Getting Started on Topsail Mark Reed Charles Davis ITS Research Computing

2  Compute Clusters  Logging In  File Spaces  User Environment and Applications, Compiling  Job Management Outline

3 Logistics  Course Format  Lab Exercises  Breaks  UNC Research Computing  Getting started Topsail page

What is a compute cluster? What is Topsail?

5 What is a compute cluster? Some Typical Components  Compute Nodes  Interconnect  Shared File System  Software  Operating System (OS)  Job Scheduler/Manager  Mass Storage

6 Compute Cluster Advantages  fast interconnect, tightly coupled  aggregated compute resources  large (scratch) file spaces  installed software base  scheduling and job management  high availability  data backup

7 Initial Topsail Cluster  Initially: 1040 CPU Dell Linux Cluster 520 dual socket, single core nodes  Infiniband interconnect  Intended for capability research  Housed in ITS Franklin machine room  Fast and efficient for large computational jobs

8 Topsail Upgrade 1  Topsail upgraded to 4,160 CPU replaced blades with dual socket, quad core  Intel Xeon 5345 (Clovertown) Processors Quad-Core with 8 CPU/node  Increased number of processors, but decreased individual processor speed (was 3.6 GHz, now 2.33)  Decreased energy usage and necessary resources for cooling system  Summary: slower clock speed, better memory bandwidth, less heat, quadrupled the core count Benchmarks tend to run at the same speed per core Topsail shows a net ~4X improvement Of course, this number is VERY application dependent

9 Topsail – Upgraded blades  52 Chassis: Basis of node names Each holds 10 blades -> 520 blades total Nodes = cmp-chassis#-blade#  Old Compute Blades: Dell PowerEdge Single core Intel Xeon EMT64T 3.6 GHZ procs 800 Mhz FSB 2MB L2 Cache per socket Intel NetBurst MicroArchitecture  New Compute Blades: Dell PowerEdge Quad core Intel 2.33 GHz procs 1333 Mhz FSB 4MB L2 Cache per socket Intel Core 2 MicroArchitecture

10 Topsail Upgrade 2  Most recent Topsail upgrade (Feb/Mar ‘09)  Refreshed much of the infrastructure  Improved IBRIX filesystem  Replaced and improved Infiniband cabling  Moved cluster to ITS-Manning building Better cooling and UPS

11 Top 500 History  Top 500 lists comes out twice a year ISC conference in June SC conference in Nov  Topsail debuted at 74 in June 2006  Peaked at 25 in June 2007  Still in the Top 500

12 Current Topsail Architecture  Login node: GHz Intel EM64T, 12 GB memory  Compute nodes: 4, GHz Intel EM64T, 12 GB memory  Shared disk: 39TB IBRIX Parallel File System  Interconnect: Infiniband 4x SDR  64bit Linux Operating System

13 Multi-Core Computing  Processor Structure on Topsail 500+ nodes 2 sockets/node 1 processor/socket 4 cores/processor (Quad-core) 8 cores/node 

14 Multi-Core Computing  The trend in High Performance Computing is towards multi-core or many core computing.  More cores at slower clock speeds for less heat  Now, dual and quad core processors are becoming common.  Soon 64+ core processors will be common And these may be heterogeneous!

15 The Heat Problem Taken From: Jack Dongarra, UT

16 More Parallelism Taken From: Jack Dongarra, UT

17 Infiniband Connections  Connection comes in single (SDR), double (DDR), and quad data rates (QDR). Topsail is SDR.  Single data rate is 2.5 Gbit/s in each direction per link.  Links can be aggregated - 1x, 4x, 12x. Topsail is 4x.  Links use 8B/10B encoding —10 bits carry 8 bits of data — useful data transmission rate is four-fifths the raw rate. Thus single, double, and quad data rates carry 2, 4, or 8 Gbit/s respectively.  Data rate for Topsail is 8 GB/s (4x SDR).

18 Topsail Network Topology

19 Infiniband Benchmarks  Point-to-point (PTP) intranode communication on Topsail for various MPI send types  Peak bandwidth: 1288 MB/s  Minimum Latency (1-way): 3.6  s

20 Infiniband Benchmarks  Scaled aggregate bandwidth for MPI Broadcast on Topsail  Note good scaling throughout the tested range (from cores)

21 Login to Topsail  Use ssh to connect: ssh Topsail.unc.edu  SSH Secure Shell with Windows  For using interactive programs with X-Windows Display: ssh –X Topsail.unc.edu ssh –Y Topsail.unc.edu  Off-campus users (i.e. domains outside of unc.edu) must use VPN connection

File Spaces

23 File Space  Home directories /ifs1/home/ anyone over 15 GB is not backed up  Scratch Space /ifs1/scr/ over 39 TB of scratch space run jobs with large output in this space  Mass Storage ~/ms

24 Mass Storage “To infinity … and beyond” - Buzz Lightyear  long term archival storage  access via ~/ms  looks like ordinary disk file system – data is actually stored on tape  “limitless” capacity  data is backed up  For storage only, not a work directory (i.e. don’t run jobs from here)  if you have many small files, use tar or zip to create a single file for better performance  Sign up for this service on onyen.unc.edu

User Environment and Applications, Compiling Code Modules

26 Modules  The user environment is managed by modules  Modules modify the user environment by modifying and adding environment variables such as PATH or LD_LIBRARY_PATH  Typically you set these once and leave them  Note there are two module settings, one for your current environment and one to take affect on your next login (e.g. batch jobs running on compute nodes)

27 Common Module Commands  module avail module avail apps  module help  module list  module add  module rm Login version  module initlist  module initadd  module initrm More on modules see

28 Parallel Jobs with MPI  There are three implementations of the MPI standard installed: mvapich mvapich2 openmpi  Performance is similar for all three, all three run on the IB fabric. Mvapich is the default. Openmpi and mvapich2 have more the the MPI-2 features implemented.

29 Compiling MPI programs  Use the MPI wrappers to compile your program mpicc, mpiCC, mpif90, mpif77 the wrappers will find the appropriate include files and libraries and then invoke the actual compiler for example, mpicc will invoke either gcc or icc depending upon which module you have loaded

30 Compiling on Topsail  Serial Programming Intel Compiler Suite for Fortran77, Fortran90, C and C++ - Recommended by Research Computing  icc, icpc, ifort GNU  gcc, g++, gfortran  Parallel Programming MPI (see previous page) OpenMP  Compiler tag: -openmp for Intel -fopenmp for GNU  Must set OMP_NUM_THREADS in submission script

Job Scheduling and Management

32 What does a Job Scheduler and batch system do? Manage Resources  allocate user tasks to resource  monitor tasks  process control  manage input and output  report status, availability, etc  enforce usage policies

33 Job Scheduling Systems  Allocates compute nodes to job submissions based on user priority, requested resources, execution time, etc.  Many types of schedulers Load Sharing Facility (LSF) – Used by Topsail IBM LoadLeveler Portable Batch System (PBS) Sun Grid Engine (SGE)

34 LSF  All Research Computing clusters use LSF to do job scheduling and management  LSF (Load Sharing Facility) is a (licensed) product from Platform Computing Fairly distribute compute nodes among users enforce usage policies for established queues  most common queues: int, now, week, month RC uses Fair Share scheduling, not first come, first served (FCFS)  LSF commands typically start with the letter b (as in batch), e.g. bsub, bqueues, bjobs, bhosts, … see man pages for much more info!

35 Simplified view of LSF bsub –n 64 –a mvapich –q week mpirun myjob Login Node Jobs Queued job routed to queue job_J job_F myjob job_7 job dispatched to run on available host which satisfies job requirements user logged in to login node submits job

36 Running Programs on Topsail  Upon ssh to Topsail, you are on the Login node.  Programs SHOULD NOT be run on Login node.  Submit programs to one of 4,160 Compute nodes.  Submit jobs using Load Sharing Facility (LSF) via the bsub command.

37 Common batch commands  bsub - submit jobs  bqueues – view info on defined queues bqueues –l week  bkill – stop/cancel submitted job  bjobs – view submitted jobs bjobs –u all  bhist – job history bhist –l

38 Common batch commands  bhosts – status and resources of hosts (nodes)  bpeek – display output of running job  Use man pages to get much more info! man bjobs

39 Submitting Jobs: bsub Command  Submit Jobs - bsub Run large jobs out of scratch space, smaller jobs can run out of your home space  bsub [-bsub_opts] executable [-exec_opts]  Common bsub options: –o  –o out.%J -q  -q week -R “resource specification”  -R “span[ptile=8]” -n  used for parallel, MPI jobs -a  -a mvapich(used on MPI jobs)

40 Two methods to submit jobs:  bsub example: submit the executable job, myexe, to the week queue and redirect output to the file out. (default is to mail output)  Method 1: Command Line bsub –q week –o out.%J myexe  Method 2: Create a file (details to follow) called, for example, myexe.bsub, and then submit that file. Note the redirect symbol, < bsub < myexe.bsub

41 Method 2 cont.  The file you submitted will contain all the bsub options you want in it, so for this example myexe.bsub will look like this #BSUB –q week #BSUB –o out.%J myexe  This is actually a shell script so the top line could be the normal #!/bin/csh, etc and you can run any commands you would like. if this doesn’t mean anything to you then nevermind :)

42 Parallel Job example Batch Command Line Method  bsub –q week –o out.%J -n 64 -a mvapich mpirun myParallelExe Batch File Method  bsub < myexe.bsub  where myexe.bsub will look like this #BSUB –q week #BSUB –o out.%J #BSUB –a mvapich #BSUB –n 64 mpirun myexe

43 Topsail Queues QueueTime LimitJobs/UserCPU/Job int2 hrs debug2 hrs64--- day24 hrs5124 – 128 week1 week5124 – cpu4 days51232 – cpu4 days51232 – cpu2 days5124 – 32 chunk4 days512Batch Jobs For access to the 512cpu queue the scalabitly should be demonstrated

44 Common Error 1  If job immediately dies, check err.%J file  err.%J file has error: Can't read MPIRUN_HOST  Problem: MPI enivronment settings were not correctly applied on compute node  Solution: Include mpirun in bsub command

45 Common Error 2  Job immediately dies after submission  err.%J file is blank  Problem: ssh passwords and keys were not correctly setup at initial login to Topsail  Solution: cd ~/.ssh/ mv id_rsa id_rsa-orig mv id_rsa.pub id_rsa.pub-orig Logout of Topsail Login to Topsail and accept all defaults

46 Interactive Jobs  To run long shell scripts on Topsail, use int queue  bsub –q int –Ip /bin/bash This bsub command provides a prompt on compute node Can run program or shell script interactively from compute node  Totalview debugger can also be run interactively from Topsail

47 MPI/OpenMP Training  Courses are taught throughout year by Research Computing  See schedule for next course MPI OpenMP

48 Further Help with Topsail  More details about using Topsail can be found on the Getting Started on Topsail help document ON CAMPUS  For assistance with Topsail, please contact the ITS Research Computing group Phone: HELP Submit help ticket at  For immediate assistance, see manual pages on Topsail: man