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Gensys-2601

Installation of virtual machine "Mint223-gensys26"

Only the necessary steps in the below list needs to be done:
1) Can be skipped if you have VirtualBox 7.2.6 or newer already installed on your computer.
2) Can be skipped if you don't want to update the documentation and the verification examples.

TOC:

1. Install and configure VirtualBox
   
2. Download and uncompress the documentation and the verification examples in the Shared Folder
   
3. Download and install the Virtual Machine
   
4. After the installation
   

1. Install and configure VirtualBox:
   If you are missing VirtualBox or if your VirtualBox-version is older than 7.2.6, it is necessary to do these steps:
   1. Make sure your machine is equipped with a 64-bits processor.
      Primary memory > 16 GB
      Free hard disk space at least 20 GB
      (If you create files inside the virtual machine its size will grow. It is therefore recommended to save all results in a folder shared with the host. How to create a shared folder is described further down under item Activate Shared Folders)
      Restart your machine and check in your BIOS that Virtualization Technology is enabled.
      Information on how to adjust BIOS-settings can be found here: wikihow or lifewire
   2. If necessary, uninstall the old VirtualBox-version.
   3. Download and install the new version of VirtualBox.
      (When running the installer you maybe will get a message: Missing dependencies Python Core package and win32api bindings. However it is not necessary to install these two packages, unless you don't plan to use Python scripts with VirtualBox)
   4. Create a Folder on your harddrive where you want to keep your Virtual Machines.
   5. Start program VirtualBox
   6. In the PullDown-menu of program VirtualBox click "File -> Preferences" and do the following
      
      1. Specify the location of your virtual machines
         On the left side select "General"
         On the right side under "Default Machine Folder"
         Specify the path to the directory where you are want to save your virtual machines
      2. Change Host Key Combination
         Select "Expert" in the upper left
         On the left side select "Input"
         On the right side select "Virtual Machine"
         As default in VirtualBox "Host Key Combination" is set equal to Right CTRL. If you wish to be able to use your "Right CTRL"-Key, please choose another key. (The "Host Key Combination" is mainly useful in case you don't have a working mouse, and when you want to leave full screen mode)
         
      Finish by clicking "OK"

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2. Download and uncompress the documentation and the verification examples in the Shared Folder
   In this step you will create the following directories: free_models, homepage and verif.
   N.B. If you have old versions of these directories, please remove/rename them before continuing with the installation.
   1. Create a directory where you want to keep Gensys documentation files, verification examples and your own workfiles. The directory must have permissions so it can be used as a Shared Folder with the virtual machine.
      E.g.: "C:\Users\Public\gensys" on a Windows-host. "$HOME/gensys" on a UNIX-host.
   2. In the above created directory. Create an empty directory "analyse", in where you can keep your work files.
      I.e.: "C:\Users\Public\gensys\analyse" on a Windows-host. "$HOME/gensys/analyse" on a UNIX-host.
   3. Download the following files:

      free_models-2601.7z = Free vehicle models
      homepage-2601.7z    = Documentation and tutorials
      verif-2601.7z       = Verification directory
      

      Webpage mega.nz requires a webbrowser that handles HTML5 and allows JavaScript to create and write to files. Currently Chrome and Firefox works best.
      Also make sure that no firewall prevents you from downloading files from the Internet.
      
      The SHA256 message digest algorithm should give you the following output:

      b13e7d25f35198c9d906bdb92b3d80a934ba4f87000c99f52d5a7d80921ebdba  free_models-2601.7z
      0fefc2d36c849d9c63fd397fd6afd486f5ca7dccea0ec0f96d04d3f344addf41  homepage-2601.7z
      b1d79a82d4adbc1ea94efc96c6d55c948f52f92618518b1191ab5a8ba54958fd  verif-2601.7z
      

      The above output can be created with the following commands:
      

      UNIX:	sha256sum [a-z]*7z
      Windows:	certutil.exe -hashfile free_models-2601.7z SHA256 certutil.exe -hashfile homepage-2601.7z SHA256 certutil.exe -hashfile verif-2601.7z SHA256

   4. Move the downloaded files to your Shared Folder (E.g. C:\Users\Public\gensys" or "$HOME/gensys"). Uncompress the files in your host computer:
      
      After 7-zipped files have been unzipped your directory should look as follows:
      
   5. The files: free_models-2601.7z, homepage-2601.7z and verif-2601.7z can now be removed.

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3. Download and install the Virtual Machine:
   Download the following 7 files:

    Mint223-gensys26.7z.001
    Mint223-gensys26.7z.002
    Mint223-gensys26.7z.003
    Mint223-gensys26.7z.004
    Mint223-gensys26.7z.005
    Mint223-gensys26.7z.006
    Mint223-gensys26.7z.007
   

   N.B webpage mega.nz requires a webbrowser that handles HTML5 and allows JavaScript to write files. Currently Chrome and Firefox works best.
   Also make sure that no firewall prevents you from downloading files from the Internet.
   
   The SHA256 message digest algorithm should give you the following output:

   5fd747053d517a6af4a5ec90a6fa6a3b921b21c8491ca26bd989157ad2566fa0  Mint223-gensys26.7z.001
   d6913af0122d9d651a16b188d8359f7edea9793251fae92a1e7ab9289990f91d  Mint223-gensys26.7z.002
   207ed16ff9102be7ad3c4c3573a4d89ef1f1af54c4798def92b891c280be915e  Mint223-gensys26.7z.003
   e4289772ba3c2f92385f0950b6e781165c54187950f2419dcbc20e850adc841b  Mint223-gensys26.7z.004
   e0025cd1f77bed40e36ec9200a78263af5c72be88a3d884cdde0c4765b25ce0f  Mint223-gensys26.7z.005
   ceda9fd5cd57d4e441cd61eb06518c01123906abdbe1ea8ed41fac01c6329ba8  Mint223-gensys26.7z.006
   363bd89af923b26d16c9d050fabc580c2ce6b7ed12640192ed0f295629551ada  Mint223-gensys26.7z.007
   

   The above table can be obtained with the following command(s):

   UNIX:	sha256sum Mint223-gensys26.7z.00?
   Windows:	certutil.exe -hashfile Mint223-gensys26.7z.001 SHA256 certutil.exe -hashfile Mint223-gensys26.7z.002 SHA256 certutil.exe -hashfile Mint223-gensys26.7z.003 SHA256 certutil.exe -hashfile Mint223-gensys26.7z.004 SHA256 certutil.exe -hashfile Mint223-gensys26.7z.005 SHA256 certutil.exe -hashfile Mint223-gensys26.7z.006 SHA256 certutil.exe -hashfile Mint223-gensys26.7z.007 SHA256

4. Contact info@gensys.se to get a link to a valid license file for your installation.
5. Create a directory for your virtual machines.
   If you are installing a virtual machine for the very first time. Please create a directory to store your virtual machines in. E.g.: "C:\Users\Public\VirtualBox_VMs" on a Windows-host or "$HOME/VirtualBox_VMs" on a UNIX-host.
6. Uncompress the file archive.
   Download and install a program that handles multiple archive files. E.g. this program: www.7-zip.org/download.html)
   After program 7-zip has been installed:
   
   • Launch program "7-zip File Manager"
   • Go to the directory where you will store your files E.g.: "C:\Users\Public\VirtualBox_VMs" on a Windows-host or "$HOME/VirtualBox_VMs" on a UNIX-host.
   • Mark file "Mint223-gensys26.7z.001"
   • Click "Extract"
   
   
   When unzipping the 7-zipped files, uncheck the checkbox under the "Extract to:"-address, otherwise the zipped files will not be extracted to the correct location. E.g.:
   After the virtual machine has been extracted, the files "Mint223-gensys26.7z.00[1-7]" can be removed.
   
7. Setup the virtual machine.
   Go to the newly created directory "Mint223-gensys26". Start VirtualBox by double-clicking the file "Mint223-gensys26.vbox". (If you cannot see the extensions of the file. Click "Options" -> "View" and uncheck "Hide extensions for known file types")
   
   Program VirtualBox will now start.
   To the left in the VirtualBox-window, mark virtual machine "Mint223-gensys26" and click "Settings".
   1. Activate "Shared Clipboard" and "Drag'n'Drop"
      On the left side in the popup-window select "General"
      On the right side select "Features"
      Under "Shared Clipboard" choose Bidirectional Under "Drag'n'Drop" choose Bidirectional
   2. Set primary memory
      On the left side in the popup-window select "System"
      On the right side select "Motherboard"
      Choose how much primary memory the virtual machine will have access to with the scale "Base Memory".
      Recommended size is ~4000MB.
      Minimum recommended size is 1280MB.
   3. Set number of processors
      On the left side in the popup-window, select "System"
      On the right side, select "Processor"
      Set number of processor(s) of your machine.
      Valid number of processors are marked in green.
   4. Activate Shared Folders
      There are mainly two reasons why we recommend to create a Shared Folder that is accessable both from the Virtual Machine and the Host Computer:
      • The hard disk of the Virtual Machine is limited to ~90 GB.
      • If a file needs to be copied into a mail or sent to a printer, it is often easier if the host can access the file.
      Setup a "Shared Folder":
      To the left in the Setting popup menu, click "Shared Folders"
      Under "Machine Folders" select "C:\Users\Public\gensys", on a Windows-host, and select "$HOME\gensys", on a UNIX-host.
      Click the middle icon to the right "Edit selected shared folder"
      Edit "Folder Path" in the popup-window, so it points to the location where you want to keep the files shared with the host computer.
      (The location shall be the same as used under Download and uncompress the documentation and the verification examples)
      Do not change "Folder Name", it must be equal to "gensys" otherwise Gensys will not find the location.
      (N.B. The "Folder Name" is case sensitive, all characters must be in lowercase)
      Do not check "Read-only".
      Do not check "Auto-mount".
      Leave text field "Mount point" blank
      Check "Make Permanent" (if the option is visible)
      Click OK
8. In the VirtualBox main window, start the virtual machine by clicking the green arrow marked "Start"
9. If your keyboard layout is something different than English(US)
   
   • Click on the -icon in the lower left corner of the window
   • Select Control Center
   • Select Keybord
   • In the Keybord popup-window. Select the "Layouts"-tab and select your keyboard layout.
10. Install Gensys license file.
    Start webbrowser firefox in the virtual machine. Enter the link mentioned under 3.2) above, and download the file. Save the license file in directory "/opt/gensys/gensys-2601/bin".
    (If you not are using gensys-2601, replace 2601 with the number of your version. You can check your version number with command: grep 'export gensys' ~/.profile_gensys or type tsim )
    
    Add execute permissions to file gen_processor_ID_check:
    

    chmod +x /opt/gensys/gensys-2601/bin/gen_processor_ID_check
    

    Test the search path to the license file with the following command:

    type gen_processor_ID_check
    

    Test the license file with the following command:

    gen_processor_ID_check
    

11. Configure the slurm queue system.
    Open the configuration file: op /etc/slurm/slurm.conf
    Under "NodeName", set number of available processors for each node in the cluster.
    (Number of available processors in your local machine can be seen with command nproc --all)
    If you have many machines in your cluster, command "NodeName" can be given multiple times.
    After the file /etc/slurm/slurm.conf has been updated, restart the slurm queue system with the following commands:
    

    sudo systemctl restart slurmctld
    sudo systemctl restart slurmd
    sudo scontrol update nodename=`hostname` state=resume reason="File /etc/slurm/slurm.conf has been updated"
    

    The password for root is: gensys1
    Check that number of cpus has been updated:
      scontrol show node `hostname` | grep -w cpu
    
    Check that the cpus are in state IDLE:
      scontrol show node `hostname` | grep -w State
    (N.B. The word after State shall be IDLE only, not IDLE+DRAIN)
    In a terminal window: Test slurm by running this command:

    sbatch --output=sbatch.out <<+
    #!/bin/sh
    /bin/hostname
    +
    

    Output from the command will be written to file sbatch.out
    If file sbatch.out don't appear in your current work directory. Check if you can see the job in the Slurm graphical user interface:
    sview &
    
    If the status of the job is "PENDING", something is not correct. If this is the case, goto Debugging SLURM for further advice.

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12. After the installation

    Please test your installation by running the three first tutorial examples: ../../tutorial/README.html