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
- Using the bash shell, assuming BLAS,
LAPACK, MPICH are not currently installed ./config/configure.py
will download &
install BLAS, LAPACK, MPICH if they are not already installed on the
system) :
export
PETSC_DIR=/home/petsc/petsc-3.1-p0
cd $PETSC_DIR
./config/configure.py
--with-cc=gcc --with-fc=gfortran --download-f-blas-lapack=1
--download-mpich=1
make
make test
- Same as above - but 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):
export
PETSC_DIR=/home/petsc/petsc-3.1-p0
cd $PETSC_DIR
./config/configure.py
--with-cc=gcc --with-fc=gfortran --with-cxx=g++
--download-f-blas-lapack=1
--download-mpich=1
--with-scalar-type=complex --with-clanguage=cxx
make
make test
- Using the bash shell, assuming BLAS,
LAPACK, MPICH software are installed at the specified locations, and
use MPI compilers mpicc/mpif90:
[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]
export
PETSC_DIR=/home/petsc/petsc-3.1-p0
cd $PETSC_DIR
./config/configure.py
--with-blas-lapack-dir=/usr/local/lib --with-mpi-dir=/usr/local/mpich
make
make test
- Using csh shell, install 2 variants of PETSc, one with gnu,
the other with intel compilers
./config/configure.py
PETSC_ARCH=linux-gnu CC=gcc FC=gfortran --download-mpich=1
make PETSC_ARCH=linux-gnu
make
PETSC_ARCH=linux-gnu test
./config/configure.py PETSC_ARCH=linux-gnu-intel
CC=icc FC=ifort --download-mpich=1
--with-blas-lapack-dir=/usr/local/mkl
make PETSC_ARCH=linux-gnu-intel
make
PETSC_ARCH=linux-gnu-intel test
PETSC_DIR and PETSC_ARCH are a couple of variables 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-3.1-p0 setenv PETSC_ARCH linux-gnu-c-debug
- specify enviornment variable for bash [can be specified in
~/.bashrc]
export PETSC_DIR=/home/balay/petsc-3.1-p0 export PETSC_ARCH=linux-gnu-c-debug
- specify variable on commandline to configure
config/configure.py PETSC_DIR=/home/balay/petsc-3.1-p0 PETSC_ARCH=linux-gnu-c-debug [other configure options]
- specify variables on command line to make
make PETSC_DIR=/home/balay/petsc-3.1-p0 PETSC_ARCH=linux-gnu-c-debug [other make options]
PETSC_DIR:
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.
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.
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Installation Instructions
Compilers:
Specify compilers and compiler options used to build PETSc [and perhaps
external packages]
- Specify compilers using the options --with-cc --with-fc --with-cxx
for c, c++, fortran compilers
- --with-cc=mpicc
--with-fc=mpif90
- --with-cc=gcc
--with-fc=gfortran
- --with-cc=gcc
--with-cxx=g++ --with-fc=gfortran --with-clanguage=cxx
- If fortran compiler is not available - then disabling using
fortran
- If no compilers are specified - configure will
automatically look for available MPI or regular compilers in users PATH
- mpicc/mpiCC/mpif90 or mpif77
- gcc/g++/gfortran or g77
- cc/CC/f77 etc..
- Its 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-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.
- ./config/configure.py
--with-cc=gcc
--with-fc=gfortran --with-debugging=0 COPTFLAGS='-O3
-march=p4
-mtune=p4' FOPTFLAGS='-O3 -qarch=p4 -qtune=p4'
- Configure cannot detect compiler libraries for certain set
of compilers. In this case one can specify additional system/compiler
libraries using the LIBS option
- ./config/configure.py
LIBS='-ldl
/usr/lib/libm.a'
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External Packages:
PETSc provides interfaces to various external packages.
Blas/Lapack and MPI are generally required packages - but one can
optionally use external solvers
like Hypre, MUMPS etc.. from within PETSc aplications.
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.
The following modes can be used to install/use external
packages with configure.
--download-PACKAGENAME=1
: Download specified package and install it. Then configure PETSc to
use this package.
- --download-f-blas-lapack=1
--download-mpich=1
- --download-blacs=1
--download-scalapack=1 --download-mumps=1
--download-PACKAGENAME=/PATH/TO/package.tar.gz
: If config/configure.py 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 package.
- --with-mpi-dir=/home/petsc/software/mpich2-1.0.4p1
--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.
- --with-parmetis-include=/home/petsc/software/parmetis/include
--with-parmetis-lib=/home/petsc/software/parmetis/lib/libparmetis.a
- --with-mpi-include=/home/petsc/software/mpich2-1.0.4p1/include
--with-mpi-lib=[/home/petsc/software/mpich2-1.0.4p1/lib/libmpich.a,-lpthread,-lrt]
Notes:
- Run config/configure.py-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.
Some architectures like Windows might have issues with these options.
In these cases, --with-PACKAGENAME-include
--with-PACKAGENAME-lib options should be prefered.
- Its best to install some external
packages like SuperLU_DIST, MUMPS, Hypre with the option --download-PACKAGENAME.
[the correct options for these packages are --download-superlu_dist=1
--download-mumps=1 --download-hypre=1]
- 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]
- All packages will be installed with the
same set of compilers - this avoids problems [for ex: wiered link time
errors] with mixing code compiled with multiple compilers [for example
mixing gfortran and ifort compiled code].
- If one had 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/PETSc/packages/SuperLU.py
for the url for download this package.
Additional options:
--with-external-packages-dir=PATH
: By default, external packages will be installed in ${PETSC_DIR}/externalpackages.
However one can choose a different location where these packages are
installed.
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Installation Instructions
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 config/configure.py command, some
of the standard locations used are
- /usr/lib/libblas.a,liblapack.a
- Intel MKL on Windows or Linux
- sunperf on solaris
- VecLib on Macs
- IBM ESSL
- [and many more]
- One can use the following options to let configure
download/install blas automatically.
- --download-f-blas-lapack=1
[when
fortran compiler is present]
- --download-c-blas-lapack=1
[when configuring without a fortran compiler - i.e --with-fc=0]
- Alternatively one can use other externalpackages
installation options like the following.
- --with-blas-lapack-lib=libsunperf.a
- --with-blas-lib=libblas.a
--with-lapack-lib=liblapack.a
- --with-blas-lapack-dir=opt/intel/mkl72
Notes:
- Sadly, IBM's ESSL
does not have all the private routines of BLAS that some packages, such
as SuperLU expect; in particular slamch, dlamch and xerbla. Therefor
you need a full implementation of blas/lapack when using these package.
In this case, use --download-f-blas-lapack=yes
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Installation Instructions
MPI:
This software provides the parallel functionality for PETSc.
- Configure will automatically look for MPI compilers
mpicc/mpif77 etc and use them if found [in default PATH]
- One can use the following options to download/install
- One can use the following options to let configure
download/install MPI automatically
- --download-mpich=1
[install
and use MPICH]
- --download-openmpi=1
[Install and useOpenMPI]
- Alternatively one can use other externalpackages installation
options.
Using MPI
Compilers:
- Its best to install PETSc with MPI compilers - 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=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]:
./config/configure.py
--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.
- ./config/configure.py
--with-mpi=0
Installing
with OpenMPI 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. The
same issue might exist with LAM as well.
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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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. And PETSc
primarily relies on a unix envirment for build tools. So to install
PETSc on windows - one has to install cygwin
[for the unix enviornment] and use win32fe
[part of PETSc sources,to interface to MS/Intel/Compaq compilers].
Install Cygwin: Please
download and install cygwin package from http://www.cygwin.com Make sure
the following cygwin components are installed.
- python
- make
- [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/bash shell]:
- mv /usr/bin/link.exe
/usr/bin/link-cygwin.exe
Setup cygwin 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 bash.exe as: c:\cygwin\bin\bash.exe --login
- verify if the compilers are useable [by running cl, ifort
in this shell]
- Now run configure with win32fe and then build the libraries
with make [as per the usual instructions]
Notes: This a new requirement as win32fe can no longer autodetect the
newer versions of compilers. They currently default to "noautodetect
mode.
Example Configure usage with Windows Compilers:
Use configure with VC2005 C and Intel Fortran 10 [With MPICH2
installed].
./config/configure.py
--with-cc='win32fe
cl' --with-fc='win32fe ifort'
--with-cxx='win32fe cl' --download-f-blas-lapack=1
If fortran usage is not required, use:
./config/configure.py --with-cc='win32fe cl' --with-fc=0
--download-c-blas-lapack=1
Using Compaq F90:
Using Microsoft C/C++ 6.0 & Compaq Fortran 6.0 with MPICH2
configure command to use:
./config/configure.py --with-cc='win32fe cl' --with-fc='win32fe f90'
--download-f-blas-lapack=1
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: --download-package
option does not
work with many external packages.
Project Files: We
provide
templates for Microsoft Visual Studio project files at
${PETSC_DIR}/projects. These work for us - with our configure build
[config/cygwin-ms.py with MPICH1 and Intel MKL 5], However they will
REQURE MODIFICATIONS to work with a user build of PETSc - as the
locations of packages & configure options used by user could be
different from our defult build.
To get these project files working for your installation of
PETSc, please do the following:
- try compiling the example from cygwin shell - using
makefile - for eg:
cd src/ksp/ksp/examples/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.
Using Cygwin gcc/g++/gfortran: One
can install and use PETSc with gcc/gfortran compilers from cygwin. In
this case follow the regular instructions.
PETSc Win32
front end - win32fe:
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.
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Installation Instructions
If one wants to install PETSc [with sources] in a common
system location like /usr/local or /opt, then sugest creating a dir for
PETSc in the required location with user previledges, 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-3.1-p0.tar.gz
- cd petsc-3.1-p0
- ./config/configure.py
- make
One can also use the gnu
prefix-install mode.
- [untar PETSc in a
non-root regular location - say /home/username]
- setenv PETSC_DIR $PWD
- ./config/configure.py
--prefix=/opt/petsc/petsc-3.1-p0 [other configure options]
- make
- sudo make install
PETSC_DIR=$PWD
After the install is done, one has to switch to using PETSC_DIR=/opt/petsc/petsc-3.1-p0.
If
you've installed PETSc with the --prefix option then you DO
NOT use a PETSC_ARCH variable. You should install different
configurations using different --prefix names.
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=1' as follows:
- run configure with the additional option '--with-batch=1' on the frontend node (compiler server)
[perhaps with the
additional option '--known-mpi-shared=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
To run any code compiled with MPI on IBM SP - one has to
go
through the job scheduler.
[So
follow the instructions from the above section 'Installing on
machine requiring job scheduler']. Alternatively check/run
config/examples/aix5.1.0.0.py for all
configure options
required on the SP with compilers defaulting to 32bit mode, and
config/examples/aix5.1.0.0-64.py with compilers defaulting to 64bit
mode.
Installing
on IBM BG/L:
IBM BG/L [as of now] requires modified compiler
script
wrappers to compile PETSc-3.1-p0. Please download http://ftp.mcs.anl.gov/pub/petsc/tmp/petsc-bgl-tools.tar.gz
and follow instructions provided in the README file
Installing
on IBM BG/P:
IBM BG/P has mpixlc and mpixlf wrappers so no additional compiler
wrappers are needed.
TAU
package and the prerequisite PDT
packages need to be installed separately. PETSc provides a wrapper
compiler for TAU. This needs to be invoked with the correct information
for the installed TAU and PDT packages. For eg:
./config/configure.py
--with-mpi-dir=/home/petsc/soft/linux-rh73/mpich-1.2.4
--with-fc=0
--with-cxx=0
-PETSC_ARCH=linux-tau --with-cc="`pwd`/bin/taucc.py
-cc=gcc
-pdt_parse=/homes/petsc/soft/linux-rh73/pdtoolkit-2.2b1/linux/bin/cparse
-tau_lib_dir=/homes/petsc/soft/linux-rh73/tau-2.11.18/i386_linux/lib"
Installing
TOPS components:
To install TOPS components one has to download and
install CCA
Tools. [linux only]
- Get the CCA Tools package from http://www.cca-forum.org/download/cca-tools/cca-tools-0.5.9.tar.gz
- Configure cca-tools using '-with-mpi' option
[prerequisites
might be
Java SDK, c++, mpich1]
- Configure PETSc with C++, babel, ccafe options.
Check config/config/asterix-tops.py for an example.
- Build PETSc libraries & TOPS components with
'make all'
- To test do: 'cd src/tops; make examples'
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