IgvFromComputeNode

From UABgrid Documentation
(Difference between revisions)
Jump to: navigation, search
(Remote display from compute node)
(Remote display from compute node)
Line 3: Line 3:
 
Example program: IGV  
 
Example program: IGV  
  
# Install & Launch X-Win on your desktop machine
+
== Install/Start X on Desktop ==
* Windows: X-Win32 from [http://www.uab.edu/it/software UAB IT]]
+
**  '''Windows''': X-Win32 from [http://www.uab.edu/it/software UAB IT]
# connect to cheaha head node with X-forwarding:
+
== ssh -X to cheaha
 +
Connect to cheaha head node with X-forwarding:
 
   ssh -X cheaha.uabgrid.uab.edu
 
   ssh -X cheaha.uabgrid.uab.edu
 
   # check that "echo $DISPLAY" shows you something
 
   # check that "echo $DISPLAY" shows you something
 
   # check that "xterm" works
 
   # check that "xterm" works
 +
== Get a compute node ==
 
* allocate compute node with qlogin, with appropriate time/memory  
 
* allocate compute node with qlogin, with appropriate time/memory  
 
** '''WARNING''': if you run IGV on the cluster head-node, you will bring on the wrath of the cluster admins!!
 
** '''WARNING''': if you run IGV on the cluster head-node, you will bring on the wrath of the cluster admins!!
Line 15: Line 17:
 
   # check that "echo $DISPLAY" shows you something
 
   # check that "echo $DISPLAY" shows you something
 
   # check that "xterm" works
 
   # check that "xterm" works
* launch IGV
+
== Launch app ==
 +
=== IGV ===
 
   # '''WARNING''': run only on compute nodes, NEVER on head-node
 
   # '''WARNING''': run only on compute nodes, NEVER on head-node
 
   /share/apps/ngs-ccts/IGV/igv.sh
 
   /share/apps/ngs-ccts/IGV/igv.sh
 
   # or
 
   # or
 
   /share/apps/ngs-ccts/IGV/igv6g  # doesn't seem to give 6G ram...
 
   /share/apps/ngs-ccts/IGV/igv6g  # doesn't seem to give 6G ram...

Revision as of 22:29, 11 September 2012

Contents

Remote display from compute node

Example program: IGV

Install/Start X on Desktop

    • Windows: X-Win32 from UAB IT

== ssh -X to cheaha Connect to cheaha head node with X-forwarding:

 ssh -X cheaha.uabgrid.uab.edu
 # check that "echo $DISPLAY" shows you something
 # check that "xterm" works

Get a compute node

  • allocate compute node with qlogin, with appropriate time/memory
    • WARNING: if you run IGV on the cluster head-node, you will bring on the wrath of the cluster admins!!
 # 4 hours, 6G RAM
 qlogin -l h_rt=0:04:00,vf=6G
 # check that "echo $DISPLAY" shows you something
 # check that "xterm" works

Launch app

IGV

 # WARNING: run only on compute nodes, NEVER on head-node
 /share/apps/ngs-ccts/IGV/igv.sh
 # or
 /share/apps/ngs-ccts/IGV/igv6g  # doesn't seem to give 6G ram...
Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox