bwgrid Treff MA/HD Sabine Richling, Heinz Kredel Universitätsrechenzentrum Heidelberg Rechenzentrum Universität Mannheim 29.

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1 bwgrid Treff MA/HD Sabine Richling, Heinz Kredel Universitätsrechenzentrum Heidelberg Rechenzentrum Universität Mannheim 29. September 2010 Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

2 Course Organization bwgrid Treff Participants Current users of the bwgrid Clusters HD/MA Students and scientists interested in Grid Computing Members of the Universities Heidelberg and Mannheim Scope bwgrid Status and Plans Lectures and/or Workshops User contributions To meet you in person Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

3 Course Organization bwgrid Treff Summer Term 2010 Main Focus: 29. April bwgrid Status and Interconnection HD/MA 20. May Batch-System and Parallel execution of serial jobs 17. June Parallel Programming with Java (Part I) 15. July Parallel Programming with Java (Part II) Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

4 Course Organization bwgrid Treff Fall/Winter 2010/2011 Lecture times: Mannheim: HS Heidelberg: WS Date Location Main Focus MA Matlab & Matlab Clones Oct 2010 MA Nov 2010 HD Dec 2010 HD Jan 2011 HD Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

5 Course Organization bwgrid Treff 29. September 2010 Agenda for today: bwgrid News Matlab on the bwgrid Cluster MA/HD Matching or Duration Models? A Monte Carlo Study (A. Uhlendorff, Department of Economics, University of Mannheim) Alternatives to Matlab: Octave & Scilab Discussion of topics for further meetings Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

6 bwgrid News bwgrid News Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

7 bwgrid News What is bwgrid? D-Grid Community project of the Universities in BW Compute Clusters at 8 locations Central storage unit in Karlsruhe Distributed system with local administration Computing centers focus on software in different fields of research Access via at least one middleware supported by D-Grid Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

8 bwgrid News bwgrid Resources Compute cluster: Mannheim/Heidelberg: 280 nodes Direct Interconnection Frankfurt Karlsruhe: 140 nodes Stuttgart: 420 nodes Tübingen: 140 nodes Mannheim (interconnected to a single cluster) Heidelberg Ulm (Konstanz): 280 nodes Hardware in Ulm Karlsruhe Stuttgart Freiburg: 140 nodes Esslingen Esslingen: 180 nodes more recent Hardware Central storage: Freiburg Tübingen Ulm (joint cluster with Konstanz) München Karlsruhe: 128 TB (with Backup) 256 TB (without Backup) Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

9 bwgrid News Access Possibilities Important! Access with local Accounts: Project numbers and User IDs (URZ); User IDs (RUM) Access only to bwgrid cluster MA/HD Access with Grid Certificate: Grid Certificate, VO membership, Grid Middleware Access to all bwgrid resources Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

10 bwgrid User Support bwgrid News General Information: Hardware and software Project descriptions Grid access (server addresses) bwgrid Portals (in development) D-Grid user support: Trouble ticket system News module for maintenances User Support available at all sites: Login messages Local webpages, wikis, mailing lists address for local support Local news man bw-grid Terms and conditions for using bwgrid Home directory, scratch/work space, /tmp Special features Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

11 bwgrid News bwgrid Cluster Mannheim/Heidelberg Belwue VORM Benutzer Benutzer PBS Benutzer Benutzer VORM LDAP Admin AD Cluster Mannheim InfiniBand Obsidian + ADVA passwd InfiniBand Cluster Heidelberg Lustre bwfs MA Lustre bwfs HD Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

12 bwgrid News bwgrid Cluster Mannheim/Heidelberg News Security update in progress (currently no 32 bit binaries on the nodes) bwgrid storage in Heidelberg available since end of August Workspaces for temporary data (no backup) $HOME now limited to 100 GB per user (with backup) New MPI modules for operating system SL 5.5 Mvapich2 1.4, 1.5 OpenMPI 1.2.8, 1.2.9, 1.3.4, Intel MPI 4.0 for GNU compiler 4.1 and Intel compiler 10.1, 11.1 Other new software modules chem/gaussian/g09a02 chem/orca/2.7.0 (Heidelberg users only!) chem/schrodinger/2009u2 vis/molden/4.8 vis/molekel/5.4.0 vis/root/5.26 math/matlab/r2010b (Mannheim users only!) math/r/2.9.2 math/r/ math/r/ Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

13 Matlab on bwgrid Matlab on bwgrid Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

14 Matlab on bwgrid Matlab License situation Available Matlab versions: R2010a and R2010b 4 Licenses for: Matlab Optimization Toolbox Parallel Computing Toolbox Statistics Toolbox Symbolic Math Toolbox 1 License for Matlab Compiler Only for users with accounts of the University of Mannheim! Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

15 Matlab on bwgrid Interactive Usage of Matlab Request a compute node qsub -I -X -l walltime=3:00:00 Load Matlab module module load math/matlab/2010b Start Matlab with GUI: without GUI (faster): matlab matlab -nodesktop Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

16 Matlab on bwgrid Matlab Batch Jobs Read Module Help module help math/matlab/2010b First try the Matlab Compiler Compile your program BEFORE job submission Start the compiled binary in your job script Matlab binaries do not consume any license tokens! Only if your program does not compile or when you use the PCT Start m-file directly in job script Use the PBS software option Occupy only 1 license at a time Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

17 Matlab on bwgrid Parallelization with Matlab Starting up to 8 programs on a node (with pbsdsh) Automatic Multithreading in Matlab Shared memory computing with Parallel Computing Toolbox Distributed computing with Distributed Computing Servern Additional licenses necessary! Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

18 Matlab on bwgrid Multithreading in Matlab Automatic Multithreading: Matlab runs computations on multiple threads No changes to Matlab code required Users can change behavior via preference Maximum gain in element-wise operations and BLAS routines Auf bwgrid: Default: Automatic. Use as many threads as cores: 8 Change number of used threads with: numthreads=2 Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

19 Matlab on bwgrid Matlab Parallel Computing Toolbox Basic commands matlabpool open 2; start Matlab workers (max. 8) matlabpool close; stop all Matlab workers Parallel Tools use parallel Matlab functions parfor parallel loops spmd for working with distributed arrays pmode interactive multithreading Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

20 Matlab Presentation (A. Uhlendorff) Matching or Duration Models? A Monte Carlo Study A. Uhlendorff, Department of Economics, Uni Mannheim Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

21 Alternatives to Matlab Free Alternatives to Matlab Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

22 Alternatives to Matlab Octave and Scilab Octave highest degree of Matlab compatibility Graphics based on Gnuplot GNU General Public License Scilab mostly compatible with Matlab (Matlab-to-Scilab translator) better Graphics, more functionality GPL compatible licence Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

23 Alternatives to Matlab Octave on bwgrid Current Version module load math/octave/3.0.3 octave starts interactive command line client octave test.m executes m-file test.m works for basic Matlab commands without changes some missing functions are provided by research projects Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

24 Alternatives to Matlab Scilab on bwgrid Current Version module load math/scilab/4.1.2 scilab starts interactive GUI (with option -nogui without GUI) mfile2sci( test.m ) converts m-file to sci-file within scilab scilab -nogui -f test.sci executes sci-file test.sci more functionality and many additional toolboxes Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25

25 Conclusion Discussion of topics for further meetings Date Location Main Focus User Contribution MA Matlab & Matlab Clones A. Uhlendorff Oct 2010 MA Nov 2010 HD Dec 2010 HD Jan 2011 HD Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 25