1. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Usage Seminar for the 64-nodes P4-Xeon Cluster in Science Faculty March 24, 2004

2. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Aims and Target audience Aims: –Usage review –Introducing news and events –Sharing among existing users Target audience –Existing and potential cluster users

3. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Today’s Outline Introduction to upgraded software and its usage Review of serial and parallel job submission Software demo Briefing of coming recurring parallel computing course Sharing and opinions from the existing users

4. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU System upgrade February 27, 2004 Upgrade to ROCKS 3.1.0 SAN adapter inserted Compute nodes all reinstalled Many application software upgrade

5. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Hardware Configuration 1 master node + 64 compute nodes + Gigabit Interconnection Master node –Dell PE2650, P4-Xeon 2.8GHz x 2 –4GB RAM, 36GB x 2 U160 SCSI (mirror) –Gigabit ethernet ports x 2 SCSI attached storage –Dell PV220S –73GB x 10 (RAID5)

6. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Hardware Configuration (cont) Compute nodes –Dell PE2650, P4-Xeon 2.8GHz x 2 –2GB RAM, 36GB U160 SCSI HD –Gigabit ethernet ports x 2 Gigabit Interconnect –Extreme Blackdiamond 6816 Gigabit ethernet –256Gb backplane –72 Gigabit ports (8 ports card x 9)

7. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Software installed Cluster operating system –ROCKS 3.1.0 from www.rocksclusters.orgwww.rocksclusters.org MPI and PVM libraries –LAM/MPI 7.0.4, MPICH 1.2.5.2, PVM 3.4.3-6beolin Compilers –GCC 3.2.3 –PGI C/C++/f77/f90/hpf version 5.1 MATH libraries –ATLAS 3.6.0, ScaLAPACK, SPRNG 2.0a Application software –MATLAB 6.1 with MPITB –R 1.8.1 –Gromacs 3.2, NAMD2.5, Gamess –Gaussian 03, Q-Chem 2.1 Editors –vi, pico, emacs, joe Queuing system –Torque/PBS, Maui scheduler

8. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Cluster O.S. – ROCKS 3.1.0 Developed by NPACI and SDSC Based on RedHat Entreprise Linux 3.0 Useful command for users to monitor jobs in all nodes. E.g. –cluster-fork date –cluster-ps morris –cluster-kill morris Web based management and monitoring –http://tdgrocks.sci.hkbu.edu.hk

9. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Ganglia

10. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Hostnames Master node –tdgrocks.sci.hkbu.edu.hk Compute nodes –comp-pvfs-0-1, …, comp-pvfs-0-64 –Short names: cp0-1, cp0-2, …, cp0-64

11. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Network diagram Master node Compute node Gigibit ethernet switch tdgrocks.sci.hkbu.edu.hk 192.168.8.1 comp-pvfs-0-1 (192.168.8.254) comp-pvfs-0-2 (192.168.8.253) comp-pvfs-0-64 (192.168.8.192)

12. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Login to the master node Login is allowed remotely in all HKBU networked PCs by ssh or vncviewer SSH Login (terminal login) –Using your favourite ssh client software, namely putty, SSHsecureshell on windows and openssh on Linux/UNIXputtySSHsecureshell openssh –E.g. on all SCI workstations (spc01 – spc30), type ssh tdgrocks.sci.hkbu.edu.hk

13. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Login to the master node VNC Login (graphical login) –Using vncviewer download from http://www.uk.research.att.com/vnc/ http://www.uk.research.att.com/vnc/ –E.g. in spc01 – spc30.sci.hkbu.edu.hk, vncviewer vnc.sci.hkbu.edu.hk:51 –E.g. in windows, run vncviewer and upon asking the server address, type vnc.sci.hkbu.edu.hk:51

14. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Username and password The unified password authentication has been implemented Same as that of your netware account Password authentication using NDS-AS Setup similar to net1 and net4 in ITSC

15. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU ssh key generation To make use of multiple nodes in the PC cluster, users are restricted to use ssh. Key generation is done once automatically during first login You may input a passphrase to protect the key pair The key pair is stored in your $HOME/.ssh/

16. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU User Policy Users are allowed to remote login from other networked PCs in HKBU. All users must use their own user account to login. The master node (frontend) is used only for login, simple editing of program source code, preparing the job dispatching script and dispatching of jobs to compute node. No foreground or background jobs can be run on it. Dispatching of jobs must be done via the PBS system.

17. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Torque/PBS system Provide a fair and efficient job dispatching and queuing system to the cluster PBS script shall be written for running job Either sequential or parallel jobs can be handled by PBS Jobs error and output are stored in different filenames according to job IDs.

18. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU PBS script example (sequential) PBS scripts are shell script with directives preceding with #PBS The above example request only 1 node and deliver the job named ‘prime’ in default queue. The PBS system will mail a message after the job executed. #!/bin/bash #PBS -l nodes=1 #PBS -N prime #PBS -m ae #PBS -q default # the above is the PBS directive used in batch queue echo Running on host `hostname` /u1/local/share/example/pbs/prime 216091

19. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Delivering PBS job Prepare and compile executable cp /u1/local/share/example/pbs/prime.c. cc –o prime prime.c -lm Prepare and edit PBS script as previous cp /u1/local/share/example/pbs/prime.bat. Submit the job qsub prime.bat

20. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU PBS script example (parallel) #!/bin/sh #PBS -N cpi #PBS -r n #PBS -e cpi.err #PBS -o cpi.log #PBS -m ae #PBS -l nodes=5:ppn=2 #PBS -l walltime=01:00:00 # This job's working directory echo Working directory is $PBS_O_WORKDIR cd $PBS_O_WORKDIR echo Running on host `hostname` echo This jobs runs on the following processors: echo `cat $PBS_NODEFILE` # Define number of processors NPROCS=`wc -l < $PBS_NODEFILE` echo This job has allocated $NPROCS nodes # Run the parallel MPI executable “cpi” /u1/local/mpich-1.2.5/bin/mpirun -v -machinefile $PBS_NODEFILE -np $NPROCS /u1/local/share/example/pbs/cpi

21. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU Delivering parallel jobs Copy the PBS script examples cp /u1/local/share/example/pbs/runcpi. Submit the PBS job qsub runcpi Note the error and output files named cpi.e??? and cpi.o???

22. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU End of Part 1 Thank you!

23. Using the P4-Xeon cluster HPCCC, Science Faculty, HKBU MPICH and LAM’s PATH MPICH 1.2.5.2 with gcc –/u1/local/mpich-1.2.5/bin MPICH 1.2.5.2 with pgi –/u1/local/mpich-pgi/bin LAM 6.5.9 –/usr/bin LAM 7.0.4 –/u1/local/lam-7.0.4/bin