The iCSF now has a node named jabberwock<\/em> containing three AMD FireGL v7800 GPUs. This node can be used to run graphical OpenGL<\/em> programs such as VMD, Paraview and Abaqus. The iCSF shares your CSF home directory and so this is a convenient place to run these visualization applications (you do not need to download large result files once a simulation running on the CSF has finished, for example).<\/p>\n By running on the jabberwock<\/em> node of the iCSF your application will use jabberwock’s<\/em> GPUs to render images, allowing you to interact with your model (e.g., a molecule or finite element mesh) while the application remains responsive.<\/p>\n Please email its-ri-team@manchester.ac.uk<\/a> to request access to the GPUs in jabberwock. Your username must be added to the correct unix group.<\/p>\n Specification<\/p>\n If you run your application on a non-GPU node then the application will send all of the data needed to render your models back to where the application’s GUI is being displayed. This might be the virtual desktop<\/em> (e.g., nyx2<\/em> or nyx3<\/em>) or it might be your local desktop. This is often slow because of the large amount of data being sent over the network (e.g., all of the data for a very dense finite element mesh). The local desktop may not have a GPU (the virtual desktops<\/em> do not have GPUs) and so slower software rendering<\/em> will be used to render the images. Hence interacting with the model can often feel sluggish.<\/p>\n By connecting to jabberwock<\/em>, and running your application using the method described below, all of the rendering will be done on the GPUs and only the final rendered image is sent back to your desktop (or the virtual desktop<\/em>). This is efficient due to the small amount of data in an image.<\/p>\n Follow the steps below to access the iCSF GPU node.<\/p>\n You must log in to the nyx3<\/strong><\/em> virtual desktop to access the iCSF GPU node. It has a fast, dedicated connection to the iCSF for accessing the GPU node.<\/p>\n Use the X2GO client<\/a> to connect to the host:<\/p>\n using your central University username and password.<\/p>\n To assist with connecting to the iCSF GPU node (named jabberwock<\/em>) for graphics use, we run an app named vglconnect<\/em> (do not<\/strong> run ssh):<\/p>\n From the nyx3<\/em> virtual desktop, open a shell window (Applications>System Tools>Terminal<\/em>) then connect to jabberwock<\/em> using:<\/p>\n This will ask for your iCSF password twice<\/strong> (it sets up two connections). <\/p>\n The vglconnect<\/em> program runs a small app on nyx3 named vglclient<\/em> which receives images from the GPUs. It then logs you in to jabberwock as normal (in fact vglconnect<\/em> uses ssh<\/em>).<\/p>\n One logged in to jabberwock<\/em> you should set up to run your application using the usual You then run your application using:<\/p>\n where myapp.exe<\/em> is the command used to run your application and args<\/em> are any optional additional flags your application may want.<\/p>\n The VMD is a graphical molecular dynamics package. We run it as follows:<\/p>\n This will display the VMD GUI on the virtual desktop but molecule rendering is done on GPU 0 of jabberwock – see diagram below. The sample molecule is available by loading in to VMD the visualization state file: <\/p>\n Paraview is a powerful scientific data visualization tool that can read many file formats and visualize the data using many different visualization techniques. We run it as follows:<\/p>\n This will display the Paraview GUI on the virtual desktop but the dataset rendering is done on GPU 2 of jabberwock (see diagram below – you will need to load in your own dataset).<\/li>\n<\/ol>\n There are three GPUs in jabberwock. They can be selected by running one of the following:<\/p>\n If no GPU number is specified then GPU 0 ( We are working on a method to automatically select a free GPU.<\/p>\n to connect to jabberwock from nyx3. Log out of jabberwock<\/em> and re-connect using the correct method.<\/dd>\n When you next run vglconnect<\/em> to log in to jabberwock it will automatically start a new copy of vglclient<\/em>.<\/dd>\n<\/dl>\n","protected":false},"excerpt":{"rendered":" UPDATE – 2016 The GPU node in the iCSF is no longer available. The iCSF now has a node named jabberwock containing three AMD FireGL v7800 GPUs. This node can be used to run graphical OpenGL programs such as VMD, Paraview and Abaqus. The iCSF shares your CSF home directory and so this is a convenient place to run these visualization applications (you do not need to download large result files once a simulation running.. Read more »<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":10,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-299","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/299","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/comments?post=299"}],"version-history":[{"count":20,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/299\/revisions"}],"predecessor-version":[{"id":660,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/299\/revisions\/660"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/10"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/media?parent=299"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}\n
Why use the GPU Node?<\/h2>\n
Connect to the nyx3<\/em> Virtual Desktop<\/h2>\n
\r\nnyx3.itservices.manchester.ac.uk\r\n<\/pre>\n
Connect to the iCSF GPU node jabberwock<\/em><\/h2>\n
\r\nvglconnect -s jabberwock\r\n<\/pre>\n
Running Graphical Application using vglrun<\/em><\/h2>\n
module load<\/code> commands (please see the software pages<\/a> for specific details).<\/p>\n\r\nvglrun myapp.exe args<\/em>\r\n<\/pre>\n
vglrun<\/code> command will run your application and force it to use GPU 0 in jabberwock for any rendering.<\/p>\nVMD example<\/h3>\n
\n
nyx3.itservices.manchester.ac.uk<\/code><\/li>\nvglconnect -s jabberwock<\/code> (enter your iCSF password twice)<\/li>\n\r\nmodule load apps\/binapps\/vmd\/1.9.1\r\nvglrun vmd\r\n<\/pre>\n
\/opt\/gridware\/apps\/binapps\/vmd\/sample_data\/1F45.vmd<\/pre>\n<\/li>\n<\/ol>\n
![\"VMD](\"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-content\/uploads\/x2go-nyx3-icsf-vmd-red.png\")
<\/a><\/p>\nParaview Example<\/h3>\n
\n
nyx3.itservices.manchester.ac.uk<\/code><\/li>\nvglconnect -s jabberwock<\/code> (enter your iCSF password twice)<\/li>\n\r\nmodule load apps\/binapps\/paraview\/4.1.0\r\nvglrun -d :0.2 paraview\r\n #\r\n # In this example we have used GPU 2 in jabberwock\r\n # (perhaps GPUs 0 and 1 are in use)\r\n<\/pre>\n
![\"Paraview](\"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-content\/uploads\/x2go-nyx3-icsf-paraview-red.png\")
<\/a><\/p>\nSelecting a GPU<\/h2>\n
\r\nvglrun -d :0.0 myapp.exe\r\nvglrun -d :0.1 myapp.exe\r\nvglrun -d :0.2 myapp.exe\r\n<\/pre>\n
:0.0<\/code>) will be used. <\/p>\nFrequently Asked Questions<\/h2>\n
\n
vglconnect -s jabberwock<\/pre>\n
vglrun app.exe<\/em><\/pre>\n<\/dd>\n
vglclient -kill<\/pre>\n