hcc unl edu HPC at HCC Jun Wang
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hcc. unl. edu HPC at HCC Jun Wang Outline of Workshop 3 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 hcc. unl. edu Jun Wang Overview of Current HPC Computing Resources at HCC Cluster Crane Tusker Sandhills Overview Processors 452 node Intel Xeon E 5 -2670 Production-mode 2. 60 GHz 2 CPU/16 LINUX cluster cores per node 106 node Production-mode LINUX cluster Opteron 6272 2. 1 GHz, 4 CPU/64 cores per node RAM 64 GB RAM per node 256 GB RAM per node 2 Nodes with 512 GB per node 140 Node 1536 Opteron 6128 44 nodes @ 128 GB Production-mode 1408 Opteron 6376 2 nodes @ 256 GB LINUX cluster 368 Opteron 2354 44 nodes @16 GB (condominium 24 Xeon E 5620 44 nodes @ 192 GB model) Connection QDR Infiniband Gigabit Ethernet Storage ~1452 TB shared Lustre storatge ~1. 8 TB local scratch per node ~500 TB shared Lustre storage ~500 GB local scratch 175 TB shared Lustre storage ~1. 5 TB per node
HPC at HCC hcc. unl. edu Jun Wang Crane Sandhills Tusker
hcc. unl. edu 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/
hcc. unl. edu 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/x 86/putty. exe
hcc. unl. edu HPC at HCC Jun Wang How to login with DUO security DUO Mobile Yubikey
hcc. unl. edu 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 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 /Some. Directory -name Some. File. Name -type f --print Exit a terminal: exit Displays command help: man command
hcc. unl. edu 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
hcc. unl. edu HPC at HCC Jun Wang Familiar with queuing system-SLURM
hcc. unl. edu HPC at HCC Jun Wang SLURM scripts for common Computational Chemistry programs GROMACS Gaussian 09 #!/bin/sh #SBATCH -J g 09 #SBATCH --nodes=1 --ntasks-per-node=4 #SBATCH --mem=10 GB #SBATCH --partition=batch #SBATCH --time=01: 00 #SBATCH --error=Test. Job. stderr #SBATCH --output=Test. Job. stdout nodelist >. /machines. LINUX echo $SLURM_JOB_ID >. /jobid source /home/chem 953/programs/g 09. sh g 09 test_g 98. com #!/bin/sh #SBATCH -J gromacs #SBATCH --nodes=1 --ntasks-per-node=16 #SBATCH --mem-per-cpu=2000 #SBATCH --time=02: 00 #SBATCH --partition=batch #SBATCH --error=Test. Job. stderr #SBATCH --output=Test. Job. 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_d
hcc. unl. edu 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 #SBATCH --partition=batch #SBATCH --error=Test. Job. stderr #SBATCH --output=Test. Job. 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 < h 2 o-64. in > h 2 o-64. out
HPC at HCC hcc. unl. edu 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 #SBATCH --partition=devel #SBATCH --error=Test. Job. stderr #SBATCH --output=Test. Job. 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/LINUX 64/nwchem o 2 au 8 -_1. nw > o 2 au 8 -_1. out
