System Basics [2017-09-14 Thu] (Slides)

ICS & HPC
ICS-ACI
Info

ICS & HPC

what is High Performance Computing? Large…
- # of processors
- # of runs
- memory requirements (finance, bio)
- storage reqs (ML, big data)
- runtime (optimization, poor coding)
HPC does not improve single processes!
resources
- internal
  - ICS-ACI
- external
  - NSF XSEDE
  - Blue Waters through GLCPC
  - DoE
people
- engagement team (Lavely, Blanton, Pavloski)
- iAsk center (help answering questions, mostly on ACI)
goal: enable research

ICS-ACI

24000 cores
very capable tool
- ACI-B for batch (high/std/basic memory)
- ACI-I for interactive (Rstudio)
- Gateways, GPUs (coming soon)
- ACI Partitions (CyberLAMP)
- Hosted resources (LIGO)
ACI-B
- access via ssh only
- log into an aci-lgn-* node to submit jobs
- process runs have dedicated resources when they start running
- what you request is specified in the submission script
- anybody can access the open allocation w/ some limitations
- slow X session launchable via -Y
- used for: production runs, high mem/proc/time
ACI-I
- access via ssh or EoD
- placed on a node and run process there
- limited to 4 procs, 12h, 48GB mem
- does not guarantee exclusive resources like a compute node
- used for: debugging, visualization, interaction

File systems

three storage location options
- home
  - /storage/home/userid
  - small (10GB) but well protected
    - not shared w/ anybody else
    - backed up frequently
- work
  - /gpfs/work/userid
  - 128GB cap
  - you can share data
  - backed up every 3 days or so
- scratch
  - /gpfs/scratch/userid
  - no file size limit
  - 1M files cap per user
  - files older than 30 days are deleted
work & scratch are linked from home
research groups can purchase
- allocations
- storage space
  - for
    - group (like work but 5TB)
    - archive
  - datamgr.aci.ics.psu
    - allow for faster data transfers

Connecting

ways to connect
- ssh in terminal
```
ssh userid@aci-b.aci.ics.psu.edu
# or
ssh userid@aci-i.aci.ics.psu.edu
        
```
  - password doesn’t show up!
- PuTTy on Windows
- Exceed onDemand to ACI-I tutorial
  - config
    - Xconfig: Desktop_mode_1280x1024.cfg
    - Xstart: Gnome_Desktop.xs
  - only 1 session
  - you can always come back (don’t log out, just quit)
  - still gonna have to use cmdline
    - Apps -> System Tools -> Terminal

Terminal

things to know
- GIYF
- man
- banana
find total and available allocation hours
```
mam-list-funds -h
    
```
manual for commands
```
man cmd
    
```
see list of options using an improper flag
```
mam-list-funds --banana
    
```

4 most basic commands

ls                            # list contents of curr dir
pwd                           # print current dir
cd scratch                    # change dir
cp logFile logFile_13Sept2017 # copy file

other useful commands

history # past commands
mv # move files
rm # remove files
mkdir # make
find # find files
grep # filter files
awk # text manipulator
id
du # disk space
clear # clear screen
env
ssh
more

special characters

cd ~ # move to home
cd . # move to here (stay here)
cd .. # move one dir up
ls *.png # list all png
ls -1 | grep png # pipe output of ls to other commands
ls > log.ls # put output in a file

Modules

wrapper for individual program
- e.g. in order to use Matlab you need to first load its module
show modules currently available
```
module avail
    
```
search for modules
```
module spider vasp
    
```
load a module optionally w/ specific version (otherwise will you the default)
```
module load ansys/18.1
    
```
better to specify version.

module families

module avail
module load gcc/5.3.1
module avail # new modules (compiled with hence conditional on gcc/5.3.1) will show up

other cmds

module list # list loaded modules
module purge # clean up loaded modules
module show modName # where libs of the module are, which env vars are setup

e.g. w/ boost module you can use show to help you set up lib paths when compiling w/ it

Transfer data

cmdline

scp lFile userid@datamgr.aci.ics.psu.edu:~/work/
rsync ...
sftp ...

programs: WinSCP, Filezilla
via Box, Dropbox w/ EoD’s Firefox interface (no syncing)
- (and no sound => no youtube!)
specific programs: Globus, Aspera

Submitting a Job

submission scripts

two sections
1. PBS directives
```
#PBS directive ...
            
```
  - used for requesting resources
  - only at beginning
2. commands
to submit
```
qsub submitScript.pbs
        
```

e.g.

#!/bin/bash
#PBS -l nodes=1:ppn=1
#PBS -l walltime=5:00
#PBS -A open

echo "Job started on $(hostname) at $(date)"

module purge
module load matlab/R2016a

# goto dir where the script lives
cd $PBS_O_WORKDIR

matlab-bin -nodisplay -nosplash < runThis.m > log.matlabRun

echo "Job ended at $(date)"

Info

ICS docs ics.psu.edu
iAsk
- iAsk at ics.psu.edu, 54275
check doc of other batch systems: TACC, OSC
seminar 2
- submitting jobs
- compiling simple codes
- allocation usage
- intro to parallelization
  - distributed vs shared memory
- data moving
  - globus, rsync
seminar 3 (Feb 2018)
- optimization techniques

About

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