI

-bash-3.3$ ./conftest
./conftest: error while loading shared libraries: libmpi.so.0: cannot open shared object file: No such file or directory

Notes:

• Avoid specifing compilers [with options --with-cc or --with-fc] when using the option --with-mpi-dir. [Option--with-mpi-dir specifies using MPI compilers - so its best to use them - and not overwride them with user specified --with-cc].
• One can specify mpiexec or mpiexec with the options --with-mpiexec

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Installation location: In-place or out-of-place

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 master or release branches since rebuilds for updates are very quick and painless, see easyrebuild.

Out-of-place installation with --prefix

To install the libraries and include files in another location use the --prefix option

• ./configure --prefix=/home/userid/petsc-3.14.0 [other configure options]

The libraries and include files needed by the users will be located in /home/userid/petsc-3.14.0/lib and /home/userid/petsc-3.14.0/include.

Installs in root location (uncommon).

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 regular/non-root user]. i.e.

• sudo mkdir /opt/petsc
• sudo chown user:group /opt/petsc
• cd /home/userid/petsc
• ./configure --prefix=/opt/petsc/petsc-3.14.0 [other configure options]
• make
• make install

If one prefers to use root access for the install they only need change the final line

• sudo make install

One should never run configure or make on any package using root access.

Installs for package managers: using DESTDIR (very uncommon)

• ./configure --prefix=/opt/petsc/petsc-3.14.0
• make
• make install DESTDIR=/tmp/petsc-pkg
• [package up /tmp/petsc-pkg The package should then be installed at /opt/petsc/petsc-3.14.0]

Multiple installs using --prefix [and DESTDIR]:

Specify a different --prefix location for each configure of different options - at configure time. For example

• ./configure --prefix=/opt/petsc/petsc-3.14.0-mpich --with-mpi-dir=/opt/mpich
• make
• make install [DESTDIR=/tmp/petsc-pkg]
• ./configure --prefix=/opt/petsc/petsc-3.14.0-openmpi --with-mpi-dir=/opt/openmpi
• make
• make install [DESTDIR=/tmp/petsc-pkg]

In-place installation

The PETSc libraries and generated included files are placed in the sub-directory off the current directory $PETSC_ARCH which is either provided by the user with, for example,

• export PETSC_ARCH=arch-debug
• ./configure
• make
• export PETSC_ARCH=arch-opt
• ./configure --with-debugging=0
• make

or

• ./configure PETSC_ARCH=arch-debug
• make
• ./configure --with-debugging=0 PETSC_ARCH=arch-opt
• make

If not provided ./configure will generate a unique value automatically (for in-place non --prefix configurations only)

• ./configure
• make
• ./configure --with-debugging=0
• make

produces the directories (on an Apple MacOS machine) arch-darwin-c-debug and arch-darwin-c-opt.

The libraries and include files needed by the users are located off the current directory in $PETSC_ARCH/lib, include and $PETSC_ARCH/include

Following master or release on Git

If you follow the master or release branches off PETSc you can update your libraries with

• git pull
• make libs

Most of the time this will work, if there are errors regarding compiling Fortran stubs you need to also do

• make allfortranstubs

If there are large changes in PETSc's configure code when you pull you may need to rerun the ./configure which you can do with

• $PETSC_ARCH/lib/petsc/conf/reconfigure-$PETSC_ARCH.py

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Environmental variables PETSC_DIR and PETSC_ARCH

Applications completely providing their own makefiles do not need to use PETSC_DIR or PETSC_ARCH

PETSC_DIR and PETSC_ARCH (in-place installs only) are used by the PETSc makefiles 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

• specify enviornment variable for csh/tcsh [can be specified in ~/.cshrc]
  • setenv PETSC_DIR /home/balay/petsc-3.14.0
  • setenv PETSC_ARCH linux-gnu-c-debug
• specify environment variable for bash [can be specified in ~/.bashrc]
  • export PETSC_DIR=/home/balay/petsc-3.14.0
  • export PETSC_ARCH=linux-gnu-c-debug
• specify variable on commandline (bash) to build an example in src/ts/tutorials
  • PETSC_ARCH=linux-gnu-c-debug make PETSC_DIR=/home/balay/petsc-3.14.0 ex1

PETSC_DIR should point to the location of the PETSc installation. For out-of-place installations this is the --prefix location. For in-place installations it is the directory where you ran configure PETSc.

PETSC_ARCH is only needed for in-place installations.

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Microsoft Windows Installation:

Are you sure you want to use Microsoft Windows? We recommend using Linux if possible [and minimize troubleshooting Microsoft Windows related issues].

Installation With GNU gcc/g++/gfortran compilers:

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).

• Cygwin 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.
• Microsoft Windows Subsystem for Linux 2 (WLS2). Untested, let us know your experience.
• Docker for Microsoft Windows. Untested, let us know your experience.
• Git bash. You must also install the GNU compilers via MinGW. Untested, let us know your experience.
• Linux virtual machine via VirtualBox. One sample tutorial is at https://www.psychocats.net/ubuntu/virtualbox. Google can provide more tutorials. Untested, let us know your experience.

---

Installation With Microsoft/Intel Windows Compilers:

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 Cygwin [for the unix enviornment] and use win32fe [part of PETSc sources, to interface to Microsoft/Intel compilers].

Install Cygwin: Please download and install Cygwin package from http://www.cygwin.com. Make sure the following Cygwin components are installed.

• python3
• make
• [default selection should already have diff and other tools]

Note: If installing PETSc with Cygwin/GNU compilers - install additional Cygwin components.

• gcc-core gcc-g++ gcc-fortran
• liblapack-devel
• openmpi libopenmpi-devel

Additional cygwin components like git cmake can be useful for installing external packages.

Remove Cygwin link.exe: Cygwin link.exe can conflict with Intel ifort compiler. If you are using ifort - please do [from Cygwin terminal/bash-shell]:

• mv /usr/bin/link.exe /usr/bin/link-cygwin.exe

Setup Cygwin terminal/bash-shell with Working Compilers: We require the compilers to be setup properly in a Cygwin bash command shell, so that "cl foo.c" or "ifort foo.f" works from this shell. For example - if using VS2005 C and Intel 10 Fortran one can do:

• 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.
• Within this shell - run Cygwin terminal/bash-shell mintty.exe as: c:\cygwin\bin\mintty.exe
• Within mintty.exe - run:/usr/bin/bash --login
• verify if the compilers are useable [by running cl, ifort in this Cygwin terminal/bash-shell]
• Now run configure with win32fe and then build the libraries with make [as per the usual instructions]

Example Configure usage with Microsoft Windows Compilers:

Use configure with VC2005 C and Intel Fortran 10 [Without MPI].

• ./configure --with-cc='win32fe cl' --with-fc='win32fe ifort' --with-cxx='win32fe cl' --with-mpi=0 --download-fblaslapack

If fortran, c++ usage is not required, use:

• ./configure --with-cc='win32fe cl' --with-fc=0 --with-cxx=0 --download-f2cblaslapack

Using MPI: We support both MS-MPI [64-bit] and Intel MPI on Microsoft Windows (MPICH2 does not work, do not use it). For example usages, check config/examples/arch-mswin*.py

Avoiding spaces in PATHs: 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 dos short form for dir names - so its best to use this notation. And cygwin tool cygpath can be used to get paths in this notation. For example

$ cygpath -u `cygpath -ms '/cygdrive/c/Program Files (x86)/Microsoft SDKs/MPI'`
/cygdrive/c/PROGRA~2/MICROS~2/MPI
$ cygpath -u `cygpath -ms '/cygdrive/c/Program Files (x86)/IntelSWTools/compilers_and_libraries/windows/mkl/lib/intel64'`
/cygdrive/c/PROGRA~2/INTELS~1/COMPIL~2/windows/mkl/lib/intel64

i.e use:

• ./configure --with-cc='win32fe cl' --with-fc='win32fe ifort' --with-cxx='win32fe cl' --with-shared-libraries=0 \
--with-mpi-include='[/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include,/cygdrive/c/PROGRA~2/MICROS~2/MPI/Include/x64]' \
--with-mpi-lib='-L/cygdrive/c/PROGRA~2/MICROS~2/MPI/lib/x64 msmpifec.lib msmpi.lib' \
--with-mpiexec=/cygdrive/c/PROGRA~1/MICROS~2/Bin/mpiexec \
--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'

ExternalPackages: The --download-package option does not work with many external packages on Microsoft Windows.

Project Files: 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.

• create an empty project file with one of the examples say src/ksp/ksp/tutorials/ex2.c
• try compiling the example from Cygwin bash shell - using makefile - for example
  • cd src/ksp/ksp/tutorials
  • make ex2
• 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.
• if errors - redo the above step. [if all the options are correctly specified - then the example should compile from MSDev.

Debugger: 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: msdev ex1.exe, Microsoft Visual Studio .NET: devenv ex1.exe, Intel Enhanced Debugger: edb ex1.exe, or GNU Debugger gdb ex1.exe.

PETSc win32 front end: 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 ${PETSC_DIR}/lib/petsc/bin/win32/win32fe without any options.

Using MinGW with Microsoft/Intel Windows Compilers:

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.

Notes on using other systems besides Cygwin to compile with Microsoft and Intel compilers

For any alternate system, we would have to redo win32fe functionality for that system. This includes

• Marshal unix type compiler options to Cl (Microsoft compiler).
• Convert paths in some of these options from this system (for example Cygwin paths) to Microsoft Windows paths.
• Have python that works with system path notation.
• Have the ability equivalent to Microsoft Windows process spawning; Cygwin process spawning produces Microsoft Windows processes. WSL1 lacked this.

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PETSc ./configure automatically generates Pkgconfig and module files for each install

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.

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Installing packages that utilize OpenMP:

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 --with-openmp

To control the number of OpenMP threads each MPI process utilizes you can set the environmental variable OMP_NUM_THREADS n or the PETSc command line option -omp_num_threads n.

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Installing on machines that use the module command:

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 ./configure with the option --with-package. For example

• module load hdf5
• ./configure --with-hdf5
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Installing on machine requiring cross compiler or a job scheduler (Batch systems):

On systems where you need to use a job scheduler or batch submission to run jobs use the configure option --with-batch. On such systems the make check option will not work

• 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 --with-cc=XXX etc Consult with the documentation and local support for such systems for information on these topics.
• On such systems you generally should not provide --with-blaslapack-dir or --download-fblaslapack since the systems provide those automatically (sometimes appropriate modules must be loaded first)
• Some packages --download-package options do not work on these systems, for example HDF5. Thus you must use modules to load those packages and --with-package to configure with the package.
• 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.

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Installing with TAU Instrumentation package:

TAU package and the prerequisite PDT packages need to be installed separately [perhaps with MPI]. Now use tau_cc.sh as compiler to PETSc configure.

• export TAU_MAKEFILE=/home/balay/soft/linux64/tau-2.20.3/x86_64/lib/Makefile.tau-mpi-pdt
• ./configure CC=/home/balay/soft/linux64/tau-2.20.3/x86_64/bin/tau_cc.sh --with-fc=0 PETSC_ARCH=arch-tau

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Installing PETSc to use NVIDIA GPUs (aka CUDA)

• Requires CUDA,
• On Linux - make sure you have compatible NVIDIA driver installed.
• In most cases you need only pass the configure option --with-cuda; check config/examples/arch-ci-linux-cuda-double.py for example usage.

CUDA build of PETSc currently works on Mac OS X, Linux, Microsoft Windows.

Examples that use CUDA have the suffix .cu; see see src/snes/tutorials/ex47.cu

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