From 191dd6db23021e084cd6ee1eced83dbb00006d91 Mon Sep 17 00:00:00 2001 From: Mark Piercy Date: Tue, 5 Sep 2023 11:48:12 -0700 Subject: [PATCH 1/4] Create schrodinger.md --- src/docs/schrodinger.md | 116 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 116 insertions(+) create mode 100644 src/docs/schrodinger.md diff --git a/src/docs/schrodinger.md b/src/docs/schrodinger.md new file mode 100644 index 000000000..aa50711e8 --- /dev/null +++ b/src/docs/schrodinger.md @@ -0,0 +1,116 @@ +## Introduction + +The [Schrodinger][url_schro] software suite is used to simulate and model molecular behavior at the atomic level. Schrodinger's software tools include molecular dynamics simulations, quantum mechanics calculations, virtual screening and visualization tools. + +Stanford Libraries has purchased a site license for the Schrodinger suite. Please contact Stanford Libraries: sciencelibrary@stanford.edu cc'ing srcc-support@stanford.edu if you would like to access Schrodinger on Sherlock. After we receive confirmation, +we will add your faculty sponsor (PI) to the sh_sw-schrodinger Sherlock group. + +## Schrodinger on Sherlock + +Schrodinger software is loaded with the module command. To load the current default version: + +```bash +module load chemistry schrodinger +``` + +To see all of our versions use the module spider command: + +```bash +$ module spider schrodinger +``` + +Once loaded your $SCHRODINGER variable is automatically set and all Schrodinger commands will run. For example to run the jaguar command: + +```bash +$ jaguar run -WAIT H20.in +``` + +To call the basic Schrodinger run command, just enter: + +```bash +$ run +``` + +or glide: +​ +```bash +$ glide +usage: glide_startup.py [options] +glide_startup.py: error: the following arguments are required: input_file +``` + +## Example batch submission + +Sample [sbatch][url_sbatch] script, requesting 1 CPU, for 10 minutes on the normal partition with default memory: + +```bash +#!/usr/bin/bash +#SBATCH -o water.%j.out +#SBATCH -e water.%j.err +#SBATCH -n 1 +#SBATCH -t 10:00 +#SBATCH -p normal +# Load required modules +module load chemistry schrodinger +# Run Schrodinger, -WAIT is often required +jaguar run -WAIT H20.in +``` + +Input file: + +``` +&gen +& +&echo +& +&zmat +O 0.0000000000000 0.0000000000000 -0.1135016000000 +H1 0.0000000000000 0.7531080000000 0.4540064000000 +H2 0.0000000000000 -0.7531080000000 0.4540064000000 +& +``` + +Save as H2O.in + + +Submit the sbatch script: +```bash +$ sbatch water.sbatch +``` + +## Maestro GUI + + +For maestro, once you load the Schrodinger module simply call the Maestro GUI with: + +$ maestro + + +If you are using a Mac, open the Terminal App and ssh with the -X option: + +```bash +ssh -X @login.sherlock.stanford.edu +sh_dev -m 16GB +ml load chemistry schrodinger +maestro & +``` +This will launch the Maestro graphical user interface in the background in an sh_dev session with 16GB of memory. + + +!!! warning GUI's +Please be aware that GUIs run over a network and X11 can be quite slow and the HPC environment is not best for GUI analysis, it's more ideal for large scale batch job submission and computation. + + +If you are using a Windows desktop/laptop you will need to use an X11 client like MobaXterm or Xming, see [X11][url_X11] at Stanford for more information. + +!!! warning OnDemand shell sessions +Note that opening an X11/GUI session will not work in a Sherlock OnDemand terminal session. You will need to use the methods mentioned above, i.e. a standard terminal session with an X11 client. + + +[comment]: # (link URLs -----------------------------------------------------) + +[url_schro]: //www.schrodinger.com/ +[url_X11]: //uit.stanford.edu/service/sharedcomputing/moreX +[url_sbatch]:      //docs/user-guide/running-jobs/#batch-jobs +[url_support]: mailto:{{ support_email }} +[comment]: # (footnotes -----------------------------------------------------) From 5076a2e36602f09d7639a0c4f674a9eb9ca96bc7 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Tue, 5 Sep 2023 16:10:16 -0700 Subject: [PATCH 2/4] add nav entry for new page --- mkdocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/mkdocs.yml b/mkdocs.yml index 063df4aee..ee704b4a5 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -286,6 +286,7 @@ nav: - Spark: docs/software/using/spark.md - MariaDB: docs/software/using/mariadb.md - PostgreSQL: docs/software/using/postgresql.md + - Schrödinger: docs/software/using/schrodinger.md - Quantum Espresso: docs/software/using/quantum-espresso.md - Advanced topics: - Connection options: docs/advanced-topics/connection.md From 33b9d900ae22cd786d05709a897cb37e314288af Mon Sep 17 00:00:00 2001 From: Mark Piercy Date: Mon, 11 Sep 2023 13:06:16 -0700 Subject: [PATCH 3/4] Update schrodinger.md fix typos --- src/docs/software/using/schrodinger.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/docs/software/using/schrodinger.md b/src/docs/software/using/schrodinger.md index a8bfa214a..97973b86d 100644 --- a/src/docs/software/using/schrodinger.md +++ b/src/docs/software/using/schrodinger.md @@ -19,11 +19,11 @@ contact [Schrödinger support][url_schrodinger_support]. [Stanford Libraries][url_sul] have purchased a site license for the Schrödinger suite. Please contact Stanford Libraries at sciencelibrary@stanford.edu and CC {{ support_email }} if you would like to access Schrödinger on Sherlock: after -we receive confirmation, your PI group will be granted access. on Sherlock. +we receive confirmation, your PI group will be granted access on Sherlock. ### Using Schrödinger -You can use Schrödinger software fater having loaded the corresponding +You can use Schrödinger software after having loaded the corresponding [software module][url_modules] with the `module` command. To load the current default version: @@ -77,7 +77,7 @@ $ maestro ``` You'll need to enable X11 forwarding in your initial connection to Sherlock, -and request it as well for your job allocationi. +and request it as well for your job allocation. Here are some example commands you can run: From 4920975de758782ef9d870f2360634c30812acbe Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Mon, 11 Sep 2023 13:27:39 -0700 Subject: [PATCH 4/4] fixes for spellcheck test --- .github/workflows/config/spellcheck.wordlist.txt | 2 ++ src/docs/software/using/schrodinger.md | 8 ++++---- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.github/workflows/config/spellcheck.wordlist.txt b/.github/workflows/config/spellcheck.wordlist.txt index 3cc6f3dd4..3568e2cf9 100644 --- a/.github/workflows/config/spellcheck.wordlist.txt +++ b/.github/workflows/config/spellcheck.wordlist.txt @@ -18,3 +18,5 @@ MPI NUMA PDU SMP +Schrödinger +OnDemand diff --git a/src/docs/software/using/schrodinger.md b/src/docs/software/using/schrodinger.md index 97973b86d..33b5a3e6f 100644 --- a/src/docs/software/using/schrodinger.md +++ b/src/docs/software/using/schrodinger.md @@ -2,7 +2,7 @@ The [Schrödinger][url_schrodinger] suite is a commercial and licensed software used to simulate and model molecular behavior at the atomic level. -Schrödinger's software tools include molecular dynamics simulations, quantum +The Schrödinger software tools include molecular dynamics simulations, quantum mechanics calculations, virtual screening and visualization tools. ### More documentation @@ -104,15 +104,15 @@ interface on your local machine's display. scheduled computations are carried over on the cluster. -For more information about X11 forwarding, you can refer to this [UIT -page][url_x11]. +For more information about X11 forwarding, you can refer to this +[page][url_x11]. ## Examples ### batch job submission -Here's an example [sbatch][url_sbatch] script, requesting 1 CPU, for 10 minutes +Here's an example [batch][url_sbatch] script, requesting 1 CPU, for 10 minutes on the `normal` partition, that can be saved as `water.sbatch`: ```bash