Compiling Source Code

Documentation on compiling source code on Negishi.

Compiling Serial Programs

A serial program is a single process which executes as a sequential stream of instructions on one processor core. Compilers capable of serial programming are available for C, C++, and versions of Fortran.

Here are a few sample serial programs:

serial_hello.f
serial_hello.f90
serial_hello.f95
serial_hello.c
serial_hello.cpp

To load a compiler, enter one of the following:

$ module load intel
$ module load gcc

The following table illustrates how to compile your serial program:
Language	Intel Compiler	GNU Compiler
Fortran 77	`$ ifort myprogram.f -o myprogram`	`$ gfortran myprogram.f -o myprogram`
Fortran 90	`$ ifort myprogram.f90 -o myprogram`	`$ gfortran myprogram.f90 -o myprogram`
Fortran 95	`$ ifort myprogram.f90 -o myprogram`	`$ gfortran myprogram.f95 -o myprogram`
C	`$ icc myprogram.c -o myprogram`	`$ gcc myprogram.c -o myprogram`
C++	`$ icc myprogram.cpp -o myprogram`	`$ g++ myprogram.cpp -o myprogram`

The Intel and GNU compilers will not output anything for a successful compilation. Also, the Intel compiler does not recognize the suffix ".f95".

Compiling MPI Programs

OpenMPI and Intel MPI (IMPI) are implementations of the Message-Passing Interface (MPI) standard. Libraries for these MPI implementations and compilers for C, C++, and Fortran are available on all clusters.

MPI programs require including a header file:
Language	Header Files
Fortran 77	`INCLUDE 'mpif.h'`
Fortran 90	`INCLUDE 'mpif.h'`
Fortran 95	`INCLUDE 'mpif.h'`
C	`#include <mpi.h>`
C++	`#include <mpi.h>`

Here are a few sample programs using MPI:

To see the available MPI libraries:

$ module avail openmpi 
$ module avail impi

The following table illustrates how to compile your MPI program. Any compiler flags accepted by Intel ifort/icc compilers are compatible with their respective MPI compiler.
Language	Intel MPI	OpenMPI
Fortran 77	`$ mpiifort program.f -o program`	`$ mpif77 program.f -o program`
Fortran 90	`$ mpiifort program.f90 -o program`	`$ mpif90 program.f90 -o program`
Fortran 95	`$ mpiifort program.f95 -o program`	`$ mpif90 program.f95 -o program`
C	`$ mpiicc program.c -o program`	`$ mpicc program.c -o program`
C++	`$ mpiicpc program.C -o program`	`$ mpiCC program.C -o program`

The Intel and GNU compilers will not output anything for a successful compilation. Also, the Intel compiler does not recognize the suffix ".f95".

Here is some more documentation from other sources on the MPI libraries:

Compiling OpenMP Programs

All compilers installed on Brown include OpenMP functionality for C, C++, and Fortran. An OpenMP program is a single process that takes advantage of a multi-core processor and its shared memory to achieve a form of parallel computing called multithreading. It distributes the work of a process over processor cores in a single compute node without the need for MPI communications.

OpenMP programs require including a header file:
Language	Header Files
Fortran 77	`INCLUDE 'omp_lib.h'`
Fortran 90	`use omp_lib`
Fortran 95	`use omp_lib`
C	`#include <omp.h>`
C++	`#include <omp.h>`

Sample programs illustrate task parallelism of OpenMP:

A sample program illustrates loop-level (data) parallelism of OpenMP:

omp_loop.c

To load a compiler, enter one of the following:

$ module load intel
$ module load gcc

The following table illustrates how to compile your shared-memory program. Any compiler flags accepted by ifort/icc compilers are compatible with OpenMP.
Language	Intel Compiler	GNU Compiler
Fortran 77	`$ ifort -openmp myprogram.f -o myprogram`	`$ gfortran -fopenmp myprogram.f -o myprogram`
Fortran 90	`$ ifort -openmp myprogram.f90 -o myprogram`	`$ gfortran -fopenmp myprogram.f90 -o myprogram`
Fortran 95	`$ ifort -openmp myprogram.f90 -o myprogram`	`$ gfortran -fopenmp myprogram.f95 -o myprogram`
C	`$ icc -openmp myprogram.c -o myprogram`	`$ gcc -fopenmp myprogram.c -o myprogram`
C++	`$ icc -openmp myprogram.cpp -o myprogram`	`$ g++ -fopenmp myprogram.cpp -o myprogram`

The Intel and GNU compilers will not output anything for a successful compilation. Also, the Intel compiler does not recognize the suffix ".f95".

Here is some more documentation from other sources on OpenMP:

Compiling Hybrid Programs

A hybrid program combines both MPI and shared-memory to take advantage of compute clusters with multi-core compute nodes. Libraries for OpenMPI and Intel MPI (IMPI) and compilers which include OpenMP for C, C++, and Fortran are available.

Hybrid programs require including header files:
Language	Header Files
Fortran 77	`INCLUDE 'omp_lib.h' INCLUDE 'mpif.h'`
Fortran 90	`use omp_lib INCLUDE 'mpif.h'`
Fortran 95	`use omp_lib INCLUDE 'mpif.h'`
C	`#include <mpi.h> #include <omp.h>`
C++	`#include <mpi.h> #include <omp.h>`

A few examples illustrate hybrid programs with task parallelism of OpenMP:

This example illustrates a hybrid program with loop-level (data) parallelism of OpenMP:

hybrid_loop.c

To see the available MPI libraries:

$ module avail impi
$ module avail openmpi

The following tables illustrate how to compile your hybrid (MPI/OpenMP) program. Any compiler flags accepted by Intel ifort/icc compilers are compatible with their respective MPI compiler.

Intel MPI
Language	Command
Fortran 77	`$ mpiifort -openmp myprogram.f -o myprogram`
Fortran 90	`$ mpiifort -openmp myprogram.f90 -o myprogram`
Fortran 95	`$ mpiifort -openmp myprogram.f90 -o myprogram`
C	`$ mpiicc -openmp myprogram.c -o myprogram`
C++	`$ mpiicpc -openmp myprogram.C -o myprogram`

OpenMPI or Intel MPI (IMPI) with Intel Compiler
Language	Command
Fortran 77	`$ mpif77 -openmp myprogram.f -o myprogram`
Fortran 90	`$ mpif90 -openmp myprogram.f90 -o myprogram`
Fortran 95	`$ mpif90 -openmp myprogram.f90 -o myprogram`
C	`$ mpicc -openmp myprogram.c -o myprogram`
C++	`$ mpiCC -openmp myprogram.C -o myprogram`

OpenMPI or Intel MPI (IMPI) with GNU Compiler
Language	Command
Fortran 77	`$ mpif77 -fopenmp myprogram.f -o myprogram`
Fortran 90	`$ mpif90 -fopenmp myprogram.f90 -o myprogram`
Fortran 95	`$ mpif90 -fopenmp myprogram.f95 -o myprogram`
C	`$ mpicc -fopenmp myprogram.c -o myprogram`
C++	`$ mpiCC -fopenmp myprogram.C -o myprogram`

The Intel and GNU compilers will not output anything for a successful compilation. Also, the Intel compiler does not recognize the suffix .f95.

Intel MKL Library

Intel Math Kernel Library (MKL) contains ScaLAPACK, LAPACK, Sparse Solver, BLAS, Sparse BLAS, CBLAS, GMP, FFTs, DFTs, VSL, VML, and Interval Arithmetic routines. MKL resides in the directory stored in the environment variable MKL_HOME, after loading a version of the Intel compiler with module.

By using module load to load an Intel compiler your environment will have several variables set up to help link applications with MKL. Here are some example combinations of simplified linking options:

$ module load intel
$ echo $LINK_LAPACK
-L${MKL_HOME}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread

$ echo $LINK_LAPACK95
-L${MKL_HOME}/lib/intel64 -lmkl_lapack95_lp64 -lmkl_blas95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread

RCAC recommends you use the provided variables to define MKL linking options in your compiling procedures. The Intel compiler modules also provide two other environment variables, LINK_LAPACK_STATIC and LINK_LAPACK95_STATIC that you may use if you need to link MKL statically.

RCAC recommends that you use dynamic linking of libguide. If so, define LD_LIBRARY_PATH such that you are using the correct version of libguide at run time. If you use static linking of libguide, then:

If you use the Intel compilers, link in the libguide version that comes with the compiler (use the -openmp option).
If you do not use the Intel compilers, link in the libguide version that comes with the Intel MKL above.

Here are some more documentation from other sources on the Intel MKL:

Intel MKL Documentation