Removed some TODOs to complete the tutorial.

Author: klust

docs/2022-CSC_and_LO/1_Intro/1_01_what_is_easybuild.md

@@ -103,16 +103,14 @@ cannot easily overwrite those.
 
 In addition to performance, **reproducibility of installations** is a core aspect of EasyBuild.
 
-TODO correct link in the next lines.
-
-Most software installations performed with EasyBuild use a **particular compiler <a href="#toolchains">toolchain</a>**,
+Most software installations performed with EasyBuild use a **particular compiler <a href="../1_05_terminology#toolchains">toolchain</a>**,
 with which we aim to be in control over the build environment and avoid relying on tools and libraries
 provided by the operating system. For similar reasons, we try to **provide all required dependencies through EasyBuild** as well,
 with a few notable exceptions, like ``OpenSSL`` for security reasons, and Infiniband and GPU drivers which
 are too closely intertwined with the operating system.
 
 For both toolchains and dependencies, **fixed software versions** are specified in the
-<a href="#easyconfig-files">easyconfig files</a>. That way, easyconfig files can easily be shared with others:
+<a href="../1_05_terminology#easyconfig-files">easyconfig files</a>. That way, easyconfig files can easily be shared with others:
 if they worked for you it is very likely that they will work for others too, because the vast majority of the
 software stack is controlled by EasyBuild.
 

docs/2022-CSC_and_LO/1_Intro/1_04_LUMI_software_stack.md

@@ -15,7 +15,34 @@ On this page we focus more on the technical implementation behind it.
 LUMI has different node types providing compute resources:
 
 -   LUMI has 16 login nodes, though many of those are reserved for special purposes and not
-    available to all users. TODO
+    available to all users. These login nodes have a zen2 CPU. These nodes have a SlingShot 10
+    interconnect.
+-   There are 1536 regular CPU compute nodes in a partition denoted as LUMI-C. These
+    compute nodes have a zen3 CPU and run a reduced version of SUSE Linux optimised
+    by Cray to reduce OS jitter. These nodes will in the future be equipped with a 
+    SlingShot 11 interconnect card.
+-   There are 2560 GPU compute nodes in a partition denoted as LUMI-G. These nodes have
+    a single zen3-based CPU with optimised I/O die linked to 4 AMD MI250X GPUs. Each node
+    has 4 SlingShot 11 interconnect cards, one attached to each GPU.
+-   The interactive data analytics and visualisation partition is really two different partitions 
+    from the software point-of-view:
+    -   8 nodes are CPU-only but differ considerably from the regular compute nodes,
+        not only in the amount of memory. These nodes are equipped with zen2 CPUs
+        and in that sense comparable to the login nodes. They also have local SSDs
+        and are equipped with SlingShot 10 interconnect cards (2 each???)
+    -   8 nodes have zen2 CPUs and 8 NVIDIA A40 GPUs each, and have 2 SlingShot 10
+        interconnect cards each.
+-   The early access platform (EAP) has 14 nodes equiped with a single 64-core
+    zen2 CPU and 4 AMD MI100 GPUS. Each node has a single SlingShot 10 interconnect
+    and also local SSDs.
+
+SlingShot 10 and SlingShot 11 are different software-wise. SlingShot 10 uses a
+Mellanox CX5 NIC that support both OFI and UCX, and hence can also use the
+UCX version of Cray MPICH. SlingShot 11 uses a NIC code-named Cassini and
+supports only OFI with an OFI provider specific for the Cassini NIC. However,
+given that the nodes that are equipped with SlingShot 10 cards are not meant
+to be used for big MPI jobs, we build our software stack solely on top of 
+libfabric and Cray MPICH.
 
 
 ---
@@ -46,7 +73,9 @@ On LUMI, two types of software stacks are currently offered:
     A deliberate choice was made to only offer a limited number of software
     packages in the globally installed stack as the setup of redundancy on LUMI
     makes it difficult to update the stack in a way that is guaranteed to not
-    affect running jobs and as a large central stack is also hard to manage.
+    affect running jobs and as a large central stack is also hard to manage, especially
+    as we expect frequent updates to the OS and compiler infrastructure in 
+    the first years of operation.
     However, the EasyBuild setup is such that users can easily install
     additional software in their home or project directory using EasyBuild build
     recipes that we provide or they develop, and that software will fully
@@ -72,12 +101,13 @@ set of target modules after loading the ``CrayEnv`` module.
 The ``LUMI`` module currently supports four partition modules, but that number may
 be reduced in the future:
 
-| Partition       | CPU target            | Accelerator                 |
-|:----------------|-----------------------|:----------------------------|
-| ``partition/L`` | ``craype-x86-rome``   | ``craype-accel-host``       |
-| ``partition/C`` | ``craype-x86-milan``  | ``craype-accel-host``       |
-| ``partition/G`` | ``craype-x86-trento`` | ``craype-accel-amd-gfx90a`` |
-| ``partition/D`` | ``craype-x86-rome``   | ``craype-accel-nvidia80``   |
+| Partition         | CPU target            | Accelerator                 |
+|:------------------|-----------------------|:----------------------------|
+| ``partition/L``   | ``craype-x86-rome``   | ``craype-accel-host``       |
+| ``partition/C``   | ``craype-x86-milan``  | ``craype-accel-host``       |
+| ``partition/G``   | ``craype-x86-trento`` | ``craype-accel-amd-gfx90a`` |
+| ``partition/D``   | ``craype-x86-rome``   | ``craype-accel-nvidia80``   |
+| ``partition/EAP`` | ``craype-x86-rome``   | ``craype-accel-amd-gfx908`` |
 
 All ``partition`` modules also load `craype-network-ofi``.
 

docs/2022-CSC_and_LO/1_Intro/1_06_installation.md

@@ -417,23 +417,20 @@ export EB_PYTHON=python3
 To keep the different versions of the LUMI software stack as independent from one another as possible,
 EasyBuild is bootstrapped for each software stack by the ``prepare_LUMI_stack.sh`` script. We use the 
 system Python 3 for running EasyBuild. That Python version currently doesn't have ``pip`` installed. 
+Our procedure is based on the ["Installing EasyBuild with EasyBuild" procedure](#method-2-installing-easybuild-with-easybuild)
+but works around the lack of `pip`. 
 EasyBuild is first installed in a temporary work directory from files downloaded from PyPi. These
 are each untarred and then installed into their location by running 
 ``python3 setup.py install --prefix=...`` in their unpacked directory.
 We do so only for the framework and easyblocks files as the easconfig files are not used to
 install EasyBuild. Instead we create our own EasyConfig file for EasyBuild which contains
 some additional packages that enable extra features in EasyBuild and also provide more information
 to Lmod. Next the configuration module for EasyBuild (see the next section, 
-["Configuring EasyBuild"](1_07_configuration), for more information) and use the temporary 
+["Configuring EasyBuild"](../1_07_configuration), for more information) and use the temporary 
 installation of EasyBuild with our own EasyConfig file to do a proper installation of EasyBuild
 with module in the final location.
 
 
-TODO: follow development setup but with downloading rather than cloning, then use that one with the
-EasyBuild configuration module to install EasyBuild with itself.
-
-
-
 ## Verifying the installation
 
 Regardless of how EasyBuild was installed, you can now run a couple of basic commands to verify the installation:
@@ -447,7 +444,8 @@ To check which EasyBuild version you have installed, run:
 eb --version
 ```
 
-The output should match with the <a href="https://pypi.org/project/easybuild/">latest EasyBuild version</a>.
+The latest version (and an overview of previous versions) can always be 
+[found on PyPi](https://pypi.org/project/easybuild/).
 
 
 #### Consulting the help output

docs/2022-CSC_and_LO/1_Intro/1_08_basic_usage.md

@@ -965,7 +965,6 @@ won't go into those here).
 
 ## Exercises
 
-TODO: Rework for LUMI and provide the necessary EasyConfig files.
 
 ***Guidelines***