LS-DYNA

Introduction

LS-DYNA is available on all our systems. It is used for many applications to solve problems in multi-physics, solid mechanics, heat transfer and fluid dynamics either as separate phenomena or as coupled physic such as thermal stress or fluid structure interaction. LSTC was recently purchased by ANSYS, therefore the software may eventually be provided as part of the ANSYS module. For now we recommended using LS-DYNA as documented in this wiki page.

Licensing

Compute Canada is a hosting provider for LS-DYNA. This means that we have LS-DYNA software installed on our clusters, but we do not provide a generic license accessible to everyone. However, many institutions, faculties, and departments already have local licenses that can be used on our clusters. Researchers can also purchase a license directly from the company to run on a SHARCNET license server for dedicated use on any Compute Canada system.

Once a license is set up, there will be remaining technical aspects. The license server on your end will need to be reachable by our compute nodes. This will require our technical team to get in touch with the technical people managing your license software. In some cases, this has already been done. You should then be able to load a ls-dyna Compute Canada module, and it should find your license automatically. For assistance please contact our Technical support.

Configuring your license file

Our module for LS-DYNA is designed to look for license information in a few places, one of which is your home folder. If you have your own license server, you can write the information to access it in the following format:

File : ls-dyna.lic

#LICENSE_TYPE: network
#LICENSE_SERVER:<port>@<server>

and put this file in the folder $HOME/.licenses/ on each cluster where you plan to submit LS-DYNA jobs. Note that firewall changes will need to be done on both our side and yours. To arrange this, send an email containing the service port and IP address of your floating license server to Technical support. To check if your new license file is responding run the following commands:

module load ls-dyna
ls-dyna_s

The output should contain defined (non-empty) values for Licensed to: and Issued by:, press ^c to exit.

Cluster batch job submission

LS-DYNA provides binaries for running jobs on a single compute node (SMP - Shared Memory Parallel using OpenMP) or across a multiple compute nodes (MPP - Message Passing Parallel using MPI). Note that for the sample slurm scripts that follow the StdEnv/2020 module must be loaded before ls-dyna/12.0 or ls-dyna-mpi/12.0 can be loaded:

Single Node Jobs

Modules for running jobs on a single compute node can be listed with: module spider ls-dyna. Jobs maybe submitted to the queue with: sbatch script-smp.sh. The following sample slurm script shows howto to run LS-DYNA with 8 cores on a single cluster compute node:

File : script-smp.sh

#!/bin/bash
#SBATCH --account=def-account  # Specify
#SBATCH --time=0-03:00         # D-HH:MM
#SBATCH --cpus-per-task=8      # Specify number of cores
#SBATCH --mem=16G              # Specify total memory
#SBATCH --nodes=1              # Do not change


module load StdEnv/2016.4      # Versions =< 11.1
module load ls-dyna/11.1

# module load StdEnv/2020      # Versions >= 12.0
# module load ls-dyna/12.0

ls-dyna_s ncpu=$SLURM_CPUS_ON_NODE i=airbag.deploy.k

where 
ls-dyna_s = single precision smp solver
ls-dyna_d = double precision smp solver

Multiple Node Jobs

The module versions available for running jobs on multiple nodes (using the prebuilt MPP prebuilt binaries provided by LS-DYNA) can be listed with module spider ls-dyna-mpi. To submit jobs to the queue use: sbatch script-mpp.sh. Sample scripts for submitting jobs to a specified total number of whole nodes (by node) *OR* a specified total number of cores (by core) are provided next:

Whole Nodes

Jobs can be submitted to a specified number of whole compute nodes with the following script:

File : script-mpp-bynode.sh

#!/bin/bash
#SBATCH --account=def-account   # Specify
#SBATCH --time=0-03:00          # D-HH:MM
#SBATCH --ntasks-per-node=32    # Specify number cores per node (graham 32 or 44, cedar 32 or 48, beluga 40)
#SBATCH --nodes=2               # Specify number compute nodes (1 or more)
#SBATCH --mem=0                 # Use all memory per compute node (do not change)

# module load StdEnv/2016.4    # Versions =< 11.1
# module load ls-dyna-mpi/11.1

module load StdEnv/2020        # Versions >= 12.0
module load ls-dyna-mpi/12.0

srun ls-dyna_d i=airbag.deploy.k

where 
ls-dyna_s = single precision mpp solver
ls-dyna_d = double precision mpp solver

Total Cores

Jobs can be submitted to an arbitrary number of compute nodes by specifying the total number of cores. This approach allows the slurm schedular to automatically determine the number of compute nodes to minimumize the wait time in the queue:

File : script-mpp-bycore.sh

#!/bin/bash
#SBATCH --account=def-account  # Specify
#SBATCH --time=0-03:00         # D-HH:MM
#SBATCH --ntasks=64            # Specify total number of cores
#SBATCH --mem-per-cpu=2G       # Specify memory per core

# module load StdEnv/2016.4    # Versions =< 11.1
# module load ls-dyna-mpi/11.1

module load StdEnv/2020        # Versions >= 12.0
module load ls-dyna-mpi/12.0

srun ls-dyna_d i=airbag.deploy.k

where 
ls-dyna_s = single precision mpp solver
ls-dyna_d = double precision mpp solver

Depending on the simulation LS-DYNA maybe unable to efficiently use many cores. Therefore before running a simulation test the scaling properties of the simulation by gradually increasing the number of cores to determine the optimal value before simulation slowdown occurs. To determine the Job Wall-clock time, CPU Efficiency and Memory Efficiency for a successfully completed job use the seff jobnumber command.

Remote visualization

LSTC provides LS-PrePost for pre- and post-processing of LS-DYNA models. This program is made available by a separate module. It does not require a license and can be used on any cluster node or on the Graham VDI nodes by following these steps:

Cluster nodes

Connect to a compute node or to a login node with TigerVNC
module load ls-prepost
lsprepost

VDI nodes

Connect to gra-vdi with TigerVNC
module load CcEnv StdEnv
module load ls-prepost
lsprepost

Message Passing Interface