kiszk commented on a change in pull request #29139: URL: https://github.com/apache/spark/pull/29139#discussion_r456874918
########## File path: docs/ml-linalg-guide.md ########## @@ -0,0 +1,85 @@ +# Spark MLlib Linear Algebra Acceleration Guide + +## Introduction + +This guide provides necessary information to enable accelerated linear algebra processing for Spark MLlib. + +Spark MLlib defines Vector and Matrix as basic data types for machine learning algorithms. On top of them, [BLAS](https://en.wikipedia.org/wiki/Basic_Linear_Algebra_Subprograms) and [LAPACK](https://en.wikipedia.org/wiki/LAPACK) operations are implemented and supported by [netlib-java](https://github.com/fommil/netlib-Java).[^1] `netlib-java` can use optimized native linear algebra libraries (refered to as "native libraries" or "BLAS libraries" hereafter) for faster numerical processing. [Intel MKL](https://software.intel.com/content/www/us/en/develop/tools/math-kernel-library.html) and [OpenBLAS](http://www.openblas.net) are two most popular ones. + +However due to license restrictions, the official released Spark binaries by default doesn't contain native libraries support for `netlib-java`. + +The following sections describe how to enable `netlib-java` with native libraries support for Spark MLlib and how to install native libraries and configure them properly. + +[^1]: The algorithms may call Breeze and it will in turn call `netlib-java`. + +## Enable `netlib-java` with native library proxies + +`netlib-java` native libraries has a dependency on `libgfortran`. It requires GFORTRAN 1.4 or above. This can be obtained by installing `libgfortran` package. After installation, the following command can be used to verify if it is installed properly. +``` +strings /path/to/libgfortran.so.3.0.0 | grep GFORTRAN_1.4 +``` + +To build Spark with `netlib-java` native library proxies, you need to add `-Pnetlib-lgpl` to Maven build command line. For example: +``` +$SPARK_SOURCE_HOME/build/mvn -Pnetlib-lgpl -DskipTests -Pyarn -Phadoop-2.7 clean package +``` + +If you only want to enable it in your project, include `com.github.fommil.netlib:all:1.1.2` as a dependency of your project. + +## Install Native Linear Algebra Libraries + +Intel MKL and OpenBLAS are two most popular native linear algebra libraries, you can choose one of them based on your preference. We described basic instructions as below. You can refer to [netlib-java documentation](https://github.com/fommil/netlib-java) for more advanced installation instructions. + +### Intel MKL + +- Download and install Intel MKL. The installation should be done on all nodes of the cluster. We assume the installation location is $MKLROOT. +- Make sure `/usr/local/lib` is in system library search path and run the following commands: +``` +$ ln -sf $MKLROOT/lib/intel64/libmkl_rt.so /usr/local/lib/libblas.so.3 +$ ln -sf $MKLROOT/lib/intel64/libmkl_rt.so /usr/local/lib/liblapack.so.3 +``` + +### OpenBLAS + +The installation should be done on all nodes of the cluster. Generic version of OpenBLAS are available with most distributions. You can install it with a distribution Package Manager (APT or YUM). + +For Debian / Ubuntu: +``` +sudo apt-get install libopenblas-base +sudo update-alternatives --config libblas.so.3 +``` +For CentOS / RHEL: +``` +sudo yum install openblas +``` + +## Check if native libraries are enabled for MLlib + +To verify native libraries are properly loaded, start `spark-shell` and run the following code +``` +scala> import com.github.fommil.netlib.BLAS; +scala> System.out.println(BLAS.getInstance().getClass().getName()); +``` + +If they are correctly loaded, it should print `com.github.fommil.netlib.NativeSystemBLAS`. Otherwise the warnings should be printed: +``` +WARN BLAS: Failed to load implementation from:com.github.fommil.netlib.NativeSystemBLAS +WARN BLAS: Failed to load implementation from:com.github.fommil.netlib.NativeRefBLAS +``` + +If native libraries are not properly configured in the system, Java BLAS implementation(f2jBLAS) will be used as fallback option. + +## Spark Configuration + +The use of multiple-threading in either Intel MKL or OpenBLAS can conflict with Spark's execution model.[^2] + +Therefore configuring these native libraries to use a single thread for operations may actually improve performance (see [SPARK-21305](https://issues.apache.org/jira/browse/SPARK-21305)). It is usually optimal to match this to the number of `spark.task.cpus`, which is `1` by default and typically left at `1`. + +You can use the options in `config/spark-env.sh` to disable multi-threading by setting thread number to 1. +``` +# You might get better performance to enable these options if using native BLAS (see SPARK-21305). +# - MKL_NUM_THREADS=1 Disable multi-threading of Intel MKL Review comment: ditto for `multi-threading` ---------------------------------------------------------------- This is an automated message from the Apache Git Service. To respond to the message, please log on to GitHub and use the URL above to go to the specific comment. For queries about this service, please contact Infrastructure at: [email protected] --------------------------------------------------------------------- To unsubscribe, e-mail: [email protected] For additional commands, e-mail: [email protected]
