Petsc, toolkit for partial di erential equations may 2015i. Role of hpc libraries and frameworks in software dev. Mathematical libraries and application software on jureca. Intel math kernel library mkl includes optimized lapack, blas, fft, vector math and statistics functions. Decomposition matrix an overview sciencedirect topics. Intel math kernel library scalapack,lapack examples. As of scalapack version 2 blacs is now builtin with the scalapack library. Very easy to use, just link with mkl of course, dont even think about writing your own gordon software suggestions. Designing numerical software premature optimization is the root of all evil first make the code produce the expected results validation. Blas, lapack, scalapack edit on github the intel mkl libraries contain a variety of optimised numerical libraries including blas, lapack, and scalapack. Mathematical libraries and application software on juqueen. Clusterbased versions of lapack, fft and sparse solver are also included to support mpi.
Intel math kernel library implements routines from the scalapack package for distributedmemory architectures. I am trying to do a cholesky decomposition via pdpotrf of mkl intels library, which uses scalapack. Petsc users manual mathematics and computer science. The portable, extensible toolkit for scientific computation petsc, pronounced petsee. Mar 30, 2020 developer reference for intel math kernel library c. Mar 21, 2018 programming environment which includes the compilers and matching libraries intel programming environment is the default on both cori and edison. Specify compilers and compiler options used to build petsc and perhaps external packages.
Provides the vector operations required for setting up and solving largescale linear and nonlinear problems. Jan 25, 2019 mkl parallel,sequential,cluster for intel compiler, use mkl flag ftn test1. Programming with big data in r oak ridge leadership. Cycle use librariesframeworks to fill software gap profiling to identify performance bottlenecks find hpc libraries or algorithm frameworks covering gaps. Jun 25, 2012 hpcc has many common libraries available, including mkl, fftw, acml, blas, scalapack, lapack, petsc. If you run your code through a job submission system, there are caveats in mpi rank mapping. Scalapack is a library of highperformance linear algebra routines for parallel distributed memory machines. Petsc solution of linear and nonlinear partial differential equations focus on problems discretized using semi or fully implicit.
Compiler optimization and libraries louisiana state university. 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. 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. Petsc solution of linear and nonlinear partial differential. Introduction to parallel programming martin cuma center for high performance computing.
I am reading the whole matrix in the master node and then distribute it like in this example. Additionally, some code samples are available as indicated by typing. Jics joint institute for computational science 714 practical scientific parallel computing 6 basic linear algebra subroutine blas blas is a library of. This manual describes the use of petsc for the numerical solution of partial differential equations and related problems. Developers need to ensure that other options are configured appropriately for their system. Petsc includes nonlinear and linear equation solvers that employ a variety of newton techniques and krylov. Portable, extensible toolkit for scientific computation petsc is a suite of data structures and routines for. Petsc, toolkit for partial differential equations parallel librariesslide 22. Scalapack solves dense and banded linear systems, least squares problems, eigenvalue problems, and singular value problems. Recommendation on sparse, direct, distributed solver. Scalapack solves dense and banded linear systems, least squares problems, eigenvalue problems, and singular value problems, and is designed to be used in mpibased parallel applications.
Comet is a dedicated xsede cluster designed by dell and sdsc delivering 2. Programming with big data in r george ostrouchov oak ridge national laboratory and university of tennessee future trends in nuclear physics computing march 1618, 2016 thomas je erson national accelerator facility newport news, va ppppbbbbddddrrrrcore team programming with big data in r. For an introduction to the online version, see pptx or pdf. There is a tar file that can be downloaded to ra that contains the source for the various programs, most in both c and fortran, a makefile, and a pbs script. Since mumps calls blas libraries, to really get performance, you should have multithreaded blas libraries such as intel mkl, amd acml, cray libsci or openblas petsc will automatically try to utilized a threaded blas if withopenmp is provided. Petsc petsc, the p ortable, e xtensible t oolkit for s cientific c omputation, provides sets of tools for the parallel as well as serial, numerical solution of pdes that require solving largescale, sparse nonlinear systems of equations. Bright cluster manager also provides environment modules to make it easy to maintain multiple versions of compilers, libraries and applications for different users on the cluster, without. Daal abstracts from underlying crossdevice communication technology, which enables use of the library in a variety of multidevice computing and data transfer scenarios including mpi, spark, and lowlevel protocols. This means that it is tightly coupled to the mpi implementation used to build it. Since the usage of scalapack depends on lapack, it involves multiple libraries. Getting started with petsc mathematics and computer science. Scalapack part of mkl, parallel blas, pblas version 2 dense linear system solvers.
Hyperlinked manual, examples, and manual pages for all routines. Clusterbased versions of lapack, fft and sparse solver are also included to support mpibased distributed memory computing. Compilers and libraries high performance computing at icer. Get routines to solve various numerical problems, such as multiplying matrices, solving a system of equations, and performing a fast fourier transform fft. These variables can be set as envirnment variables or specified on the command line to both configure and make specify enviornment variable for cshtcsh can be specified in. Other available compilers, such as bupc, llvm, etc, will not be covered in this presentation. On desktop linux, make sure that you have lapackdev or atlasdev installed. Scalapack, petsc, nag, fftw mkl dense and sparse matrices. This has been built with the extra packages mumps and scalapack.
Parallel programming paradigms george ostrouchov oak ridge national laboratory and university of tennessee and pppppbbbbdddrrrrrcore team course at it4innovations, ostrava, october 67, 2016. Read 19 answers by scientists with 18 recommendations from their colleagues to the question asked by eduardo sanchez on aug 8, 2012. Scalapack package available in mkl and supporting distributed processing of the data relies on mpi communication technology. Petsc plasma mkl intel dplasma libsci cray scalapack pblas blacs cublas nvidia magma papi tau mpi mpip fpmpi netcdf4 adios magma hiplarmhiplar pbdmpi pbdpapi pbdncdf4 pbdadios pppbbbddprofprofprof acml amd combblas cusparse nvidia pbddmatpbddmat pbddmat pbdbase pbdslap ppppbbbbddddrrrrcore team. Code optimization cornell university center for advanced. Everything works fine when the dimension of the spd matrix is even.
Mathematical libraries and application software on. Petsc includes a set of python configuration files which support the use of various compilers, mpi implementations and math libraries. A read is counted each time someone views a publication summary such as the title, abstract, and list of authors, clicks on a figure, or views or downloads the fulltext. Hpcc has many common libraries available, including mkl, fftw, acml, blas, scalapack, lapack, petsc. Highperformance libraries and tools fsu computer science. Everything else trilinos, mumps, metis, etc will be reused. Optimization and scalability cornell university center for. Intel mkl users guide and reference manual intel mkl user forum petsc web site. Intel math kernel library mkl optimization for intel processors. Using intel mkl blas and lapack with petsc intel software. The standard compute nodes consist of intel xeon e52680v3 formerly codenamed haswell processors, 128 gb ddr4 dram 64 gb per socket, and 320 gb of ssd. Other libraries, including global arrays, hdf5, iipp, tbb, netcdf and petsc. Petsc matlab and even more matrixsparse solver matrix node vector sparse dense scalapack lapack blas pastix paradiso plapack blas. This page gives a number of intel math kernel library mkl examples, in particular calls to routines that are part of the scalapack group of routines.
The module names and available link flags are summarized in the following table. We will post more detailed instructions later, but for feb 24, click here lecture notes for mar 3. Intel mkl math kernel library includes highly vectorized and threaded linear algebra, fast fourier transforms fft, vector math and statistics functions. Scalapack is a library of highperformance linear algebra routines for distributedmemory messagepassing mimd computers. Petsc plasma mkl intel dplasma libsci cray scalapack pblas blacs cublas nvidia magma papi tau mpi mpip fpmpi netcdf4 adios magma hiplarmhiplar pbdmpi pbdpapi pbdncdf4 pbdadios pppbbbddprofprofprof acml amd combblas cusparse nvidia pbddmatpbddmat pbddmat pbdbase pbdslap ppppbbbbddddrrrrcore team sustainable scalable statistical. The intel math kernel library intel mkl cookbook includes key recipes and building blocks to help you solve more complex problems.