OpenVnmrJ Version 3.2 Installation or Upgrade
For upgrade information, see the end of this document.
OpenVnmrJ Version 3.2 has been installed on RHEL systems running 8 and 9. It has also been installed on AlmaLinux 8 and 9 and on Ubuntu Version 20, 22, and 24 systems. Note the last CentOS version 7 had its end of like in June, 2024. This release does not support CentOS.
The MacOS version of OpenVnmrJ has been installed on versions High Sierra (10.13) to Sequoia (15). Installation on RHEL, AlmaLinux, and Ubuntu systems can be used to run a spectrometer. The MacOS version is for data-processing only.
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For AlmaLinux systems, one can start by downloading one of the x86_64 images available from https://mirrors.almalinux.org/isos
For Ubuntu systems, one can start by downloading one of the images available from https://ubuntu.com/download/desktop
A typical OpenVnmrJ RHEL or AlmaLinux installation may involve selecting, in the "SOFTWARE SELECTION" options, the GNOME Desktop as the base environment and the GNOME applications, Legacy X Window System Compatibility, Compatibility Libraries, and Development Tools as add-ons. One does not need to set a hostname or connect to a network at this time. After clicking "Begin Installation", set the root password and click the "USER CREATION" button to make vnmr1, which will be the default OpenVnmrJ administrator.
Following installation and a reboot, login in as root, accept the license, turn on the network and click the "Finish configuration" button. After a few more configuration items, it is ready for installation of OpenVnmrJ.
The OpenVnmrJ installer may be downloaded from https://github.com/OpenVnmrJ/OpenVnmrJ/releases Move the zip file to /tmp and unzip it. If you are logged in as root, do not try to install it from the root home directory (/root). It will not work. First unzip the file and cd into dvdimageOVJ (or dvdimageOVJMI). Run ./load.nmr. The first thing it will do is install missing OS packages. It uses yum and will require network access. Since it turns off SELinux, a reboot is needed after the packages are installed.
After reboot, log in as root again and cd to the dvdimageOVJ directory and run ./load.nmr again. It will find that all required packages have been installed and start a normal OpenVnmrJ installation. Following that, it will prompt you to set up some standard accounts (walkup and service), install the latest version of NMRPipe, install the VnmrJ 4.2 manual set, install the VnmrJ 4.2 fidlib, and setup the network for console communications. If you make the walkup and service accounts, on Ubuntu systems, they will be given the initial password of abcd1234. On RHEL, and AlmaLinux systems, they will not be given a password.
Note that access to the network is tested by trying to "ping" google.com Some firewalls disable ping. If you are sure you have network access, one can bypass the "ping" test by using ./load.nmr noPing
Note that the default OS package installation downloads them from the network. To support installation of OpenVnmrJ without network access, two new scripts have been implemented. They are in the dvdimageOVJ directory along with load.nmr. The ovjGetRepo command is a link to the installpkgs script. Network access is required for this command. It will download and save the required packages and their dependencies. It will also install them. For this to work, a system with a minimum of packages is needed, since if the package is already installed, the ovjGetRepo script will not download it. To create the repository described below, a fresh install of AlmaLinux 8.4 with only the Gnome desktop and "Development tools" selection was used. The ovjGetRepo script puts the packages in a directory named openvnmrj.repo in the parent directory of the dvdimageOVJ direcory. The openvnmrj.repo directories were zipped and given names to reflect the specific OS. They can be downloaded with these links:
https://www.dropbox.com/s/hsav3k3flowkhxn/ovj3AlmaLinux84.repo.zip?dl=0
The second script is ovjUseRepo. It takes an optional path name for the openvnmrj.repo but defaults to the parent of the dvdimageOVJ directory. This script makes a repository and adds it to the list of yum repos. If the installpkgs script, called by load.nmr, detects openvnmrj.repo, it will not do the ping test and it disables all other repositories. Internet access is not required. A typical process would be to download the OpenVnmrJ installer and one of the above OS repositories. Move both files to /tmp and then do unzip unzip cd dvdimageOVJ ./ovjUseRepo ./load.nmr
Installations on Ubuntu systems are similar to those for RHEL and AlmaLinux. One difference is that the user account created during the installation of Ubuntu will be given "admin" privileges. That is, by using sudo, that account can do anything the root account on RHEL can do. Some may prefer that the vnmr1 account does not have those privileges. One could then create an initial account, such as ovjroot. During the installation of OpenVnmrJ, the vnmr1 account will be created with no admin privileges. It will be given the initial password of abcd1234.
After the OpenVnmrJ installation is complete, log out and log in before using the administrator (vnmr1) account.
Newer systems use the Gnome 3 display manager. The "Standard" display manager no longer has desktop icons. Rather, it has an Activities button at the upper left corner. Clicking that button will display a "Type to search..." entry field. If you enter vnmrj or openvnmr, the OpenVnmrJ launch icon will appear. This can be dragged to the favorites toolbar or right-clicked and select "Add to Favorites". If the OpenVnmrJ launch icon does not appear, re-run makeuser on that account. You may also need to log out and log in again.
Gnome 3 also supports the "Classic" display manager, where desktop icons are displayed. One can select the display manager from the login screen. A settings icon is available after selecting the user, but before entering the password. On RHEL, it is next to the "Sign in" button. Select the "Classic (Wayland display server)" and then log in. On Ubuntu, the settings icon is at the lower right-hand corner of the display. Select either of the "Ubuntu" settings. The OpenVnmrJ desktop launch icons will be displayed. Before they can be used, they must be enabled by clicking the right mouse button on them and selecting "Allow Launching".
The MacOS version needs java version 1.8 or newer to be installed. To install on the Mac, open the "Finder" and navigate to the OpenVnmrj.pkg file. Right-click on the icon and select "Open". If you double-click on the icon, it may result in System security complaining it’s “not registered developer” and then quit. To get around this security issue, go to Apple Pull down menu System Preferences Security & Privacy Click on lock icon bottom left of window and enter administrator password General Tab Bottom Section Allow apps downloaded from: Select OpenVnmrJ and choose “Open Anyways”
Also, if installed on MacOS Catalina (10.15) or newer version of MacOS, the Mac must be rebooted following installation of OpenVnmrJ. If one installs OpenVnmrJ Version 3.2 on a Mac running Mojave or older versions and subsequently upgrades to Catalina or newer MacOS versions, OpenVnmrJ will stop working. This is because Catalina and newer MacOS versions have implemented a "read-only" system directory and OpenVnmrJ will have been moved to a different disk locations and the /vnmr link will have been removed. To re-enable OpenVnmrJ, run the script
~/vnmrsys/vnmr/bin/ovjFixMac
A system reboot will then be necessary.
The open-source version of java for MacOS may be obtained from https://jdk.java.net. Download, for example, the JDK 14.0.2 release. Unpack the java package with the commands
gunzip openjdk-14.0.2_osx-x64_bin.tar.gz
tar xvf openjdk-14.0.2_osx-x64_bin.tar
Then move the jdk-14.0.2.jdk directory with the command
sudo mv jdk-14.0.2.jdk /Library/Java/JavaVirtualMachines
OpenVnmrJ is stored as a subdirectory of /Applications/OpenVnmrJ.app on MacOS systems. In that directory, there is a symbolic link "Contents" which will point to one of the OpenVnmrJ versions. Older versions of OpenVnmrJ can be removed by, for example, cd /APplications/OpenVnmrJ.app rm -rf Contents_3.1_BETA4
There are a number of tools that OpenVnmrJ uses that may not be present in a standard MacOS installation. The script ovjMacTools is provided to install these tools. It installs GhostScript, which has the PostScript to PDF conversion tool (ps2pdf). It installs ImageMagick, which has the convert tool to convert various image formats. It installs xterm, along with xQuartz, which is used by NMRpipe, for example. The ovjMacTools script uses brew to install these tools.
The first time OpenVnmrJ starts on MacOS, a popup asking Do you want the application "VnmrBg" to accept incoming netwrk connections? may appear. You can click Deny. That popup should not appear again.
Running ./load.nmr will install the new release as described above. If one instead runs ./upgrade.nmr then OpenVnmrJ will be upgraded in place. That is, a new directory to hold the release will not be created. The current system and user configuration files will be maintained, along with any gradient shimming, probe, or other calibration files. All other files that have changed or been added since the previous version will be installed. There is no graphical interface when the upgrade is performed. The upgrade.nmr process only upgrades the files in /vnmr. It does not upgrade files in individual user accounts. For that, one should use either "vnmrj adm" or makeuser. Note that when installing a new version of OVJ, it is best to use the load.nmr script. After installing the latest release of OVJ from github and you subsequently build a newer version with the ovjBuild script, then the upgrade.nmr is very useful.