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CSC Quick Reference: Getting Help File Transfer

This document provides a quick reference to common commands, tools, and resources for using CSC computing environments and services. It includes summaries of commands for getting help, file transfer, networking, programming, file storage, and system monitoring. Resources listed include supercomputers, interactive servers, software environments, compilers, and ways to contact CSC support.

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raul yondo
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61 views

CSC Quick Reference: Getting Help File Transfer

This document provides a quick reference to common commands, tools, and resources for using CSC computing environments and services. It includes summaries of commands for getting help, file transfer, networking, programming, file storage, and system monitoring. Resources listed include supercomputers, interactive servers, software environments, compilers, and ways to contact CSC support.

Uploaded by

raul yondo
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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CSC Quick Reference

Getting help File Transfer


 man program (manual pages)  scp computer1:file1 computer2:file2 (copy
 apropos stuff (looks for stuff in all files from computer1 to computer2)
documentation)  An example of scp usage:
 firefox (html browser)  scp nobel.tex [email protected]: (copies
 CSC services for researchers: the file nobel.tex (from current directory
http://research.csc.fi (see pwd above) to machine top.univ.fi)
 module load application (initialize the Because the directory in the target
environment of an application) machine was not specified the file goes to
 module avail (list applications on current the home directory of user laureate.)
server, module spider on Taito)  You can also install a graphical file transfer
 module list (list of loaded applications) program e.g. FileZilla
 module purge application (remove application  iput file (copies file to the iRODS archive)
environment)  iget file (copies file from iRODS archive to
 FAQ: https://research.csc.fi/faq-knowledge- current directory)
base  ils (shows content of your iRODS archive)
 General Guide: http://research.csc.fi/csc-guide  Files can be copied also using the web
browser via the Scientist's User Interface:
https://sui.csc.fi
Unix commands
 ls (list directory)
 less (print a file to the screen, quit with q) Networking
 cp (copy a file)  ssh computer (open a new secure session)
 rm (delete a file)  In Linux use ssh -X computer or ssh -Y
 mv (move or rename a file) computer to enable X-connection
 cd (change the current directory)  In Windows use NoMachine client instead as
 cat (sends the file to standard output) Windows does not have native support for
 pwd (print name of the current directory) remote graphics (much better than X-
 mkdir (create a directory) emulators like XMing)
 rmdir (delete a directory)  dos2unix changes Windows (DOS) format
 exit (quit the session) text files into Unix-format.
 passwd (change password)
 history (list all commands given previously)
 !stuff (executes the last command that started
Paging With less
with "stuff")  less file (print a file to the screen)
 head nobel.tex (list ten first lines of the file  ls -la | less (page the output of a command)
nobel.tex)  [return] (next line)
 tail -100 nobel.tex (list the last hundred lines of  [space] (next screen)
the file nobel.tex)  b (previous screen)
 tail -f nobel.tex (keeps listing the end of file  /stuff [enter] looks for the next occurrence of
nobel.tex. Handy for following an output "stuff", n gives the next, n the next, ...
file when lines are appended to it.)  h (list the commands of less)
 grep stuff nobel.tex (print lines containing the  q (quit the less program)
word stuff from the file nobel.tex)
 ls -la > file (output of a command to a file)
 ls -la | grep "nobel" (Chaining (piping)
Computers
multiple commands)  sisu.csc.fi (Cray XC supercomputer for
 tar cvf nob.tar nobel.* (make a tar-file nob.tar massively parallel jobs)
from all files whose names begin with  taito.csc.fi (HP supercluster for serial and
nobel You can also tar a directory.) parallel jobs)
 tar xvf nob.tar (extract all files from the tar-  taito-shell.csc.fi (HP supercluster, interactive
archive nob.tar) use)
 gzip nob.tar (compress file nob.tar to save  http://research.csc.fi/csc-s-servers
space)  nxkajaani.csc.fi NoMachine gateway to CSC's
 gunzip nob.tar.gz (uncompress file nob.tar.gz) servers. Some GUIs directly available.

CSC Quick Reference to Unix commands and CSC Computing Environment 2017-02-13 1/2
Command Line Shell Emacs Editor
 bash is CSC's standard command shell with  emacs file (start the emacs editor)
advanced command-line editing  emacs -nw file (emacs without X-windows)
 Up and down arrow keys recall old command  Notation [Ctrl]-c means: "hold down the
lines Control key and press the c key"
 [Ctrl]-d is the end-of-file character on Unix  Moving: cursor keys and page up/down keys
systems  [Ctrl]-x [Ctrl]-c (quit and save)
 [Ctrl]-d or the tab key lists possible choice  [Ctrl]-x [Ctrl]-s (save)
while you write a file name or a command  [Ctrl]-g (interrupt an emacs command if you
name get stuck in the minibuffer)
 [Ctrl]-z moves the current program or  [Ctrl]-h [Ctrl]-h (Emacs help system)
command to the background, e.g. goes  Other text editors are e.g. nano, and vi
from gnuplot to command prompt
 bg (makes the current job in the background to Program Development
continue execution)  Compilers on CSC machines (Fortran, C):
 fg (brings a job to the foregound)  GNU, Intel, Cray
 [ctrl]-r looks for a matching command from  Environment is different on different servers,
history backwards while typing check the server pages (see above)
 use the module command to check the
version and to load the environment. It will
File Storage Areas also put libraries in the path.
 $HOME User's home directory. Kajaani home  An example of compiling a program with gcc
is shared by Sisu and Taito and available  module load PrgEnv-gnu/5.0.41
on compute nodes, regular backups  cc -o prog -fast prog.c
 $TMPDIR Temporary directory. Local on each  Run the program: ./prog
node, old files are removed, no backup,
not available on Sisu compute nodes. Use
System Status
for compiling code.  saldo (show CPU quota)
 $WRKDIR Temporary directory. Local on each  quota -v (disk quota)
machine (except shared on Sisu and  ps (process status)
Taito), good place for large scratch files,  top (continuous process status)
files not accessed in 90 days are removed,  uptime (show the load of the computer, in
no backup. Hippu, you can use huptime)
 ARCHIVE long term storage used via the  who (list logged-in users)
iRODS commands. Module load irods  finger user (gives information about user)
needed in Vuori, Sisu and Hippu. ils: list  df -h (disk status in human readable units)
contents, iput file copy a file to archive,  du -hs * (disk space used by a directories)
iget file: copy a file from archive.  sbatch, squeue, scancel
Save only large files here. Use the tar and  sacct –j JOBID (info about completed jobs)
gzip commands to make one file of your  A graphical presentation of the server usage
directory before copying here. with history:
Recommended single file size: 10MB - https://sui.csc.fi/web/guest/host-monitor
300GB. Shared between machines, files
are kept during customership, within
backup. How to contact CSC
 IDA long term iRODS storage with flexible  User homepage: https://research.csc.fi/
sharing and access options.  Address: CSC - IT Center for Science Ltd.,
http://avointiede.fi/ida P.O.-BOX 405, 02101 Espoo
 $USERAPPL Directory to keep your  Street address: Keilaranta 14, Espoo
executables. Local to each machine, Is  Phone: (09) 457 2001,
visible to compute nodes and is within  ServiceDesk (09) 457 2821 between 8:30-
backup service. 16:00 or by email [email protected]
 Project directory. Can be requested from User  Forgotten password: https://sui.csc.fi
manager by project leader. Within backup  New user accounts:
service. https://research.csc.fi/accounts-and-
 http://research.csc.fi/csc-guide-directories-and- projects
data-storage-at-csc

CSC Quick Reference to Unix commands and CSC Computing Environment 2017-02-13 2/2

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