CSC Quick Reference: Getting Help File Transfer

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 laureate@top.univ.fi: (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 servicedesk@csc.fi
 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
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CSC Quick Reference: Getting Help File Transfer

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