Basic Unix/Linux

Home , Echo (command), Head (Unix), History (command), Tail (Unix), Tar (computing)

Useful Links

MGHPCC: wiki.umassrc.org

General and detailed info as well as a number of tutorials available: (1) Intro to Linux and HPC, (2) Crash Course in Perl Programming and (3) Crash Course in Python Programming

HPC seminar webpage: this week’s tutorials will be posted here

http://people.math.umass.edu/~johnston/HPC_MGHPCC_S15.html

Google: www.google.com everything else! UMass HPC Tutorial

Using the UMass Shared Cluster at the MGHPCC UMass Shared Cluster

Enables faculty to focus on research! (rather than facilities/IT management)

• ~10,000 cores (Intel & AMD) including a handful of K80 GPU enabled nodes • GNU & Intel compilers and libraries along with a large number of loadable modules • Inﬁniband network with 400TB of high speed storage • LSF batch scheduler • Direct ﬁber connections from Amherst campus to MGHPCC to handle large data transfers Obtaining an Account

There is absolutely no cost for using the Shared Cluster!

https://ghpcc06.umassrc.org/hpc/index.php

students: you will need to be sponsored by a PI, most likely your professor, in order to obtain an account Basic Unix/Linux commands bash shell: ssh, scp man ls cd & pwd Top 11! mkdir & rmdir cp, mv & rm cat, more, head & tail env & echo history & grep chmod tar, gzip & gunzip editors: vi, emacs or xemacs login via ssh & transferring data via scp

Secure SHell (ssh): add -X for window forwarding

ssh [email protected] ! or

ssh -l username ghpcc-6.umassrc.org

Secure CoPy (scp): scp filename [email protected]:. ! or ! scp [email protected]:filename . man format and display online manuals (man): e.g. man ls ls, cd & pwd list directory contents (ls): ls ls * * is a wildcard ls -lt ls -a change directory (cd): cd cd /usr/local cd .. print working directory (pwd): displays current directory Unix/Linux file system mkdir & rmdir make directory (mkdir): mkdir junk mkdir junk/new remove directory (rmdir): rmdir -p junk

cp, mv & rm

copy file (cp): cp file_a file_b move file (mv): mv file_a file_b remove file (mv): mv file_a file_b cat, more, head & tail

concatenate and print (cat): cat file cat file_a file_b > file_c

> is ﬁle/output redirect

file perusal filter (more): more file cat file | more I is the pipe ‘operator’ output portion of file (head & tail): head file head -10 file tail file Basic Unix/Linux commands bash shell: ssh, scp man ls cd & pwd Top 11! mkdir & rmdir cp, mv & rm cat, more, head & tail env & echo history & grep chmod tar, gzip & gunzip editors: vi/vim, emacs or xemacs env & echo environment (env): display environment vars & settings echo variable (echo): echo $HOME echo $OMP_NUM_THREADS echo $LD_LIBRARY_PATH

history & grep

history (history): display command history

ﬁnd expression (grep): print lines matching a pattern

e.g. history | grep ssh I is the pipe ‘operator’ chmod change ﬁle mode bits (chmod):

tar, gzip & gunzip tape archive (tar): create/extract a file ‘archive’ tar -cvf directory.tar directory_name tar -xvf directory.tar zip and unzip (gzip & gunzip): compress & uncompress a file gzip file gunzip file.gz vi/vim vi & vim are the basic Unix/Linux file editors available modules & software packages

http://wiki.umassrc.org/wiki/index.php/Provided_Software example: using Intel compilers

you must load the needed modules

$ module load intel/composer_xe_2013_sp1

$ module load intel/intel/mkl_libraries_from_composer_xe_2013_sp1 $ module list batch jobs and the LSF system

IBM Load Sharing Facility, a commercial product!

http://ghpcc06.umassrc.org/doc/lsf/

http://wiki.umassrc.org/wiki/index.php/Submitting_Cluster_Jobs more to come

Wednesday: MATLAB & R

Thursday: C/C++/Fortran, linking to Optimized libraries & basic OpenMP programming

Thank You!