diff --git a/_episodes/02-lammps-performance.md b/_episodes/02-lammps-performance.md index 03e96f0..5be1a00 100644 --- a/_episodes/02-lammps-performance.md +++ b/_episodes/02-lammps-performance.md @@ -60,7 +60,7 @@ For this course, we have prepared a number of exercises. You can get a copy of these exercises by running (make sure to run this from `/work`): ```bash -git clone --depth=1 git@github.com:EPCCed/archer2-advanced-use-of-lammps.git +git clone --depth=1 https://www.github.com/EPCCed/archer2-advanced-use-of-lammps.git ``` Once this is downloaded, please `cd exercises/1-performance-exercise/`. diff --git a/_episodes/03-lammps-performance.md b/_episodes/03-lammps-performance.md index 03e96f0..5be1a00 100644 --- a/_episodes/03-lammps-performance.md +++ b/_episodes/03-lammps-performance.md @@ -60,7 +60,7 @@ For this course, we have prepared a number of exercises. You can get a copy of these exercises by running (make sure to run this from `/work`): ```bash -git clone --depth=1 git@github.com:EPCCed/archer2-advanced-use-of-lammps.git +git clone --depth=1 https://www.github.com/EPCCed/archer2-advanced-use-of-lammps.git ``` Once this is downloaded, please `cd exercises/1-performance-exercise/`. diff --git a/_episodes/04-post-run-analysis.md b/_episodes/04-post-run-analysis.md index 5438c0b..60b58c2 100644 --- a/_episodes/04-post-run-analysis.md +++ b/_episodes/04-post-run-analysis.md @@ -37,7 +37,7 @@ For this course, we have prepared a number of exercises. If you have not done so yet, you can get a copy of these exercises by running (make sure to run this from `/work`): ```bash -git clone --depth=1 git@github.com:EPCCed/archer2-advanced-use-of-lammps.git +git clone --depth=1 https://www.github.com/EPCCed/archer2-advanced-use-of-lammps.git cd exercises/2-post-analysis/ ``` diff --git a/_episodes/05-replica-exchange.md b/_episodes/05-replica-exchange.md index 61d5cc8..475fe6c 100644 --- a/_episodes/05-replica-exchange.md +++ b/_episodes/05-replica-exchange.md @@ -60,7 +60,7 @@ For computational efficiency, it is the temperatures that are swapped between re The code for this section can be downloaded from the git repository: ```bash -git clone --depth=1 git@github.com:EPCCed/archer2-advanced-use-of-lammps.git +git clone --depth=1 https://www.github.com/EPCCed/archer2-advanced-use-of-lammps.git cd exercises/3-replica-exchange-exercise ``` diff --git a/_episodes/06-lammps-python.md b/_episodes/06-lammps-python.md index 4f5fd25..3b0bd03 100644 --- a/_episodes/06-lammps-python.md +++ b/_episodes/06-lammps-python.md @@ -72,11 +72,18 @@ Of note here: the MPI version of LAMMPS is built, and that it has access to the correct fast Fourier transform (FFTW) and Eigen3 libraries. -Once this is built, you should be able to run LAMMPS from the compute nodes by loading the appropriate module. +Once this is built, you should be able to run LAMMPS from the compute nodes by loading the python virtual environment and adding the LAMMPS binary to the `$PATH`. +But, in this course we will be using the `lammps-python` module available in ARCHER2. ## Running LAMMPS through Python +After loading the module: + +```bash +module load lammps-python +``` + Running LAMMPS through Python is quite a simple task: you can import the LAMMPS Python library, start the LAMMPS environment, and run a LAMMPS simulation by running the following commands: ```python @@ -102,7 +109,7 @@ For this course, we have prepared a number of exercises. If you have not already done so, you can get a copy of these exercises by running (make sure to run this from `/work`): ```bash -svn checkout https://github.com/EPCCed/archer2-advanced-use-of-lammps/trunk/exercises +git clone --depth=1 https://www.github.com/EPCCed/archer2-advanced-use-of-lammps.git ``` Once this is downloaded, please `cd exercises/4-python/`. diff --git a/exercises/1-performance-exercise/run.slurm b/exercises/1-performance-exercise/run.slurm index 1c9f532..9e8ffcd 100644 --- a/exercises/1-performance-exercise/run.slurm +++ b/exercises/1-performance-exercise/run.slurm @@ -6,7 +6,7 @@ #SBATCH --cpus-per-task=1 #SBATCH --time=0:20:0 -#SBATCH --account=z19 +#SBATCH --account=ta132 #SBATCH --partition=standard #SBATCH --qos=short @@ -15,4 +15,4 @@ module load lammps/15Dec2023 export OMP_NUM_THREADS=1 export SRUN_CPUS_PER_TASK=$SLURM_CPUS_PER_TASK -srun lmp -in in.ethanol -l log.out +srun lmp -in in.ethanol -l log.out_${SLURM_TASKS_PER_NODE} diff --git a/exercises/2-post-analysis/in.lj_rerun b/exercises/2-post-analysis/in.lj_rerun index f5fd21f..fd9948e 100644 --- a/exercises/2-post-analysis/in.lj_rerun +++ b/exercises/2-post-analysis/in.lj_rerun @@ -19,7 +19,7 @@ pair_coeff * * 1.0 1.0 neighbor 0.3 bin neigh_modify delay 0 -timestep 0.0005 +timestep 0.005 thermo_style custom step temp etotal pe ke press vol density thermo 1000 diff --git a/exercises/2-post-analysis/run.slurm b/exercises/2-post-analysis/run.slurm index 7cfbf88..e6281e7 100644 --- a/exercises/2-post-analysis/run.slurm +++ b/exercises/2-post-analysis/run.slurm @@ -6,7 +6,7 @@ #SBATCH --cpus-per-task=1 #SBATCH --time=0:20:0 -#SBATCH --account=z19 +#SBATCH --account=ta132 #SBATCH --partition=standard #SBATCH --qos=short diff --git a/exercises/3-replica-exchange-exercise/run.slurm b/exercises/3-replica-exchange-exercise/run.slurm index 48112d8..aa150e9 100644 --- a/exercises/3-replica-exchange-exercise/run.slurm +++ b/exercises/3-replica-exchange-exercise/run.slurm @@ -6,7 +6,7 @@ #SBATCH --cpus-per-task=1 #SBATCH --time=00:10:00 -#SBATCH --account=z19 +#SBATCH --account=ta132 #SBATCH --partition=standard #SBATCH --qos=short diff --git a/exercises/4-python/run.slurm b/exercises/4-python/run.slurm index 2b625fd..3763450 100644 --- a/exercises/4-python/run.slurm +++ b/exercises/4-python/run.slurm @@ -4,7 +4,7 @@ #SBATCH --nodes=1 #SBATCH --time=0:5:0 -#SBATCH --account=z19 +#SBATCH --account=ta132 #SBATCH --partition=standard #SBATCH --qos=short #SBATCH --cpus-per-task=1