Gnu compiler build instructions use below command to find the latest gcc and impi version on ikt. These packages provide some basic numeric kernels used by petsc. Petsc fails on cluster could not find a functional blas. Petsc portable, extensible toolkit for scientific computation is an open source suite of data structures and routines for the parallel solution of scientific applications modelled by partial differential equations. Browse, download lapack routines with online documentation browser. About petsc installation computational science stack exchange. When a need for running sets of standard tests and comparing them against known solutions arose, a new structure for the tests was designed with the. Cray, blue gene loosely coupled such as network of workstations gpu clusters many vector and sparse matrix kernels operating systems linux, mac, windows, bsd, proprietary unix any compiler realcomplex, singledoublequad precision, 3264bit int. Gnumakefile a makefile that can be used with minor modification to compile and run all the lapack examples. From the installation instructions on the petsc website, i saw that, if i wanted to download blas, lapack, and the mpi compilers that petsc needs, i should add these lines to the list in the above file.
Thanks artem, i reduced number of parameters and now configured petsc with mkl. Is this a common trend or are there other factors at play. For damask, petsc needs to be compiled with support for all fortran 2003. Libmeshusers weird petsc errors with multiple variables on code modified from transientex1 libmeshusers weird petsc errors with multiple variables on code. But when compiling my lib that uses petsc, even though i linked all petsc libs its complain at runtime of. If you are not using the reference blas, you will need to modify change the properties linker general additional library directory to tell visual studio where the libraries are, and also add the name of. The examples below show options for configuring petsc to link to intel mkl blas and lapack. Open a terminal and go to the directory where you have saved it. Getting started with petsc argonne national laboratory. I installed cygwin default installation with python, make, diff. Run with withblaslib to indicate the library containing blas. The first example we only list c sources in this book. It is an extension of petsc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic.
I found with the petsc configure option download fblas lapack my program runs twice as fast over running it with mkl. I am trying to install petsc library on windows 7 to be used with visual studio express 2008, but i didnt succeed so far. Using intel mkl blas and lapack with petsc intel software. Hyak installing petsc hyak user documentation uwit wiki. Summary this document describes how to build the portable extensible toolkit for scientific computation petsc with intel math kernel library intel mkl blas and lapack it also introduces how to enable sparse linear operation include sparse blas and intel mkl pardiso and cluster pardiso as direct solver in petsc applications. A suite of data structures and routines for the scalable parallel solution of scientific applications modeled by partial differential equations. Parallel implementation of finite element code using petsc. If i compare results for typical model poisson equation, 220220220 cells, pretty sparse matrix, kspbcgs i dont see any improvements. If these libraries are not already available on the users machine, he can download and install the software from the respective webpages petsc homepage, and aztec homepage. What i need from you tell me if you do not understand tell me if an example does not work suggest better wording or.
Download development version of petsc from bitbucket repository or latest released petsc version from official website. It is also possible to get petsc to download and install mumps see mumps. Petsc is developed as opensource software and can be downloaded from the argonne national laboratory. It can also be used for computing a partial svd of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. Be sure when calling the lapack routing that all arguments are passed by reference. Last edited by julien langou on fri jan 31, 2014 11.
You may want to choose the debug config if you choose gotoblas. Software package like trilinos and petsc also have a complete iterative eigensolver suite. Download the lapack vs example visual studio project and unzip move or copy the libraries from step 1 in the lapack vs example folder. Enabling intel mkl in petsc applications intel software. Download lapack packages for alpine, arch linux, centos, fedora, freebsd, kaos, netbsd, opensuse, slackware. 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. Mar 28, 2018 this document contains instructions for linking to intel mkl blas and lapack functions when building the petsc libraries. If you only want to use tao and petsc, and you have no interest in using blas and lapack elsewhere, then you do not need to manually download and install blas and lapack. Now you need to change the directory of blas in the file c. Examples on vec, mat, ksp, snes download petsc source to better follow the discussion.
Lapackscalapack development view topic calculate a. Because of the new api the function matsetoptions in sourcematrix. There will probably be some kind of configure program that might need to be run first, to setup. Petsc objects home texas advanced computing center. Petsc fails on cluster could not find a functional. Troubleshooting massachusetts institute of technology. See using petsc parallel for an example of how to run a petsc job on more than one processor.
Before it may be compiled petsc must be configured with the following commands. In below instructions use the latest gcc and impi version from output of above module command. How to install openmpi, mpi4py, petsc and petsc4py for use. The petsc interface is compatible with petsc, version 2. Introduction portable extensible toolkit for scienti. Therefore, prior to discussing specific objects in detail, we briefly discuss how petsc treats distributed objects.
Download the petsc source by grabbing the current gzipped tarball at. Please, visit petsc website for advanced configuration options. These test packages duplicated much of the infrastructure both within and between packages. Retrieve, configure, build, and run a petsc example. Libraries like this should be located in usrlocallib or elsewhere asneeded in usrlocal. Instructions for download can be found on petsc website. Hello, i am trying to modify the entries of the system matrix in the main function. If you have any other examples you would like to run for example, ex19 do the following. Requests tell me if you do not understand tell me if an example does not work suggest better wording. The petsc fortran libraries are built automatically during the installation outlined above. To compile and test the fortran examples, use the command. As discussed in the machines file, most of the difficulties that beginners experience with petsc are related to linking the correct system libraries often those associated with fortran. Petsc and boost on windows cygwin and linux materials. Several issues discussed below deal with this problem.
Nov 12, 2017 mkl sparse blas ie for aij and baij matrix operations petsc 3. It supports mpi, shared memory pthreads, and gpus through cuda or opencl, as well as hybrid mpishared memory pthreads or mpigpu parallelism. Introduction what i need from you tell me if you do not understand tell me if an example does not work suggest better wording or. To build and run the example file using the project provided. There is a little problem compiling openfvm parallel version with petsc 3. Nonlinear pde example using trilinos preconditioner ml. Petsc portable, extensible toolkit for scienti c computing. The easiest way to configure petsc for damask is to let petsc download and. Lapack is written in fortran 90 and provides routines for solving systems of simultaneous linear equations, leastsquares solutions of linear systems of equations, eigenvalue problems, and singular value problems. Better to use than petsc use the package with the highest level of abstraction that uses petsc eigenvalues slepc, optimizationation with pde constraints tao finite elements deal. In order to avoid incompatibilities between petsc, petsc4py and petgem, we highly recommend the following configuration lines. Petsc releases are available for download from the petsc web site at. Blas and lapack are software libraries for numerical linear algebra that.
Petsc extensible toolkit for scientific computation petsc. Arkode installation procedure the installation of any sundials package is accomplished by installing the sundials suite as a whole, according to the instructions that follow. Jics joint institute for computational science 714 practical scientific parallel computing 6 basic linear algebra subroutine blas blas is a library of standardized basic linear algebra computational kernels created to perform efficiently on serial computers taking into. Before testing the fortran examples, please make sure that the cversion of the examples work correctly. The same procedure applies whether or not the downloaded file contains one or all solvers in sundials. When building petsc for two or more machine types that share a common filesystem, for example sun4 and hpux, multiple petsc directory trees are not needed.
Doing a search below will usually lead straight to the problem. Xt5, bgp, earth simulator loosely coupled such as network of workstations gpu clusters many vector and sparse matrix kernels. These examples will open an x window and draw some graphics. Petsc portable, extensible toolkit for scientific computation. Since you are downloading blaslapack, that example would not be necessary, but it may be for other libraries you are using. If you have a clean environment not working mpiblas lapack, then run. Petsc automatically places the libraries for each machine in a different location. Petsc is based on the spmd model, and all its objects act like they exist in parallel, spread out over all the processes.
Petsc now downloads a decent version of mpi during installation, so no. If enabled by the user with the appropriate toggle for cmake, the examples distributed with sundials will be built together with the solver libraries but the installation step will result in exporting. Assuming blas, lapack, mpich are not currently installed. The above code changes the variables in system matrix.
There are two packages that petsc is capable of downloading and install, but that you may want to avoid. Apr 01, 2020 petgem is a parallel python code for 3d controlledsource electromagnetic method 3d csem in geophysics using highorder edge finite elements nedelec finite elements. Configure the petsc that you downloaded and unpacked. Ii, libmesh, fenics, petscfem, oofem, finite elements and multiphysics moose finite volumes freecfd, openfvm wave propagation pyclaw. This is the actual commandfile that tells make what to do. Getting started with petsc mathematics and computer science. Several examples are also included that represent the interoperability with other numerical software packages in the xsdk toolkit.
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