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Hands-on #3

Singularity and MPI

Singularity has a good integration with MPI. With Singularity, the MPI usage model is to call ‘mpirun’ from outside the container, and reference the container from the ‘mpirun’ command. It has to be installed on all of the nodes that are going to use it. A centralized filesystem works best for this. The mpirun command communicates with the binary via the Process Management Interface (PMI) used by OpenMPI. When MPI run gets executed it forks an Orted process that launches Singularity as a container process. The MPI application within the container is linked to the MPI runtime libraries within the container. The MPI runtime libraries then connect and communicate back to the Orted process via a universal PMI.
Singularity MPI application process
MPI application process for Singularity
Usage would look like this:
mpirun -np 20 singularity exec container.img /path/to/contained_mpi_prog
Warning MPI must be newer or equal to the version inside the container

Building LAMMPS MPI Singularity configuration file

Create/use the lammps template configuration file lammps-mpi.cfg in the /home directory.
BootStrap: yum
OSVersion: 7
MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/
Include: yum
%setup
cd $SINGULARITY_ROOTFS/opt
wget http://www.mpich.org/static/downloads/3.2/mpich-3.2.tar.gz
wget http://lammps.sandia.gov/tars/lammps-stable.tar.gz
%post
yum -y groupinstall "Development Tools"
mkdir -p /opt/mpich
cd /opt/mpich
tar xf ../mpich-3.2.tar.gz --strip-components 1
./configure --prefix=/usr/local |& tee log.configure
make -j |& tee log.make
make install |& tee log.make_install
mkdir -p /opt/lammps
cd /opt/lammps
tar xf ../lammps-stable.tar.gz --strip-components 1
cd src
make yes-granular |& tee log.make_yes_granular
make -j mpi |& tee log.make_mpi
%runscript
/opt/lammps/src/lmp_mpi "[email protected]"

Creating the container image

  • Create a container called lammps-mpi.img and modify the size to 2048 MiB.
singularity create --size 2048 lammps-mpi.img`
  • Bootstrap the lammps configuration file created in the previous step.
sudo singularity build lammps-mpi.img lammps-mpi.cfg
Note Bootstrapping step requires root access.

Running the container image

To execute the container
mpirun -np 4 singularity run ~/lammps-mpi.img -i in.granregion.mixer
To run LAMMPS on Cambridge HPC
srun -Atraining -pbiocloud-normal --reservation=singularity --mpi=pmi2 -N1 -n24 singularity run ~/lammps.img -i ~/in.mixer