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HPC at HCC Jun 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 . Commonly Used Linux commands. How to change password . Familiar with SLURM queuing system.
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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 Commonly Used Linux commands How to change password Familiar with SLURM queuing system SLURM scripts for common Computational Chemistry programs
HPC at HCCJun Wang hcc.unl.edu Overview of Current HPC Computing Resources at HCC
HPC at HCCJun Wang hcc.unl.edu Crane Tusker Sandhills
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/students http://hcc.unl.edu/newusers/
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.exe
HPC at HCCJun Wang hcc.unl.edu How to login with DUO security DUO Mobile Yubikey
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/directory Lists files: ls Copies files: cpthisfile.txt /home/thisdirectory Moves files: mv thisfile.txt /home/thisdirectory Deletes files: rmthisfile.txt Creates a directory: mkdirdirectory 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 HCCJun Wang hcc.unl.edu 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 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 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 HCCJun Wang hcc.unl.edu Familiar with queuing system-SLURM
HPC at HCCJun Wang hcc.unl.edu SLURM scripts for common Computational Chemistry programs GROMACS Gaussian09 #!/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 mpirunmdrun_mpi_d #!/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.LINUXecho $SLURM_JOB_ID > ./jobidsource /home/chem953/programs/g09.shg09 test_g98.com
HPC at HCCJun Wang hcc.unl.edu 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 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/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
