IgvFromComputeNode

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(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]] ...")
 
 
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= Remote display from compute node =
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= Remote X11 display from compute node =
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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
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== Install/Start X on Desktop ==
* Windows: X-Win32 from [http://www.uab.edu/it/software UAB IT]]
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*   '''Windows''': X-Win32 from [http://www.uab.edu/it/software UAB IT]
# connect to cheaha head node with X-forwarding:
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== ssh conection with X11 support ==
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=== ssh -X to cheaha  ===
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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
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=== Windows/ PuTTY ssh ===
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Check that Connection > SSH > X11 has a checkmark next to "Enable X11 forwarding"
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== Get a compute node ==
 
* allocate compute node with qlogin, with appropriate time/memory  
 
* allocate compute node with qlogin, with appropriate time/memory  
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** '''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
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   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
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== Launch app ==
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=== IGV ===
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  # '''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 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...
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