Merge pull request #95 from gkaf89/refactor/VASP

Refactor/vasp Explain the settings required for OpenMP
ULHPC · Dec 2, 2024 · a12a13a · a12a13a
2 parents 3aca179 + 465e512
commit a12a13a
Showing 1 changed file with 154 additions and 47 deletions.
diff --git a/docs/software/computational-chemistry/electronics/vasp.md b/docs/software/computational-chemistry/electronics/vasp.md
@@ -1,60 +1,167 @@
 [![](https://www.vasp.at/images/logo.png){: style="width:300px;float: right;" }](https://www.vasp.at/)
-[VASP](https://www.vasp.at/documentation/) is a package for performing ab initio quantum-mechanical molecular dynamics (MD)
-using pseudopotentials and a plane wave basis set. The approach implemented in VASP
-is based on a finite-temperature local-density approximation (with the free energy as variational quantity)
-and an exact evaluation of the instantaneous electronic ground state at each MD step
-using efficient matrix diagonalization schemes and an efficient Pulay mixing.
-
-## Available versions of VASP in ULHPC
-To check available versions of VASP at ULHPC type `module spider vasp`.
-The following list shows the available versions of VASP in ULHPC.
+
+[VASP](https://www.vasp.at/documentation/) is a package for performing ab initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD step using efficient matrix diagonalization schemes and an efficient Pulay mixing.
+
+## Accessing VASP in UL HPC clusters
+
+VASP is a proprietary software. If your group has access to VASP, then the UL HPC team can compile the source code and provide your group with a module that is optimally configured for use in our clusters.
+
+All software is installed in the group project directory which is [backed up](/data/backups/#directories-on-the-ulhpc-clusters-infrastructure).
+```
+${PROJECTHOME}/<project name>/backup/easubuild
+```
+Add the following to your `bascrc` to access the project modules.
 ```bash
-phys/VASP/5.4.4-intel-2017a
-phys/VASP/5.4.4-intel-2018a
-phys/VASP/5.4.4-intel-2019a
+if command -v module >/dev/null 2>&1 ; then
+    module use "${PROJECTHOME}/<project name>/backup/easubuild/${ULHPC_CLUSTER}/2023b/${RESIF_ARCH}/modules/all"
+fi
 ```
 
-## Interactive mode
-To open VASP in the interactive mode, please follow the following steps:
+After refreshing your environment you can check for the available versions of VASP by typing `module spider vasp`:
+```
+$ module spider vasp
+...
+phys/VASP/6.4.3-foss-2023b
+...
+```
 
-```bash
-# From your local computer
-$ ssh -X iris-cluster
+## Working with VASP
 
-# Reserve the node for interactive computation
-$ salloc -p interactive --time=00:30:00 --ntasks 1 -c 4 --x11 # OR si --x11 [...]
+VASP support both interactive session with a graphical GUi and batch jobs submitted through a job scheduler.
 
-# Load the module vasp and needed environment 
-$ module purge
-$ module load swenv/default-env/devel # Eventually (only relevant on 2019a software environment) 
-$ module load phys/VASP/5.4.4-intel-2019a
+### Interactive mode
 
-$ vasp_[std/gam/ncl]
-```
+To open VASP in the interactive mode, please follow these steps.
 
-## Batch mode
-```bash
-#!/bin/bash -l
-#SBATCH -J VASP
-#SBATCH -N 2
-#SBATCH -A <project name>
-#SBATCH -M --cluster iris 
-#SBATCH --ntasks-per-node=28
-#SBATCH --time=00:30:00
-#SBATCH -p batch
-
-# Load the module vasp and needed environment 
-module purge 
-module load swenv/default-env/devel # Eventually (only relevant on 2019a software environment) 
-module load phys/VASP/5.4.4-intel-2019a
-
-srun -n ${SLURM_NTASKS} vasp_[std/gam/ncl]
-```
+=== "Iris"
+    ```bash
+    # From your local computer
+    $ ssh -X iris-cluster
+
+    # Reserve the node for interactive computation
+    $ salloc -p interactive -A <project name> -t 1:00:00 -n 1 -c 14 --x11
+    # OR si -A <project name> -t 1:00:00 -n 1 -c 14 --x11 [...]
+
+    # Load the vasp module
+    $ module purge
+    $ module load phys/VASP/6.4.3-foss-2023b
+
+    $ vasp_[std/gam/ncl]
+    ```
+=== "Aion"
+    ```bash
+    # From your local computer
+    $ ssh -X iris-cluster
+
+    # Reserve the node for interactive computation
+    $ salloc -p interactive -A <project name> -t 1:00:00 -n 1 -c 16 --x11
+    # OR si -A <project name> -t 1:00:00 -n 1 -c 16 --x11 [...]
+
+    # Load the vasp module
+    $ module purge
+    $ module load phys/VASP/6.4.3-foss-2023b
+
+    $ vasp_[std/gam/ncl]
+    ```
+
+### Batch mode
+
+VASP jobs can also be executed as batch scripts with the job scheduler. Please execute all large jobs in batch scripts.
+
+When executing very large VASP jobs you should take advantage of OpenMP to reduce the limitations imposed by cache size and memory bandwidth when using multiple MPI processes. According to the VASP documentation, you should
+
+- setup a single process per L3 level cache (`OMP_NUM_THREADS`),
+- assign cores to threads so that all threads run on cores that share the same L3 cache (`OMP_PLACES` and `OMP_PROC_BIND`), and
+- increase the stack size per OpenMP process to at least `512 Mbytes` to avoid segmentation faults, as VASP is called a significant number of functions per OpenMP process (`OMP_STACKSIZE`).
+
+=== "Aion"
+    The [processors of Aion](https://en.wikichip.org/wiki/amd/epyc/7h12) are composed by [Core Complexes (CCX)](https://en.wikichip.org/wiki/amd/microarchitectures/zen_2#Core_Complex), with each CCX having 4 core and an L3 cache where all cores have uniform access. Thus,
+
+    - assign a process per CCX with 4 threads per process by setting the number of `OMP_NUM_THREADS=4`, and
+    - bind all threads to the cores where they where assigned with `OMP_PLACES=cores` and `OMP_PROC_BIND=close`.
+
+    ```bash
+    #!/usr/bin/bash --login
+
+    #SBATCH --account=<project name>
+    #SBATCH --job-name=VASP-casename
+    #SBATCH --nodes=2
+    #SBATCH --ntasks-per-node=32
+    #SBATCH --cpus-per-task=4
+    #SBATCH --time=0-08:00:00
+    #SBATCH --partition=batch
+    #SBATCH --qos=normal
+
+    # Set output and error files
+    #SBATCH --error=%x-%j.err
+    #SBATCH --output=%x-%j.out
+
+    print_error_and_exit() {
+      echo "***ERROR*** $*"
+      exit 1
+    }
+
+    # Load the vasp module
+    module purge || print_error_and_exit "No 'module' command found"
+    module load module load phys/VASP/6.4.3-foss-2023b
+
+    export OMP_NUM_THREADS=4
+
+    export OMP_PLACES=cores
+    export OMP_PROC_BIND=close
+
+    export OMP_STACKSIZE=512m
+
+    srun vasp_[std/gam/ncl]
+    ```
+
+=== "Iris"
+    The L3 cache structure of Iris is considerably simpler, with each socket having a [single L3 cache where all cores have uniform access](https://en.wikichip.org/wiki/intel/xeon_e5/e5-2680_v4). Thus,
+
+    - assign a process per socket with 14 threads per process by setting the number of `OMP_NUM_THREADS=14`, and
+    - bind all threads to the cores where they where assigned with `OMP_PLACES=cores` and `OMP_PROC_BIND=close`.
+
+    ```bash
+    #!/usr/bin/bash --login
+
+    #SBATCH --account=<project name>
+    #SBATCH --job-name=VASP-casename
+    #SBATCH --nodes=2
+    #SBATCH --ntasks-per-node=2
+    #SBATCH --cpus-per-task=14
+    #SBATCH --time=0-08:00:00
+    #SBATCH --partition=batch
+    #SBATCH --qos=normal
+
+    # Set output and error files
+    #SBATCH --error=%x-%j.err
+    #SBATCH --output=%x-%j.out
+
+    print_error_and_exit() {
+      echo "***ERROR*** $*"
+      exit 1
+    }
+
+    # Load the vasp module
+    module purge || print_error_and_exit "No 'module' command found"
+    module load module load phys/VASP/6.4.3-foss-2023b
+
+    export OMP_NUM_THREADS=14
+
+    export OMP_PLACES=cores
+    export OMP_PROC_BIND=close
+
+    export OMP_STACKSIZE=512m
+
+    srun vasp_[std/gam/ncl]
+    ```
+
+!!! info "Sources"
+    1. [The VASP Manual: Combining MPI and OpenMP](https://www.vasp.at/wiki/index.php/Combining_MPI_and_OpenMP)
 
 ## Additional information
-To know more information about VASP tutorial and documentation,
-please refer to [VASP manual](https://www.vasp.at/wiki/index.php/The_VASP_Manual).
+
+To know more information about VASP tutorial and documentation, please refer to [VASP manual](https://www.vasp.at/wiki/index.php/The_VASP_Manual).
 
 !!! tip
-    If you find some issues with the instructions above,
-    please report it to us using [support ticket](https://hpc.uni.lu/support).
+    If you find some issues with the instructions above, please report it to us using [support ticket](https://hpc.uni.lu/support).