parsed mds by for chatbot parser script for account.md, connecting.md, compiling_your_software.md (FOR REVIEW ONLY, NO MERGE!)

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_1.txt

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+Getting an HPC Account
+Getting ready to request an account
+All users of AUGent can request
+an
+account on the HPC, which is part of the Flemish Supercomputing Centre (VSC).
+See HPC policies for more information on who is entitled to an account.
+The VSC, abbreviation of Flemish Supercomputer Centre, is a virtual
+supercomputer centre. It is a partnership between the five Flemish
+associations: the Association KU Leuven, Ghent University Association,
+Brussels University Association, Antwerp University Association and the
+University Colleges-Limburg. The VSC is funded by the Flemish
+Government.
+There are two methods for connecting to HPC-UGent infrastructure:
+- Using a terminal to connect via SSH.
+- Using the web portal

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_10.txt

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+After you have uploaded your public key you will receive an e-mail with
+a link to confirm your e-mail address. After confirming your e-mail
+address the VSC staff will review and if applicable approve your
+account.
+Welcome e-mail
+Within one day, you should receive a Welcome e-mail with your VSC
+account details.
+Dear (Username), 
+Your VSC-account has been approved by an administrator.
+Your vsc-username is vsc40000
+Your account should be fully active within one hour.
+To check or update your account information please visit
+https://account.vscentrum.be/
+For further info please visit https://www.vscentrum.be/user-portal
+Kind regards,
+-- The VSC administrators
+Now, you can start using the HPC. You can always look up your VSC id later
+by visiting <https://account.vscentrum.be>.

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_10_metadata.json

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+{
+    "main_title": "account",
+    "subtitle": "Welcome-e-mail",
+    "source_file": "../../mkdocs/docs/HPC/account.md",
+    "title_depth": 3,
+    "directory": "account",
+    "parent_title": "",
+    "previous_title": "account_paragraph_9",
+    "next_title": "account_paragraph_11",
+    "OS": "generic",
+    "reference_link": "https://docs.hpc.ugent.be/account/#welcome-e-mail"
+}

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_12.txt

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+Computation Workflow on the HPC
+A typical Computation workflow will be:
+1.  Connect to the HPC
+2.  Transfer your files to the HPC
+3.  Compile your code and test it
+4.  Create a job script
+5.  Submit your job
+6.  Wait while
+    1.  your job gets into the queue
+    2.  your job gets executed
+    3.  your job finishes
+7.  Move your results
+We'll take you through the different tasks one by one in the following
+chapters.

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_12_metadata.json

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+{
+    "main_title": "account",
+    "subtitle": "Computation-Workflow-on-the-HPC",
+    "source_file": "../../mkdocs/docs/HPC/account.md",
+    "title_depth": 2,
+    "directory": "account",
+    "parent_title": "",
+    "previous_title": "account_paragraph_11",
+    "next_title": null,
+    "OS": "generic",
+    "reference_link": "https://docs.hpc.ugent.be/account/#computation-workflow-on-the-hpc"
+}

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_1_metadata.json

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+{
+    "main_title": "account",
+    "subtitle": "Getting-ready-to-request-an-account",
+    "source_file": "../../mkdocs/docs/HPC/account.md",
+    "title_depth": 2,
+    "directory": "account",
+    "links": {
+        "0": "https://docs.hpc.ugent.be/sites/hpc_policies",
+        "1": "https://docs.hpc.ugent.be/web_portal"
+    },
+    "parent_title": "",
+    "previous_title": null,
+    "next_title": "account_paragraph_2",
+    "OS": "generic",
+    "reference_link": "https://docs.hpc.ugent.be/account/#getting-ready-to-request-an-account"
+}

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_2.txt

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+The web portal offers a convenient way to upload files and gain shell access to the HPC-UGent infrastructure from a standard web browser (no software installation or configuration required).
+If you would like use a terminal with SSH as this gives you more flexibility continue reading.
+However if you prefer to use the web portal, you can skip ahead to the following section: Applying for the account.
+Once you have successfully obtained an account, you can then delve into the details of utilizing the HPC-UGent web portal by reading Using the HPC-UGent web portal.
+The HPC-UGent infrastructure clusters use public/private key pairs for user authentication
+(rather than passwords). Technically, the private key is stored on your
+local computer and always stays there; the public key is stored on the HPC.
+Access to the HPC is granted to anyone who can prove to have access to the
+corresponding private key on his local computer.

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_2_metadata.json

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+{
+    "main_title": "account",
+    "subtitle": "Getting-ready-to-request-an-account",
+    "source_file": "../../mkdocs/docs/HPC/account.md",
+    "title_depth": 2,
+    "directory": "account",
+    "links": {
+        "0": "https://docs.hpc.ugent.be/account/#applying-for-the-account",
+        "1": "https://docs.hpc.ugent.be/web_portal"
+    },
+    "parent_title": "",
+    "previous_title": "account_paragraph_1",
+    "next_title": "account_paragraph_3",
+    "OS": "generic",
+    "reference_link": "https://docs.hpc.ugent.be/account/#getting-ready-to-request-an-account"
+}

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_3.txt

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+How do SSH keys work?
+-   an SSH public/private key pair can be seen as a lock and a key
+-   the SSH public key is equivalent with a lock: you give it to the
+    VSC and they put it on the door that gives access to your account.
+-   the SSH private key is like a physical key: you don't hand it out
+    to other people.
+-   anyone who has the key (and the optional password) can unlock the
+    door and log in to the account.
+-   the door to your VSC account is special: it can have multiple
+    locks (SSH public keys) attached to it, and you only need to open
+    one lock with the corresponding key (SSH private key) to open
+    the door (log in to the account).
+Since all VSC clusters use Linux as their main operating system, you
+will need to get acquainted with using the command-line interface and
+using the terminal (see tutorial).

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_3_metadata.json

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+{
+    "main_title": "account",
+    "subtitle": "How-do-SSH-keys-work",
+    "source_file": "../../mkdocs/docs/HPC/account.md",
+    "title_depth": 3,
+    "directory": "account",
+    "links": {
+        "0": "https://docs.hpc.ugent.be/linux-tutorial"
+    },
+    "parent_title": "",
+    "previous_title": "account_paragraph_2",
+    "next_title": "account_paragraph_4",
+    "OS": "generic",
+    "reference_link": "https://docs.hpc.ugent.be/account/#how-do-ssh-keys-work"
+}

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_8.txt

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+Applying for the account
+Visit <https://account.vscentrum.be/>
+You will be redirected to our WAYF (Where Are You From) service where
+you have to select your "Home Organisation".
+Select "UGent" in the dropdown box and optionally select "Save my preference"
+and "permanently".
+Click "Confirm"
+You will now be taken to the authentication page of your institute.
+You will now have to log in with CAS using your UGent account.
+You either have a login name of maximum 8 characters, or a (non-UGent)
+email address if you are an external user. In case of problems with your
+UGent password, please visit: <https://password.ugent.be/>. After
+logging in, you may be requested to share your information. Click "Yes,
+continue".

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/account/account_paragraph_8_metadata.json

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+{
+    "main_title": "account",
+    "subtitle": "Applying-for-the-account",
+    "source_file": "../../mkdocs/docs/HPC/account.md",
+    "title_depth": 2,
+    "directory": "account",
+    "parent_title": "",
+    "previous_title": "account_paragraph_7",
+    "next_title": "account_paragraph_9",
+    "OS": "generic",
+    "reference_link": "https://docs.hpc.ugent.be/account/#applying-for-the-account"
+}

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_1.txt

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+Compiling and testing your software on the HPC
+All nodes in the HPC cluster are running the "RHEL 8.8 (accelgor, doduo, donphan, gallade, joltik, skitty)" 
+Operating system, which is a specific version of Red Hat Enterprise Linux. This means that all the 
+software programs
+(executable) that the end-user wants to run on the HPC first must be
+compiled for RHEL 8.8 (accelgor, doduo, donphan, gallade, joltik, skitty). It also means that you first have to install all the
+required external software packages on the HPC.
+Most commonly used compilers are already pre-installed on the HPC and can be
+used straight away. Also, many popular external software packages, which
+are regularly used in the scientific community, are also pre-installed.

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_10.txt

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+The "mpi_hello.c" program is a simple source file, written in C with MPI
+library calls.
+Then, check the command line options for *"mpicc" (GNU C-Compiler with
+MPI extensions)*, then we compile and list the contents of the directory
+again:
+mpicc --help
+mpicc -o mpihello mpihello.c
+ls -l
+A new file "hello" has been created. Note that this program has
+"execute" rights.
+Let's test this program on the "login" node first:
+$ ./mpihello
+Hello World from Node 0.
+It seems to work, now run it on the HPC.
+qsub mpihello.pbs
+Compiling a parallel program in Intel Parallel Studio Cluster Edition
+We will now compile the same program, but using the Intel Parallel
+Studio Cluster Edition compilers. We stay in the examples directory for
+this chapter:

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_10_metadata.json

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+{
+    "main_title": "compiling_your_software",
+    "subtitle": "Compiling-a-parallel-program-in-Intel-Parallel-Studio-Cluster-Edition",
+    "title_depth": 3,
+    "directory": "compiling_your_software",
+    "parent_title": "",
+    "previous_title": "compiling_your_software_paragraph_9",
+    "next_title": "compiling_your_software_paragraph_11",
+    "OS": "generic",
+    "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-a-parallel-program-in-intel-parallel-studio-cluster-edition"
+}

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_11.txt

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+cd ~/examples/Compiling-and-testing-your-software-on-the-HPC
+We will compile this C/MPI -file into an executable with the Intel
+Parallel Studio Cluster Edition. First, clear the modules (purge) and
+then load the latest "intel" module:
+module purge
+module load intel
+Then, compile and list the contents of the directory again. The Intel
+equivalent of mpicc is mpiicc.
+mpiicc -o mpihello mpihello.c
+ls -l
+Note that the old "mpihello" file has been overwritten. Let's test this
+program on the "login" node first:
+$ ./mpihello
+Hello World from Node 0.
+It seems to work, now run it on the HPC.
+qsub mpihello.pbs
+Note: The AUGent only has a license for the Intel Parallel Studio Cluster
+Edition for a fixed number of users. As such, it might happen that you
+have to wait a few minutes before a floating license becomes available
+for your use.

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_11_metadata.json

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+{
+    "main_title": "compiling_your_software",
+    "subtitle": "Compiling-a-parallel-program-in-Intel-Parallel-Studio-Cluster-Edition",
+    "title_depth": 3,
+    "directory": "compiling_your_software",
+    "parent_title": "",
+    "previous_title": "compiling_your_software_paragraph_10",
+    "next_title": "compiling_your_software_paragraph_12",
+    "OS": "generic",
+    "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-a-parallel-program-in-intel-parallel-studio-cluster-edition"
+}

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_12.txt

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+Note: The Intel Parallel Studio Cluster Edition contains equivalent
+compilers for all GNU compilers. Hereafter the overview for C, C++ and
+Fortran compilers.
+|             | Sequential Program |           | **Parallel Program (with MPI)** |           |
+|-------------|------------------------|-----------|---------------------------------|-----------|
+|             | GNU                | Intel | GNU                         | Intel |
+| C       | gcc                    | icc       | mpicc                           | mpiicc    |
+| **C++**     | g++                    | icpc      | mpicxx                          | mpiicpc   |
+| Fortran | gfortran               | ifort     | mpif90                          | mpiifort  |

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_12_metadata.json

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+{
+    "main_title": "compiling_your_software",
+    "subtitle": "Compiling-a-parallel-program-in-Intel-Parallel-Studio-Cluster-Edition",
+    "title_depth": 3,
+    "directory": "compiling_your_software",
+    "parent_title": "",
+    "previous_title": "compiling_your_software_paragraph_11",
+    "next_title": null,
+    "OS": "generic",
+    "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-a-parallel-program-in-intel-parallel-studio-cluster-edition"
+}

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_1_metadata.json

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+{
+    "main_title": "compiling_your_software",
+    "subtitle": "Compiling-and-testing-your-software-on-the-HPC",
+    "title_depth": 1,
+    "directory": "compiling_your_software",
+    "parent_title": "",
+    "previous_title": null,
+    "next_title": "compiling_your_software_paragraph_2",
+    "OS": "generic",
+    "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-and-testing-your-software-on-the-hpc"
+}

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_2.txt

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+Check the pre-installed software on the HPC
+In order to check all the available modules and their version numbers,
+which are pre-installed on the HPC enter:
+When your required application is not available on the HPC please contact
+any HPC member. Be aware of potential "License Costs". "Open Source"
+software is often preferred.
+Porting your code
+To port a software-program is to translate it from the operating system in
+which it was developed (e.g., Windows 7) to another operating system
+(e.g., Red Hat Enterprise Linux on our HPC) so that it can be used there. Porting implies some
+degree of effort, but not nearly as much as redeveloping the program in
+the new environment. It all depends on how "portable" you wrote your
+code.

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_2_metadata.json

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+{
+    "main_title": "compiling_your_software",
+    "subtitle": "Porting-your-code",
+    "title_depth": 2,
+    "directory": "compiling_your_software",
+    "parent_title": "",
+    "previous_title": "compiling_your_software_paragraph_1",
+    "next_title": "compiling_your_software_paragraph_3",
+    "OS": "generic",
+    "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#porting-your-code"
+}

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_3.txt

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+In the simplest case the file or files may simply be copied from one
+machine to the other. However, in many cases the software is installed
+on a computer in a way, which depends upon its detailed hardware,
+software, and setup, with device drivers for particular devices, using
+installed operating system and supporting software components, and using
+different directories.
+In some cases software, usually described as "portable software" is
+specifically designed to run on different computers with compatible
+operating systems and processors without any machine-dependent
+installation; it is sufficient to transfer specified directories and
+their contents. Hardware- and software-specific information is often
+stored in configuration files in specified locations (e.g., the registry
+on machines running MS Windows).

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_3_metadata.json

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+{
+    "main_title": "compiling_your_software",
+    "subtitle": "Porting-your-code",
+    "title_depth": 2,
+    "directory": "compiling_your_software",
+    "parent_title": "",
+    "previous_title": "compiling_your_software_paragraph_2",
+    "next_title": "compiling_your_software_paragraph_4",
+    "OS": "generic",
+    "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#porting-your-code"
+}

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_4.txt

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+Software, which is not portable in this sense, will have to be
+transferred with modifications to support the environment on the
+destination machine.
+Whilst programming, it would be wise to stick to certain standards
+(e.g., ISO/ANSI/POSIX). This will ease the porting of your code to other
+platforms.
+Porting your code to the RHEL 8.8 (accelgor, doduo, donphan, gallade, joltik, skitty) platform is the responsibility of the end-user.
+Compiling and building on the HPC
+Compiling refers to the process of translating code written in some
+programming language, e.g., Fortran, C, or C++, to machine code.
+Building is similar, but includes gluing together the machine code
+resulting from different source files into an executable (or library).
+The text below guides you through some basic problems typical for small
+software projects. For larger projects it is more appropriate to use
+makefiles or even an advanced build system like CMake.

scripts/HPC_chatbot_preprocessor/parsed_mds/generic/compiling_your_software/compiling_your_software_paragraph_4_metadata.json

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+{
+    "main_title": "compiling_your_software",
+    "subtitle": "Compiling-and-building-on-the-HPC",
+    "title_depth": 2,
+    "directory": "compiling_your_software",
+    "parent_title": "",
+    "previous_title": "compiling_your_software_paragraph_3",
+    "next_title": "compiling_your_software_paragraph_5",
+    "OS": "generic",
+    "reference_link": "https://docs.hpc.ugent.be/compiling_your_software/#compiling-and-building-on-the-hpc"
+}