| • | basic commands | • | using Condor | • | managing jobs | • | file permissions | • | shell scripts | • | more info | • |
| Basic commands | [top] |
| cd | <path> | changes directory to path |
| .. | changes to parent directory | |
| ~ | changes to home directory | |
| (s)cp | <source path> <destination path> | (secure) copies from source path to destination path |
| du | find disk usage (in directory) | |
| -hs | find disk usage (in "human-readable" form) | |
| -a <path> |sed -n '$= ' | count number of files in path | |
| find | <path> \*<string>\* | find all files below path |
| finger | <username> | shows login information about username |
| grep | <pattern> <file> | scans file for instances of patternand prints the relevant lines |
| -c <pattern> <file> | counts instances of pattern in file | |
| hostname | displays name of current machine (in a cluster) | |
| -i <machine name> | displays IP address of a machine (in a cluster) | |
| ls | lists all files and directories in current location | |
| <path> | lists files in path | |
| -a | lists all files (including "hidden" files) | |
| -l | lists files, showing file info (permissions, dates) | |
| | more | lists files one page at a time (advanced by space) | |
| mkdir | <directory name> | creates a directory directory name |
| mv | <original path> <destination path> | moves/renames file(s) from original path to destination path |
| pssh | executes a command on all machines in a cluster | |
| "ps -fu maman" | shows all processes of user maman | |
| w | shows who is logged in on each machine (individually) | |
| "top -n 1 -b" | shows top 4 processes on each machine (individually) | |
| <command> <file> | executes command for cluster machines listed in file (each machine on a separate line) | |
| rm | <path> | removes (deletes) a file with specified path |
| -R <directory name> | removes (deletes) a directory and all files contained within it | |
| rmdir | <directory name> | removes a directory specified by directory name (must be empty) |
| who | lists all usernames logged into a system |
| Using Condor | [top] |
Condor is a job submission and queue management system for computer clusters. Here are a few basic commands:
| condor_prio | -p <value> <jobno> | changes priority of jobno within user to value (values range from -20 to +20, with +20 being best priority) |
| condor_q | shows the condor queue, including job status and runtime | |
| -run | shows only the running jobs, with host machine information | |
| -submitter <username> | shows the job info for a specific user | |
| condor_rm | <jobno> | removes the job jobno from the queue |
| condor_status | shows the status of the cluster, including activity and job runtime | |
| -run | shows the machines in the cluster with running jobs, including user allocation | |
| condor_submit | <command file> | submits jobs described within command file to the condor queue |
| condor_userprio | shows (active) user queue priorities | |
| -all | shows full user queue priority info (effective and real priorities, resources used...) | |
| -setprio <username> <value> | changes queue priority of username to value | |
| -setfactor <username> <value> | changes queue priority factor of username to value |
Examples of some of these commands and Condor command files are here and more fully here (departmental documents). The official Condor manual is useful for setup and extra commands.
| Managing jobs | [top] |
| kill -<value> <pid> | kills process with pid pid with option flag value (eg. kill -9 <pid> will hard kill the job) |
| ps ux | finds (user-)running processes on a terminal |
| top | shows all processes running on a machine (incl. info about memory/cpu usage, pid etc) |
| renice <value> <pid> | changes priority of process with pid pid to nice value value (eg. renice -19 <pid> will set the job to priority 19) |
| Shell scripts | [top] |
A bit of information about running scripts...
| at now -f <file> | &larr runs an executable file from the shell prompt |
Example of a simple executable file:
| nice -19 | R | --save -q | < inscone | > outscone.out |
| &uarr | &uarr | &uarr | &uarr | &uarr |
| set priority of job | application | arguments to application | input file (eg R commands) | output file (screen output) |
You can use a "master" file to e.g. run different scripts depending on specific machines (in a cluster):
| #!/bin/csh | ||
| setenv HOSTNAME `hostname -s` | &larr | sets HOSTNAME variable to short hostname (without domain) |
| cd /home/maman/mydir | &larr | sets directory containing executable |
| if ($HOSTNAME == "zeppo") then | ||
| at now -f runscone1 | &larr | runs executable |
| else if ($HOSTNAME == "chico") then | ||
| at now -f runscone2 | ||
| ... | ||
| else | ||
| echo "Unknown host" | ||
| endif |
| More info... | [top] |