News Rel.2101

Gensys.2101

Installation of virtual machine "Mint20-gensys21"

Only the necessary steps in the below list needs to be done.
Section 1) can be skipped if you have VirtualBox 6.1.4 or newer already installed on your computer.
Section 2) can be skipped if you don't want to update the documentation and the verification examples.

Install and configure program VirtualBox:
If you are missing VirtualBox or if your VirtualBox-version is older than 6.1.4, it is necessary to do these steps:
1. Make sure your machine is equipped with a 64-bits processor.
  Primary memory > 1 GB
  Free hard disk space > 55 GB
  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 VirtualBox version 6.1.4 or newer.
4. Start program VirtualBox
5. In the PullDown-menu of program VirtualBox click "File -> Preferences"
  On the left side in the popup-window 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"
Download and uncompress the documentation and the verification examples:
N.B. In this step you will create the following three directories: free_models, homepage and verif. If you have old versions of these directories, they will be overritten.
If you want to keep your old versions of free_models, homepage and verif. You can skip this part, or you can uncompress the files at another location, and then compare the directories with each other using script opdiff_dir.
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 or "$HOME/gensys" on a UNIX-host.
2. In the newly created work directory. Also create a directory where you can keep your own work files.
  E.g.: "analyse"
3. Download the following files:
```
free_models-2101.7z    = Free vehicle models
homepage-2101.7z       = Documentation and tutorials
verif-2101.7z          = 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:
```
 0 sha256sum [a-z]*7z
81d504d52e49654e47515fad31a3e1ce54fe096f6240cf77ae694dadfbb6409b  free_models-2101.7z
7b005bba859cfa8e17618b7def091e1b2c0fb686d2b05a4c77ce5b5dfaed0067  homepage-2101.7z
17876d1ff731da06f72d33057a1a155b19907d3ab10e850d6890bca2afee70a4  verif-2101.7z
```
4. Move the downloaded files to your Shared Folder (E.g. C:\Users\Public\gensys" or "$HOME/gensys"). Uncompress the files in program that handle 7-zip files. (If you don't have a program for 7-zip files, you can download a program with this link: www.7-zip.org/download.html)
5. The files free_models-2101.7z, homepage-2101.7z and verif-2101.7z can now be removed.
Download and install the virtual machine:
1. Download the following 7-zip files:
```
Mint20-gensys21.7z.001
Mint20-gensys21.7z.002
Mint20-gensys21.7z.003
Mint20-gensys21.7z.004
Mint20-gensys21.7z.005
```
  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:
```
 0 sha256sum Mint20-gensys21.7z.00?
d7052f9d53e8a0bed6bacb9afbf79e86968214e83f7f3fa934df1ad4728e60bf  Mint20-gensys21.7z.001
18cae6114f7045d8e9556be468137cf6d0ef018b86e47e624bddd49225ff911e  Mint20-gensys21.7z.002
3e204138ceb29b7dee52d112f00ec00bde34950fbfc76150097b0ec42d4d2aa4  Mint20-gensys21.7z.003
943c676aa8e2a49f19a01e103b31da812d589b5297436edb308d758bb14a0ef0  Mint20-gensys21.7z.004
07c7165967c4179d81744e3bb936c82179b025ee562d3dfe53353fea92d00b04  Mint20-gensys21.7z.005
```
2. Contact info@gensys.se to get a link to a valid license file for your installation.
3. 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.
4. Uncompress the file archive.
  Move the five files downloaded under 3.1) to the location created under 3.3).
  Mark file "Mint20-gensys21.7z.001" and with your right mouse button and select 7z -> Open Archive -> Extract.
  After the virtual machine has been extracted, the five files "Mint20-gensys21.7z.00[1-5]" can be removed.
  (If you don't have a program for 7-zip files, you can download a program with this link: www.7-zip.org/download.html)
5. Setup the virtual machine.
  Go to the newly created directory "Mint20-gensys21". Start VirtualBox by double-clicking file "Mint20-gensys21.vbox".
  Mark the virtual machine "Mint20-gensys21" and click "Settings".
  1. Activate Shared Clipboard
    On the left side in the popup-window select "General"
    On the right side select "Advanced"
    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". Minimum recommended size is 1280MB. Maximum recommended size depend on the size of the primary memory of your host computer. You must choose a size within the green marked area of the scale.
  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
    On the left side in the popup-window select "Shared Folders"
    On the right side select "gensys /home/gensys/gensys"
    Click right mouse button and select "Edit Shared Folder"
    Change "Folder Path" so it points to your "Shared Folder"-location. See under "Download and uncompress the documentation and the verification examples" above.
    Folder Name: "gensys" must not be changed (N.B. Folder Name is case sensitive)
    Check "Make Permanent" (if the option is visible)
    Do not check "Auto-mount".
    If option "Mountpoint" is visible write "gensys" in this field.
    Click OK
6. In the VirtualBox main window, start the virtual machine by clicking the green arrow marked "Start"
7. 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-2101/bin".
  Add execute permissions to file gen_processor_ID_check:
```
chmod +x /opt/gensys/gensys-2101/bin/gen_processor_ID_check
```
8. Configure the slurm queue system by editing file: /etc/slurm-llnl/slurm.conf
  Under "NodeName", set number of available processors for each node in the cluster.
  If you have many machines in your cluster, command "NodeName" can be given multiple times.
  After the file /etc/slurm-llnl/slurm.conf has been updated, the virtual machine must be restarted in order to make the changes to take effect.
  In a terminal window: Test slurm by running program "/bin/hostname" via command sbatch:
```
sbatch --output=sbatch.out <<+
#!/bin/sh
/bin/hostname
+
```
  Output from the command will be sent 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". Open program "Oracle VM VirtualBox Manager" and go to Settings -> System -> Processor, and check that number of processors are greater or equal to the number defined in file /etc/slurm-llnl/slurm.conf.
  If not, update file /etc/slurm-llnl/slurm.conf again, or shutdown the virtual machine and update number of processors in "Oracle VM VirtualBox Manager".

After installation

Please test your installation by running the tutorial examples: README

Updates in the new machine

Gensys is now compiled with the new compiler gcc-10, which gives better warning messages and improves execution times.