fixes

.wordlist.txt

@@ -3307,6 +3307,13 @@ lxc
 subcommands
 multiqc
 sortmerna
+Sylabs
+sylabs
+multiqc
+sortmerna
+lxc
+testcontainer
+testdefinition
 
 
 

docs/software/directly-from-IG/openmolcas.md → docs/software/openmolcas.md

@@ -1,40 +1,46 @@
 # MOLCAS user guide
-https://www.uppmax.uu.se/support/user-guides/molcas-user-guide/
 
-How to run the program MOLCAS on UPPMAX
+> How to run the program MOLCAS on UPPMAX
 
-Information
+## Information
 MOLCAS is an ab initio computational chemistry program. Focus in the program is placed on methods for calculating general electronic structures in molecular systems in both ground and excited states. MOLCAS is, in particular, designed to study the potential surfaces of excited states
 
-This guide will help you get started running MOLCAS on UPPMAX. More detailed information on how to use Molcas can be found on the official website.
+This guide will help you get started running MOLCAS on UPPMAX. More detailed information on how to use Molcas can be found on the [official website](https://molcas.org/).
 
-Licensing
+## Licensing
 A valid license key is required to run Molcas on UPPMAX. The licence key should be kept in a directory named .Molcas under the home directory.
 
-Molcas is currently free of charge for academic researchers active in the Nordic countries. You can get hold of a license by following these instructions.
+Molcas is currently free of charge for academic researchers active in the Nordic countries. You can get hold of a license by following [these instructions](https://www.molcas.org/order.html).
 
-Versions installed at UPPMAX
+## Versions installed at UPPMAX
 At UPPMAX the following versions are installed:
 
-8.0 (serial)
-7.8 (serial)
-Modules needed to run MOLCAS
+- 8.0 (serial)
+- 7.8 (serial)
+## Modules needed to run MOLCAS
 In order to run MOLCAS you must first load the MOLCAS module. You can see all available versions of MOLCAS installed at UPPMAX with:
 
+```bash
 module avail molcas
+```
 Load a MOLCAS module with, eg:
 
+```bash
 module load molcas/7.8.082
-How to run MOLCAS interactively
+```
+## How to run MOLCAS interactively
 If you would like to do tests or short runs, we recommend using the interactive command:
-
+```bash
 interactive -A your_project_name
+```
 This will reserve a node for you to do your test on. Note that you must provide the name of an active project in order to run on UPPMAX resources. After a short wait you will get access to the node. Then you can run MOLCAS by:
-
+```bash
 module load molcas/7.8.082
 molcas -f test000.input
-The test000.input looks like:
+```
+The `test000.input` looks like:
 
+``` 
 *$Revision: 7.7 $
 ************************************************************************
 * Molecule: H2
@@ -75,11 +81,13 @@ Ras2
  &SLAPAF
  
  &CASPT2
-See the SLURM user guide for more information on the interactive command. Don't forget to exit your interactive job when you have finished your calculation. Exiting will free the resource for others to use.
+```
+See the [SLURM user guide](../cluster_guides/slurm.md) for more information on the interactive command. Don't forget to exit your interactive job when you have finished your calculation. Exiting will free the resource for others to use.
 
-Batch scripts for slurm
+## Batch scripts for slurm
 It's possible to run MOLCAS in the batch queue. Here is an example running MOLCAS on one core:
 
+```sbatch
 #!/bin/bash -l
 #
 #SBATCH -A <em>your_project_name</em>
@@ -93,9 +101,10 @@ module load molcas/7.8.082
 export MOLCASMEM=2000
  
 molcas -f test000.input
+```
 Again you'll have to provide your project name.
 
-If the script is called test000.job you can submit it to the batch queue with:
-
+If the script is called `test000.job` you can submit it to the batch queue with:
+```bash
 sbatch test000.job
-This example will not take many seconds to run on e.g. Tintin or Milou.
+```

docs/software/singularity.md

@@ -51,13 +51,13 @@ See [https://www.sylabs.io/guides/2.6/user-guide/container_recipes.html](https:/
 ## Using the sylabs cloud remote builder, an example
 Even if you don't run Linux on your desktop system, you can still build your own images. Typically software pages contain enough information as installation instructions to create a modified recipe to build images for software.
 
-[Sylabs](https://www.sylabs.io/) (the company currently developing singularity) offer an experimental cloud service for building images from recipies. Here's an example on how to use that to build an image for a software (for this example, we picked [sortmerna](https://github.com/biocore/sortmerna)  as it was the first user software request that came up).
+[Sylabs](https://www.sylabs.io/) (the company currently developing singularity) offer an experimental cloud service for building images from recipes. Here's an example on how to use that to build an image for a software (for this example, we picked [sortmerna](https://github.com/biocore/sortmerna)  as it was the first user software request that came up).
 
 - First, we need to sign in to the sylabs remote builder, available at https://cloud.sylabs.io. It allows sign in through various providers (currently Google, Microsoft, GitHub, GitLab). If you don't have an account with one of these, at least one of them is likely to offer free registration.
 
 - Once signed in, we want to create a project for this software, so we click on "Singularity Library" in the top menu and select "Create a new project", set ourselves as owner and enter sortmerna as project name. We also select to make images for this project public.
 
-- Once we click onwards, we can create our first image for the project. This can be done either by pushing an image from a client (commands are given) or by building in the cloud service.
+- Once we click onward, we can create our first image for the project. This can be done either by pushing an image from a client (commands are given) or by building in the cloud service.
 
 - Since we want to use the cloud service, we click remote builder and get a box to fill in an image recipe. We also get a box to enter a tag or version and the possibility to enter a description.