Quick Instructions:
Invoke the following commands from the top level PETSc directory:
./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-fblaslapack --download-mpich
make all test
Encounter problems?
Read the error message from ./configure!
If you get the message 'No such file or directory' try: python ./configure
make problems? Just copy/paste make command printed by configure including PETSC_DIR and PETSC_ARCH options
Do not have fortran compiler? check
the latest patched tarball
For most users we recommend installing PETSc as a regular/non-root user, perhaps in /home/username/soft
To extract the sources use: gunzip -c petsc-3.7.0.tar.gz | tar -xof -
Please check: ./configure --help
Please check
To install in
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
If BLAS, LAPACK, MPI 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-blas-lapack-dir=/usr/local/blaslapack --with-mpi-dir=/usr/local/mpich
./configure --with-blas-lapack-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]
(add the option --with-fortran-kernels=generic to get
possibly faster complex number performance on some systems):
./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-blas-lapack-dir=/usr/local/mkl
make PETSC_ARCH=linux-gnu-intel all test
PETSC_DIR and PETSC_ARCH are a couple of variables that control the
configuration and build process of PETSc. These variables can be set as
envirnment variables or specified on the command line [to both configure and make]
specify enviornment variable for csh/tcsh [can be specified in ~/.cshrc]
setenv PETSC_DIR /home/balay/petsc-3.7.0
setenv PETSC_ARCH linux-gnu-c-debug
specify enviornment variable for bash [can be specified in ~/.bashrc]
export PETSC_DIR=/home/balay/petsc-3.7.0
export PETSC_ARCH=linux-gnu-c-debug
specify variable on commandline to configure
./configure PETSC_DIR=/home/balay/petsc-3.7.0 PETSC_ARCH=linux-gnu-c-debug [other configure options]
specify variables on command line to make
make PETSC_DIR=/home/balay/petsc-3.7.0 PETSC_ARCH=linux-gnu-c-debug [other make options]
this variable should point to the location of the PETSc
installation that is used. Multiple PETSc versions can
coexist on the same file-system. By changing PETSC_DIR
value, one can switch between these installed versions of
PETSC_ARCH:
this variable gives a name to a configuration/build.
Configure uses this value to stores the generated config
makefiles in ${PETSC_DIR}/${PETSC_ARCH}/conf. And make
uses this value to determine this location of these
makefiles [which intern help in locating the correct
include and library files].
Thus one can install multiple variants of PETSc libraries
- by providing different PETSC_ARCH values to each
configure build. Then one can switch between using these
variants of libraries [from make] by switching the
PETSC_ARCH value used.
If configure doesn't find a PETSC_ARCH value [either in
env variable or command line option], it automatically
generates a default value and uses it. Also - if make
doesn't find a PETSC_ARCH env variable - it defaults to
the value used by last successful invocation of previous
configure.
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 --with-clanguage=cxx
Note that --with-clanguage=cxx means that the PETSc source code is compiled with the C++ compiler. This is not normally needed and we don't recommend it. One can use 'c' build of PETSc from both C and C++. One can also have a complex build with C99.
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 or mpif77
gcc/g++/gfortran or g77
cc/CC/f77 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/g77] 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 toggle
option --with-debugging [defaults to debug enabled].
Additionally one can specify more suitable optimization
flags with the options COPTFLAGS, FOPTFLAGS,
CXXOPTFLAGS. For ex: 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'
PETSc provides interfaces to various .
Blas/Lapack is a required package, MPI is not required if running sequentially. One can optionally use
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-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. Then 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 alternaive means [perhaps wget 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
--with-mpi-dir=/home/petsc/software/mpich2-1.0.4p1
Note that except for MPI we hightly recommend you have PETSc download and install the external packages rather than you installing them separately first.
--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 eg:
--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]
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 prefered.
It's best to install some external packages like SuperLU_DIST, MUMPS,
Hypre, METIS, and ParMETIS with the option --download-PACKAGENAME.
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/config.packages/SuperLU.py for the url for
download this package.
Additional options:
--with-external-packages-dir=PATH: By default,
external packages will be unpacked in ${PETSC_DIR}/externalpackages.
However one can choose a different location where these packages are unpacked.
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-blas-lapack-lib=libsunperf.a
--with-blas-lib=libblas.a --with-lapack-lib=liblapack.a
--with-blas-lapack-dir=/soft/com/packages/intel/13/079/mkl
Intel provides blas/lapack via
It usually works from GNU/Intel compilers on linux and MS/Intel compilers on Windows.
One can specify it to PETSc configure with for eg: --with-blas-lapack-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
and specify with the configure option --with-blas-lapack-lib
Sadly, IBM's ESSL does not have all the routines of BLAS and LAPACK
that some packages, such as SuperLU in particular slamch,
dlamch and xerbla. In this case instead of using ESSL we suggest
--download-fblaslapack. If you really want to use ESSL,
This software provides the parallel functionality for PETSc.
Configure will automatically look for MPI compilers mpicc/mpif77 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]
for other installation options.
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
Vendor provided MPI might already be installed. IBM, SGI, Cray etc provide their own:
./config/confiure.py --with-cc=mpcc --with-fc=mpf77
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
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/mpif77 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
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
Are you sure you want to use MS/Windows? We recommend using linux
if possible [and minimize troubleshooting windows related issues].
And most externalpackages will not work on windows.
If you have access to only a windows machine and not a linux machine,
consider using linux virtual machine via .
One sample tutorial is at .
Google can provide more tutorials.
You can consider using GNU compilers from .
Our regular [linux] instructions would work with cygwin/gnu compilers.
And most externalpackages will also work.
Installation With MS/Intel/Compaq Compilers:
Microsoft Windows OS does not provide the same unix shell enviornment
as the other OSes. Also the default MS/Intel/Compaq compilers behave
differently than other unix compilers. So to install PETSc on Microsoft
Windows - one has to install
[for the unix enviornment] and use
of PETSc sources,to interface to MS/Intel/Compaq compilers].
Install Cygwin: Please download and install
cygwin package from .
Make sure the following cygwin components are installed.
[default selection should already have diff and other tools]
Remove Cygwin link.exe: Cygwin link.exe can
conflict with Intel ifort and Comapq F90 compilers. If you are using
these compilers - 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
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 Windows Compilers:
Use configure with VC2005 C and Intel Fortran 10 [With MPICH2 installed].
./configure --with-cc='win32fe cl' --with-fc='win32fe ifort' --with-cxx='win32fe cl' --download-fblaslapack
If fortran usage is not required, use:
./configure --with-cc='win32fe cl' --with-fc=0 --download-f2cblaslapack
Using Compaq F90:
Using Microsoft C/C++ 6.0 & Compaq Fortran 6.0 with MPICH2 configure command to use:
./configure --with-cc='win32fe cl' --with-fc='win32fe f90' --download-fblaslapack
Note: MPICH2 mpif.h needs a fix for it to work with Compaq F90
[specifically remove line with MPI_DISPLACEMENT_CURRENT - which uses
'integer*8' - which is unsupported by Compaq F90]
ExternalPackages: The --download-package
option does not work with many external packages on Microsoft
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/examples/tutorials/ex2.c
try compiling the example from cygwin bash shell - using makefile - for eg:
cd src/ksp/ksp/examples/tutorials
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
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.
Using Cygwin gcc/g++/gfortran: One can install
and use PETSc with gcc/gfortran compilers from cygwin.
In this case
follow the regular Unix instructions.
This tool is used as a wrapper to Microsoft/ Borland/ Intel compilers
and associated tools - to enable building PETSc libraries using cygwin
make and other UNIX tools. For additional info, run
${PETSC_DIR}/bin/win32/win32fe without any options.
If one wants to install PETSc [with sources] in a common system
location like /usr/local or /opt, then we suggest creating a dir for
PETSc in the required location 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 /opt/petsc
tar -xzf petsc-3.7.0.tar.gz
cd petsc-3.7.0
./configure
Installing with --prefix:
One can also use the GNU --prefix install mode.
./configure --prefix=/opt/petsc/petsc-3.7.0
[other configure options]
[sudo] make install
[user can now use this PETSc install with:] make PETSC_DIR=/opt/petsc/petsc-3.7.0 ex1
Note: one has to switch to using PETSC_DIR=/opt/petsc/petsc-3.7.0 after
install is done - and NOT use PETSC_ARCH anymore.
These can be found in ${PETSC_DIR}/${PETSC_ARCH}/lib/pkgconfig/PETSc.pc and ${PETSC_DIR}/${PETSC_ARCH}/lib/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.
If one has to use a cross compiler - or go through the job scheduler to
use MPI on a given machine - use the configure option
--with-batch as follows:
run configure with the additional option --with-batch on
the frontend node (compiler server) [perhaps with the
additional option --known-mpi-shared-libraries=0]
the above configure run will create a binary conftest.
Run this binary conftest on one compute node
using the job scheduler.
The above run of conftest will create a new python script
reconfigure.
Run python reconfigure again
on the frontend node (compiler server) to complete the
configuration process
package and the prerequisite
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
Requires ,
Thrust has been included in CUDA since the 4.0 release - so a separate install is not needed.
Currently using CUDA-4.1 or CUDA-4.2 with Cusp-v0.3.1 or CUDA-5 with Cusp-v0.4.0.
On Linux - make sure you have
compatible
installed.
check config/examples/arch-cuda-double.py for example usage.
Cuda build of PETSc curently works on Apple OSX, Linux [Ubuntu 10.04], Microsoft Windows [Server 2003].
and the OpenCL shared library, which is shipped in the vendor graphics driver.
Make sure the OpenCL headers are available on your system by e.g. downloading them from the
Package managers on Linux provide these headers through a package named 'opencl-headers' or similar.
Always make sure you have the latest GPU driver installed. There are several known issues with older driver versions.
check config/examples/arch-viennacl.py for example usage.
OpenCL/ViennaCL builds of PETSc currently work on Apple OSX, Linux, and Microsoft Windows. OpenCL is less a burden on the build system than CUDA, so installation is often easier and works with any host compiler.}