Intel(R) - Computational and Systems Biology at MIT

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9 Intel® Math Kernel Library User’s Guide is one of -lmkl_blacs, -lmkl_blacs_intelmpi,-lmkl_blacs_intelmpi20,-mkl_blacs_openmpi is -lmkl_scalapack_core and/or -lmkl_cdft_core is forScaLAPACK, and for Cluster FFTs. are LAPACK, processor optimized kernels,threading library, and system library for threading support linked as described at thebeginning of section Link Command Syntax in Chapter 5.For example, if you are using Intel MPI 3.x, wish to statically use the LP64 interface withScaLAPACK and to have only one MPI process per core (and thus do not employ threading),provide the following linker options:-L$MKLPATH -I$MKLINCLUDE -Wl,--start-group $MKLPATH/libmkl_intel_lp64.a$MKLPATH/libmkl_scalapack_lp64 $MKLPATH/libmkl_blacs_intelmpi20_lp64$MKLPATH/libmkl_sequential.a $MKLPATH/libmkl_core.a -static_mpi-Wl,--end-group -lpthread –lmFor more examples, see Examples for Linking with ScaLAPACK and Cluster FFT.Note that and library should correspond to the MPIversion. For instance, if it is Intel MPI 2.x, then andlibmkl_blacs_intelmpi20 libraries are used. To link with Intel MPI 3.0 or 3.1, alsolibmkl_blacs_intelmpi20 should be used.For information on linking with Intel® MKL libraries, see Chapter 5 Linking Your Applicationwith Intel® Math Kernel Library.Setting the Number of ThreadsThe OpenMP* software responds to the environmental variable OMP_NUM_THREADS. Intel®MKL 10.0 has also introduced other mechanisms to set the number of threads, such asMKL_NUM_THREADS or MKL_DOMAIN_NUM_THREADS (see section “Using Additional ThreadingControl” in chapter 6). Make certain that the relevant environment variable has the sameand correct value on all the nodes. Intel MKL 10.0 also no longer sets the default numberof threads to 1, but depends on the compiler to set the default number. For the threadinglayer based on the Intel® compiler (libmkl_intel_thread.a), this value is the numberof CPUs according to the OS. Be cautious to avoid over-prescribing the number of threads,which may occur, for instance, when the number of MPI ranks per node and the number ofthreads per node are both greater than one.The best way to set, for example, the environment variable OMP_NUM_THREADS is in thelogin environment. Remember that mpirun starts a fresh default shell on all of the nodesand so, changing this value on the head node and then doing the run (which works on anSMP system) will not effectively change the variable as far as your program is concerned.In .bashrc, you could add a line at the top, which looks like this:9-2
Working with Intel® Math Kernel Library Cluster Software 9OMP_NUM_THREADS=1; export OMP_NUM_THREADSIt is possible to run multiple CPUs per node using MPICH, but the MPICH must be built toallow it. Be aware that certain MPICH applications may not work perfectly in a threadedenvironment (see the Known Limitations section in the Release Notes). The safest thing formultiple CPUs, although not necessarily the fastest, is to run one MPI process perprocessor with OMP_NUM_THREADS set to one. Always verify that the combination withOMP_NUM_THREADS=1 works correctly.Using Shared LibrariesAll needed shared libraries must be visible on all the nodes at run time. One way toaccomplish this is to point these libraries by the LD_LIBRARY_PATH environment variable inthe .bashrc file. If Intel MKL is installed only on one node, you should link statically whenbuilding your Intel MKL applications.The Intel® compilers or GNU compilers can be used to compile a program that uses IntelMKL. However, make certain that MPI implementation and compiler match up correctly.ScaLAPACK TestsTo build NetLib ScaLAPACK tests for IA-32, IA-64, or Intel® 64 architectures, addlibmkl_scalapack_core.a to your link command.Examples for Linking with ScaLAPACK and Cluster FFTFor information on detailed MKL structure of the architecture-specific directories of thecluster libraries, see section Directory Structure in Detail in Chapter 3.Examples for C ModuleSuppose the following conditions are met:• MPICH 1.2.5 or higher is installed in /opt/mpich,• Intel® MKL 10.0 is installed in /opt/intel/mkl/10.0.xxx, where xxx is the IntelMKL package number, for example, /opt/intel/mkl/10.0.039.• You use the Intel® C Compiler 8.1 or higher and the main module is in C.9-3
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