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howto:tipsandtricks [2019/04/16 08:49]
ccrosby [Please slow down and work methodically]
howto:tipsandtricks [2019/07/15 13:20] (current)
ccrosby [Transferring files to the cluster]
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 ===== Running software with GUI's ===== ===== Running software with GUI's =====
 The usual ssh-session and interactive PBS sessions do not by default support any graphics. ​ If you need to run a software package with a GUI (many pre-processors,​ for example), you need a session with graphics capability. ​ There are two ways of getting this: The usual ssh-session and interactive PBS sessions do not by default support any graphics. ​ If you need to run a software package with a GUI (many pre-processors,​ for example), you need a session with graphics capability. ​ There are two ways of getting this:
-  - Use a VNC session to connect to one of the two visualization nodes, as per the instructions on [[howto:​remote_viz|Remote visualization]].+  - Use a VNC session to connect to one of the two visualization nodes, as per the instructions on [[howto:​remote_viz|Remote visualization]].  Keep in mind that it is possible and practical to get a VNC session directly on a compute node, without using one of the dedicated visualization nodes.
   - Use X-forwarding. ​ This is only a realistic option if you are on a fast connection to the CHPC.  ssh -X into lengau, then ssh -X from there to your compute node that you already have interactive PBS session on (see above). ​ Thanks to the wonders of Mesa and software rendering, quite sophisticated graphics processing may be done this way.  Look for the Mesa modules if you need OpenGL-capable software to run in this manner.   - Use X-forwarding. ​ This is only a realistic option if you are on a fast connection to the CHPC.  ssh -X into lengau, then ssh -X from there to your compute node that you already have interactive PBS session on (see above). ​ Thanks to the wonders of Mesa and software rendering, quite sophisticated graphics processing may be done this way.  Look for the Mesa modules if you need OpenGL-capable software to run in this manner.
   - You can also get an X-capable interactive PBS session by appending ''​ -X ''​ to your ''​qsub -I ''​ instruction. ​ This will only work if your ssh-session into the login node has X-forwarding turned on, that is, ''​ssh -X user@lengau.chpc.ac.za''​ or ''​ssh -Y user@lengau.chpc.ac.za''​   - You can also get an X-capable interactive PBS session by appending ''​ -X ''​ to your ''​qsub -I ''​ instruction. ​ This will only work if your ssh-session into the login node has X-forwarding turned on, that is, ''​ssh -X user@lengau.chpc.ac.za''​ or ''​ssh -Y user@lengau.chpc.ac.za''​
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 ===== Transferring files to the cluster ===== ===== Transferring files to the cluster =====
-Command line scp and rsync are the usual methods for data transfer. ​ However, it is easy to make mistakes, and you need to have the path right. ​ MobaXterm (see above) has an easy to use "drag & drop" interface. ​ [[https://​filezilla-project.org|FileZilla]] is fast, easy to use and runs on Linux, Windows and OSX.  A different option is to use sshfs to mount your lengau directory directly on your workstation. ​ There is a [[https://​github.com/​Foreveryone-cz/​win-sshfs/​releases|Windows sshfs client]] that sort-of works. ​ Sometimes.+Large amounts of data should be transferred by means of [[howto:​globus|Globus]],​ which provides a GUI for managing your data transfers. ​ Globus is based on the GridFTP protocol, and is faster and more robust than scp-based methods. 
 + 
 +Command line scp and rsync are the usual methods for data transfer ​of smaller files. ​ Remember to transfer files to scp.chpc.ac.za rather than lengau.chpc.ac.za  ​However,​ it is easy to make mistakes, and you need to have the path right. ​ MobaXterm (see above) has an easy to use "drag & drop" interface. ​ [[https://​filezilla-project.org|FileZilla]] is fast, easy to use and runs on Linux, Windows and OSX.  A different option is to use sshfs to mount your lengau directory directly on your workstation. ​ There is a [[https://​github.com/​Foreveryone-cz/​win-sshfs/​releases|Windows sshfs client]] that sort-of works. ​ Sometimes.
  
  
 ===== How to qsub from a compute node ===== ===== How to qsub from a compute node =====
-Lengau is set up in such way that it is not possible to submit another ​PBS script (qsub) ​from a compute node.  However, it is possible to have an ssh command in a PBS script, so the obvious solution is to ssh to the login node in order to submit another PBS script, if you wanted to submit another PBS script at the completion of the current one, you could insert a line like this at the end of your first script:+You may have difficulties submitting ​a PBS job from a compute node.  However, it is possible to have an ssh command in a PBS script, so the obvious solution is to ssh to the login node in order to submit another PBS script, if you wanted to submit another PBS script at the completion of the current one, you could insert a line like this at the end of your first script:
 <​code>​ <​code>​
 ssh login2 qsub /​mnt/​lustre/​users/​jblogs/​scripts/​PBS_Script1 ssh login2 qsub /​mnt/​lustre/​users/​jblogs/​scripts/​PBS_Script1
/var/www/wiki/data/attic/howto/tipsandtricks.1555397372.txt.gz · Last modified: 2019/04/16 08:49 by ccrosby