Workshop 3

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HPC at HCC
Jun Wang
Outline of Workshop3
Overview of Current HPC Computing Resources at HCC
How to obtain an account at HCC
How to login with DUO security
Commonly Used Linux commands
How to change password
Familiar with SLURM queuing system
SLURM scripts for common Computational
Chemistry programs
HPC at HCC
Jun Wang
Overview of Current HPC Computing Resources at HCC
Cluster
Crane
Tusker
Sandhills
Overview
Processors
452 node
Intel Xeon E5-2670
Production-mode 2.60GHz 2 CPU/16
LINUX cluster
cores per node
106 node
Production-mode
LINUX cluster
Opteron 6272
2.1GHz, 4 CPU/64
cores per node
RAM
64GB RAM per
node
256 GB RAM per
node
2 Nodes with
512GB per node
140 Node
1536 Opteron 6128 44 nodes @ 128GB
Production-mode 1408 Opteron 6376 2 nodes @ 256GB
LINUX cluster
368 Opteron 2354 44 nodes @16GB
(condominium
24 Xeon E5620 44 nodes @ 192GB
model)
Connection
QDR Infiniband
QDR Infiniband
QDR Infiniband
Gigabit Ethernet
Storage
~1452 TB shared
Lustre storatge
~1.8 TB local
scratch per node
~500 TB shared
Lustre storage
~500GB local
scratch
175TB shared
Lustre storage
~1.5TB per node
HPC at HCC
Jun Wang
Crane
Sandhills
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 with DUO security
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 with DUO security
DUO Mobile
Yubikey
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
How to change password
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
Additional Rules:
Password can not have any dictionary word
New password can not have similar pattern to your username, current password and most
recent previous password
HCC password valid only for 100 days-->Reset your password every 100 days
HPC at HCC
Jun Wang
Familiar with queuing system-SLURM
HPC at HCC
Jun Wang
SLURM scripts for common Computational
Chemistry programs
GROMACS
Gaussian09
#!/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.stdout
nodelist > ./machines.LINUX
echo $SLURM_JOB_ID > ./jobid
source /home/chem953/programs/g09.sh
g09 test_g98.com
#!/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/gromacs4.5.5/exe-mkl/bin/GMXRC.bash
nodelist > ./machines.LINUX
echo $SLURM_JOB_ID > ./jobid
mpirun mdrun_mpi_d
HPC at HCC
Jun Wang
SLURM scripts for common Computational
Chemistry programs
Quantum Espresso
#!/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/4.7
module load openmpi/1.6
module load intel-mkl/13
echo 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
HPC at HCC
Jun Wang
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/13
module load openmpi/1.6
module 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
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