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PBS Batch System, Catalina scheduler. Intel Compilers

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Title: PBS Batch System, Catalina scheduler. Intel Compilers


1
Using SDSC TeraGrid IA-64 Cluster
  • July 2005
  • Don Frederick
  • http//www.sdsc.edu/user_services

2
Agenda
  • SDSC IA-64 Cluster Hardware Summary
  • Logging In to SDSC TeraGrid IA-64 Cluster
  • ssh
  • gsi-ssh
  • User Environment softenv
  • Compilers
  • Fortran
  • C/C
  • Running Jobs
  • Batch
  • Interactive
  • Example

3
SDSC IA-64 Cluster
  • CPUs
  • Intel Intanium II 1.5 GHz, 6 MB L3 cache
  • System Design
  • 262 dual CPU nodes
  • 2 GB memory per node
  • 2 login nodes 8 cpus/node
  • 16 special data transfer nodes
  • Interconnect
  • Myrinet 2000
  • OS
  • SUSE Linux 8.0
  • Disk
  • 60 TB GPFS
  • 1.7 TB NFS

4
SDSC IA-64 Cluster
  • PBS Batch System, Catalina scheduler
  • Intel Compilers Fortran, C,C, version 8.0
    default

5
Logging on to SDSC TeraGrid IA-64 Cluster
  • ssh l username tg-login.sdsc.teragrid.org
  • MUST use ssh or other secure login method
    gsi-ssh
  • File copying
  • scp original_file username_at_tg-login1.sdsc.teragrid
    .org/to_dir/copied_file
  • System status
  • http//clumon.sdsc.edu/

6
User Environment
  • Common TeraGrid Software Stack (CTSS) provides
    common set of software across TG sites
  • Compilers
  • Utilities

7
User Environment
  • Defined using softenv package allows user
    and/or sysadmins to define default user
    environment search paths, other Unix
    environment variables
  • Complete reference
  • http//www.teragrid.org/docs/softenv/
  • Users can customize their environment using
    softenv commands and mods to the .soft file

8
Using softenv
  • To add and remove the softenv settings from shell
    environments run the respective script from the
    command line
  • /usr/sdsc/bin/add-softenv
  • /usr/sdsc/bin/remove-softenv

9
b
Manipulating the Environment
  • /home/ltusernamegt/.soft
  • softenv
  • Displays symbolic software key names
  • soft add ltpackage-namegt
  • Temporary addition of package to environment
  • soft delete ltpackage-namegt
  • Temporary package removal from environment
  • resoft
  • Modify dotfile and apply to present environment
  • softdb examine softenv database
  • man softenv

10
TeraGrid IA-64 Compilers
  • Fortran90
  • Intel efc 8.1 is default compiler
  • C/C
  • Intel icc 8.1 is default compiler
  • MPI several flavors
  • mpich-gm mpicc, mpif90 default mpi compilers
    mpich MPI library compiled using GM (Myrinet
    network primitives)
  • mpich-vmi mpicc, mpif90 mpich implementation
    allowing cross-site MPI
  • mpich-g2 - mpicc, mpif90 mpich implementation
    allowing cross-site MPI

11
Running Jobs - Batch
  • Portable Batch System (PBS) is the batch
    software. SDSC uses the Catalina job scheduler.
  • To run in batch, create batch job script, using
    PBS syntax and use PBS commands to submit job to
    batch queue

12
Running Jobs - Batch
  • Example of a PBS batch script for running an MPI
    job, executable a.out on 10 nodes, 2 MPI
    processes/node

!/bin/csh PBS -q dque PBS -N my_job PBS -l
nodes10ppn2 PBS -l walltime05000 PBS -o
file.out PBS -e file.err PBS -V cd
/work/username mpirun -v -machinefile
PBS_NODEFILE -np 20 ./a.out
13
Running Jobs Batch (Continued)
  • Job is submitted to PBS batch system via the qsub
    command
  • qsub script-name
  • Where script-name is the job script (see
    previous page). must be executable.
  • Job status checked with qstat command
  • qstat or
  • qstat jobname
  • Cancel jobs in queue or running with qcancel
    jobname

14
Running Interactive
  • Interactive use is via PBS
  • qsub -I -V -l walltime003000 -l nodes4ppn2
  • This request is for 4 nodes for interactive use
    (using 2 cpus/node) for a maximum wall-clock time
    of 30 minutes. Once the scheduler can honor the
    request, PBS responds with ready and gives the
    node names.
  • Once nodes are assigned, ubser can now run any
    interactive command. For example, to run an MPI
    program, parallel-test on the 4 nodes, 8 cpus
    mpirun -np 8 -machinefile PBS_NODEFILE
    parallel-test

15
TeraGrid IA-64 Numerical Libraries
  • Intel Math Kernel Library (MKL) main numerical
    library, optimized for IA-64
  • Basic linear algebra subprograms (BLAS) with
    additional sparse routines.
  • Fast Fourier Transforms (FFT) in 1 and 2
    dimensions, complex and real.
  • The linear algebra package, LAPACK
  • A C interface to BLAS
  • Vector Math Library (VML)
  • Vector Statistical Library (VSL)
  • Multi-dimensional Discrete Fourier Transforms
    (DFTs)

16
TG IA-64 Software Software
  • Suse linux sles8 rc4
  • Intel c 8.0
  • Intel fortran 8.0
  • Intel MKL 6.0.012
  • Globus 2.4.3
  • Condor-G 6.5.3
  • MPICH-1.2.5.10-pre3
  • Open-PBS 2.3.16
  • Torque 1.1.0
  • Catalina
  • Open SSH/SSL 3.7.1
  • XCAT 1.2.0beta7
  • Python w/ XML

17
TG IA-64 Software
  • The available grid services (inside Globus) are
  • GPT 2.2.9 (installer)
  • Globus 2.4.3
  • gsi-openssh 1.9
  • gsi-ncftp 3.0.3
  • Condor-G (NMI 2.1 binary bundle) gahp_server
    6.4.7 rebuild
  • Myproxy 1.4

18
Using TG IA-64 - Example
  • Example files are in /usr/local/sdsc/training/TG.
  • Log onto TG IA-64 using ssh
  • Copy directory contents to your home directory
  • Run make to create executable
  • Use qsub to submit batch job script
  • Use qsub to submit interactive job

19
References
  • SDSC TeraGrid User Guide
  • http//www.sdsc.edu/teragrid/guide.html
  • TeraGrid Getting Started Guide
  • http//www.teragrid.org/userinfo/index.html
  • TeraGrid Tutorial from Supercomputing 04
  • Applications in the TeraGrid Environment
  • http//teragrid.org/userinfo/docs/SC04-TeraGrid-tu
    torial.ppt
  • TeraGrid Tutorial on Cross-Site Data Transfer
  • http//teragrid.org/userinfo/docs/crosssite_xfer-s
    c04.ppt
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