From ba6e5b5ebad4a561d0007a67921e764fcfc07b8f Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Wed, 10 Aug 2011 16:07:37 +0000 Subject: [PATCH] Drop support for VirtualBox git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4484 e3abac25-378b-4346-85de-24260fe3988d --- website/man_servervm.html | 55 +++++++++++++++------------------------------ 1 file changed, 18 insertions(+), 37 deletions(-) diff --git a/website/man_servervm.html b/website/man_servervm.html index 1a14d3d..e24e333 100644 --- a/website/man_servervm.html +++ b/website/man_servervm.html @@ -52,55 +52,42 @@ -

Troubleshooting

- +

 

What is the JABAWS Server Virtual Appliance?

The JABAWS Virtual Appliance is a way to run JABAWS server locally without the need to connect to the internet or configure JABAWS. What the appliance provides is a 'virtual server machine' (or more simply - virtual machine or VM), running an installation of the JABAWS Web Application Archive (WAR) on TurnKey Linux. Once this has started up, it displays a message indicating the IP address of the JABAWS server, allowing any JABAWS client (such as Jalview or the JABAWS command line client) to connect to it.
-You can run the appliance with freely available programs such as VMWare Player or -Oracle VirtualBox 3.2.x, but you will need to install them first. We have tested the JABAWS appliance -with VMware Player v 3.1.2 on Windows and Linux, and VirtualBox v. 3.2.12 on Windows, Linux and Mac. - However, you are not limited to these virtualization systems and can use the JABAWS appliance with any commercial alternative.

+You can run the appliance with freely available program such as VMware Player, but you will need to install it first. We have tested the JABAWS appliance +with VMware Player v 3.1.2 on Windows and Linux, and VMware Fusion on Mac. + However, you are not limited to these virtualization systems and can use the JABAWS appliance with any other virtualization platform. You can use VMware OVF tool to convert JABAWS image to a different virtualization format e.g. OVF.

When to use the JABAWS Virtual Appliance

-

The appliance best suits users who would like to use the JABA web services locally. This might be because they do want to access -systems over an internet or local intranet connection, or alternately, want to keep their data private. It is also -the recommended option for users who want to install JABAWS on Windows, which does not support all the bioinformatics programs that JABAWS can run. -
Since the appliance is a self contained unit of software, it is also an attractive option for Linux, UNIX or Mac users wishing to set up JABAWS services quickly.

-

When not to use the JABAWS Virtual Appliance

+

The appliance best suits users who would like to use the JABA web services locally. This might be because they do not want to access +systems over an internet, or just want to keep their data private. It is also +the recommended option for users who want to install JABAWS on Windows, which does not support all the bioinformatics programs that JABAWS can run.

+

When not to use the JABAWS Virtual Appliance

+

For servers that will be used heavily, we recommend that a JABAWS Server WAR distribution is deployed, rather than the Virtual Appliance version of JABAWS. This is because the JABAWS appliance is pre-configured to use only 1 CPU and 512M of memory (where the minimum amount of memory required for a JABAWS server is about 378M), which is unlikely to be sufficient for heavy computation. It is possible to reconfigure the virtual appliance so it uses more computation resources, -but for most production environments, the JABAWS WAR distribution will be more easy to deploy and tune to take advantage of the resources available.

+but for most production environments, the JABAWS WAR distribution will be easier to deploy and fine tune to take advantage of the available resources.

-

How to install VMWare Player or VirtualBox

+

How to install VMware Player

Please see the VMware Player -and Oracle VirtualBox web sites for up to date instructions and downloads.

+ web sites for up to date instructions and downloads.

VMware Player appliance configuration

-

The free VMware Player can be used to run the JABAWS services from the Windows and Linux host operating systems, there is no support for Mac at the time of writing (December 2010). -However, VMware Fusion, a commercial VMware product, offers virtual machine support for Mac computers too.

+

The free VMware Player can be used to run the JABAWS services from the Windows and Linux host operating systems. VMware Fusion, a commercial VMware product, offers virtual machine support for Mac.

To run the JABAWS server on VMware player, unpack the JABAWS VM into one of the folders on your local hard drive. Open VMware Player, click "Open Virtual Machine" and point the Player to the location of the JABAWS, then choose the JABAWS.vmx file to open an appliance.

When you play the machine for the first time the Player might ask you whether "This virtual machine may have been moved or copied.", say that you have copied it. That is all.

-

VirtualBox appliance configuration

-

VirtualBox can be used to run JABAWS services from Windows, Linux, Solaris or Mac host operating systems. Use the VitualBox "Import Appliance" option to import the JABAWS. Please bear in mind that to benefit from multiple CPU support under the VirtualBox software you need to enable hardware virtualization extensions, such as Intel Virtualization VT-x or AMD-V support in the BIOS of your computer. Unfortunately, we were unable to find a reliable way to do it on Mac, so some Macs running VirtualBox will be limited to one CPU only, irrespective of the number of CPUs of the host machine.

-

We found that, by default, virtualization extensions are enabled in VirtualBox irrespective of whether your computer supports them. You will get the VERR_VMX_MSR_LOCKED_OR_DISABLED exception if your computer does not support the extensions or their support is disabled. Just deselect the checkboxes shown on the screen shot below to solve the problem.

-

VirtualBox JABAWS VM configuration screen shot displaying virtualization settings.

-

VT-x extension on VirtualBox

JABAWS Appliance details

By default, the JABAWS virtual appliance is configured with 512M of memory and 1 CPU, but you are free to change these settings. If you have more than one CPU or CPU core on your computer you can make them available for the JABAWS virtual machine by editing virtual machine settings. Please bear in mind that more CPU power will not make a single calculation go faster, but it will enable the VM to do calculations in parallel. Similarly, you can add more memory to the virtual machine. More memory lets your VM deal with larger tasks, e.g. work with large alignments.

The VMware Player screen shot below displays JABAWS VM CPU settings.

@@ -115,7 +102,7 @@ However, VMware Fusi - VMware tools : Installed

OS info
- OS : TurnKey Linux, based on Ubuntu 8.0.4 JEOS (Just-Enough-Operation-System)
- - Installation : Oracle Java 6, Tomcat 6, JABAWS v. 1.0
+ - Installation : Oracle Java 6, Tomcat 7, JABAWS v. 2.0
- Hostname : tomcat
- IPv4 address : dhcp
- IPv6 address : auto
@@ -138,7 +125,7 @@ However, VMware Fusi

  • SSH/SFTP
    Access: root@VM_IP
    • -

    Where VM_IP is the VM IP address. Under VMware Player host only networking, the first VM may have 192.168.227.128 IP address. Under VirtualBox host only networking, first VM may have 192.168.56.101 IP address.

    +

    Where VM_IP is the VM IP address. Under VMware Player host only networking, the first VM may have 192.168.227.128 IP address.

    Configuring Jalview to work with your JABAWS VM

    After booting the JABAWS VM, you should see similar screen, however, the IP address of your VM may be different. To enable Jalview to work with your JABAWS appliance you need to go to Jalview->Tools->Preferences->Web Services -> New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview help pages.

    JABAWS welcome screen

    @@ -146,17 +133,11 @@ However, VMware Fusi

    JABAWS welcome screen

    If you need to configure a static IP address the configuration console will help you with this. Shutting down the VM is best from the configuration console as well.

    VM Network Settings

    -

    By default the JABAWS VM is configured to use host-only networking. This means that the host can communicate with the VM via a network, but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect to the Internet from the VM, configure your VM to use NAT network. However, you will not be able to connect to the VM from the host in such case. If you want to be able to connect to your VM and let VM connect to the internet at the same time you would have to use a Bridged network. In such a case you would have to configure the VM IP address manually (unless of course your network has a DHCP server to do that)

    -

    VirtualBox fails to open the VM due to VERR_VMX_MSR_LOCKED_OR_DISABLED exception

    -

    VERR_VMX_MSR_LOCKED_OR_DISABLED exception means that Intel Virtualization technology is disabled or not supported by your computer. If you have such a problem, please make sure you have configured the JABAWS VM with 1 CPU and disabled VT-X extensions. Alternatively you can enable virtualization extensions ion from the BIOS of your computer. Unfortunately, we cannot give you exact instructions on how to do this, as this would depend on your computer BIOS manufacturer. For MACs it may not be possible at all.

    -

    VirtualBox 4.0.0 fails to import the VM due to VBOX_E_INVALID_OBJECT_STATE exception

    -

    VirtualBox version 4.x.x is not compatible with JABAWS virtual appliance. Please download the previous version of VirtualBox 3.2.12 to use with JABAWS VA.

    -

    VMWare Player fails to open the VM with "Fail to query source for information" exception

    -

    At the time of writing, the latest version of VMware Player 3.1.2 supported only a legacy OVF version 0.9. Whereas OVF packaged with JABAWS VM is version 1.0. Please use VMX - VMware specific configuration file with all VMware products.

    +

    By default the JABAWS VM is configured to use host-only networking. This means that the host can communicate with the VM via a network, but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect to the Internet from the VM, configure your VM to use NAT network. However, you will not be able to connect to the VM from the host in such case. If you want to be able to connect to your VM and let VM connect to the internet at the same time you would have to use a Bridged network. In such a case you would have to configure the VM IP address manually (unless of course your network has a DHCP server to do that)

    - -- 1.7.10.2