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The MPICH2 programs use mpd daemon or ssh connection to spawn processes, no PBS support is needed. However the PBS allocation is required to access compute nodes. On Anselm, the **Intel MPI** and **mpich2 1.9** are MPICH2 based MPI implementations.
!!! Note "Note"
Use the mpirun to execute the MPICH2 code.
$ qsub -q qexp -l select=4:ncpus=16 -I
qsub: waiting for job 15210.srv11 to start
qsub: job 15210.srv11 ready
$ module load impi
$ mpirun -ppn 1 -hostfile $PBS_NODEFILE ./helloworld_mpi.x
Hello world! from rank 0 of 4 on host cn17
Hello world! from rank 1 of 4 on host cn108
Hello world! from rank 2 of 4 on host cn109
Hello world! from rank 3 of 4 on host cn110
In this example, we allocate 4 nodes via the express queue interactively. We set up the intel MPI environment and interactively run the helloworld_mpi.x program. We request MPI to spawn 1 process per node.
Note that the executable helloworld_mpi.x must be available within the same path on all nodes. This is automatically fulfilled on the /home and /scratch filesystem.
You need to preload the executable, if running on the local scratch /lscratch filesystem
$ pwd
/lscratch/15210.srv11
$ mpirun -ppn 1 -hostfile $PBS_NODEFILE cp /home/username/helloworld_mpi.x .
$ mpirun -ppn 1 -hostfile $PBS_NODEFILE ./helloworld_mpi.x
Hello world! from rank 0 of 4 on host cn17
Hello world! from rank 1 of 4 on host cn108
Hello world! from rank 2 of 4 on host cn109
Hello world! from rank 3 of 4 on host cn110
In this example, we assume the executable helloworld_mpi.x is present on shared home directory. We run the cp command via mpirun, copying the executable from shared home to local scratch . Second mpirun will execute the binary in the /lscratch/15210.srv11 directory on nodes cn17, cn108, cn109 and cn110, one process per node.
!!! Note "Note"
MPI process mapping may be controlled by PBS parameters.
The mpiprocs and ompthreads parameters allow for selection of number of running MPI processes per node as well as number of OpenMP threads per MPI process.
Follow this example to run one MPI process per node, 16 threads per process. Note that no options to mpirun are needed
$ qsub -q qexp -l select=4:ncpus=16:mpiprocs=1:ompthreads=16 -I
$ module load mvapich2
$ mpirun ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI application, using 1 MPI processes per node and 16 threads per socket, on 4 nodes.
Follow this example to run two MPI processes per node, 8 threads per process. Note the options to mpirun for mvapich2. No options are needed for impi.
$ qsub -q qexp -l select=4:ncpus=16:mpiprocs=2:ompthreads=8 -I
$ module load mvapich2
$ mpirun -bind-to numa ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI application, using 2 MPI processes per node and 8 threads per socket, each process and its threads bound to a separate processor socket of the node, on 4 nodes
Follow this example to run 16 MPI processes per node, 1 thread per process. Note the options to mpirun for mvapich2. No options are needed for impi.
$ qsub -q qexp -l select=4:ncpus=16:mpiprocs=16:ompthreads=1 -I
$ module load mvapich2
$ mpirun -bind-to core ./helloworld_mpi.x
In this example, we demonstrate recommended way to run an MPI application, using 16 MPI processes per node, single threaded. Each process is bound to separate processor core, on 4 nodes.
In the previous two examples with one or two MPI processes per node, the operating system might still migrate OpenMP threads between cores. You might want to avoid this by setting these environment variable for GCC OpenMP:
As of OpenMP 4.0 (supported by GCC 4.9 and later and Intel 14.0 and later) the following variables may be used for Intel or GCC:
The mpirun allows for precise selection of how the MPI processes will be mapped to the computational nodes and how these processes will bind to particular processor sockets and cores.
Process mapping may be controlled by specifying a machinefile input to the mpirun program. Altough all implementations of MPI provide means for process mapping and binding, following examples are valid for the impi and mvapich2 only.
cn110.bullx
cn109.bullx
cn108.bullx
cn17.bullx
cn108.bullx
$ mpirun -machinefile machinefile helloworld_mpi.x
Hello world! from rank 0 of 5 on host cn110
Hello world! from rank 1 of 5 on host cn109
Hello world! from rank 2 of 5 on host cn108
Hello world! from rank 3 of 5 on host cn17
Hello world! from rank 4 of 5 on host cn108
In this example, we see that ranks have been mapped on nodes according to the order in which nodes show in the machinefile
The Intel MPI automatically binds each process and its threads to the corresponding portion of cores on the processor socket of the node, no options needed. The binding is primarily controlled by environment variables. Read more about mpi process binding on [Intel website](https://software.intel.com/sites/products/documentation/hpc/ics/impi/41/lin/Reference_Manual/Environment_Variables_Process_Pinning.htm). The MPICH2 uses the -bind-to option Use -bind-to numa or -bind-to core to bind the process on single core or entire socket.
### Bindings verification
In all cases, binding and threading may be verified by executing
$ mpirun -bindto numa numactl --show
$ mpirun -bindto numa echo $OMP_NUM_THREADS
The[MPI section of Intel Xeon Phi chapter](../intel-xeon-phi/) provides details on how to run Intel MPI code on Xeon Phi architecture.