News Rel.1901

Gensys.1901

Installation of virtual machine Mint191-gensys-1901
Do the following steps:

1) Install and configure program VirtualBox:

2) Download and uncompress the documentation and the verification examples:

N.B. In this step you will create the 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 directory above. Also create a directory where you can keep your own work files.
  E.g.: "analyse"
3. Download the following files:
```
free_models-1901.exe    = Free vehicle models
homepage-1901.tgz       = Documentation and tutorials
verif-1901.exe          = Verification directory

The files can be downloaded with the following links:
https://mega.nz/#!eBtREaYA!mTIpInfaklR4hVppeUI7ePZgIL_EQVCob_dgmhIztuo  (free_models-1901.exe)  
https://mega.nz/#!vR9DiaqI!qV95zVlu4vRZXgv-j6PBjgGkECy50ufzBkQDwSuQiwA  (homepage-1901.tgz)     
https://mega.nz/#!vAdzFIoZ!j_1id7sSifUb6iX-HSVNEbkvc-U68OhkEf81loGUoMw  (verif-1901.exe)
```
  N.B webpage mega.nz requires a webbrowser that handles HTML5 and allows JavaScript to write files. Currently Chrome and Firefox works best.
  The MD5 message-digest algorithm should give you the following output if all files has been downloaded without errors:
```
md5sum *
0cd121397927fcb270cead5e1c9d45cd  free_models-1901.exe  
03c5ab5bfb1149d4a8eacdb60c26af41  homepage-1901.tgz     
060ae9f949f71b57c73ae298da4ca7a6  verif-1901.exe
```
4. Move the downloaded files to your Shared Folder (Users\Public\gensys" or "$HOME/gensys"). Execute the downloaded files, and they will unpack themselves. (If you are extracting the files on a Linux host via "wine". Make sure the exe-files have read and execute permissions)
5. File homepage-1901.tgz must be treated a bit different, because it is not a self-extractor. In order to unpack file homepage-1901.tgz please use the command:
```
tar -xzkpf homepage-1901.tgz
```
  If command "tar" is not available in your host machine. You can skip this step for now and unpack it later, when you have unpacked and started the virtual machine under step 3) below.

3) Download and install the virtual machine:

1. Download the following self-extractors:
```
Mint191-gensys-1901.exe        = The virtual machine
Mint191-gensys-1901.7z.00[1-5] = Sub-files to Mint191-gensys-1901.exe
The files can be downloaded with the following links:
https://mega.nz/#!3MVkySaT!sxqtekMG4_gWDY083qvVYWCXTer-ZI06F-I-NyBsYHI  (Mint191-gensys-1901.exe)
https://mega.nz/#!uZEkCSbI!lMBT1pBvjDBKgVtvmRj_KUslyyKaYI7U0w5_230LkGI  (Mint191-gensys-1901.7z.001)
https://mega.nz/#!OQESFIwA!s7EqOL9LE1G3fkRFt-jfEF-KnnxgViLC18zvd2xQRaM  (Mint191-gensys-1901.7z.002)
https://mega.nz/#!zcNmgAoY!ABM57PWiIzU3csLvQiYHloU0q5cSCDrt6iSkK_oklwE  (Mint191-gensys-1901.7z.003)
https://mega.nz/#!qAdQiYqI!GHTgN5fH6kcSbFniZPERoVXXrSXuOEt5YiBoFTvHHsQ  (Mint191-gensys-1901.7z.004)
https://mega.nz/#!XYFGUCZZ!CNbVWbOAKqUqWuOd5-gmGOj9P-zZ7xEBTLt9a9n9b2s  (Mint191-gensys-1901.7z.005)
```
  N.B webpage mega.nz requires a webbrowser that handles HTML5 and allows JavaScript to write files. Currently Chrome and Firefox works best. The MD5 message-digest algorithm should give you the following output if all files has been downloaded without errors:
```
md5sum *
dcd81f5dba1a842a50fc8d6b7ca14150  Mint191-gensys-1901.7z.001
3bc139d1ad33fb92296cfacfd894011a  Mint191-gensys-1901.7z.002
4c214a75daab5966dae9b06fefc6865e  Mint191-gensys-1901.7z.003
250bf6e2312427f83305c961c8691e97  Mint191-gensys-1901.7z.004
fa445b2384dc0027c0a22e0df1da4264  Mint191-gensys-1901.7z.005
9b6b0267ab36f41cc365ca44c9724f19  Mint191-gensys-1901.exe
```
2. Contact info@gensys.se to get a link to a valid license file for your installation.
3. 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 "$HOME/VirtualBox VMs" on a UNIX-host.
4. Move file Mint191-gensys-1901.exe and its sub-files to the directory containing your virtual machines ("C:\Users\Public\VirtualBox VMs" or "$HOME/VirtualBox VMs"). File Mint191-gensys-1901.exe is a self-extractor file. Execute the file and the whole virtual machine will be unpacked. (If you are extracting the files on a Linux host via "wine". Make sure the exe-files have read and execute permissions)
5. Go to directory Mint191-gensys-1901 created by Mint191-gensys-1901.exe. Start the virtual machine by double-clicking file Mint191-gensys-1901.vbox.
6. Activate Shared Clipboard
  Mark virtual machine "Mint191-gensys-1901" and click "Settings".
  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
7. Set primary memory
  Mark virtual machine "Mint191-gensys-1901" and click "Settings".
  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 of primary memory is 1500MB - 2000MB. Choosing too high value can lead to slow a execution, because the host machine may start swapping its memory.
8. Set number of processors
  Mark virtual machine "Mint191-gensys-1901" and click "Settings".
  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 with green.
9. Activate Shared Folders
  Mark virtual machine "Mint191-gensys-1901" and click "Settings".
  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
  Check "Make Permanent" (if the option is visible)
  If option "Mountpoint" is visible write "gensys" in this field.
  Click OK
10. Start the virtual machine by clicking the green arrow marked "Start" in the VirtualBox main window.
11. Install Gensys license file.
  Start webbrowser firefox in the virtual machine. Enter the link mentioned under 2) above, and download the file. Save the license file in directory "/opt/gensys/gensys-1901/bin".
  Add execute permissions to file gen_processor_ID_check:
```
chmod +x /opt/gensys/gensys-1901/bin/gen_processor_ID_check
```
12. Configure the slurm queue system by editing file: /etc/slurm-llnl/slurm.conf
  Under "NodeName", set number of processors that the queue system may use. Restart the slurm queue system by writing:
```
systemctl stop slurmctld
systemctl start slurmctld
```
  (Password: gensys1)
  Test slurm by sending the "hostname"-command:
```
sbatch --output=sbatch.out <<+
#!/bin/sh
/bin/hostname
+
```
  Output from the command will be sent to file sbatch.out
  If you are experiencing problems. Check if these three processes are running on your machine: munged, slurmd and slurmctld. If these processes are not running, you can start them with:
```
sudo munged          ;# For authenticating local MUNGE clients and servicing.
sudo slurmd          ;# Start the compute node daemon of Slurm.
sudo slurmctld       ;# Start the central management daemon of Slurm.
```

You only need to do the necessary steps in the above list.
Part 1) can be skipped if you have VirtualBox already installed on your computer.
Part 2) can be skipped if you don't want to update the documentation and the verification examples.

Troubleshooting

If you have problems with file downloading.
Please check the following:

Make sure that no firewall prevents you from downloading files from the Internet.
Try different web-browsers, including modern versions of Firefox and Chrome.

After installation

Please test your installation by running the tutorial examples by following the instructions given in README

Adding own source code

If you want to be able to compile own subroutines. It is necessary to install new compilers in the virtual machine. To do so, please give the following commands:

gen_apt-get_install.sh g++-8
gen_apt-get_install.sh gfortran-8
gen_apt-get_install.sh gcc-8

The output from command "gen_apt-get_install.sh" is appended to file "~/Downloads/installed.out". In this file you can track all packages installed with the "gen_apt-get_install.sh"-command.