Running Lethe on Digital Research Alliance of Canada Clusters#
Setting-up the Folder Structure#
In your $HOME
, create a “dealii” folder and a “lethe” folder, each containing “build” and “inst” folders:
The deal.II and Lethe projects can then be cloned in their corresponding folders, as indicated later in this tutorial.
After installation is complete, the folder structure will be, for deal.II (and likewise for Lethe):
$HOME/dealii/dealii
for deal.ii git,$HOME/dealii/build
for compilation (cmake
command),$HOME/dealii/inst
for installation (ninja install
command)
Folders can be open with the cd
command (cd $folder_path
).
For the sake of clarity, this is the folder structure considered for the rest of this tutorial.
Installing deal.II#
All operations must be performed on login nodes.
Load Trilinos
, Parmetis
and P4est
, and their prerequisite modules and set the appropriate environment variables. It is convenient to create a .dealii
file in your $HOME
directory that contains the following lines to source the appropriate libraries:
This file needs to be sourced every time you launch a job or you compile deal.II and/or Lethe. Once the file has been created, you can then source it on the terminal with:
and use it in your .sh
script when launching a job (see Launching Simulations below).
Although Lethe always supports the master branch of deal.II, we maintain an identical deal.II fork on the CHAOS laboratory organization. This fork is always tested to make sure it works with Lethe. To clone this deal.II fork, execute in $HOME/dealii
directory:
We can compile dealii
in the $HOME/dealii/build
folder, by defining the paths to installation folders of Trilinos
, Parmetis
and P4est
. To increase the speed of this step, we skip dealii
tests and compile in release mode only.
Tip
The -DCMAKE_CXX_FLAGS=”-march=native” works on both Rorqual, Nibi, and Trillium. To ensure that the flag has worked correctly, the cmake output should contain the following information : Vectorization level: 512 bit (sse2 avx2 avx512*)
.
Warning
If you wish to run simulations with over 4B (\(4\cdot 10^9\)) degrees of freedom, you must compile with the DEAL_II_WITH_64BIT_INDICES = ON
flag. Such large simulations should be carried out using the lethe-fluid-matrix-free
application.
and:
The argument -jX
specifies the number of processors used for the compilation. On login nodes, a maximum of 6 cores should be used in order to ensure that other users can continue using the cluster without slowdowns. If you use more than 6 cores, your compilation may be terminated automatically.
Installing Lethe#
After installing deal.II, compiling Lethe is relatively straightforward. To compile Lethe, the Trilinos
, Parmetis
and P4est
modules should be loaded.
In the $HOME/lethe
directory, download Lethe:
To install Lethe in the $HOME/lethe/inst
directory (applications will be in inst/bin
), run in the $HOME/lethe/build
directory:
Copying Local Files#
We use Globus to transfer files between your local machine and the cluster. For more information, visit the Globus documentation.
Launching Simulations#
Simulations are sent to the scheduler via batch scripts. Visit the Digital Research Alliance of Canada (Alliance) wiki page for more information about the scheduler and running jobs. For your convenience, an example of job.sh
is given below:
Tip
The --ntasks-per-node
option is the number of parallel tasks per node. When using a full node, this should correspond to the number of cores available on the node. For example, on Narval, this should be set to 64.
Tip
If you have jobs that need to be launched one after the other, you can add #SBATCH --dependency=$previous-slurm-job-id
to your launching script. This will make sure that the job will only start once the previous job has finished.
The job is sent using:
Status can be followed with the sq
command: under ST
, PD
indicates a pending job, and R
a running job.
Console outputs are written in slurm-$jobID.out
. For instance, to display the 20 last lines from this file, use:
Clusters Specifications#
Please consult the documentation for the machine you are using for the specification of the nodes:
Cluster |
Tasks per Node |
Memory per Node |
URL |
---|---|---|---|
Narval |
64 |
248 Go |
|
Trillium |
192 |
755 Go |
|
Rorqual |
192 |
760 Go |
|
Nibi |
192 |
754 Go |
Saving a SSH Key (Linux)#
To save your key on the cluster, so that it is not asked for each log, generate your ssh-key with:
which defaults to an RSA key. If you want to specify the key type you want to generate (i.e. ED25519 key), type
Note
ED25519 keys are preferred to RSA keys since they are more secure and performant. Seek more information in the GitLab Documentation.
To upload this local key to your Compute Canada Database account (CCDB) use: