added ANSYS/MAPDL

_data/sidebars/merlin6_sidebar.yml

@@ -75,10 +75,12 @@ entries:
       url: /merlin6/openmpi.html
     - title: IntelMPI
       url: /merlin6/impi.html
-    - title: ANSYS/Fluent
-      url: /merlin6/ansys-fluent.html
     - title: ANSYS/CFX
       url: /merlin6/ansys-cfx.html
+    - title: ANSYS/Fluent
+      url: /merlin6/ansys-fluent.html
+    - title: ANSYS/MAPDL
+      url: /merlin6/ansys-mapdl.html
   - title: Announcements
     folderitems:
     - title: Downtimes

pages/merlin6/05 Software Support/ansys-cfx.md

@@ -28,16 +28,20 @@ module load ANSYS/2020R1-1
 
 ### Non-interactive: sbatch
 
-Running jobs with `sbatch` is always the recommended method. This makes the use of the resources more efficient.
+Running jobs with `sbatch` is always the recommended method. This makes the use of the resources more efficient. Notice that for
+running non interactive Mechanical APDL jobs one must specify the `-batch` option.
 
 #### Serial example
 
+This example shows a very basic serial job.
+
 ```bash
 #!/bin/bash
 #SBATCH --job-name=CFX       # Job Name
 #SBATCH --partition=hourly   # Using 'daily' will grant higher priority than 'general'
 #SBATCH --time=0-01:00:00    # Time needed for running the job. Must match with 'partition' limits.
 #SBATCH --cpus-per-task=1    # Double if hyperthreading enabled
+#SBATCH --ntasks-per-core=1  # Double if hyperthreading enabled
 #SBATCH --hint=nomultithread # Disable Hyperthreading
 #SBATCH --error=slurm-%j.err # Define your error file
 
@@ -48,6 +52,9 @@ SOLVER_FILE=/data/user/caubet_m/CFX5/mysolver.in
 cfx5solve -batch -def "$JOURNAL_FILE" 
 ```
 
+One can enable hypertheading by defining `--hint=multithread`, `--cpus-per-task=2` and `--ntasks-per-core=2`.
+However, this is in general not recommended, unless one can ensure that can be beneficial.
+
 #### MPI-based example
 
 An example for running CFX using a Slurm batch script is the following:
@@ -60,7 +67,7 @@ An example for running CFX using a Slurm batch script is the following:
 #SBATCH --nodes=1            # Number of nodes
 #SBATCH --ntasks=44          # Number of tasks
 #SBATCH --cpus-per-task=1    # Double if hyperthreading enabled
-#SBATCH --ntasks-per-core=1  # Run one task per core
+#SBATCH --ntasks-per-core=1  # Double if hyperthreading enabled
 #SBATCH --hint=nomultithread # Disable Hyperthreading
 #SBATCH --error=slurm-%j.err # Define a file for standard error messages
 ##SBATCH --exclusive         # Uncomment if you want exclusive usage of the nodes
@@ -72,5 +79,6 @@ JOURNAL_FILE=/data/user/caubet_m/CFX/myjournal.in
 cfx5solve -batch -def "$JOURNAL_FILE" -part $SLURM_NTASKS
 ```
 
-In the above example, one can increase the number of *nodes* and/or *ntasks* if needed. One can remove
+In the above example, one can increase the number of *nodes* and/or *ntasks* if needed and combine it
-`--nodes`` for running on multiple nodes, but may lead to communication overhead.
+with `--exclusive` whenever needed. In general, **no hypertheading** is recommended for MPI based jobs.
+Also, one can combine it with `--exclusive` when necessary.

pages/merlin6/05 Software Support/ansys-fluent.md

@@ -38,6 +38,8 @@ For running it as a job, one needs to run in no graphical mode (`-g` option).
 
 #### Serial example
 
+This example shows a very basic serial job.
+
 ```bash
 #!/bin/bash
 #SBATCH --job-name=Fluent    # Job Name
@@ -54,6 +56,9 @@ JOURNAL_FILE=/data/user/caubet_m/Fluent/myjournal.in
 fluent 3ddp -g -i ${JOURNAL_FILE}
 ```
 
+One can enable hypertheading by defining `--hint=multithread`, `--cpus-per-task=2` and `--ntasks-per-core=2`.
+However, this is in general not recommended, unless one can ensure that can be beneficial.
+
 #### MPI-based example
 
 An example for running Fluent using a Slurm batch script is the following:
@@ -79,7 +84,9 @@ fluent 3ddp -g -t ${SLURM_NTASKS} -i ${JOURNAL_FILE}
 ```
 
 In the above example, one can increase the number of *nodes* and/or *ntasks* if needed. One can remove
-`--nodes`` for running on multiple nodes, but may lead to communication overhead.
+`--nodes`` for running on multiple nodes, but may lead to communication overhead. In general, **no
+hyperthreading** is recommended for MPI based jobs. Also, one can combine it with `--exclusive` when necessary.
+
 
 ## Interactive: salloc
 

pages/merlin6/05 Software Support/ansys-mapdl.md

@@ -0,0 +1,119 @@
+---
+title: ANSYS / MAPDL
+#tags:
+last_updated: 30 June 2020
+keywords: software, ansys, mapdl, slurm, apdl
+summary: "This document describes how to run ANSYS/Mechanical APDL in the Merlin6 cluster"
+sidebar: merlin6_sidebar
+permalink: /merlin6/ansys-mapdl.html
+---
+
+This document describes the different ways for running **ANSYS/Mechanical APDL**
+
+## ANSYS/Mechanical APDL
+
+Is always recommended to check which parameters are available in Mechanical APDL and adapt the below examples according to your needs.
+For that, please refer to the official Mechanical APDL documentation.
+
+## Running Mechanical APDL jobs
+
+### PModules
+
+Is strongly recommended the use of the latest ANSYS software **ANSYS/2020R1-1** available in PModules.
+
+```bash
+module use unstable
+module load ANSYS/2020R1-1
+```
+
+### Non-interactive: sbatch
+
+Running jobs with `sbatch` is always the recommended method. This makes the use of the resources more efficient. Notice that for 
+running non interactive Mechanical APDL jobs one must specify the `-b` option.
+
+#### Serial example
+
+This example shows a very basic serial job.
+
+```bash
+#!/bin/bash
+#SBATCH --job-name=MAPDL     # Job Name
+#SBATCH --partition=hourly   # Using 'daily' will grant higher priority than 'general'
+#SBATCH --time=0-01:00:00    # Time needed for running the job. Must match with 'partition' limits.
+#SBATCH --cpus-per-task=1    # Double if hyperthreading enabled
+#SBATCH --ntasks-per-core=1  # Double if hyperthreading enabled
+#SBATCH --hint=nomultithread # Disable Hyperthreading
+#SBATCH --error=slurm-%j.err # Define your error file
+
+module use unstable
+module load ANSYS/2020R1-1
+
+SOLVER_FILE=/data/user/caubet_m/MAPDL/mysolver.in
+mapdl -b -i "$SOLVER_FILE"
+```
+
+One can enable hypertheading by defining `--hint=multithread`, `--cpus-per-task=2` and `--ntasks-per-core=2`.
+However, this is in general not recommended, unless one can ensure that can be beneficial.
+
+#### SMP-based example
+
+This example shows how to running Mechanical APDL in Shared-Memory Parallelism mode. It limits the use 
+to 1 single node, but by using many cores. In the example below, we use a node by using all his cores
+and the whole memory.
+
+```bash
+#!/bin/bash
+#SBATCH --job-name=MAPDL     # Job Name
+#SBATCH --partition=hourly   # Using 'daily' will grant higher priority than 'general'
+#SBATCH --time=0-01:00:00    # Time needed for running the job. Must match with 'partition' limits.
+#SBATCH --nodes=1            # Number of nodes
+#SBATCH --ntasks=1           # Number of tasks
+#SBATCH --cpus-per-task=44   # Double if hyperthreading enabled
+#SBATCH --hint=nomultithread # Disable Hyperthreading
+#SBATCH --error=slurm-%j.err # Define a file for standard error messages
+#SBATCH --exclusive          # Uncomment if you want exclusive usage of the nodes
+
+module use unstable
+module load ANSYS/2020R1-1
+
+SOLVER_FILE=/data/user/caubet_m/MAPDL/mysolver.in
+mapdl -b -np ${SLURM_CPUS_PER_TASK} -i "$SOLVER_FILE"
+```
+
+In the above example, one can reduce the number of **cpus per task**. Here usually `--exclusive` 
+is recommended if one needs to use the whole memory. 
+
+For **SMP** runs, one might try the hyperthreading mode by doubling the proper settings 
+(`--cpus-per-task`), in some cases it might be beneficial.
+
+Please notice that `--ntasks-per-core=1` is not defined here, this is because we want to run 1 
+task on many cores! As an alternative, one can explore `--ntasks-per-socket` or `--ntasks-per-node` 
+for fine grained configurations.
+
+#### MPI-based example
+
+This example enables Distributed ANSYS for running Mechanical APDL using a Slurm batch script.
+
+```bash
+#!/bin/bash
+#SBATCH --job-name=MAPDL     # Job Name
+#SBATCH --partition=hourly   # Using 'daily' will grant higher priority than 'general'
+#SBATCH --time=0-01:00:00    # Time needed for running the job. Must match with 'partition' limits.
+#SBATCH --nodes=1            # Number of nodes
+#SBATCH --ntasks=44          # Number of tasks
+#SBATCH --cpus-per-task=1    # Double if hyperthreading enabled
+#SBATCH --ntasks-per-core=1  # Run one task per core
+#SBATCH --hint=nomultithread # Disable Hyperthreading
+#SBATCH --error=slurm-%j.err # Define a file for standard error messages
+##SBATCH --exclusive         # Uncomment if you want exclusive usage of the nodes
+
+module use unstable
+module load ANSYS/2020R1-1
+
+SOLVER_FILE=/data/user/caubet_m/MAPDL/mysolver.in
+mapdl -b -dis -np ${SLURM_NTASKS} -i "$SOLVER_FILE"
+```
+
+In the above example, one can increase the number of *nodes* and/or *ntasks* if needed and combine it
+with `--exclusive` when necessary. In general, **no hypertheading** is recommended for MPI based jobs.
+Also, one can combine it with `--exclusive` when necessary.