1. Installation and Running¶
1.1. Docker¶
Note
For use on supercomputers, use singularity instead
First, docker needs to be installed. Docker Desktop can be installed at https://docs.docker.com/get-docker/
docker pull dejac001/mcccs-mn
docker run -ti -v $PWD:/home/ dejac001/mcccs-mn # run interactively inside container
Then, the image can be accessed interactively by
docker run -ti -v $PWD:/home/ dejac001/mcccs-mn # run interactively inside container
1.2. Singularity¶
module load singularity
singularity pull docker://dejac001/mcccs-mn
Note
It is a good practice to move the singularity image, which is large,
to a shared directory (e.g., /home/<groupname>/shared/
)
The code can then be run using
module load singularity
cd ${workdir} # change to working directory where input files are
singularity exec path/to/mcccs-mn_latest.sif topmon
where path/to/mcccs-x_latest.sif
is the relative or absolute path to the singularity image
made during installation.
To run with multiple processors (e.g. 2), the last line is be replaced with
singularity exec path/to/mcccs-mn_latest.sif mpirun -np 2 topmon
1.3. Windows 10¶
On Windows 10, installing and running can be performed using Docker or Ubuntu. The instructions for Docker are given above. Otherwise, install Windows-Subsystem-for-Linux
then install Ubuntu from the App store and then follow the instructions below for Ubuntu.
1.4. Ubuntu¶
The dockerfiles and docker image is made in ubuntu, so the same commands can be made as those in the docker files.
First, the dependencies need to be installed. The associated dockerfile looks like the following
1 2 3 4 5 6 | FROM ubuntu
MAINTAINER <dejac001@umn.edu>
RUN apt-get update
RUN DEBIAN_FRONTEND="noninteractive" \
apt-get -y install gfortran cmake git mpi mpich
|
To install the ubuntu dependencies,
type in the commands after RUN
.
Second, the code needs to be cloned from the repository. The associated dockerfile looks like
1 2 3 4 5 6 7 8 | FROM dejac001/mcccs-x-base
MAINTAINER <dejac001@umn.edu>
RUN cd /lib \
&& git clone https://github.com/dejac001/desorption.git MCCCS-MN \
&& mkdir -p MCCCS-MN/build && cd MCCCS-MN/build/ \
&& cmake -D CMAKE_BUILD_TYPE=RELEASE .. && make -j 2 \
&& ln -sf /lib/MCCCS-MN/build/src/topmon /usr/bin/topmon
|
Again, installation in ubuntu requires using the same
commands after RUN
.