CSCE569 Parallel Computing

1. CSCE569 Parallel Computing Lecture 2 TTH 03:30AM-04:45PM Dr. Jianjun Huhttp://mleg.cse.sc.edu/edu/csce569/ University of South Carolina Department of Computer Science and Engineering

2. Outline • Clusters and SMP systems at USC CEC • Ways of using High Performance Systems • PBS Job Queuing System • How to write Job file • How to submit, delete, manage jobs submitted to Linux Cluster • How to submit a large Number of Jobs

3. Systems: NICK Linux OS Hardware • 76 Compute Nodes w/ dual 3.4 GHz XEON 2ML2, 4GB RAM1 Master Node w/ dual 3.2 GHz 2ML2, 4GB RAM • Topspin Infiniband Interconnect • Storage: 1 terabyte network storage Software • Rocks 4.3 CentOS Base, OpenMPI, OpenPBS/Torque • Absoft Compilers • Intel Compilers • Bio Roll that includes the following bio-informatics packages: HMMER, NCBI BLAST, MpiBLAST, biopython, ClustalW, MrBayes, T_Coffee, Emboss, Phylip, fasta, Glimmer, and CPAN • Intel Math Kernel Library • TURBOMOLE • VASP • STAR-CD

4. Systems: Optimus Hardware • 64 Nodes: Dual CPU, 2.0 GHz Dual-Core AMD Opterons, Totaling 256 Cores • 8GB RAM • 1 Terabyte of Storage in Headnode • Gigabit Ethernet Interconnect Software • ROCKS 5.1 • OpenMPI • OpenPBS Scheduler • GNU Compilers

5. Systems: ZIA SGI Altix 4700 Shared-memory system Hardware • 128 Itanium Cores @ 1.6 GHz/ 8MB Cache • 256 GB RAM • 8TB storage • NUMAlink Interconnect Fabric Software • SUSE10 w/SGI PROPACK • Intel C/C++ and Fortran Compilers • VASP • PBSPro scheduling software • Message Passing Toolkit • Intel Math Kernel Library • GNU Scientific Library • Boost library

6. Other Systems Nataku • 8 Nodes: Dual CPU, 2.0 GHz Dual-Core AMD Opterons, Totaling 32 Cores • 16 GB RAM in Headnode, 8GB RAM in compute nodes • Chemical Engineering machine for Star-CD Jaws2 • 8 Compute Nodes w/ dual XEON 2.6 GHz, 2GB RAM • Remaining parts of original Jaws cluster, currently being rebuilt • 1 Terabyte attached storage Dr. Flora’s 12 CPU VASP Cluster Dr. Heyden’s MAC Cluster for VASP

7. Distributed Multiprocessor Cluster HD2 HD3 HD1 NFS Front End Node

8. Question How can we utilize large high performance machines like these to speed up applications?

9. Ways of using Linux Clusters • App. Type1: Each data set is computed in a function independently as a job and can be run independently on one CPU data1 Regular program data2 Collect results data3 dataK

10. Ways of using Linux Clusters • App. Type2: Parallel program compute1 data Communication between processes compute2 result compute3 Parallel processes can be executed on multiple CPUs and can be summarized together in the main process Compute 4

11. PBS System for Clusters • PBS is a workload management system for Linux clusters • It supplies commands for • job submittion • job monitoring (tracing) • job deletion • It consists of the following components: • Job server (pbs_server) • provides the basic batch services • receiving/creating a batch job • modifying the job • protecting the job against system crashes • running the job

12. PBPBS System for Clusterssing • Job Executor (pbs_mom) • receives a copy of the job from the job server • sets the job into execution • creates a new session as identical user • returns the job's output to the user. • Job Scheduler (pbs_sched) • runs site's policy controlling which job is run and where and when it is run • PBS allows each site to create its own Scheduler • Currently Nick uses the Torque/Maui Scheduler

13. OpenPBS Batch Processing • Maui communicates • with Moms: monitoring the state of a system's resources • with Server: retrieving information about the availability of jobs to execute

14. Steps needed to run your first production code Suppose your application experiments are: $myprog data1 2 30 $myprog data2 3 12 ... Steps to use PBS: 1. Create a job script for each running experiment • containing the PBS options to request the needed resources (i.e. number of processors, wall-clock time, etc.) • and user commands to prepare for execution of the executable (i.e. cd to working directory, etc.). 2. Submit the job script file to PBS queue qsub prog1.sh 3. Monitor the job

15. First example: job1.sh jobfile #!/bin/bash #PBS -N MyAppName #PBS -l nodes=1 #PBS -l walltime=00:01:00 #PBS -e /home/dgtest/dgtest0200/test.err #PBS -o /home/dgtest/dgtest0200/test.out #PBS -V Export PATH=$PATH:yourdir/bin; myprog data1 2 30 Where is your output file located? Where is the screen output?

16. Jobfile for use on ZIA #!/bin/s#PBS -N helloMPI #PBS -o hello.out#PBS -e hello.err#PBS -l select=1:ncpus=4#PBS -l place=free:sharedcd /home/<username>/testmpirun -np 4 /home/<username>/test/hello

17. PBS Options • #PBS -N myJob • Assigns a job name. The default is the name of PBS job script. • #PBS -l nodes=4:ppn=2 • The number of nodes and processors per node. • #PBS -l walltime=01:00:00 • The maximum wall-clock time during which this job can run. • #PBS -o mypath/my.out • The path and file name for standard output. • #PBS -e mypath/my.err • The path and file name for standard error. • #PBS -j oe • Join option that merges the standard error stream with the standard output stream

18. PBS Options • #PBS -k oe • Define which output of the batch job to retain on the execution host. • #PBS -W stagein=file_list • Copies the file onto the execution host before the job starts. • #PBS -W stageout=file_list • Copies the file from the execution host after the job completes. • #PBS -r n • Indicates that a job should not rerun if it fails. • #PBS –V • Exports all environment variables to the job.

19. Procedure • Use command line • Use editor to create an executable script: • vi myExample.sh • Use first example code • Make myExample.sh executable: • chmod +x myExample.sh • Test your script • ./ myExample.sh • Submit your script: • qsub myExample.sh • remember your job identifier • i.e. 96682

20. Monitor / Control a Job • Check wether your job runs • qstat • qstat –a • check status of jobs, queues, and the PBS server • qstat –f • get all the information about a job, i.e. resources requested, resource limits, owner, source, destination, queue, etc. • qdel job.ID • delete a job from the queue • qhold job.ID • hold a job if it is in the queue • qrls job.ID • release a job from hold

21. Exercise • Problem: Given 10000 html pages, count the frequency of all words and report it as: keyword frequeny Keyword1 frequency1... • Use PBS to submit 100 jobs

22. How to submit 100 jobs • Typical ways: 1. read file list 2. for each file, create a job file, and submit it to the PBS queue • Write a bash script, which submits a jobs for different datasets • Write a perl script to submit jobs • Write a C program to submit jobs

23. Quick psub • Psub is a perl script that can wrap a command line program into a job file and submit to the cluster queue • >psub jobname.sh “prog.pl –i=1” this will create a job file “jobname.sh” and submit to the server for running. No need to edit a job file anymore

24. Local Disk of Computing Node • Normally, the computing node of clusters can directly read and write files on NFS storage space • If your program has intense write-read operation, reading and writing to NFS directory will cause high traffics • Solution:direct your output and input to local directories at computing nodes and after execution, copy the results file to NSF directory • /temp, /tmp /state/partition1

25. Summary • TypeI parallel computing application • How PBS works in Linux Cluster Computers • How to submit jobs to Linux clusters

26. Homework • Programming Problem: Given a html page, count the frequency of all words and report it as: keyword frequeny Keyword1 frequency1... • Use PBS to submit 100 jobs to count frequency for 10000 html pages in next Lab session.

27. Homework • Learn how to compile C programs on Linux • Learn how to create PBS job file • Learn how to submit jobs • Learn how to submit multiple jobs • Learn how to compile and run MPI program on NICK