Rework 16-modules lesson

_episodes/15-modules.md

@@ -94,9 +94,9 @@ message telling you so
 ## Loading and Unloading Software
 
 To load a software module, use `module load`. In this example we will use
-Python 3.
+R.
 
-Initially, Python 3 is not loaded. We can test this by using the `which`
+Initially, R is not loaded. We can test this by using the `which`
 command. `which` looks for programs the same way that Bash does, so we can use
 it to tell us where a particular piece of software is stored.
 
@@ -105,13 +105,13 @@ it to tell us where a particular piece of software is stored.
 ```
 {: .language-bash}
 
-{% include {{ site.snippets }}/modules/missing-python.snip %}
+{% include {{ site.snippets }}/modules/missing-r.snip %}
 
-We can load the `python3` command with `module load`:
+We can load the `R` command with `module load`:
 
-{% include {{ site.snippets }}/modules/module-load-python.snip %}
+{% include {{ site.snippets }}/modules/module-load-r.snip %}
 
-{% include {{ site.snippets }}/modules/python-executable-dir.snip %}
+{% include {{ site.snippets }}/modules/r-executable-dir.snip %}
 
 So, what just happened?
 
@@ -134,14 +134,15 @@ there's only one difference: the different directory at the beginning. When we
 ran the `module load` command, it added a directory to the beginning of our
 `$PATH`. Let's examine what's there:
 
-{% include {{ site.snippets }}/modules/python-ls-dir-command.snip %}
+{% include {{ site.snippets }}/modules/r-ls-dir-command.snip %}
 
-{% include {{ site.snippets }}/modules/python-ls-dir-output.snip %}
+{% include {{ site.snippets }}/modules/r-ls-dir-output.snip %}
 
 Taking this to its conclusion, `module load` will add software to your `$PATH`.
 It "loads" software. A special note on this - depending on which version of the
 `module` program that is installed at your site, `module load` will also load
-required software dependencies.
+required software dependencies. For instance loading the 
+module `lammps/openmpi/intel/20231214` also loads:
 
 {% include {{ site.snippets }}/modules/software-dependencies.snip %}
 
@@ -180,16 +181,16 @@ Let's examine the output of `module avail` more closely.
 
 > ## Using Software Modules in Scripts
 >
-> Create a job that is able to run `python3 --version`. Remember, no software
+> Create a job that is able to run `R --version`. Remember, no software
 > is loaded by default! Running a job is just like logging on to the system
 > (you should not assume a module loaded on the login node is loaded on a
 > compute node).
 >
 > > ## Solution
 > >
 > > ```
-> > {{ site.remote.prompt }} nano python-module.sh
-> > {{ site.remote.prompt }} cat python-module.sh
+> > {{ site.remote.prompt }} nano r-module.sh
+> > {{ site.remote.prompt }} cat r-module.sh
 > > ```
 > > {: .language-bash}
 > >
@@ -199,9 +200,9 @@ Let's examine the output of `module avail` more closely.
 > > {{ site.sched.comment }} {{ site.sched.flag.qos }}
 > > {% endif %}{{ site.sched.comment }} {{ site.sched.flag.time }} 00:00:30
 > > 
-> > module load {{ site.remote.module_python3 }}
+> > module load r/gcc/4.4.0
 > >
-> > python3 --version
+> > R --version
 > > ```
 > > {: .output}
 > >

_includes/snippets_library/NYU_Greene_slurm/modules/missing-r.snip

@@ -0,0 +1,16 @@
+```
+/usr/bin/which: no R in 
+(share/apps/singularity/bin:
+/share/apps/local/bin:
+/home/yourUsername/.local/bin:
+/home/yourUsername/bin:
+/share/apps/singularity/bin:
+/share/apps/local/bin:
+/usr/local/bin:
+/usr/bin:
+/usr/local/sbin:
+/usr/sbin:
+/usr/lpp/mmfs/bin:
+/opt/slurm/bin:)
+```
+{: .output}

_includes/snippets_library/NYU_Greene_slurm/modules/module-load-r.snip

@@ -0,0 +1,5 @@
+```
+{{ site.host_prompt }} module load r/gcc/4.4.0 
+{{ site.host_prompt }} which R
+```
+{: .language-bash}

_includes/snippets_library/NYU_Greene_slurm/modules/python-module-path.snip

@@ -1,10 +1,14 @@
 ```
-/cluster/software/Python/3.8.2-GCCcore-9.3.0/bin:
-/cluster/software/XZ/5.2.5-GCCcore-9.3.0/bin:
-/cluster/software/bzip2/1.0.8-GCCcore-9.3.0/bin:
-/cluster/software/binutils/2.34-GCCcore-9.3.0/bin:
-/cluster/software/GCCcore/9.3.0/bin:/node/bin:/usr/local/bin:
-/usr/bin:/usr/local/sbin:/usr/sbin:/cluster/bin:
-/cluster/home/sabryr/.local/bin:/cluster/home/sabryr/bin
+/share/apps/r/4.4.0/gcc/bin:
+/share/apps/singularity/bin:
+/share/apps/local/bin:
+/home/yourUsername/.local/bin:
+/home/yourUsername/bin:
+/usr/local/bin:
+/usr/bin:
+/usr/local/sbin:
+/usr/sbin:
+/usr/lpp/mmfs/bin:
+/opt/slurm/bin:
 ```
 {: .output}

_includes/snippets_library/NYU_Greene_slurm/modules/r-executable-dir.snip

@@ -0,0 +1,4 @@
+```
+/share/apps/r/4.4.0/gcc/bin/R
+```
+{: .output}

_includes/snippets_library/NYU_Greene_slurm/modules/r-ls-dir-command.snip

@@ -0,0 +1,4 @@
+```
+{{ site.host_prompt }} ls /share/apps/r/4.4.0/gcc/bin
+```
+{: .language-bash}

_includes/snippets_library/NYU_Greene_slurm/modules/r-ls-dir-output.snip

@@ -0,0 +1,4 @@
+```
+ R  Rscript  __run_base.bash
+```
+{: .output}

_includes/snippets_library/NYU_Greene_slurm/modules/software-dependencies.snip

@@ -6,69 +6,40 @@ software modules.
 ```
 {: .language-bash}
 ```
-
-Currently Loaded Modules:
-  1) StdEnv                     (S)      6) libreadline/8.0-GCCcore-8.2.0 (H)
-  2) GCCcore/8.2.0                       7) XZ/5.2.4-GCCcore-8.2.0        (H)
-  3) bzip2/1.0.6-GCCcore-8.2.0  (H)      8) GMP/6.1.2-GCCcore-8.2.0       (H)
-  4) zlib/1.2.11-GCCcore-8.2.0  (H)      9) libffi/3.2.1-GCCcore-8.2.0    (H)
-  5) ncurses/6.1-GCCcore-8.2.0  (H)     10) Python/3.7.2-GCCcore-8.2.0
-
-  Where:
-   S:  Module is Sticky, requires --force to unload or purge
-   H:             Hidden Module
-
+No modules loaded
 ```
 {: .output}
 
 ```
-{{ site.host_prompt }} module load Beast/2.5.2-GCC-8.2.0-2.31.1
+{{ site.host_prompt }} module load lammps/openmpi/intel/20231214
 {{ site.host_prompt }} module list
 ```
 {: .language-bash}
 
 ```
+
 Currently Loaded Modules:
-  1) StdEnv                        (S)   9) libffi/3.2.1-GCCcore-8.2.0
-  2) GCCcore/8.2.0                      10) Python/3.7.2-GCCcore-8.2.0
-  3) bzip2/1.0.6-GCCcore-8.2.0     (H)  11) binutils/2.31.1-GCCcore-8.2.0
-  4) zlib/1.2.11-GCCcore-8.2.0     (H)  12) GCC/8.2.0-2.31.1
-  5) ncurses/6.1-GCCcore-8.2.0     (H)  13) Java/11.0.2
-  6) libreadline/8.0-GCCcore-8.2.0 (H)  14) beagle-lib/3.1.2-GCC-8.2.0-2.31.1
-  7) XZ/5.2.4-GCCcore-8.2.0        (H)  15) Beast/2.5.2-GCC-8.2.0-2.31.1
-  8) GMP/6.1.2-GCCcore-8.2.0       (H)
+  1) szip/intel/2.1.1               5) gsl/intel/2.6              9) python/intel/3.8.6
+  2) hdf5/intel/1.12.0              6) openmpi/intel/4.0.5       10) boost/intel/1.74.0
+  3) netcdf-c/intel/4.7.4           7) fftw/openmpi/intel/3.3.9  11) plumed/openmpi/intel/2.8.3
+  4) pnetcdf/openmpi/intel/1.12.1   8) intel/19.1.2              12) lammps/openmpi/intel/20231214
 
-  Where:
-   S:  Module is Sticky, requires --force to unload or purge
-   H:             Hidden Module
 
 ```
 {: .output}
 
-So in this case, loading the `beast` module (a bioinformatics software
-package), also loaded `Java/11.0.2` and `beagle-lib/3.1.2-GCC-8.2.0-2.31.1` as
-well. Let's try unloading the `beast` package.
+So in this case, loading the `lammps` module (a molecular dynamics
+software package), also loaded 11 other modules as well. Let's try 
+unloading the `lammps` package.
 
 ```
-{{ site.host_prompt }} module unload Beast/2.5.2-GCC-8.2.0-2.31.1
+{{ site.host_prompt }} module unload lammps/openmpi/intel/20231214
 {{ site.host_prompt }} module list
 ```
 {: .language-bash}
 
 ```
-Currently Loaded Modules:
-  1) StdEnv                        (S)   8) GMP/6.1.2-GCCcore-8.2.0       (H)
-  2) GCCcore/8.2.0                       9) libffi/3.2.1-GCCcore-8.2.0    (H)
-  3) bzip2/1.0.6-GCCcore-8.2.0     (H)  10) Python/3.7.2-GCCcore-8.2.0
-  4) zlib/1.2.11-GCCcore-8.2.0     (H)  11) binutils/2.31.1-GCCcore-8.2.0 (H)
-  5) ncurses/6.1-GCCcore-8.2.0     (H)  12) GCC/8.2.0-2.31.1
-  6) libreadline/8.0-GCCcore-8.2.0 (H)  13) Java/11.0.2
-  7) XZ/5.2.4-GCCcore-8.2.0        (H)  14) beagle-lib/3.1.2-GCC-8.2.0-2.31.1
-
-  Where:
-   S:  Module is Sticky, requires --force to unload or purge
-   H:             Hidden Module
-
+No modules loaded
 ```
 {: .output}
 
@@ -81,13 +52,6 @@ everything).
 ```
 {: .language-bash}
 ```
-The following modules were not unloaded:
-  (Use "module --force purge" to unload all):
-
-  1) StdEnv
+No modules loaded
 ```
 {: .output}
-
-Note that `module purge` is informative. It lets us know that all but a default
-set of packages have been unloaded (and how to actually unload these if we
-truly so desired).

_includes/snippets_library/NYU_Greene_slurm/modules/wrong-nextflow-version.snip

@@ -0,0 +1,37 @@
+Let's take a closer look at the `nextflow` module. Nextflow is a scientific 
+workflow system predominantly used for bioinformatic data analysis
+In this case, we have:
+
+```
+   nextflow/20.07.1    nextflow/20.11.0-edge    nextflow/21.10.5    nextflow/23.04.1
+   nextflow/20.10.0    nextflow/21.04.3         nextflow/21.10.6    nextflow/24.04.3
+```
+{: .language-bash}
+
+How do we load each copy and which copy is the default?
+
+```
+{{ site.host_prompt }} module load Nextflow
+```
+{: .language-bash}
+
+```
+Lmod has detected the following error:  The following module(s) are unknown: "Nextflow"
+
+Please check the spelling or version number. Also try "module spider ..."
+It is also possible your cache file is out-of-date; it may help to try:
+  $ module --ignore-cache load "Nextflow"
+
+Also make sure that all modulefiles written in TCL start with the string #%Module
+
+
+```
+{: .output}
+
+To load a software module we must specify the full module name:
+
+```
+{{ site.host_prompt }} module load nextflow/24.04.3
+{{ site.host_prompt }} nextflow -version
+```
+{: .language-bash}