Development/FFTW: Difference between revisions
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| module load |
| module load |
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| numlib/ |
| numlib/mkl |
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| Availability |
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| [[bwUniCluster]] | [[BwForCluster_Chemistry]] |
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|- |
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| License |
| License |
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| Commercial. See [https://software.intel.com/en-us/articles/end-user-license-agreement EULA]. |
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| [http://www.fftw.org/faq/section1.html#isfftwfree GPL] | [http://www.fftw.org/fftw3_doc/License-and-Copyright.html License and Copyright] |
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|Citing |
|Citing |
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| n/a |
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| [https://github.com/FFTW/fftw3/blob/master/AUTHORS Authors] |
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| Links |
| Links |
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| [ |
| [https://software.intel.com/en-us/intel-mkl Intel MKL Homepage] | [http://www.fftw.org/ FFTW Homepage] |
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|- |
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| Graphical Interface |
| Graphical Interface |
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| No |
| No |
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<br> |
<br> |
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= Description = |
= Description = |
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'''FFTW''' is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications. |
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<br> |
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[http://www.fftw.org/ More infos about FFTW] |
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<br> |
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This package provides three versions of the fftw3 library depending on precision: |
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* libfft3 |
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* libfftw3f |
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* libfftw3l <small>for double, single and long-double precision libraries</small> |
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<br> |
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= Documentation = |
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== Online == |
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[http://www.fftw.org/fftw3_doc/ Online Documentation] |
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== Local == |
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* info fftw3 |
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* man fftw-wisdom |
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* man fftw-wisdom-to-conf |
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<br> |
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See also documentation folder pointed to by shell variable $FFTW_DOC_DIR |
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<br> |
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<br> |
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= Versions and Availability = |
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A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the |
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<br> |
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<big> |
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[https://cis-hpc.uni-konstanz.de/prod.cis/ Cluster Information System CIS] |
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</big> |
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{{#widget:Iframe |
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|url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/numlib/fftw |
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|width=99% |
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|height=200 |
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|border=0 |
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}} |
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On the command line interface of any bwHPC cluster you'll get a list of available versions |
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by using the command 'module avail chem/gamess'. |
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<pre> |
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$ module avail chem/gamess |
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------------------------ /opt/bwhpc/common/modulefiles ------------------------- |
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chem/gamess/12052014 |
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</pre> |
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<br> |
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= Loading the Module = |
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Load the fftw module, and, if needed, the corresponding openmpi module. |
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You can load the default version of 'FFTW'' with the command<br> |
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'module load numlib/fftw'. |
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<pre> |
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$ module load numlib/fftw |
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Loading module dependency 'compiler/intel/13.1'. |
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</pre> |
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The module will try to load modules it needs to function (e.g. compiler, mpi, numlibs). |
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<br> |
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If loading the module fails, check if you have already loaded one of those modules with<br> |
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the command 'module list'. |
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If you wish to load a specific (older) version (if available), you can do so using e.g. |
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'module load numlib/fftw/'version' to load the version you desires. |
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<pre> |
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$ module avail numlib/fftw |
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------------------------ /opt/bwhpc/common/modulefiles ------------------------- |
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numlib/fftw/3.3.3-impi-4.1.1-gnu-4.4 |
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numlib/fftw/3.3.3-impi-4.1.1-intel-13.1(default) |
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$ |
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$ module load numlib/fftw/3.3.3-impi-4.1.1-gnu-4.4 |
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$ module list |
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Currently Loaded Modulefiles: |
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1) numlib/fftw/3.3.3-impi-4.1.1-gnu-4.4 |
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</pre> |
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<font color=red>Beware!</font> Compiler and numerical library must fit! |
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<br> |
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<br> |
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= Hints for compiling and linking = |
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== FFTW Specific Environments == |
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To see a list of all FFTW environments set by the 'module load'-command use the command |
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'module display numlib/fftw'. |
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<br> |
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After having loaded the appropriate module(s), you can use several environment variables to compile and link your application. |
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<pre> |
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$ module display numlib/fftw |
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------------------------------------------------------------------- |
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/opt/bwhpc/common/modulefiles/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1: |
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FTW_VERSION = 3.3.3-impi-4.1.1-intel-13.1 |
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FFTW_HOME = /opt/bwhpc/common/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1 |
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FFTW_BIN_DIR = /opt/bwhpc/common/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1/bin |
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FFTW_INC_DIR = /opt/bwhpc/common/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1/include |
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FFTW_LIB_DIR = /opt/bwhpc/common/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1/lib |
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FFTW_STA_DIR = /opt/bwhpc/common/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1/lib |
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FFTW_SHA_DIR = (empty) |
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FFTW_MAN_DIR = /opt/bwhpc/common/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1/share/man |
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FFTW_INF_DIR = /opt/bwhpc/common/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1/share/info |
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FFTW_DOC_DIR = /opt/bwhpc/common/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1/doc |
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FFTW_EXA_DIR = /opt/bwhpc/common/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1/examples |
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FFTW_WWW = http://www.fftw.org/ |
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PATH = /opt/bwhpc/common/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1/bin:$PATH |
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MANPATH = /opt/bwhpc/common/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1/share/man:$MANPATH |
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INFOPATH = /opt/bwhpc/common/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1/share/info:$INFOPATH |
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LD_LIBRARY_PATH = /opt/bwhpc/common/numlib/fftw/3.3.3-impi-4.1.1-intel-13.1/lib:$LD_LIBRARY_PATH |
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[...] |
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</pre> |
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== Compile a Serial Program == |
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<pre> |
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$ gcc example.c -o example -I$FFTW_INC_DIR -L$FFTW_LIB_DIR -lfftw3 -lm |
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</pre> |
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=== with POSIX Threads === |
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Compile program with support for POSIX threads: |
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<pre> |
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$ gcc example.c -o example -I$FFTW_INC_DIR -L$FFTW_LIB_DIR -lfftw3_threads -lfftw3 -lpthread -lm |
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</pre> |
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The '''Fastest Fourier Transform in the West (FFTW)''' is a software library for computing discrete Fourier transforms in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). FFTW was developed by Matteo Frigo and Steven G. Johnson at the Massachusetts Institute of Technology. |
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== Compile program with support for OpenMP threads == |
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<pre> |
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$ gcc example.c -o example -fopenmp -I$FFTW_INC_DIR -L$FFTW_LIB_DIR -lfftw3_omp -lfftw3 -lm |
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</pre> |
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The '''Intel Math Kernel Library (Intel MKL)''' offers FFTW2 (for version 2.x) and FFTW3 (for version 3.x) interfaces to the Intel MKL Fast Fourier Transform and Trigonometric Transform functionality. These interfaces enable applications using FFTW to gain performance with Intel MKL without changing the application source code. Therefore, it is highly recommended to use Intel MKL instead of a separate FFTW installation. |
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== Compile program with support for MPI == |
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<pre> |
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$ mpicc example.c -o example -I$FFTW_INC_DIR -L$FFTW_LIB_DIR -lfftw3_mpi -lfftw3 -lm |
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</pre> |
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= FAQ = |
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== Run program with MPI support == |
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<pre> |
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$ mpirun -n <ncpu> ./example |
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</pre> |
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[[File:comparison.png|right|border|300px|Copyright: KIZ (Ulm University)]] |
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(Replace <ncpu> by number of processor cores.) |
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'''Q:''' Why is there no FFTW module on the cluster? |
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Replace -lfftw3, -lfftw3_threads, etc. by -lfftw3f, -lfftw3f_threads, etc. for single |
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precision and by -lfftw3l, -lfftw3l_threads etc. for long-double precision codes, respectively. |
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'''A:''' MKL exhibits better performance than FFTS libraries (see Figure on the right). Therefore, we recommend to use MKL and do not offer a separate FFTW installation. |
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These commands will compile your program with dynamic fftw library versions in |
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which case you also have to have the fftw module loaded for running the program. |
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Alternatively, you may want to link your program with static fftw library versions. |
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With static fftw libraries it is only necessary to load the fftw module for compiling |
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but not for executing the program. |
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'''Q:''' Why does my code complain about <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080"> argument of type "long double *" is incompatible with parameter of type "double *" </span>? |
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== Compile program with static fftw library versions == |
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Example for POSIX threads support |
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<pre> |
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$ gcc example.c -o example -I$FFTW_INC_DIR $FFTW_LIB_DIR/{libfftw3_threads.a,libfftw3.a} -lpthread -lm |
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</pre> |
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or: |
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<pre> |
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$ gcc example.c -o example -I$FFTW_INC_DIR -L$FFTW_LIB_DIR -Wl,-Bstatic -lfftw3 -lfftw3_threads \ |
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-Wl,-Bdynamic -lpthread -lm |
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</pre> |
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'''A:''' The interfaces do not support long double precision because Intel MKL FFT functions operate only on single- and double-precision floating point data types. For the very rare case that you need extended data types, please submit a support ticket at https://www.bwhpc.de/supportportal. |
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Environment variables $FFTW_INC_DIR, $FFTW_LIB_DIR etc. are available after |
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loading the module. |
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= Useful links = |
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Sample code for various test cases is provided in folder pointed to by environment |
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variable $FFTW_EXA_DIR. |
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* [https://software.intel.com/content/www/us/en/develop/articles/intel-math-kernel-library-documentation.html Documentation (english)] |
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<!-- |
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* [https://de.wikipedia.org/wiki/Math_Kernel_Library Wikipedia article (german)] |
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[[Category:Numerical_libraries]][[Category:bwUniCluster]] |
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* [https://en.wikipedia.org/wiki/Math_Kernel_Library Wikipedia article (english)] |
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--> |
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Latest revision as of 00:04, 15 March 2023
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The main documentation is available via |
| Description | Content |
|---|---|
| module load | numlib/mkl |
| License | Commercial. See EULA. |
| Citing | n/a |
| Links | Intel MKL Homepage | FFTW Homepage |
| Graphical Interface | No |
Description
The Fastest Fourier Transform in the West (FFTW) is a software library for computing discrete Fourier transforms in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). FFTW was developed by Matteo Frigo and Steven G. Johnson at the Massachusetts Institute of Technology.
The Intel Math Kernel Library (Intel MKL) offers FFTW2 (for version 2.x) and FFTW3 (for version 3.x) interfaces to the Intel MKL Fast Fourier Transform and Trigonometric Transform functionality. These interfaces enable applications using FFTW to gain performance with Intel MKL without changing the application source code. Therefore, it is highly recommended to use Intel MKL instead of a separate FFTW installation.
FAQ
Q: Why is there no FFTW module on the cluster?
A: MKL exhibits better performance than FFTS libraries (see Figure on the right). Therefore, we recommend to use MKL and do not offer a separate FFTW installation.
Q: Why does my code complain about argument of type "long double *" is incompatible with parameter of type "double *" ?
A: The interfaces do not support long double precision because Intel MKL FFT functions operate only on single- and double-precision floating point data types. For the very rare case that you need extended data types, please submit a support ticket at https://www.bwhpc.de/supportportal.