Jun Wang

Report
HPC at HCC
Jun Wang
Outline of Workshop1
Overview of HPC Computing Resources at HCC
How to obtain an account at HCC
How to login a Linux cluster at HCC
How to Copy files to/from Linux cluster at HCC
Commonly Used Linux commands
Change password to your own after first login
How to edit a file using Linux vi editor
HPC at HCC
Jun Wang
Overview of HPC Computing Resources at HCC
Cluster
Firefly
Sandhills
Red
Tusker
Overview
Processors
RAM
871 (2.8 GHz , 64
bit)
720 node
Opteron, 4-Core
production-mode
8 GB per node
Per Node
LINUX cluster
280 2.2 GHz,
8-Core Per Node
1344 cores 2.2 GHz 42 Nodes with
44 Node
AMD Opteron 6128 128GB per node
Production-mode
96 cores at 1.9GHz
2 Nodes with
LINUX cluster
AMD Opteron 6168 256GB per node
40x Opteron 2261
70x Opteron 2354
266 node
43x Xeon E5520
Production-mode
40x Xeon E5530
LINUX cluster
~2500 Condor job
slots
106 node
Production-mode
LINUX cluster
Opteron 6272
2.1GHz, 4 CPU/64
cores per node
1.5-2GB RAM per
job slot
256 GB RAM per
node
Connection
Storage
800 MB/sec
Infiniband
interconnect
150 TB shared
Panasas storage
6 TB SATA RAID
73 GB per node
QDR Infiniband
Gigabit Ethernet
~1.5TB per node
Gigabit Ethernet
~2 PB of raw
storage space
QDR Infiniband
~350 TB shared
Lustre storage
~500GB local
scratch
HPC at HCC
Jun Wang
Firefly
Sandhills
Red
Tusker
HPC at HCC
Jun Wang
How to obtain an account at HCC
Group account application for faculty http://hcc.unl.edu/newusers/newgroup.index.php
User account application for faculty/postdocs/students
http://hcc.unl.edu/newusers/
HPC at HCC
Jun Wang
How to login a Linux cluster at HCC
On PC:
Download putty.exe to your desktop from
http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe
HPC at HCC
Jun Wang
How to login a Linux cluster at HCC
On Mac:
Click “Applications”-->”Utilities”-->”Terminal”
Type “ssh [email protected]
HPC at HCC
Jun Wang
How to Copy files to/from Linux cluster at HCC
On PC:
Download a free app WinSCP http://winscp.net/download/winscp514setup.exe
Install it using all default options
Note: You may need to convert file generated on Windows to Linux format
Type “dos2unix xxx” in a Linux terminal, where xxx the file name
HPC at HCC
Jun Wang
How to Copy files to/from Linux cluster at HCC
On Mac:
Open a terminal and type “scp -r $PWD/xxx [email protected]: ” to upload
Open a terminal and type “scp -r [email protected]:xxx ./ ” to download
HPC at HCC
Jun Wang
Commonly Used Linux commands
http://www.centos.org/docs/2/rhl-gsg-en-7.2/ch-doslinux.html
Changes directories:
cd /directory/directory
Lists files:
ls
Copies files:
cp thisfile.txt /home/thisdirectory
Moves files:
mv thisfile.txt /home/thisdirectory
Deletes files:
rm thisfile.txt
Creates a directory:
mkdir directory
View a file:
less thisfile.txt
Displays your present working directory:
pwd
Reset your password:
passwd
Finds a string of text in a file:
grep -i “Phrase” * -R
Search a file in a directory: find /SomeDirectory -name SomeFileName -type f --print
Exit a terminal:
exit
Displays command help:
man command
HPC at HCC
Jun Wang
Change password to your own after first login
Type “passwd” after login to any HCC cluster
Note: HCC uses LDAP to share users account and password info across all HCC clusters
HCC password rule:
Password minimum length 8
Minimum required digit characters 1
Minimum required alpha characters 1
Minimum required upper case characters 1
Minimum required character categories 1
Minimum token length 1
HPC at HCC
Jun Wang
How to edit a file using Linux vi editor
Type “vi test-vi” to create a file called test-vi
Press “i” key to enter edit mode
Press “Enter” key to enter command mode
Type some characters
HPC at HCC
Jun Wang
How to edit a file using Linux vi editor
Press “Esc” key to switch to command mode
Type“:wq” and Press ”Enter” key to save
file and exit to command line
Retype “vi test-vi” to check saved test-vi
Type “q” to quit. Press “i” key to re-edit
and “Esc” when done. Type “q!” to quit
without save or “wq” to save and quit
HPC at HCC
Jun Wang
Thank you for your attention!
Hands-on practice on zeng-cuda.unl.edu if you do not have a HCC account
Username: workshop
Create your own directory
HPC at HCC
Jun Wang
To be continued:
Familiar with Linux file system
Familiar with Shell environment
Familiar with queuing system
How to submit a serial job
How to submit a MPI parallel job
You may download this ppt file at the newly
designed electronics shop website
http://chem.unl.edu/eshop

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