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<h3>JABAWS on VM (Virtual Machine)</h3>\r
<h4><a name="vmbexc" id="vmbexc"/>I cannot open VM using VirtualBox due to VERR_VMX_MSR_LOCKED_OR_DISABLED exception. Can you help?</h4>\r
- <p>VERR_VMX_MSR_LOCKED_OR_DISABLED exception means that Intel Virtualization technology is disabled or not supported by your computer. If you have such problem, please make sure you have configured 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. </p>\r
+ <p>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. </p>\r
<h4><a name="ovfOnVmware" id="ovfOnVmware"/>VMWare Player - Failed to query source for information. I cannot open OVF file using VMware player. Why is this?</h4>\r
- <p>At a time of writing, the latest version of VMware Player 3.1.2 support 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. </p>\r
+ <p>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. </p>\r
<h4><a name="vmiaccess" id="vmiaccess"/>I want to connect to the Internet from my VM. Can I do that?</h4>\r
\r
-<p>By default JABAWS VM is configured to use host-only networking. This means that the host can communicate with the VM via 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 Bridged network. In such case you would have to configure the VM IP address manually (unless of cause your network have a DHCP server to do that). </p>\r
+<p>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). </p>\r
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<div id="copyright">Last update: 17 November 2010<br/>\r
Peter Troshin and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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<p> JABAWS can be deployed on nearly any operation system, it can operate on a stand alone server as well as submit the jobs to the cluster. Thanks to <a href="http://www.drmaa.org/">DRMAA</a> it integrates well with a large variety of cluster job management systems. <a href="http://www.jalview.org">Jalview</a> from version 2.6 integrates with JABAWS and can be configured to submit jobs to different versions of JABAWS, for example to your local, lab version, or publicly available version elsewhere. As JABAWS can be installed in your lab, or indeed on your personal computer, it eliminates the need to send your private information to the outside, to one of the publicly accessible servers. JABAWS can run programs with additional parameters defined by you, so you are no longer limited to defaults. JABAWS is safe to install for public access as it could limit the size of the tasks which it accepts and denies access to resources within web application folder. Please look in the how to for more information on <a href="howto.html#wjaba">JABAWS benefits</a>. </p>\r
<h4>Public JABAWS Server</h4>\r
+<p class="attention">Please note that JABAWS computing cluster is going for a maintenance shutdown on the weekend starting from the 8-th of January. Therefore, no services will be available from <span class="style1">6pm Friday the 7th of January</span>, until <span class="style1">12am Monday the 10th of January 2011 GMT</span>. </p>\r
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-For programmatic access to JABAWS please refer to the How To section <a href="howto.html#connectto">using JABAWS in your program</a>. \r
+<p>For programmatic access to JABAWS please refer to the How To section <a href="manual.html#connectto">using JABAWS in your program</a>.</p>\r
+<p>Please feel free to post your questions/issues to the <a href="http://www.jalview.org/mailman/listinfo/jabaws-discuss">jabaws-discuss</a> mailing list. </p>\r
<h4>Authors</h4>\r
<p>Peter Troshin and Geoff Barton are the authors of the JABA Web\r
Services. Jim Procter helped with the JABAWS design process and web\r
<li><a href="#warfile">JABAWS War File Content</a></li>\r
</ul>\r
<h3>JABAWS Virtual Appliance </h3>\r
-<h4><a name="whenvm" id="whenvm"/></a>When to use virtual appliance </h4>\r
-<p>The appliance best suits for individual users who want to use JABA web services locally, without Internet connection, want to keep their data private and uses Windows as their main OS. The appliance is a self contained unit of software and as such may be an attractive option for Linux, UNIX or Mac users but they can always deploy a <a href="#instwar">war distribution</a> instead. <br />\r
+<h4><a name="whenvm" id="whenvm"/></a>When to use the virtual appliance </h4>\r
+<p>The appliance best suits for individual users who want to use the JABA web services locally, without Internet connection, want to keep their data private and uses Windows as their main OS. The appliance is a self contained unit of software and as such may be an attractive option for Linux, UNIX or Mac users but they can always deploy a <a href="#instwar">war distribution</a> instead. <br />\r
To run the appliance you would need to have relatively powerful computer. The appliance comes pre configured to use 1 CPU and 512M of memory and the minimum amount of memory required is about 378M. </p>\r
<h4><a name="virtualbox" id="virtualbox"/>VirtualBox appliance configuration</h4>\r
-<p>VirtualBox can be used to run JABAWS services from Windows, Linux, Solaris or Mac host operation systems. Use VitualBox "Import Appliance" option to import JABAWS. Please bear in mind that to benefit from multiple CPU support under VirtualBox software you need to enable<a href="http://en.wikipedia.org/wiki/X86_virtualization"> hardware virtualization extensions</a>, 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. </p>\r
-<p>We found that, by default, virtualization extensions are enabled in VirtualBox irrespective of whether your computer supports them. You will get the <a href="howto.html#vmbexc"></a><a href="howto.html#vmbexc">VERR_VMX_MSR_LOCKED_OR_DISABLED</a> exception if you 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. </p>\r
+<p>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<a href="http://en.wikipedia.org/wiki/X86_virtualization"> hardware virtualization extensions</a>, 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. </p>\r
+<p>We found that, by default, virtualization extensions are enabled in VirtualBox irrespective of whether your computer supports them. You will get the <a href="howto.html#vmbexc"></a><a href="howto.html#vmbexc">VERR_VMX_MSR_LOCKED_OR_DISABLED</a> 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. </p>\r
<p>VirtualBox JABAWS VM configuration screen shot displaying virtualization settings.</p>\r
<p><img src="images/vmb_virtual.png" alt="VT-x extension on VirtualBox" width="669" height="535" /></p>\r
<h4><a name="vmplayer" id="vmplayer"/>VMware Player appliance configuration </h4>\r
-<p>Free <a href="http://downloads.vmware.com/d/info/desktop_downloads/vmware_player/3_0">VMware Player</a> can be used to run JABAWS services from Windows and Linux host operation system, there is no support for Mac in time of writing. However, <a href="https://www.vmware.com/vmwarestore/buyfusion.html">VMware Fusion</a>, a commercial VMware product, offer virtual machine support for Mac computers too. </p>\r
-<p>To run JABAWS server on VMware player, unpack JABAWS VM into one of the folders on your local hard drive. Open VMware Player, and click "Open Virtual Machine" and point the Player to the location of the JABAWS, choose JABAWS.vmx file to open an appliance. </p>\r
+<p>The free <a href="http://downloads.vmware.com/d/info/desktop_downloads/vmware_player/3_0">VMware Player</a> can be used to run the JABAWS services from the Windows and Linux host operating systems, there is no support for Mac in time of writing. However, <a href="https://www.vmware.com/vmwarestore/buyfusion.html">VMware Fusion</a>, a commercial VMware product, offers virtual machine support for Mac computers too. </p>\r
+<p>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. </p>\r
<p>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. </p>\r
<h4><a name="jabawsAppliance" id="jabawsAppliance"/>JABAWS Appliance details</h4>\r
-<p>By default, 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 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 let your VM deal with larger tasks, e.g. work with large alignments.</p>\r
+<p>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.</p>\r
<p>The VMware Player screen shot below displays JABAWS VM CPU settings. </p>\r
<p><img src="images/VMware_cpu.png" alt="vmware cpu settings" width="852" height="267" border="1" /></p>\r
<p><strong>JABAWS appliance configuration: </strong></p>\r
- Date of creation: 8 October 2010<br />\r
- CPUs : 1<br />\r
- RAM : 512 MB<br />\r
- - Networking : Host only (the VM has no access to the outside network, nothing from outside network can access the VM)<br />\r
+ - Networking : Host only (the VM has no access to the outside network, nothing from the outside network can access the VM)<br />\r
- Hard disk : 20 GB (expanding)<br />\r
- VMware tools : Installed</p>\r
<p><strong>OS info</strong><br />\r
</ul>\r
<p>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.</p>\r
<h4><a name="jalviewWithJaba" id="jalviewWithJaba"/>Configuring Jalview to work with your JABAWS VM</a> </h4>\r
-<p>After you booted 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 <a href="http://www.jalview.org/help/html/webServices/JABAWS.html">help pages</a>. </p>\r
+<p>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 <a href="http://www.jalview.org/help/html/webServices/JABAWS.html">help pages</a>. </p>\r
<p><img src="images/vm_welcome_screen.png" alt="JABAWS welcome screen" width="734" height="461" /></p>\r
<p>If you click on Advanced Menu, you will see the configuration console, similar to the one below. </p>\r
<p><img src="images/VMware_booted.png" alt="JABAWS welcome screen" width="735" height="461" /></p>\r
git://source.jalview.org / jabaws.git / commitdiff