Outline of Workshop3 Overview of Current HPC Computing Resources at HCC How to obtain an account at HCC How to login with DUO security Familiar with SLURM queuing system Commonly Used Linux commands ID: 699737
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Slide1
HPC at HCCJun Wang
hcc.unl.edu
Outline of
Workshop3
Overview of Current HPC Computing Resources at HCC
How to obtain an account at HCC
How to login with DUO security
Familiar with SLURM queuing system
Commonly Used Linux commands
How to change password
SLURM scripts for common Computational Chemistry programsSlide2
HPC at HCCJun Wang
hcc.unl.edu
Overview of
Current HPC Computing Resources at HCC
Cluster
Overview
Processors
RAM
Connection
Storage
Crane
452
node
Production-mode LINUX cluster
Intel Xeon E5-2670 2.60GHz 2 CPU/16 cores per node
64GB RAM per node
QDR Infiniband
~1452 TB shared Lustre storatge
~1.8 TB local scratch per node
Tusker
106 node Production-mode LINUX cluster
Opteron 6272 2.1GHz, 4 CPU/64 cores per node
256 GB RAM per node
2 Nodes with 512GB per node
QDR
Infiniband
~500 TB shared
Lustre
storage
~500GB local scratch
Sandhills
140 Node Production-mode LINUX cluster
(condominium model)
1536 Opteron 6128
1408 Opteron 6376
368 Opteron 2354
24 Xeon E5620
44 nodes @ 128GB
2 nodes @ 256GB
44 nodes @16GB
44 nodes @ 192GB
QDR Infiniband
Gigabit Ethernet
175TB shared
Lustre
storage
~1.5TB per nodeSlide3
HPC at HCCJun Wang
hcc.unl.edu
Crane
Sandhills
TuskerSlide4
HPC at HCCJun Wang
hcc.unl.edu
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/studentshttp://hcc.unl.edu/newusers/Slide5
HPC at HCCJun Wang
hcc.unl.edu
How to login
with DUO security
On PC:Download putty.exe to your desktop from http://the.earth.li/~sgtatham/putty/latest/x86/putty.exeSlide6
HPC at HCCJun Wang
hcc.unl.edu
How to login
with DUO security
DUO Mobile
YubikeySlide7
HPC at HCCJun Wang
hcc.unl.edu
Commonly Used Linux commands
http://www.centos.org/docs/2/rhl-gsg-en-7.2/ch-doslinux.html
Changes directories: cd
/directory/directoryLists files: ls
Copies files: cp thisfile.txt /home/thisdirectory
Moves files: mv thisfile.txt /home/thisdirectory
Deletes files: rm thisfile.txtCreates a
directory: mkdir directoryView 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
commandSlide8
HPC at HCCJun Wang
hcc.unl.edu
How to change password
Type “
passwd” after login to any HCC clusterNote: 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 1Minimum required alpha characters
1 Minimum required upper case characters 1Minimum required character categories 1 Minimum token length 1
Additional Rules:Password can not have any dictionary wordNew password can not have similar pattern to your username, current password and most recent previous passwordHCC password valid only for 100 days-->Reset your password every 100 daysSlide9
HPC at HCCJun Wang
hcc.unl.edu
Familiar with queuing
system-SLURMSlide10
HPC at HCCJun Wang
hcc.unl.edu
SLURM scripts for common Computational Chemistry programs
#!/bin/
sh#SBATCH -J g09#SBATCH --nodes=1 --ntasks-per-node=4
#SBATCH --mem=10GB#SBATCH --partition=batch#SBATCH --time=01:00:00#SBATCH --error=TestJob.stderr
#SBATCH --output=TestJob.stdoutnodelist > ./machines.LINUX
echo $SLURM_JOB_ID > ./jobidsource /home/chem953/programs/g09.shg09 test_g98.com
Gaussian09
GROMACS
#!/bin/
sh
#SBATCH -J
gromacs
#SBATCH --nodes=1 --
ntasks
-per-node=16
#SBATCH --
mem
-per-
cpu
=2000
#SBATCH --time=02:00:00
#SBATCH --
partition=batch
#SBATCH --error=
TestJob.stderr
#SBATCH --output=
TestJob.stdout
source /home/
zeng
/programs/gromacs-4.5.5/exe-
mkl
/bin/
GMXRC.bash
nodelist
> ./
machines.LINUX
echo $SLURM_JOB_ID > ./
jobid
mpirun
mdrun_mpi_dSlide11
HPC at HCCJun Wang
hcc.unl.edu
SLURM scripts for common Computational Chemistry programs
#!/bin/
sh#SBATCH -J espresso#SBATCH --nodes=1 --ntasks-per-node=32
#SBATCH --mem-per-cpu=1024#SBATCH --time=08:00:00#SBATCH --
partition=batch#SBATCH --error=TestJob.stderr#SBATCH --output=TestJob.stdout
module load compiler/gcc/4.7module load openmpi/1.6module load intel-
mkl/13echo nodelist > ./machines.LINUX
echo $SLURM_JOB_ID > ./
jobid
export ESPRESSO_TMPDIR=/scratch
mpiexec
/home/
zeng
/programs/espresso-5.0.2/bin/
cp.x
< h2o-64.in > h2o-64.out
Quantum EspressoSlide12
HPC at HCCJun Wang
hcc.unl.edu
SLURM scripts for common Computational Chemistry programs
NWChem
#!/bin/
sh#SBATCH -J nwchem#SBATCH --nodes=1 --ntasks-per-node=64
#SBATCH --mem-per-cpu=4000#SBATCH --time=01:00:00#SBATCH --partition=devel
#SBATCH --error=TestJob.stderr#SBATCH --output=TestJob.stdout
module load compiler/intel/13module load openmpi/1.6module load intel-
mkl
/13
nodelist
> ./
machines.LINUX
echo $SLURM_JOB_ID > ./
jobid
export SCRATCH_DIR=$TMPDIR
mpiexec
/home/
zeng
/programs/nwchem-6.3/bin/LINUX64/
nwchem
o2au8-_1.nw > o2au8-_1.out