IgvFromComputeNode: Difference between revisions

From Cheaha
Jump to navigation Jump to search
(Created page with "= Remote display from compute node = Example program: IGV # Install & Launch X-Win on your desktop machine * Windows: X-Win32 from [http://www.uab.edu/it/software UAB IT]] ...")
 
No edit summary
 
(6 intermediate revisions by the same user not shown)
Line 1: Line 1:
= Remote display from compute node =
= Remote X11 display from compute node =
 
Alternately, you can use VNC which can be faster for slow connections: [[Setting_Up_VNC_Session]]


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 conection with X11 support ==
 
=== 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
=== Windows/ PuTTY ssh ===
Check that Connection > SSH > X11 has a checkmark next to "Enable X11 forwarding"
== 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!!
   # 4 hours, 6G RAM
   # 4 hours, 6G RAM
   qlogin -l h_rt=0:04:00,vf=6G
   qlogin -N IGV_6g -l h_rt=0:04:00,vf=6G
   # 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
   /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...

Latest revision as of 16:22, 20 March 2014

Remote X11 display from compute node

Alternately, you can use VNC which can be faster for slow connections: Setting_Up_VNC_Session

Example program: IGV

Install/Start X on Desktop

ssh conection with X11 support

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

Windows/ PuTTY ssh

Check that Connection > SSH > X11 has a checkmark next to "Enable X11 forwarding"

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 -N IGV_6g -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...