IgvFromComputeNode

From UABgrid Documentation
(Difference between revisions)
Jump to: navigation, search
(Install/Start X on Desktop)
 
(3 intermediate revisions by one 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/Start X on Desktop ==
 
== 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]
== ssh -X to cheaha  ==
+
 
 +
== ssh conection with X11 support ==
 +
 
 +
=== ssh -X to cheaha  ===
 
Connect to cheaha head node with X-forwarding:
 
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 ==
 
== Get a compute node ==
Line 15: Line 24:
 
** '''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!!
 
   # 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 app ==
 
== Launch app ==
 
=== IGV ===
 
=== IGV ===

Latest revision as of 10:22, 20 March 2014

Contents

[edit] 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

[edit] Install/Start X on Desktop

  • Windows: X-Win32 from UAB IT

[edit] ssh conection with X11 support

[edit] 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

[edit] Windows/ PuTTY ssh

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

[edit] 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

[edit] Launch app

[edit] 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