Merge pull request #3 from RuiApostolo/gh-pages

Budget codes, git typos, python
EPCCed · Jan 17, 2024 · b7ed6c5 · b7ed6c5
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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