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OpenVnmrJ Version 2 Installation

OpenVnmrJ Version 2 has been installed on RedHat/CentOS systems running versions 6.8, 6.9, and 6.10, and versions 7.5, 7.6, and 7.7. It has also been installed on Ubuntu Version 14, 16, and 18 systems. The MacOS version of OpenVnmrJ has been installed on versions Yosemite (10.10) to Catalina (10.15). Installation on RHEL/CentOS systems can be used to run a spectrometer. Installation on Ubuntu systems may function as a spectrometer, but this has not been verified. The MacOS version is for data-processing only.

To install on CentOS 6.x systems, we recommend using the CentOS KickStart DVD available from Agilent ( see SpinSights https://spinsights.chem.agilent.com/docs/DOC-12723 )

For CentOS 7.x systems, one can start by installing a standard OS using the CentOS-7-x86_64-DVD-*.iso images available from https://www.centos.org/download/

For Ubuntu systems, one can start by downloading one of the images available from https://ubuntu.com/download/desktop

If earlier versions of OS, for example, CentOS_6.9, Centos_7.6, or Ubuntu_16, were chosen, then the system, if connected to network, will prompt for OS updates at a later stage. It is up to the user and/or user's organization policies to opt for OS updates or not.

A typical CentOS 7.x 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 root's home directory (/root). It will not work. After unzipping the file, cd into dvdimageOVJ (or dvdimageOVJMI) and run ./load.nmr. The first thing it will do is install missing CentOS 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, and setup the network for console communications. If you make the walkup and service accounts, they will be given passwords abcd1234.

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 repositories described below, a fresh install of CentOS 7 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. For the repositories described below, this was repeated for CentOS 7.5, 7.6, and 7.7, since each has different package dependencies. The openvnmrj.repo directories were zipped to files named ovjCentos75.repo.zip, ovjCentos76.repo.zip, and ovjCentos77.repo.zip. They can be downloaded with these links:

https://www.dropbox.com/s/1abfx71q7ppnz5k/ovjCentos75.repo.zip?dl=0

https://www.dropbox.com/s/n95wnuyhmmccpby/ovjCentos76.repo.zip?dl=0

https://www.dropbox.com/s/rx0fiprusehf78r/ovjCentos77.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 CentOS 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 CentOS. 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 CentOS 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.

The MacOS version needs java version 1.8 or newer to be installed. Also, if installed on MacOS Catalina (10.15), the Mac must be rebooted following installation of OpenVnmrJ. If one installs OpenVnmrJ Version 2 on a Mac running Yosemite to Mojave and subsequently upgrades to Catalina, OpenVnmrJ will stop working. This is because Catalina has 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 13.0.2 release. Unpack the java package with the commands

gunzip openjdk-13.0.2_osx-x64_bin.tar.gz

tar xvf openjdk-13.0.2_osx-x64_bin.tar

Then move the jdk-13.0.2.jdk directory with the command

sudo mv jdk-13.0.2.jdk /Library/Java/JavaVirtualMachines