Author Topic: Welcome to VM alphaMELTS 1.9 (Lubuntu 16.04)  (Read 5761 times)

Paula

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Welcome to VM alphaMELTS 1.9 (Lubuntu 16.04)
« on: October 25, 2012, 05:34:42 pm »
VM (virtual machine) alphaMELTS is a lightweight Linux (Lubuntu) 32-bit or 64-bit installation for use with the VirtualBox program. The download includes alphaMELTS and the rhyolite-MELTS/pMELTS graphic user interface. Also installed are Jon Snow's Meltsout program (see here) and a copy of the VMD program (the 32-bit version does not have the full VMD feature set but can be used for basic visualization).

Running the VM alphaMELTS guest on a Windows host provides an alternative to installing Perl for alphaMELTS users and, until the introduction of the Windows Subsystem for Linux, was the only way to run the rhyolite-MELTS GUI on Windows (see this post for more details about WSL alphaMELTS and rhyolite-MELTS). It is the main way to try out the new alphaMELTS 2 beta (see the alphaMELTS 2 version of the MELTS tutorial). It does require several GB free hard disk space for installation (~5GB is used permanently) and at least 1GB RAM total (preferably 2GB+) but on modern machines both alphaMELTS and rhyolite-MELTS should run well within Linux, without impacting the host operating system too much.

You can download VM alphaMELTS at the alphaMELTS download site. Installation instructions are given there. Once you start the virtual machine you are logged in as the user 'melts'. No password is needed to log in but it will be needed to update or install software. The password is case-sensitive and is the former name of alphaMELTS, as detailed here. You can change both automatic log in, the (lack of) requirement for a password for log in, and the password itself.

The first time you start the virtual machine you may be prompted to update VirtualBox Guest Additions. You will need the password for this and some other system maintenance e.g. to check for Lubuntu security updates. To update VirtualBox Guest Additions:
  • Start the alphaMELTS Lubuntu machine.
  • Select 'Devices' -> 'Insert Guest Additions CD image...' in the VirtualBox menu, and click OK to open it in File Manager.
  • Select 'Tools' -> 'Open Current Folder in Terminal' from the File Manager menu.
  • Type 'sudo ./VBoxLinuxAdditions.run' (or 'sudo ./VBoxLinux' and then the tab key) and press the return key.
  • Enter the password and then wait while it removes the old version and installs the new one.
  • Finally click the 'eject' button next to the CD image in the File Manager.
The rhyolite-MELTS executable is in a folder called 'MELTS' in the user's home space. alphaMELTS 1.8, 1.9, and 2.0 are also located in the MELTS folder, together with copies of the examples and tutorial files. alphaMELTS 1.9, which includes some features for forwards compatibility with alphaMELTS 2.0, is the installed version. If you prefer to use alphaMELTS 1.8 (which should be slightly more backwards compatible) then open LXTerminal; type 'cd MELTS/linux_alphamelts_1-8', then './install.command', and take the default values for all the questions.

The links_folder, which is included in the user's PATH, is in the default location ('/home/melts/bin' - see the alphaMELTS documentation for more details). There are also links to the rhyolite-MELTS executable in '/home/melts/bin'. The rhyolite-MELTS, linux_alphamelts_1-8, linux_alphamelts_1-9, linux_alphamelts_2-0, and Meltsout-II folders should be left in place (else the links will break) but it is fine to move the examples or tutorial files.

The default desktop has icons for programs that will be useful for running alphaMELTS and rhyolite-MELTS placed next the start menu. From left to right, they are:
  • LXTerminal - needed to start rhyolite-MELTS and for running alphaMELTS in command line mode
  • Leafpad - a text editor with Windows-like short cuts (e.g. ctrl-C, ctrl-V for copy and paste respectively)
  • Gnumeric - a simple spreadsheet program that is nice as it opens space delimited text files automatically
  • Web browser - Firefox
  • Customize tool - to change look and feel of the Desktop e.g. font sizes
  • Software Updater - to keep the Lubuntu operating system up to date
  • File Manager - PCManFM that opens in the melts user's home space
The panel is located at the top of the screen, by default, so that it may be more easily integrated with the host Desktop (which, for Windows at least, tends to have the panel at the bottom of the screen). Four keyboard layouts have been installed: English (QUERTY) - US and GB layouts -, French (AZERTY), and German (QUERTZ) keyboards. You can switch between them by clicking the keyboard icon in the top right.

The system puts an icon for the Shared folder on the Desktop, assuming the target folder exists. It should point to a folder on the host operating system (see the VM alphaMELTS installation instructions for more details). You can double-click this icon to open the folder in the File Manager, PCManFM. Go to 'Tools' -> 'Open Current Folder in Terminal' in PCManFM to open the Terminal so that you can start alphaMELTS or rhyolite-MELTS where the input / output files are located. There is also a link to the Shared folder in the user's home space, so you can open LXTerminal and then type 'cd Shared' to get to the files on your host system. You can take advantage of the tab-completion on the command line and within alphaMELTS (which uses with-readline).

Note that alphaMELTS on Lubuntu is generally less tolerant of file or folder names containing spaces than on other systems, including other versions of Linux, and drag-and-drop of filenames does not work in the same way. It is fine for the Shared folder location on the host machine to have spaces (the 'Folder Path' setting in VirtualBox, e.g. "C:\Users\username\Documents\My Folder"). For the names other folders and files, within the Shared folder and elsewhere on the Lubuntu system, we recommend using '_' instead of spaces.

There is a double-clickable launcher for alphaMELTS 1.9 on the Desktop, that will automatically open LXTerminal. Use is somewhat like the alphaMELTS (double-click) version of the MELTS tutorial, but dragging and dropping files does not work in quite the same way in Lubuntu as in other operating systems. One workaround is to right-click the file and choose 'Copy Paths'; then right-click in the LXTerminal window and select 'Paste'. Make sure to specify an output folder with '-p' or all the files will end up in the melts user's home space.

There is also a Desktop icon for rhyolite-MELTS that you can double-click and it will open rhyolite-MELTS with the LXTerminal so that you can choose between rhyolite-MELTS 1.0.2, 1.1.0, 1.2.0, and pMELTS. Double-clicking the actual Melts-rhyolite-public executable will not give you these choices. Note, however, that if you use the Desktop rhyolite-MELTS, the program will open in the melts user's home space, and all output will go there (similar to what happens if you double-click Melts-rhyolite-public on MacOS); you will need to specifically move all the .tbl files out of the folder between rhyolite-MELTS runs, ideally to somewhere in the Shared folder instead. Otherwise, if the phase assemblage differs between run 1 and run 2, melts.out and all the .tbl files for phases in run 2 will be overwritten but any other .tbl files from run 1 will still be hanging around.

A convenient way to invoke rhyolite-MELTS or alphaMELTS is to open a terminal in Lubuntu, navigate to where the files are and type 'Melts-rhyolite', 'run_alphamelts.command' (with or without command line switches), or 'run-alphamelts.command' (for alphaMELTS 2). Wait for the MELTS GUI windows to be initialized, if appropriate, and then switch to 'Seamless' mode in VirtualBox (Host+L). alphaMELTS or rhyolite-MELTS with have their own window(s) on the host Desktop and output will be written to the Shared folder; data can easily be imported to into programs on the host operating system, such as ExcelTM and MatlabTM, for plotting (see the Tips, tools & add-ons board, and the alphaMELTS links page for more details).

The Meltsout program can be run by typing 'meltsout filename' at the LXTerminal command line, or for the default 'melts.out' file, simply type 'meltsout'. VMD can be run by typing 'vmd' at the terminal command line. If you use the VMD program, please sign up on the download site so that you can accept the terms of the VMD software license.

Note that you probably want to exclude the 'alphaMELTS Lubuntu.vdi' virtual hard drive from any automatic backups to avoid filling up the backup disk. (The exact name and location of the virtual hard drive may differ slightly and can be found under 'Storage' in the VirtualBox machine settings.) Backing up strategies that don't generate such huge files include copying files to the Shared folder, or using this as the working directory, and uploading files to a cloud-based service, such as Dropbox or Google Drive.

More information for getting started with VirtualBox, Linux / Unix type systems in general, and Lubuntu in particular will be added to the Operating system specific boards as needed. A few posts on the Linux and Mac OS X boards will be relevant and this VirtualBox tricks page is useful too. If there are any problems please let me know.

Cheers,
Paula
« Last Edit: November 18, 2020, 08:06:45 pm by Paula »

Paula

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Re: Welcome to VM alphaMELTS 1.9
« Reply #1 on: September 20, 2018, 04:29:31 pm »
Note the link to Meltsout is missing in the links_folder in the currently posted VM alphaMELTS version. It will be in the next version. In the meantime, you can fix this by opening LXTerminal. Type:

Quote
cd bin
ln -sf ../MELTS/Meltsout-II/meltsout .

You need only do this once. 'ln' stands for 'link'; '-s' is for 'symbolic', so if you delete the link you do not delete the original file (much like Windows shortcuts); '-f' is for 'force', which makes no difference unless you move the 'Meltsout-II' location and need to remake the link.

Update: the current version (as of October 31st, 2018) has the link fixed.
« Last Edit: October 31, 2018, 02:26:44 pm by Paula »