High Performance Computing in Aachen

Transcription

1 High Performance Computing in Aachen Samuel Sarholz aachen.de Center for Computing and Communication RWTH Aachen University HPC unter Linux Sep 15, RWTH Aachen

2 Agenda o Hardware o Development Tools and Software o Usage o Support 2

3 The RZ Compute Cluster History o since 1958: Vector and other super computers o 1994: The Unix Cluster started with IBM machines o : main compute power in UltraSparc III IV CPUs o 2004: 64 Opteron nodes mainly with Linux o 2006: first Windows compute nodes o 2008: Intermediate Xeon Cluster o : new large procurement 3

4 The RZ Compute Cluster #nodes accumulated performance [TFLOPS] accumulated memory [TB] processor clock memory model type #procs #cores #threads [MHz] [GB] network 2 SF E25K UltraSPARC IV GE 0,60 0,58 20 SF T5120 UltraSPARC T GE 0,45 0,64 64 SF V40z Opteron GE 1,13 0,51 4 SF V40z Opteron GE + IB 0,14 0,06 2 SF X4600 Opteron GE 0,17 0,06 60 FuSi Rx200 S4 Xeon X GE + IB 5,76 0,96 2 FuSi Rx600 S4 Xeon E GE + IB 0,38 0, sum ,80 3,01 4

5 Harpertown based InfiniBand Cluster o Recently installed Cluster: Fujitsu Siemens Primergy Rx 200 S4 servers 2x Intel Xeon 5450 (quad core, 3.0 GHz) 16 / 32 GB memory per node 4x DDR InfiniBand: MPI latency: 3.6 us MPI bandwidth: 1250 MB/s 5 o 270 machines; RZ + other hosted machines (from RWTH institutes) o On place 100 in the Top500 list

6 Integrative Hosting o Machines are installed as the RZ Cluster Linux, Solaris, (Windows) Filesystems are shared o Resources preferably will be shared with other clusters Less idling machines, institutes can use more machines if needed E.g. the Institute for Scientific Computing cluster o Login and batch jobs may be restricted to certain user groups 6

7 Some Hosted Machines Vendor Machine Type Machine Count Processor Sockets Cores Fujitsu Simens Rx Xeon 2 8 Sun X Opteron 2 4 Sun X Opteron 2 4 Dell Xeon 2 4 Sun V20z 10 Opteorn 2 2 Hosted compute power about 4x more than the RZ cluster 7

8 Institutes we host for 8 o Lehr und Forschungsgebiet Theoretische Chemie (IPC), FB 1 Prof. Arne Lüchow o Lehrstuhl für Mathematik ( CCES), FB 1 Prof. Dieter Bothe o Lehrstuhl für Theoretische Physik C und Institut für Theoretische Physik (ThPhC), FB 1 Prof. Ulrich Schollwöck o Lehrstuhl für Werkstoffchemie (MCh), FB 1 Prof. Jochen Schneider o Lehrstuhl für Informatik 12 (Hochleistungsrechnen) (SC), FB 1 Prof. Christian Bischof o Ultra High Speed Mobile Information and Communication (UMIC) Exzellenzcluster o Aachen Institute for advanced study in Computational Engineering Science (AICES) Graduiertenschule im Rahmen der Exzellenzinitiative o Tailor Made Fuels from Biomass (TMFB) Exzellenzcluster

9 Agenda o Hardware o Development Tools and Software o Login o Support 9

10 Cluster Environment 10 o Processors / operating systems 4 platforms : 1. Opteron/Linux and Xeon/Linux 2. Xeon/Windows 3. SPARC/Solaris 4. Opteron/Solaris o All platforms are suited for serial programming, shared memory parallelization, message passing o We offer support for programming and parallelization Compilers, MPI libraries, debugging and performance analysis tools

11 Programming Tools 11 o Compiler o Debugger TotalView Visual Studio o Correctness tools Sun Thread Analyzer Intel Thread Checker Marmot o Performance analysis Intel VTune Sun Analyzer Vampir Scalasca Acumem

12 Compiler Company Compiler Version Language OpenMP support Autopar Sun Studio 11 F95/C/C++ F95/C/C++ F95/C/C++ Debugger dbx sunstudio Runtime Analysis analyzer, collect, er_print, gprof GNU 4.3 F95/C/C++ F95/C/C++ F95/C/C++ gdb gprof Intel 10.1 F95/C/C++ F95/C++ Threading Tools F95/C/C++ idb vtune GNU 4.1 F95/C/C++ F95/C++ Threading Tools F95/C/C++ gdb gprof Sun Studio 12 F95/C/C++ F95/C/C++ F95/C/C++ dbx sunstudio analyzer, collect, er_print, gprof Microsoft Visual Studio 2005 C/C++ C/C++ Visual Studio VS 2008 Intel 10.1 F95/C/C++ F95/C/C++ F95/C/C++ Visual Studio vtune 12

13 MPI Libraries Company Version Debugger Runtime Analysis Plattform Network Sun HPC ClusterTools 6 TotalView analyzer, mpprof Solaris tcp, shm Sun HPC ClusterTools >7 based on OpenMPI TotalView analyzer, vampir Solaris tcp, shm, InfiniBand OpenMPI 1.2 TotalView analyzer, vampir Solaris tcp, shm, InfiniBand Intel 3.1 (based on mpich2) TotalView Intel TraceCollector Linux tcp, shm, InfiniBand & Analyzer OpenMPI 1.2 TotalView Vampir Linux tcp, shm, InfiniBand Microsoft based on mpich2 Visual Studio w/ MS Compute Cluster Pack Windows tcp, shm, IniniBand 13

14 Software Packages 14 FEM o Abaqus o Ansys o Hyperworks o Ls Dyna o Marc/Mentat o Nastran/Patran Chemie o Gaussian o Turbomole o Vasp o abinit o meep Site license Parallel version available No site license CFD o CFX/TASCFlow o Fluent o ICEM CFD o StarCD o gerris Mathematik o Maple o Mathematica Misc o Matlab/Simulink o Tecplot o Siesta

15 Agenda o Hardware o Development Tools and Software o Usage o Support 15

16 o Frontend nodes for login Login Unix Frontends (ssh protocol) (or NX* on Linux) cluster.rz.rwth-aachen.de (Sparc Solaris) cluster-solaris-sparc.rz... (cl-sol-s) cluster-solaris-opteron.rz... (cl-sol-o) cluster-linux.rz... (Xeon Linux) cluster-linux-xeon.rz... (cl-lin-x) cluster-linux-operon.rz... (cl-lin-o) Windows Frontends (rdp protocol) cluster-win.rz.rwth-aachen.de (Xeon Windows) cluster-win2003.rz... cluster-win-beta.rz * You can get an NX client from

17 Interactive Usage o Interactive frontend systems are meant for short test runs, GUIs and debugging. Compute jobs should be submitted to the batch system On Linux we offer a few nodes for MPI tests and debugging to avoid overloaded frontends mpiexec determines the hosts with the lowest load to run on On Unix different program version and tools are managed by the module system 17

18 Batch System o The batch system manages the distribution of compute jobs Makes sure systems are not overloaded to guarantee good performance On Unix the Sun Grid Engine (SGE) is employed On Windows the Microsoft Compute Cluster Pack is used For more info and examples see our documentation 18

19 19 HPC unter Linux File Storage o We offer several filesystems on all compute nodes /home/<userid> or H: for permanent files, e.g programs, batch scripts and config files Snapshots to cover for accidental file deletion.zfs/snapshot/ Downside: they use quota as well /work/<userid> or W: for temporary compute results Offers more space and better performance than /home Unused files will be deleted after a month! /lustre/work/ <userid> fast parallel file system available on request Tape archive for long term storage o $TMP or %TMP% Limited space on a local disc May be deleted after logout o X: (Windows only) On a windows fileserver to offer better meta data performance You can use UNC as well e.g.: \\cifs\cluster\home\<userid>

20 Agenda o Hardware o Development Tools and Software o Usage o Support 20

21 Links o Information related to HPC at the RWTH Aachen o RWTH Compute Cluster User s Guide o Usage of the Windows HPC systems o Information on Hosting 21

22 Support Just send an to our trouble ticket system: Support inquiries: Software and Licensing: Programming, Debugging, Tuning, Parallelization: 22

23 Questions Thank you for your attention! Questions? 23