Difference between revisions of "MPI Libraries"
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On the HPC cluster, | On the HPC cluster, there are two different kinds of MPI libraries: | ||
'''OpenMPI''' and '' | '''OpenMPI''' and ''Intel MPI'' ('''impi''') | ||
The [http://www.open-mpi.org OpenMPI] library is an open source implementation for the MPI protocol. | The [http://www.open-mpi.org OpenMPI] library is an open source implementation for the MPI protocol. | ||
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module avail openmpi | module avail openmpi | ||
module avail impi | module avail impi | ||
The currently installed versions are available... | |||
... on envirnoment ''hpc-uniol-env'': | |||
'''OpenMPI/1.10.4'''-GCC-4.9.4 | |||
'''OpenMPI/2.0.1'''-GCC-5.4.0 | |||
'''OpenMPI/2.0.1'''-GCC-6.2.0 | |||
'''OpenMPI/2.0.2'''-GCC-5.4.0-2.26 | |||
'''impi/5.1.3.210''' | |||
...on environment ''hpc-env/6.4'': | |||
'''OpenMPI/2.1.0'''-iccifort-2018a | |||
'''OpenMPI/2.1.1'''-GCC-6.4.0-2.28 | |||
'''impi/2018a'''-iccifort-2018a | |||
'''impi/2018.1.163'''-GCC-6.4.0-2.28 | |||
For performance reasons the latest release of OpenMPI / impi should be used. | For performance reasons the latest release of OpenMPI / impi should be used. | ||
The following instructions and examples are based on the environment '''hpc-env/6.4''', which is currently our environment for the newest stable software versions that we install. | |||
Therefor we encourage you to use this environment when working with MPI. | |||
== Compiling with OpenMPI == | == Compiling with OpenMPI == | ||
Before compiling [[User environment - The usage of module|load the actual module]] of OpenMPI, e.g. | Before compiling [[User environment - The usage of module|load the actual module]] of OpenMPI, e.g. | ||
module load | module load OpenMPI/2.1.1-GCC-6.4.0-2.28 | ||
for using the GNU compiler. | for using the GNU compiler. | ||
Line 42: | Line 63: | ||
These programs are only wrappers which means that the scripts sets additional flags for OpenMPI (e.g. include path, flags for linking OpenMPI libraries, ...). For using the Intel Compiler please use the module | These programs are only wrappers which means that the scripts sets additional flags for OpenMPI (e.g. include path, flags for linking OpenMPI libraries, ...). For using the Intel Compiler please use the module | ||
module load | module load OpenMPI/2.1.0-iccifort-2018a | ||
Below there is a list of all environment variables for setting other compiler. | Below there is a list of all environment variables for setting other compiler. | ||
Line 66: | Line 87: | ||
|} | |} | ||
</center> | </center> | ||
However, in general the module's toolchain (as indicated by the version suffix, e.g iccifort-2018a) already defines the compiler that will used by the wrappers listed above. In principle it should be possible to change the default behaviour but this is not recommended. In case of Fortran 90 or newer, the module files will most likely cause problems. | |||
== | == Compiling with Intel MPI == | ||
Before compiling an MPI program you need to [[User environment - The usage of module|load the actual module]] for Intel MPI, e.g. with the commands | |||
$ module load hpc-env/6.4 | |||
$ module load impi/2018a-iccifort-2018a | |||
Other versions of Intel MPI are available, you may have to load a different environment before you can load them (use <tt>module spider impi</tt> to find out which versions exist and which environments have to be loaded). Note, that the following has been tested for <tt>impi/2018a-iccifort-2018a</tt>, other versions may behave slightly different. | |||
In general, you can use Intel MPI with the Intel compilers '''or''' the GNU compilers. Both families of compilers are loaded together with the Intel MPI module, and it is recommended that use the versions that are loaded automatically. Compilation of your MPI program is done using a wrapper command, e.g. | |||
$ mpicc MPI_HelloWorld.c -o MPI_HelloWorld | |||
for a C-program. These wrapper commands set the required additional flags for Intel MPI (e.g. include path, flags for linking Intel MPI libraries, ...) which are then used by the underlying compiler (e.g. GNU compiler, Intel Compiler), in addition to any other options given to the wrapper. The available wrapper commands are listed below (and also [https://software.intel.com/en-us/mpi-developer-reference-linux-compilation-commands here]). '''Note:''' the actual compiler called by the standard wrappers is from the GNU compiler family. You can verify this by typing e.g.: | |||
$ mpicc | |||
This script invokes an appropriate specialized C MPI compiler driver. | |||
The following ways (priority order) can be used for changing default | |||
compiler name (gcc): | |||
1. Command line option: -cc=<compiler_name> | |||
2. Environment variable: I_MPI_CC (current value '') | |||
3. Environment variable: MPICH_CC (current value '') | |||
Alternatively, and to get more details, you can also use the command | |||
$ mpicc --version | |||
(likewise for other wrappers) which will give the name and version of the underlying compiler. In the first command (w/o <tt>--version</tt> you can also see how to change the default behaviour of the wrapper. Therefore, | |||
$ mpicc -cc=icc ... | |||
would compile your program using the Intel C compiler. | |||
The following standard wrappers of Intel MPI can be used for compilation of your MPI programs: | |||
<center> | <center> | ||
{| style="background-color:#eeeeff;" cellpadding="10" border="1" cellspacing="0" | {| style="background-color:#eeeeff;" cellpadding="10" border="1" cellspacing="0" | ||
|- style="background-color:#ddddff;" | |- style="background-color:#ddddff;" | ||
! Name | ! Name | ||
!Description | ! Description | ||
! Default compiler | |||
! Compiler cmd-line option | |||
! Compiler ENV variable | |||
|- | |- | ||
| ''mpicc'' | | ''mpicc'' | ||
| C compiler | | C compiler | ||
| <tt>gcc</tt> | |||
| <tt>-cc=<compiler_name></tt> | |||
| <tt>I_MPI_CC</tt> | |||
|- | |- | ||
| ''mpicxx'' | | ''mpicxx'' | ||
| C++ compiler | | C++ compiler | ||
| <tt>g++</tt> | |||
| <tt>-cxx=<compiler_name></tt> | |||
| <tt>I_MPI_CXX</tt> | |||
|- | |- | ||
| ''mpifc'' | | ''mpifc'' | ||
| Fortran compiler | | Fortran compiler | ||
| <tt>gfortran</tt> | |||
| <tt>-fc=<compiler_name></tt> | |||
| <tt>I_MPI_FC</tt> | |||
|- | |- | ||
| ''mpif77'' | | ''mpif77'' | ||
| Fortran 77 compiler | | Fortran 77 compiler | ||
| <tt>gfortran</tt> | |||
| <tt>-f77=<compiler_name></tt> | |||
| <tt>I_MPI_F77</tt> | |||
|- | |- | ||
| ''mpif90'' | | ''mpif90'' | ||
| Fortran 90 compiler | | Fortran 90 compiler | ||
| <tt>gfortran</tt> | |||
| <tt>-f90=<compiler_name></tt> | |||
| <tt>I_MPI_F90</tt> | |||
|- | |- | ||
|} | |} | ||
</center> | </center> | ||
As you can see, each of the wrappers above used a GCC default compiler. This can be changed by chosing the compiler using a cmd-line option as shown above or by setting the corresponding environment variables, e.g. | |||
export I_MPI_CC=icc | export I_MPI_CC=icc | ||
for using the Intel C | for using the Intel C compiler. | ||
Alternatively for GNU compilers and Intel Compilers there exists following wrapper scripts which needs no special environment variables settings. | Alternatively for GNU compilers and Intel Compilers there exists following wrapper scripts which needs no special environment variables settings. | ||
Line 173: | Line 193: | ||
|} | |} | ||
</center> | </center> | ||
'''Important note for Fortran 90/2008''': Newer Fortran standards can use special module files. Intel MPI in general supports the Fortran 90/95 standard (if the underlying compiler supports it which is usually the case nowadays). Therefore, you can include the MPI module with | |||
use mpi | |||
If you are using the Intel compiler <tt>ifort</tt> you can also use the new Fortran 2008 standard with | |||
use mpi_f08 | |||
which is recommended (mainly for code robustness). This standard is '''not''' supported for the combination Intel MPI and GCC compiler (see [https://software.intel.com/en-us/articles/intel-mpi-library-release-notes-linux also here]) |
Latest revision as of 12:29, 28 June 2019
On the HPC cluster, there are two different kinds of MPI libraries: OpenMPI and Intel MPI (impi)
The OpenMPI library is an open source implementation for the MPI protocol. The Intel MPI library is an optimized implementation for the MPI protocol. Different versions compiled with different compilers are available. A list is given by typing
module avail openmpi module avail impi
The currently installed versions are available...
... on envirnoment hpc-uniol-env:
OpenMPI/1.10.4-GCC-4.9.4 OpenMPI/2.0.1-GCC-5.4.0 OpenMPI/2.0.1-GCC-6.2.0 OpenMPI/2.0.2-GCC-5.4.0-2.26 impi/5.1.3.210
...on environment hpc-env/6.4:
OpenMPI/2.1.0-iccifort-2018a OpenMPI/2.1.1-GCC-6.4.0-2.28 impi/2018a-iccifort-2018a impi/2018.1.163-GCC-6.4.0-2.28
For performance reasons the latest release of OpenMPI / impi should be used. The following instructions and examples are based on the environment hpc-env/6.4, which is currently our environment for the newest stable software versions that we install. Therefor we encourage you to use this environment when working with MPI.
Compiling with OpenMPI
Before compiling load the actual module of OpenMPI, e.g.
module load OpenMPI/2.1.1-GCC-6.4.0-2.28
for using the GNU compiler.
The compilation can be done by following wrappers of OpenMPI:
Name | Description |
---|---|
mpicc | C compiler |
mpic++, mpiCC or mpicxx | C++ compiler |
mpif77 | Fortran 77 compiler |
mpif90 | Fortran 90 compiler |
These programs are only wrappers which means that the scripts sets additional flags for OpenMPI (e.g. include path, flags for linking OpenMPI libraries, ...). For using the Intel Compiler please use the module
module load OpenMPI/2.1.0-iccifort-2018a
Below there is a list of all environment variables for setting other compiler.
Environment variable | Description |
---|---|
OMPI_CC | Set the C compiler |
OMPI_CXX | Sets the C++ compiler |
OMPI_F77 | Sets the Fortran 77 compiler |
OMPI_FC | Sets the Fortran 90 compiler |
However, in general the module's toolchain (as indicated by the version suffix, e.g iccifort-2018a) already defines the compiler that will used by the wrappers listed above. In principle it should be possible to change the default behaviour but this is not recommended. In case of Fortran 90 or newer, the module files will most likely cause problems.
Compiling with Intel MPI
Before compiling an MPI program you need to load the actual module for Intel MPI, e.g. with the commands
$ module load hpc-env/6.4 $ module load impi/2018a-iccifort-2018a
Other versions of Intel MPI are available, you may have to load a different environment before you can load them (use module spider impi to find out which versions exist and which environments have to be loaded). Note, that the following has been tested for impi/2018a-iccifort-2018a, other versions may behave slightly different.
In general, you can use Intel MPI with the Intel compilers or the GNU compilers. Both families of compilers are loaded together with the Intel MPI module, and it is recommended that use the versions that are loaded automatically. Compilation of your MPI program is done using a wrapper command, e.g.
$ mpicc MPI_HelloWorld.c -o MPI_HelloWorld
for a C-program. These wrapper commands set the required additional flags for Intel MPI (e.g. include path, flags for linking Intel MPI libraries, ...) which are then used by the underlying compiler (e.g. GNU compiler, Intel Compiler), in addition to any other options given to the wrapper. The available wrapper commands are listed below (and also here). Note: the actual compiler called by the standard wrappers is from the GNU compiler family. You can verify this by typing e.g.:
$ mpicc This script invokes an appropriate specialized C MPI compiler driver. The following ways (priority order) can be used for changing default compiler name (gcc): 1. Command line option: -cc=<compiler_name> 2. Environment variable: I_MPI_CC (current value ) 3. Environment variable: MPICH_CC (current value )
Alternatively, and to get more details, you can also use the command
$ mpicc --version
(likewise for other wrappers) which will give the name and version of the underlying compiler. In the first command (w/o --version you can also see how to change the default behaviour of the wrapper. Therefore,
$ mpicc -cc=icc ...
would compile your program using the Intel C compiler.
The following standard wrappers of Intel MPI can be used for compilation of your MPI programs:
Name | Description | Default compiler | Compiler cmd-line option | Compiler ENV variable |
---|---|---|---|---|
mpicc | C compiler | gcc | -cc=<compiler_name> | I_MPI_CC |
mpicxx | C++ compiler | g++ | -cxx=<compiler_name> | I_MPI_CXX |
mpifc | Fortran compiler | gfortran | -fc=<compiler_name> | I_MPI_FC |
mpif77 | Fortran 77 compiler | gfortran | -f77=<compiler_name> | I_MPI_F77 |
mpif90 | Fortran 90 compiler | gfortran | -f90=<compiler_name> | I_MPI_F90 |
As you can see, each of the wrappers above used a GCC default compiler. This can be changed by chosing the compiler using a cmd-line option as shown above or by setting the corresponding environment variables, e.g.
export I_MPI_CC=icc
for using the Intel C compiler.
Alternatively for GNU compilers and Intel Compilers there exists following wrapper scripts which needs no special environment variables settings.
Wrapper for Intel Compiler | Wrapper for GNU Compiler | Description |
---|---|---|
mpiicc | mpigcc | C compiler |
mpiicpc | mpigxx | C++ compiler |
mpiifort | Fortran 77 compiler |
Important note for Fortran 90/2008: Newer Fortran standards can use special module files. Intel MPI in general supports the Fortran 90/95 standard (if the underlying compiler supports it which is usually the case nowadays). Therefore, you can include the MPI module with
use mpi
If you are using the Intel compiler ifort you can also use the new Fortran 2008 standard with
use mpi_f08
which is recommended (mainly for code robustness). This standard is not supported for the combination Intel MPI and GCC compiler (see also here)