added ANSYS/Fluent

Gemfile.lock

@@ -1,13 +1,14 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (4.2.11.1)
+    activesupport (6.0.3.2)
-      i18n (~> 0.7)
+      concurrent-ruby (~> 1.0, >= 1.0.2)
+      i18n (>= 0.7, < 2)
       minitest (~> 5.1)
-      thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
-    addressable (2.6.0)
+      zeitwerk (~> 2.2, >= 2.2.2)
-      public_suffix (>= 2.0.2, < 4.0)
+    addressable (2.7.0)
+      public_suffix (>= 2.0.2, < 5.0)
     bigdecimal (1.4.4)
     coffee-script (2.4.1)
       coffee-script-source
@@ -16,8 +17,8 @@ GEM
     colorator (1.1.0)
     commonmarker (0.17.13)
       ruby-enum (~> 0.5)
-    concurrent-ruby (1.1.5)
+    concurrent-ruby (1.1.6)
-    dnsruby (1.61.2)
+    dnsruby (1.61.3)
       addressable (~> 2.5)
     em-websocket (0.5.1)
       eventmachine (>= 0.12.9)
@@ -26,33 +27,32 @@ GEM
       ffi (>= 1.3.0)
     eventmachine (1.2.7)
     execjs (2.7.0)
-    faraday (0.15.4)
+    faraday (1.0.1)
       multipart-post (>= 1.2, < 3)
-    ffi (1.11.1)
+    ffi (1.13.1)
     forwardable-extended (2.6.0)
     gemoji (3.0.1)
-    github-pages (198)
+    github-pages (206)
-      activesupport (= 4.2.11.1)
       github-pages-health-check (= 1.16.1)
-      jekyll (= 3.8.5)
+      jekyll (= 3.8.7)
-      jekyll-avatar (= 0.6.0)
+      jekyll-avatar (= 0.7.0)
       jekyll-coffeescript (= 1.1.1)
-      jekyll-commonmark-ghpages (= 0.1.5)
+      jekyll-commonmark-ghpages (= 0.1.6)
       jekyll-default-layout (= 0.1.4)
-      jekyll-feed (= 0.11.0)
+      jekyll-feed (= 0.13.0)
       jekyll-gist (= 1.5.0)
-      jekyll-github-metadata (= 2.12.1)
+      jekyll-github-metadata (= 2.13.0)
-      jekyll-mentions (= 1.4.1)
+      jekyll-mentions (= 1.5.1)
-      jekyll-optional-front-matter (= 0.3.0)
+      jekyll-optional-front-matter (= 0.3.2)
       jekyll-paginate (= 1.1.0)
-      jekyll-readme-index (= 0.2.0)
+      jekyll-readme-index (= 0.3.0)
-      jekyll-redirect-from (= 0.14.0)
+      jekyll-redirect-from (= 0.15.0)
-      jekyll-relative-links (= 0.6.0)
+      jekyll-relative-links (= 0.6.1)
-      jekyll-remote-theme (= 0.3.1)
+      jekyll-remote-theme (= 0.4.1)
       jekyll-sass-converter (= 1.5.2)
-      jekyll-seo-tag (= 2.5.0)
+      jekyll-seo-tag (= 2.6.1)
-      jekyll-sitemap (= 1.2.0)
+      jekyll-sitemap (= 1.4.0)
-      jekyll-swiss (= 0.4.0)
+      jekyll-swiss (= 1.0.0)
       jekyll-theme-architect (= 0.1.1)
       jekyll-theme-cayman (= 0.1.1)
       jekyll-theme-dinky (= 0.1.1)
@@ -62,19 +62,18 @@ GEM
       jekyll-theme-midnight (= 0.1.1)
       jekyll-theme-minimal (= 0.1.1)
       jekyll-theme-modernist (= 0.1.1)
-      jekyll-theme-primer (= 0.5.3)
+      jekyll-theme-primer (= 0.5.4)
       jekyll-theme-slate (= 0.1.1)
       jekyll-theme-tactile (= 0.1.1)
       jekyll-theme-time-machine (= 0.1.1)
-      jekyll-titles-from-headings (= 0.5.1)
+      jekyll-titles-from-headings (= 0.5.3)
-      jemoji (= 0.10.2)
+      jemoji (= 0.11.1)
       kramdown (= 1.17.0)
-      liquid (= 4.0.0)
+      liquid (= 4.0.3)
-      listen (= 3.1.5)
       mercenary (~> 0.3)
-      minima (= 2.5.0)
+      minima (= 2.5.1)
-      nokogiri (>= 1.8.5, < 2.0)
+      nokogiri (>= 1.10.4, < 2.0)
-      rouge (= 2.2.1)
+      rouge (= 3.19.0)
       terminal-table (~> 1.4)
     github-pages-health-check (1.16.1)
       addressable (~> 2.3)
@@ -82,13 +81,13 @@ GEM
       octokit (~> 4.0)
       public_suffix (~> 3.0)
       typhoeus (~> 1.3)
-    html-pipeline (2.11.0)
+    html-pipeline (2.13.0)
       activesupport (>= 2)
       nokogiri (>= 1.4)
     http_parser.rb (0.6.0)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    jekyll (3.8.5)
+    jekyll (3.8.7)
       addressable (~> 2.4)
       colorator (~> 1.0)
       em-websocket (~> 0.5)
@@ -101,49 +100,50 @@ GEM
       pathutil (~> 0.9)
       rouge (>= 1.7, < 4)
       safe_yaml (~> 1.0)
-    jekyll-avatar (0.6.0)
+    jekyll-avatar (0.7.0)
-      jekyll (~> 3.0)
+      jekyll (>= 3.0, < 5.0)
     jekyll-coffeescript (1.1.1)
       coffee-script (~> 2.2)
       coffee-script-source (~> 1.11.1)
     jekyll-commonmark (1.3.1)
       commonmarker (~> 0.14)
       jekyll (>= 3.7, < 5.0)
-    jekyll-commonmark-ghpages (0.1.5)
+    jekyll-commonmark-ghpages (0.1.6)
       commonmarker (~> 0.17.6)
-      jekyll-commonmark (~> 1)
+      jekyll-commonmark (~> 1.2)
-      rouge (~> 2)
+      rouge (>= 2.0, < 4.0)
     jekyll-default-layout (0.1.4)
       jekyll (~> 3.0)
-    jekyll-feed (0.11.0)
+    jekyll-feed (0.13.0)
-      jekyll (~> 3.3)
+      jekyll (>= 3.7, < 5.0)
     jekyll-gist (1.5.0)
       octokit (~> 4.2)
-    jekyll-github-metadata (2.12.1)
+    jekyll-github-metadata (2.13.0)
-      jekyll (~> 3.4)
+      jekyll (>= 3.4, < 5.0)
       octokit (~> 4.0, != 4.4.0)
-    jekyll-mentions (1.4.1)
+    jekyll-mentions (1.5.1)
       html-pipeline (~> 2.3)
-      jekyll (~> 3.0)
+      jekyll (>= 3.7, < 5.0)
-    jekyll-optional-front-matter (0.3.0)
+    jekyll-optional-front-matter (0.3.2)
-      jekyll (~> 3.0)
+      jekyll (>= 3.0, < 5.0)
     jekyll-paginate (1.1.0)
-    jekyll-readme-index (0.2.0)
+    jekyll-readme-index (0.3.0)
-      jekyll (~> 3.0)
+      jekyll (>= 3.0, < 5.0)
-    jekyll-redirect-from (0.14.0)
+    jekyll-redirect-from (0.15.0)
-      jekyll (~> 3.3)
+      jekyll (>= 3.3, < 5.0)
-    jekyll-relative-links (0.6.0)
+    jekyll-relative-links (0.6.1)
-      jekyll (~> 3.3)
+      jekyll (>= 3.3, < 5.0)
-    jekyll-remote-theme (0.3.1)
+    jekyll-remote-theme (0.4.1)
-      jekyll (~> 3.5)
+      addressable (~> 2.0)
-      rubyzip (>= 1.2.1, < 3.0)
+      jekyll (>= 3.5, < 5.0)
+      rubyzip (>= 1.3.0)
     jekyll-sass-converter (1.5.2)
       sass (~> 3.4)
-    jekyll-seo-tag (2.5.0)
+    jekyll-seo-tag (2.6.1)
-      jekyll (~> 3.3)
+      jekyll (>= 3.3, < 5.0)
-    jekyll-sitemap (1.2.0)
+    jekyll-sitemap (1.4.0)
-      jekyll (~> 3.3)
+      jekyll (>= 3.7, < 5.0)
-    jekyll-swiss (0.4.0)
+    jekyll-swiss (1.0.0)
     jekyll-theme-architect (0.1.1)
       jekyll (~> 3.5)
       jekyll-seo-tag (~> 2.0)
@@ -171,8 +171,8 @@ GEM
     jekyll-theme-modernist (0.1.1)
       jekyll (~> 3.5)
       jekyll-seo-tag (~> 2.0)
-    jekyll-theme-primer (0.5.3)
+    jekyll-theme-primer (0.5.4)
-      jekyll (~> 3.5)
+      jekyll (> 3.5, < 5.0)
       jekyll-github-metadata (~> 2.9)
       jekyll-seo-tag (~> 2.0)
     jekyll-theme-slate (0.1.1)
@@ -184,44 +184,43 @@ GEM
     jekyll-theme-time-machine (0.1.1)
       jekyll (~> 3.5)
       jekyll-seo-tag (~> 2.0)
-    jekyll-titles-from-headings (0.5.1)
+    jekyll-titles-from-headings (0.5.3)
-      jekyll (~> 3.3)
+      jekyll (>= 3.3, < 5.0)
     jekyll-watch (2.2.1)
       listen (~> 3.0)
-    jemoji (0.10.2)
+    jemoji (0.11.1)
       gemoji (~> 3.0)
       html-pipeline (~> 2.2)
-      jekyll (~> 3.0)
+      jekyll (>= 3.0, < 5.0)
-    json (2.2.0)
+    json (2.3.0)
     kramdown (1.17.0)
-    liquid (4.0.0)
+    liquid (4.0.3)
-    listen (3.1.5)
+    listen (3.2.1)
-      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-fsevent (~> 0.10, >= 0.10.3)
-      rb-inotify (~> 0.9, >= 0.9.7)
+      rb-inotify (~> 0.9, >= 0.9.10)
-      ruby_dep (~> 1.2)
     mercenary (0.3.6)
     mini_portile2 (2.4.0)
-    minima (2.5.0)
+    minima (2.5.1)
-      jekyll (~> 3.5)
+      jekyll (>= 3.5, < 5.0)
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
-    minitest (5.11.3)
+    minitest (5.14.1)
     multipart-post (2.1.1)
-    nokogiri (1.10.3)
+    nokogiri (1.10.9)
       mini_portile2 (~> 2.4.0)
-    octokit (4.14.0)
+    octokit (4.18.0)
+      faraday (>= 0.9)
       sawyer (~> 0.8.0, >= 0.5.3)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
-    public_suffix (3.0.3)
+    public_suffix (3.1.1)
-    rb-fsevent (0.10.3)
+    rb-fsevent (0.10.4)
-    rb-inotify (0.10.0)
+    rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rouge (2.2.1)
+    rouge (3.19.0)
-    ruby-enum (0.7.2)
+    ruby-enum (0.8.0)
       i18n
-    ruby_dep (1.5.0)
+    rubyzip (2.3.0)
-    rubyzip (1.2.3)
     safe_yaml (1.0.5)
     sass (3.7.4)
       sass-listen (~> 4.0.0)
@@ -234,11 +233,12 @@ GEM
     terminal-table (1.8.0)
       unicode-display_width (~> 1.1, >= 1.1.1)
     thread_safe (0.3.6)
-    typhoeus (1.3.1)
+    typhoeus (1.4.0)
       ethon (>= 0.9.0)
-    tzinfo (1.2.5)
+    tzinfo (1.2.7)
       thread_safe (~> 0.1)
-    unicode-display_width (1.6.0)
+    unicode-display_width (1.7.0)
+    zeitwerk (2.3.1)
 
 PLATFORMS
   ruby
@@ -250,4 +250,4 @@ DEPENDENCIES
   json (~> 2.2)
 
 BUNDLED WITH
-   2.0.2
+   2.1.4

_data/sidebars/merlin6_sidebar.yml

@@ -75,6 +75,8 @@ entries:
       url: /merlin6/openmpi.html
     - title: IntelMPI
       url: /merlin6/impi.html
+    - title: ANSYS/Fluent
+      url: /merlin6/ansys-fluent.html
   - title: Announcements
     folderitems:
     - title: Downtimes

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

@@ -0,0 +1,122 @@
+---
+title: ANSYS / Fluent
+#tags:
+last_updated: 30 June 2020
+keywords: software, ansys, fluent, slurm
+summary: "This document describes how to run ANSYS/Fluent in the Merlin6 cluster"
+sidebar: merlin6_sidebar
+permalink: /merlin6/ansys-fluent.html
+---
+
+This document describes the different ways for running **ANSYS/Fluent**
+
+## ANSYS/Fluent
+
+Is always recommended to check which parameters are available in Fluent and adapt the below example according to your needs.
+For that, run `fluent -help` for getting a list of options. However, as when running Fluent one must specify one of the 
+following flags:
+* **2d**: This is a 2D solver with single point precision.
+* **3d**: This is a 3D solver with single point precision.
+* **2dpp**: This is a 2D solver with double point precision.
+* **3dpp**: This is a 3D solver with double point precision.
+
+## Running Fluent 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
+
+Using `sbatch` is always recommeneded.
+
+#### Serial example
+
+```bash
+#!/bin/bash
+#SBATCH --job-name=Fluent    # 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 --hint=nomultithread # Disable Hyperthreading
+#SBATCH --output=%j.out      # Define your output file
+#SBATCH --error=%j.err       # Define your error file
+
+module use unstable
+module load ANSYS/2020R1-1
+
+JOURNAL_FILE=/data/user/caubet_m/Fluent/myjournal.in
+fluent 3ddp -g -i ${JOURNAL_FILE}
+```
+
+#### MPI-based exampke
+
+An example for running Fluent using a Slurm batch script is the following:
+
+```bash
+#!/bin/bash
+#SBATCH --job-name=Fluent    # 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=%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
+
+JOURNAL_FILE=/data/user/caubet_m/Fluent/myjournal.in
+fluent 3ddp -g -t ${SLURM_NTASKS} -i ${JOURNAL_FILE}
+```
+
+In the above example, one can increase the number of *nodes* and/or *ntasks* if needed. 
+
+## Interactive: salloc
+
+Running Fluent interactively is strongly not recommended and one should whenever possible use `sbatch`.
+However, sometimes interactive runs are needed. For jobs requiring only few CPUs (in example, 2 CPUs) **and** for a short period of time, one can use the login nodes.
+Otherwise, one must use the Slurm batch system using allocations:
+   * For short jobs requiring more CPUs, one can use the Merlin shortest partitions (`hourly`).
+   * For longer jobs, one can use longer partitions, however, interactive access is not always possible (depending on the usage of the cluster).
+
+Please refer to the documentation **[Running Interactive Jobs](/merlin6/interactive-jobs.html)** for firther information about different ways for running interactive
+jobs in the Merlin6 cluster.
+
+### Considerations
+
+For running Fluent using Slurm computing nodes, one needs to get the list of the reserved nodes. For getting that list, once you have the allocation, one can run
+the following command:
+
+```bash
+scontrol show hostname
+```
+
+This list must be included in the settings as the list of hosts where to run Fluent. Alternatively, one can give that list as parameter (`-cnf` option) when running `fluent`,
+as follows:
+
+<details>
+<summary>[Running Fluent with 'salloc' example]</summary>
+<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
+(base) [caubet_m@merlin-l-001 caubet_m]$ salloc --nodes=2 --ntasks=88 --hint=nomultithread --time=0-01:00:00 --partition=test $SHELL
+salloc: Pending job allocation 135030174
+salloc: job 135030174 queued and waiting for resources
+salloc: job 135030174 has been allocated resources
+salloc: Granted job allocation 135030174
+
+(base) [caubet_m@merlin-l-001 caubet_m]$ module use unstable
+(
+base) [caubet_m@merlin-l-001 caubet_m]$ module load ANSYS/2020R1-1
+module load: unstable module has been loaded -- ANSYS/2020R1-1
+
+(base) [caubet_m@merlin-l-001 caubet_m]$ fluent 3ddp -t$SLURM_NPROCS -cnf=$(scontrol show hostname | tr '\n' ',')
+</pre>
+</details>