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SW:MKL

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MKL

The Intel Math Kernel Library (MKL) is a library of optimized and threaded math routines such as BLAS, LAPACK, sparse solvers, fast fourier transforms, vector math, and more for all the latest Intel architectures. This page will show you how to use MKL on ada and terra, with examples to demonstrate its common use.

Environment

Before using the MKL library, you need to load the MKL module file:

module load imkl/2017.1.132-iompi-2017A

This command loads the default MKL library and all the modules that imkl depends on or is associated with, including icc, ifort, and impi. It sets the $MKLROOT environment variable that will be used in our examples.

The Intel MKL library can be used by various compilers, including the Intel compilers, the GNU compilers, and the PGI compilers. However, the options required by each brand of compilers are different. Our discussion below is based on the Intel compilers.

How To Link

Linking to the MKL library can be much involved if all possible usage senarios are considered. In this user guide, we focus only on dynamic linking using the -mkl compiler option, with consideration of the commonly used BLAS95/LAPACK95 static libraries.

General forms of linking to the MKL library using the -mkl flag, with options of linking to the MKL BLAS95/LAPACK95 Fortran libraries, are as follows:

ifort myprog.f   -mkl[=lib] [options] [-lmkl_blas95_lp64] [-lmkl_lapack95_lp64] ...
icc   myprog.c   -mkl[=lib] [options] ...
icpc  myprog.cpp -mkl[=lib] [options] ...

The flag -mkl[=lib] tells the compiler to link to certain parts of MKL, where lib can be one of three values shown in the table.

Value Meaning
parallel Tells the compiler to link using the threaded part of MKL. This is the default if the option is specified with no lib.(-mkl=parallel is equivalent to -mkl)
The threaded part of MKL includes multithreaded BLAS, LAPACK, FFT, etc. The environment variable OMP_NUM_THREADS must be set to control the number of threads at run time for the threaded MKL library.
sequential Tells the compiler to link using the non-threaded part of MKL, which includes sequential BLAS, LAPACK, FFT, etc.
cluster Tells the compiler to link using the cluster part and the sequential part of MKL. The cluster part of MKL includes distributed FFT (DCFT), ScaLAPACK, and other sub-libraries for distributed computing. The Intel MPI library is required when -mkl=cluster.

Dynamic linking is the preferred way of linking to the MKL library. In most cases, the -mkl flag provides all that you need.

Example 1 Link to the sequential part of MKL.

ifort example.f -mkl=sequential -o example.exe

Example 2 Link to the threaded part of MKL.

icc example.c -mkl=parallel -o example.exe

Example 3 Link to the cluster part of MKL, being it DCFT or ScaLAPACK. For this to compile, you must load the intel/mpi module first.

mpiifort example.f -mkl=cluster -o example.exe

When -mkl=cluster is used, the non-cluster part of MKL linked will be sequential. If we want to use the cluster part of MKL and the threaded part of MKL at the same time, we have to link each and every library explicitly.

Example 4 Link to ScaLAPACK and the threaded part of MKL.

mpiicpc example.cpp -openmp -I${MKLROOT}/composrxe/mkl/include  \
-L$(MKLROOT}/composerxe/mkl/lib -lmkl_scalapack_lp64 -lmkl_intel_lp64 \
-lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -o example.exe

Link with BLAS95/LAPACK95

Dynamic linking to the right part of the MKL library has been made easy with the -mkl flag. However, not all commonly used libraries are shared libraries and hence cannot be linked dynamically. More specifically, the MKL BLAS Fortran95 and LAPACK Fortran 95 libraries are static and have no dynamic counterparts. These libraries must be stated explicitly at the command line for linking. Again, the -mkl flag can work with the BLAS95/LAPACK95 libraries to make things much easier.

Example 5 Link to the sequential part of MKL and BLAS95.

ifort example.f -mkl=sequential -lmkl_blas95_lp64 -o example.exe

Example 6 Link to the threaded part of MKL and LAPACK95.

ifort example.f -mkl -lmkl_lapack95_lp64 -o example.exe

Linking a code with a static library must place the code before the static library to allow symbols from the static library referenced in the code to be resolved correctly, as shown in the examples above. To allow arbitrary orders between the library and the source code, we can use -Wl,--start-group archives -Wl,--end-group. The flag -Wl tells the compiler to pass the linker option following the comma to the linker. --start-group and --end-group are linker options to enclose the archives in between (can be libraries, source codes, and object files) as a group, and these files will be searched repeatedly until no new undefined references are created.

Example 7 Link to the threaded part of MKL and LAPACK95 in arbitrary order. Notice that the source file is placed after the static library.

ifort -mkl -Wl,--start-group -lmkl_lapack95_lp64 example.f -Wl,--end-group -o example.exe 

ScaLAPACK

The MKL library implemens routines from the ScaLAPACK package for distributed-memory architectures. ScaLAPACK solves dense and banded linear systems, least square problems, eigenvalue problems, and singular value problems. It is built on top of BLAS, LAPACK, and BLACS (Basic Linear Algebra Communication Subprograms). The latter includes a set of routines that support a linear algebra oriented messages passing interface for a large range of distributed memory platforms. Except a few supporting utility routines that are implemented in C, majority of ScaLAPACK routines are implemented in Fortran 77.

Before calling a ScaLAPACK routine, the processor grid has to be set up by the programmer and all global matrices must be distributed manually on the process grid. In ScaLAPACK, block cyclic distribution is used for dense matrices and block distribution is used for banded matrices.

In general, four basic steps are required to call a ScaLAPACK routine.

  1. Initialize the process grid
  2. Distribute the matrix on the process grid
  3. Call ScaLAPACK routine
  4. Release the process grid

A pseudo program that calls a ScaLAPACK dense linear solver (pdgesv) is shown as follow:

! Step 1: nitialize the process grid working environment

  call blacs_pinfo
  call blacs_setup
  call blacs_gridinit
  call balcs_gridinfo

! Step 2: distribute the data if they are not in place on each process

  if (i am the root process) then
      ! send data to each non-root process
      do i=0, np-1
        if (i.NE.root) call dgesd2d   
  else
      call dgerv2d   ! non-root process receives data
  endif
  call descinit      ! create descriptors about the global matrix 

! Step 3: call the scalapack routine

  call pdgesv

! Step 4: release the process grid.

  call blacs_gridexit
  call blacs_exit

Complete sample programs in Fortran 90 and C can be downloaded from here: mypdgesvdriver.f90 and mypdgesvdriver.c. These programs have been tested on Eos with the Intel compilers and the Intel MPI library.

[login1]$ mpiifort -mkl=cluster mypdgesvdriver.f90 -o mypdgesvdriver_f.exe
[login1]$ mpiicc -mkl=cluster mypdgesvdirver.c -o mypdgesvdriver_c.exe
[login1]$ mpirun -np 6 ./mypdgesvdriver_c.exe
0.00000000 -0.16666667 -0.50000000 0.16666667 
0.50000000 0.00000000 0.00000000 
0.00000000 0.00000000 

FFTW wrappers

(needs documentation)

Automatic Offloading

MKL provides automatic offloading to a PHI co processor for some of its compute intensive routines. Offloading is done in a completely transparent manner and requires no change to the code or use of special compilation flags.The table below shows the environmental variables MKL provides to guide automatic offloading


Env var Description
MKL_MIC_ENABLE Enables automatic offloading; 0 (disabled), 1 (enabled)
OFFLOAD_DEVICES Specifies list of PHI co processors to use. If not set, default is to use all available PHI processors
MKL_HOST_WORKDIVISION Specifies what fraction of work should be done on host; value between 0 and 1.0
MKL_MIC_WORKDIVISION Specifies what fraction of work should be done on all PHI co processors within the node; value between 0 and 1.
MKL_MIC_<N>_WORKDIVISION Specifies what fraction of work should be done on PHI co processors with id N; value between 0 and 1.
MKL_MIC_MAX_MEMORY Specifies the maximum memory that can be used on all PHI co processors within the node.
MKL_MIC_<N>_MAX_MEMORY Specifies the maximum memory that can be used on PHI co processors with id N.
OFFLOAD_REPORT Specifies the profiling report level for Automatic Offload; values [0..2], where 0 is no report and 2 is most detailed report.

The most important environmental variable from the table above is MKL_MIC_ENABLE . If this variable is not set, MKL will not offload any computation.

To specify the number of threads use the environmental variable MKL_NUM_THREADS or MIC_MKL_NUM_THREADS (assuming MIC is the prefix used with MIC_ENV_PREFIX environmental variable). It is recommended to use MIC_MKL_NUM_THREADS to distinguish number of threads on host and PHI.

NOTE: Every PHI co processor has 60 cores and every core has 4 hardware threads. Therefore, in general the recommended value for MIC_MKL_NUM_THREADS is 240

Example 1: Enable Automatic offloading, and set the number of threads to 240

[login8]$ export MKL_MIC_ENABLE=1
[login8]$ export MIC_MKL_NUM_THREADS=240 


Example 2: Set the fraction of work to offload to the PHI to 0.7. Use 240 Threads on the PHI and 16 threads on the host.

[login8]$ export MKL_MIC_ENABLE=1
[login8]$ export MKL_MIC_WORKDIVISION=0.7
[login8]$ export MKL_HOST_WORKDIVISION=0.3
[login8]$ export MIC_MKL_NUM_THREADS=240 
[login8]$ export MKL_NUM_THREADS=16

Further Information

Our examples show some basic use of compiling and linking the MKL library with the Intel compilers and how to do automatic offloading. For other usage, such as static linking, Single Dynamic Library, linking with MPICH2, compiling with the GNU compilers, compiling with the PGI compilers, please check with the Intel MKL Linking Advisor.

We also show an example (in C and Fortran) on how to program with ScaLAPACK, a distributed linear algebra package provided in MKL. For more examples on how to program with MKL routines, please see files in $MKLROOT/composrxe/mkl/examples on Ada. To get the complete source files, copy the *.tgz file to your scratch and untar them with tar xzvf *.tgz

For a complete reference of MKL, check the Intel MKL Reference Manual.