modified: jobs/batch.md

modified:   jobs/dos_and_donts.md
modified:   jobs/job_management.md
modified:   jobs/slurm_parameter.md
deleted:    software/modules.md

jobs/batch.md

+---
+sort: 2
+---
+
 # Batch system
 
 The Star cluster is a resource that is shared between many of users and

jobs/dos_and_donts.md

+---
+sort: 1
+---
 
 # Dos and don'ts
 

jobs/job_management.md

@@ -6,7 +6,7 @@ commands:
 1.  Submit the job with `sbatch <script_name>`.
 2.  Check the job status with `squeue`. (to limit the display to only
     your jobs use `squeue -u <user_name>`.)
-3.  (optional) Delete the job with `scancel <job_id>`.
+3.  (optional) Delete/kill the job with `scancel <job_id>`.
 
 You can also hold the start of a job:
 

jobs/slurm_parameter.md

+---
+sort: 3
+---
+
+
 # SLURM Workload Manager
 
 Slurm Workload Manager, or SLURM (Simple Linux Utility for Resource Management), is a free and open-source job scheduler for managing workloads on Linux and Unix-based clusters, such as Star.

software/modules.md

-# Software Module Scheme
-
-Since a HPC cluster is shared among many users, and also holds a
-significant size in contrast to most desktop compute machinery around,
-the amount of installed software spans many applications in many
-different versions and quite a few of them are installed typically
-non-standard places for easier maintenance (for admin crew), practical
-and security reasons. It is not possible (nor desirable) to use them all
-at the same time, since different versions of the same application may
-conflict with each other. Therefore, it is practical to provide the
-production environment for a given application outside of the
-application itself. This is done using a set of instructions and
-variable settings that are specific for the given application called an
-application module. This also simplifies control of which application
-versions are available in a specific session.
-
-We are also using the Easybuild system for installing software on Star
-(see <https://easybuilders.github.io/easybuild/>).
-
-The main command for using this system is the *module* command. You can
-find a list of all its options by typing:
-
-    module --help
-
-We use the lmod module system; for more info see
-<https://lmod.readthedocs.io/en/latest/> on Star. Below we listed the
-most commonly used options, but also feel free to ivestigate options in
-this toolset more thoroughly on developers site.
-
-## Which modules are currently loaded?
-
-To see the modules currently active in your session, use the command:
-
-    module list
-
-  Which modules are available? ----------------------------
-
-In order to see a complete list of available modules, issue the command:
-
-    module avail
-
-The resulting list will contain module names conforming to the following
-pattern:
-
--   name of the module
--   /
--   version
--   (default) if default version
-
-## How to load a module
-
-In order to make, for instance, the NetCDF library available issue the
-command:
-
-    module load netCDF
-
-This will load the default NetCDF version. To load a specific version,
-just include the version after a slash:
-
-    module load netCDF/4.3.3.1-intel-2016a
-
- 
-
-## How to unload a module
-
-Keeping with the above example, use the following command to unload the
-NetCDF module again:
-
-    module unload netcdf
-
-## Which version of a module is the default?
-
-In order to see, for instance, which version of NetCDF is loaded by the
-module, use:
-
-    module show netcdf
-
-This will show the version and path of the module.  
-
-## How do I switch to a different version of a module?
-
-Switching to another version is similar to loading a specific version.
-As an example, if you want to switch from the default (current) Intel
-compilers version to version 2016b (aka 2016.3), type:
-
-    module switch intel intel/2016b
-
-**Beware: by default on Star, you are not able to have two conflicting
-modules - f.e. openmpi and impi - loaded at the same time.** This is
-only partially true for these new packages. With the new packages it is
-also more common that when you load one package it will automatically
-load several other packages that it needs to function. We recommend
-doing ml after every load and unloading any conflicting packages.