introduction to euler - eth z · introduction to euler. claudia thurnherr ... introduction and...
TRANSCRIPT
||
Christian Loosli and Claudia Thurnherr *
* Contact: [email protected], [email protected]
Laboratory of Composite Materials and Adaptive Structures
20.09.2016Claudia Thurnherr 1
Introduction to Euler
|| 20.09.2016Claudia Thurnherr 2
Outline
Introduction and ideal simulation procedure
How to connect to Euler
How to exchange files
Most important Unix commands
How to get around on Euler
Euler example: Ansys
Euler example: Abaqus
Euler example: COMSOL
|| 20.09.2016Claudia Thurnherr 3
Outline
Introduction and ideal simulation procedure
How to connect to Euler
How to exchange files
Most important Unix commands
How to get around on Euler
Euler example: Ansys
Euler example: Abaqus
Euler example: COMSOL
|| 20.09.2016Claudia Thurnherr 4
Introduction and ideal simulation procedure
Euler is the high performance computing cluster at ETH
Every ETH member has access to Euler and can login (at the moment each user has available
storage of 16GB in the home folder with back-up and 2.5TB scratch without back-up)
Although you sometimes need to wait to start your batch job, there are a lot of resources
available which help you to run your simulation as fast as possible
1. Pre-processing:
• Modeling/mesh
• On your own
laptop/computer
2. Pre-processing
(if needed):
• Meshing/high
fidelity
• On griffin server
Solving:
• On your own
laptop/computer
(if small)
• On Euler
Post-processing:
• On your own
laptop/computer
• On griffin server (if
needed)
|| 20.09.2016Claudia Thurnherr 5
Outline
Introduction and ideal simulation procedure
How to connect to Euler
How to exchange files
Most important Unix commands
How to get around on Euler
Euler example: Ansys
Euler example: Abaqus
Euler example: COMSOL
|| 20.09.2016Claudia Thurnherr 6
How to connect to Euler
Euler is Unix based, hence you
need SSH (Secure Shell) as a
network protocol
We recommend to use the
program PuTTY
Host Name: euler.ethz.ch
Login with your nethz credentials
|| 20.09.2016Claudia Thurnherr 7
How to connect to Euler
Euler is Unix based, hence you
need SSH (Secure Shell) as a
network protocol
We recommend to use the
program PuTTY
Host Name: euler.ethz.ch
Login with your nethz credentials
|| 20.09.2016Claudia Thurnherr 8
Outline
Introduction and ideal simulation procedure
How to connect to Euler
How to exchange files
Most important Unix commands
How to get around on Euler
Euler example: Ansys
Euler example: Abaqus
Euler example: COMSOL
|| 20.09.2016Claudia Thurnherr 9
How to exchange files
To upload files to your Euler-
folder you need a ftp client
(File Transfer Protocol)
We recommend to use
FileZilla or WinSCP
Use SFTP (Secure File
Transfer Protocol):
sftp://euler.ethz.ch
|| 20.09.2016Claudia Thurnherr 10
Outline
Introduction and ideal simulation procedure
How to connect to Euler
How to exchange files
Most important Unix commands
How to get around on Euler
Euler example: Ansys
Euler example: Abaqus
Euler example: COMSOL
|| 20.09.2016Claudia Thurnherr 11
Most important Unix commands (use Tab-key for auto-completion)
Command Meaning example
cd Change directory cd folder
cd .. Go to parent directory cd ../otherFolder
cp Copy cp file1 folder1
mkdir Make directory mkdir folder1
touch Make new file touch file1
mv Move or rename mv file1 folder1/folder2/folder3
mv file1 file2
rm Remove rm file1
-f Force (potentially dangerous) rm -f file1
-r Recursive (to address subfolders as well) cp -r folder1 folder 2 (if folder 1
contains other folders)
|| 20.09.2016Claudia Thurnherr 12
Most important Unix commands (use Tab-key for auto-completion)
Command Meaning example
ls Show files in the current directory
pwd Show path
emacs filename Opens a file in the text editor emacs
gzip filename Compresses files
gunzip Uncompresses files
* To replace some letters file_*.txt
exit Close terminal / connection
Most things can also be done with the GUI of the FTP client (e.g. FileZilla, WinSCP)
|| 20.09.2016Claudia Thurnherr 13
Outline
Introduction and ideal simulation procedure
How to connect to Euler
How to exchange files
Most important Unix commands
How to get around on Euler
Euler example: Ansys
Euler example: Abaqus
Euler example: COMSOL
|| 20.09.2016Claudia Thurnherr 14
How to get around on Euler
All the important information are available in
the Euler-WIKI:
http://www.clusterwiki.ethz.ch/brutus/Getting_
started_with_Euler
|| 20.09.2016Claudia Thurnherr 15
How to get around on Euler
Before you start: check which version of your
needed software is installed on Euler
See also:
http://www.clusterwiki.ethz.ch/brutus/Euler_Ap
plications#Applications_on_Euler
Euler Command Meaning
module avail Displays available versions of an
application / library
module list Displays the currently loaded modules
module load Loads a specific version of an application
module purge Unloads all currently loaded modules
|| 20.09.2016Claudia Thurnherr 16
How to get around on Euler
Euler Command Meaning Example
bsub [command] Start job as a batch job (By default it will
start with 1 core for 4 hours using at most 1
GB of RAM.)
bsub matlab my_matlab_code.m
bsub matlab my_matlab_code.m
batch job Module /
software
File name
|| 20.09.2016Claudia Thurnherr 17
How to get around on Euler: special commands for Euler
Euler Command Meaning Example
bsub [command] Start job as a batch job (By default it will
start with 1 core for 4 hours using at most 1
GB of RAM.)
bsub matlab my_maltab_code.m
bqueues Shows the running and pending jobs for all
the different queues
Available for us: 4h, 24h, 120h, 30days,
recommended: 4h, 24h
bjobs / bbjobs Shows status of submitted jobs
busers Shows how many resources you can use
Also refer to: http://www.clusterwiki.ethz.ch/brutus/LSF_mini_reference
On the application webpage you find links for various software specific commands
http://www.clusterwiki.ethz.ch/brutus/Euler_Applications#Applications_on_Euler
|| 20.09.2016Claudia Thurnherr 18
Outline
Introduction and ideal simulation procedure
How to connect to Euler
How to exchange files
Most important Unix commands
How to get around on Euler
Euler example: Ansys
Euler example: Abaqus
Euler example: COMSOL
|| 20.09.2016Claudia Thurnherr 19
Euler example: Ansys
Upload your infile.inp to Euler
If you work with Ansys classic, your input file is just your APDL file
If you work with Ansys Workbench, you need to export your input file:
|| 20.09.2016Claudia Thurnherr 20
Euler example: Ansys
Upload your infile.inp to Euler
Type the command:
module load ansys/17
bsub –n 4 –W 4:00 –R “rusage[mem=2000]” “ansys170 –np 4 <infile.inp>
outfile.out”
-n / -np: number of processors
-W: desired time slot (4:00, 24:00, 120:00, …)
-mem: RAM memory allocationAlso refer to:
http://www.clusterwiki.ethz.ch/
brutus/Ansys_MECHANICAL
|| 20.09.2016Claudia Thurnherr 21
Euler example: Ansys
To use distributed computing
Type the command:
module load ansys/17
bsub –n 4 –W 4:00 –R “rusage[mem=2000]” “ansys170 -dis –np 4 <infile.inp>
outfile.out”
-n / -np: number of processors
-W: desired time slot (4:00, 24:00, 120:00, …)
-mem: RAM memory allocationAlso refer to:
http://www.clusterwiki.ethz.ch/
brutus/Ansys_MECHANICAL
|| 20.09.2016Claudia Thurnherr 22
Euler example: Ansys
For the post-processing in Ansys classic: Click on “General Postproc Read Results”
For the post-processing in Workbench: download the solution files (.rst) from Euler and import it
as follows:
|| 20.09.2016Claudia Thurnherr 23
Outline
Introduction and ideal simulation procedure
How to connect to Euler
How to exchange files
Most important Unix commands
How to get around on Euler
Euler example: Ansys
Euler example: Abaqus
Euler example: COMSOL
|| 20.09.2016Claudia Thurnherr 24
Euler example: Abaqus
Upload your infile.inp to Euler
Type the command:
module load abaqus
bsub –n 4 –W 4:00 –R “rusage[mem=2000]” abaqus job=infile cpus=4 [Abaqus-
Parameters]
-n / -np: number of processors
-W: desired time slot (4:00, 24:00, 120:00, …)
-mem: RAM memory allocation
Also refer to: http://www.clusterwiki.ethz.ch/brutus/Abaqus
|| 20.09.2016Claudia Thurnherr 25
Euler example: Python
Upload your infile.py to Euler
Type the command:
module load python/VERSION
bsub [commands] python infile.py
(in connection with Abaqus type first: module load abaqus)
|| 20.09.2016Claudia Thurnherr 26
Outline
Introduction and ideal simulation procedure
How to connect to Euler
How to exchange files
Most important Unix commands
How to get around on Euler
Euler example: Ansys
Euler example: Abaqus
Euler example: COMSOL
|| 20.09.2016Claudia Thurnherr 27
Euler example: COMSOL
Upload your infile.mph file to Euler
Type the command: module load comsol/5.2
Shared memory:
bsub –n 4 –W 4:00 –R “rusage[mem=8000]” “comsol batch –np 4 –inputfile
infile.mph –outputfile outfile.mph”
-n / -np: number of processors
-W: desired time slot (4:00, 24:00, 120:00, …)
-mem: RAM memory allocation
Replace infile.mph with the name of your input file (must be a .mph file)
|| 20.09.2016Claudia Thurnherr 28
Euler example: COMSOL
Upload your infile.mph file to Euler
Type the command: module load comsol
Shared memory:
bsub –n 4 –W 4:00 –R “rusage[mem=8000]” “comsol batch –np 4 –inputfile
infile.mph –outputfile outfile.mph”
Distributed memory:
bsub –n 4 comsol batch –clustersimple –inputfile infile.mph –outputfile
outfile.mph
Also refer to: http://www.clusterwiki.ethz.ch/brutus/Comsol_Multiphysics
Thank you for your attention
Contact:
Christian Loosli ([email protected]), Claudia Thurnherr ([email protected])