Metabolomics 2008 4th Annual Conference, Sept. 2-6, 2008
SetupX becomes open source
ClusterSupport
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Running cluster jobs from Windows requires 3 tools (curtesy of GW).
1) Putty - a free telnet SSH client (whats getty?)
2) WINCSP - a free ftp and transfer client
3) Cygwin/X - a free X-Windows client (activate XWindows if you use setup.exe from cygwin)
...don't forget to start your Cygwin bash shell and enter startx
...enter your login name and pwd and enter the clustername in Putty and WINSCP, setup X11 forwarding in PUTTY, voila!
The Sun Grid Engine can be configured via qmon
The 8 GByte nodes on Shiraz can be accessed via qmon -q highmem.q
The Explorer style File Manager can be started on the head node with nautilus
See other explanations in this PPT.
Some general command line tools for UNIX and LIN.X
We have access to two clusters.
Shiraz
1) Putty - a free telnet SSH client (whats getty?)
2) WINCSP - a free ftp and transfer client
3) Cygwin/X - a free X-Windows client (activate XWindows if you use setup.exe from cygwin)
...don't forget to start your Cygwin bash shell and enter startx
...enter your login name and pwd and enter the clustername in Putty and WINSCP, setup X11 forwarding in PUTTY, voila!
The Sun Grid Engine can be configured via qmon
The 8 GByte nodes on Shiraz can be accessed via qmon -q highmem.q
The Explorer style File Manager can be started on the head node with nautilus
See other explanations in this PPT.
| Command | Description | |
| qacct | Extract accounting information from cluster | |
| qalter | Changes the attributes of submitted but pending jobs | |
| qconf | SGE's cluster, queue etc configuration | |
| qdel | Job deletion | |
| qhold | Holds back submitted jobs for execution | |
| qhost | Shows status information about SGE hosts | |
| qmod | Modify queue statues: enabled or suspended | |
| qmon | X-windows Motif interface | |
| qrsh | SGE queue based rsh facility | |
| qselect | List queue matching selection criteria | |
| qsh | Opens an interactive shell on a low-loaded hosts | |
| qstat | Status listing of jobs and queues | |
| qsub | Commandline interface to submit jobs to SGE | |
| qtcsh | SGE queue based TCSH facility | |
| qtcsh, qsh | extended command shells that can transparently distribute execution of programs/applications to least loaded hosts via SGE. | |
Some general command line tools for UNIX and LIN.X
| find something in files | find . -print | xargs grep "findmestring" |
| list files |
ls -l |
| which java version | which java |
| which java compiler | which javac |
| show free memory | free |
| show detailed memory info | cat /proc/meminfo |
| show number of CPUs or processors | cat /proc/cpuinfo|grep processor|wc -l |
| show CPU type | cat /proc/cpuinfo |
| show running programs or tasks | ps aux|sort -n +2 |
| show tasks | ps aux|sort -rn +2|head -10 |
| history | show command history you typed |
| env | show environment variables |
| show processor and memory load 5x |
vmstat 2 5 |
| show every 2 sec. cpu san mem info | vmstat 2 |
| show running tasks | top |
| show running tasks from user B. Gates | top -u bgates |
| check largest memory pages: | cat /proc/meminfo | grep Huge |
| startx | start X-Windows |
| break some command or task | Ctrl-C or Strg-C |
| show free space on disk or HD |
df |
We have access to two clusters.
Shiraz
- 111 nodes, dual socket dual core Opteron running Rocks 4.1
- 2 Opteron 270 (2.0 GHz) processors per node
- 37 nodes w/ 8GB Ram, the rest have 4GB per node
- 6.4 TB (raw) backed up redundant storage
- 24 nodes, dual Opteron running Rocks 4.1
- Dual Opteron 248 (2.2 GHz) processors, 4GB RAM per node
- 3.2 TB (raw) backed up redundant storage
Created by
kind
Last modified 2008-07-08 10:32 PM
Last modified 2008-07-08 10:32 PM
