From 29a5731eee5037b133ef8bd1a4d38ecaebad5d54 Mon Sep 17 00:00:00 2001 From: "J. George" Date: Sat, 11 May 2024 22:15:35 +0200 Subject: [PATCH] Document the option to run LOBSTER with one jobscript only (#811) * Update LOBSTER documentation --- docs/user/codes/vasp.md | 39 ++++++++++++++++++++++++++++++++++++++- pyproject.toml | 4 ++-- 2 files changed, 40 insertions(+), 3 deletions(-) diff --git a/docs/user/codes/vasp.md b/docs/user/codes/vasp.md index 274cc0567c..e836303001 100644 --- a/docs/user/codes/vasp.md +++ b/docs/user/codes/vasp.md @@ -247,7 +247,7 @@ adjust them if necessary. The default might not be strict enough for your specific case. ``` -### Lobster +### LOBSTER Perform bonding analysis with [LOBSTER](http://cohp.de/) and [LobsterPy](https://github.com/jageo/lobsterpy) @@ -367,6 +367,43 @@ for number, (key, cohp) in enumerate( plotter.add_cohp(key, cohp) plotter.save_plot(f"plots_cation_anion_bonds{number}.pdf") ``` +# Running the LOBSTER workflow without database and with one job script only + +It is also possible to run the VASP-LOBSTER workflow with a minimal setup. +In this case, you will run the VASP calculations on the same node as the LOBSTER calculations. +In between, the different computations you will switch from MPI to OpenMP parallelization. + +For example, for a node with 48 cores, you could use an adapted version of the following SLURM script: + +```bash +#!/bin/bash +#SBATCH -J vasplobsterjob +#SBATCH -o ./%x.%j.out +#SBATCH -e ./%x.%j.err +#SBATCH -D ./ +#SBATCH --mail-type=END +#SBATCH --mail-user=you@you.de +#SBATCH --time=24:00:00 +#SBATCH --nodes=1 +#This needs to be adapted if you run with different cores +#SBATCH --ntasks=48 + +# ensure you load the modules to run VASP, e.g., module load vasp +module load my_vasp_module +# please activate the required conda environment +conda activate my_environment +cd my_folder +# the following script needs to contain the workflow +python xyz.py +``` + +The `LOBSTER_CMD` now needs an additional export of the number of threads. + +```yaml +VASP_CMD: <> +LOBSTER_CMD: OMP_NUM_THREADS=48 <> +``` + (modifying_input_sets)= Modifying input sets diff --git a/pyproject.toml b/pyproject.toml index 80a3516779..0fb602268c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,7 @@ requires-python = ">=3.9" dependencies = [ "PyYAML", "click", - "custodian>=2024.2.15", + "custodian>=2024.4.18", "emmet-core>=0.78.0rc4", "jobflow>=0.1.11", "monty>=2024.2.2", @@ -84,7 +84,7 @@ strict = [ "cclib==1.8.1", "chgnet==0.3.5", "click==8.1.7", - "custodian==2024.3.12", + "custodian==2024.4.18", "dscribe==2.1.0", "emmet-core==0.82.2", "ijson==3.2.3",