KAUST Supercomputing Laboratory Orientation Workshop October 13, 2009

Agenda 1Introduction to KAUST SL and team 2Computational resources currently available 3Computational resources available in the near future 4Getting an account on KAUST SL machines 5Q & A 6Machine-room viewing KAUST King Abdullah University of Science and Technology2

3 KAUST Supercomputer Lab Our Mission To offer resources that are world-class in both capacity and diversity HPC systems (BG/P, GPUs, SMP, Linux) Data systems (on-demand filesystems, archive) To assist KAUST researchers to fully exploit these resources Via a talented, skilled and experienced staff Joint research collaborations between SL team and researchers SL team will conduct its own HPC exploitation research Thank you for your continued patience and understanding!!

4 The KAUST SL team Management Jim Sexton Richard Orme Systems Administration Jonathon Anderson Iain Georgeson Research & Enablement Aron Ahmadia Samar Aseeri Dodi Heryadi Mark Cheeseman Ying Qian **Possibility of getting IBM expertise as part of CDCR collaboration

KAUST King Abdullah University of Science and Technology5 Currently available resources Capability machines (Blue Gene/P) WATSONshaheen Shaheen (early user access only) Capacity machines (linux clusters) WATSONlinux Shaheen (early user access only) Texas A&M University linux clusters Data stores Storage available at WATSON (not backed up) 0.5TB shared on Shaheen

Available Blue Gene/P Systems KAUST SL Orientation Session October 13, 2009

7 Blue Gene/P – compute design CPU 4 850MHz 13.6 GF/s Compute Card 1 cpu, 4GB DDR2 Node Card 32 compute cards, 0-2 IO cards 128GB DDR2, 435 GF/s Rack 32 node cards, IO cards 4TB DDR2, 13.9 TF/s Shaheen System 4 or 8 racks 16 or 32TB DDR or TF/s

8 Blue Gene/P – communication networks 3D Torus point-to-point communication twelve 425 MB/s links per compute node (5.1 GB/s total) 41 or 167 TB/s for system Collective Optimized collective operations (broadcast, reduction, …) Three 850 MB/s links per compute/IO node (5.1 GB/s total) Serves as connection between compute and IO nodes Low latency barriers and interrupt External 10GbE connection for external communication (file IO)

9 Accessing the Shaheen platforms KAUST researchers have access to 2 BG/P’s –WATSONshaheen (4 racks) –Shaheen (8 racks) Need to ssh/sftp into a front-end machine kstfen1.watson.ibm.com kstfen2.watson.ibm.com shaheen.hpc.kaust.edu.sa NOTE: front-end machines are of a different architecture Power6 (32-way) 64 GB Access to shared GPFS filesystems

Filesystem layout WATSONshaheen 5 PB scratch GPFS (not backed up) No archive access for KAUST users –Users responsible for backing up important Shaheen Currently only 0.5PB available Archive is not available 3 GPFS file-systems shared between BG/P and Xeon cluster –Home –Project (to be shared between users of the same project) –scratch 10

11 Shaheen – programming environment Full IBM and GNU compiler suite available on both BG/P systems MPI and OpenMP supported applications abinit cpmd dlpoly espresso games gromacs nwchem openfoam siesta math libraries blas/lapack boost essl fftw hypre parmetis petsc scalapack trilinos IO libraries hdf5 netcdf pnetcdf debugging gdb Totalview (Shaheen only) performance analysis fpmpi gprof ipm mpiP mpitrace tau Supported software: located under /soft Control by MODULES Please allow some time for Shaheen supported software stack to be built

Shaheen - compiling Do not use normal compiler calls (gcc, gfortran, xlc, …) – create binaries that run on login nodes NOT the compute nodes –Architecture difference between login and compute nodes Use IBM-provided wrapper compiler commands –create binaries for the compute nodes –Includes native MPI support 12 mpicc –o test.exe test.cc mpicxx –o test.exe test.cpp mpif90 –o test.exe test.f mpif77 –o test.exe test.f90 mpixlc –o test.exe test.cc mpixlcxx –o test.exe test.cpp mpixlf90 –o test.exe test.f90 GNU IBM

13 Shaheen – running a job WATSONshaheen No job management or queuing system present –All jobs ran interactively via the mpirun command mpirun –np 16 –partition r001n00-c32i2 –VN –cwd pwd –exe test.exe where MPI tasks -np indicates # of MPI tasks -partition indicates BG/P partition to use -VN indicates the run mode -cwd gives the rutime directory -exe gives the name of the executable to be ran In above example, test.exe is ran on 4 quad-core CPUs in the current directory How do I find an appropriate BG/P partition? /soft/bgp_partition_finder NOTE: only a simple script that may fail sometimes

14 Shaheen – running a job continued WATSONshaheen continued… Run modes –SMP: 1 MPI task per CPU. 4GB available to task –DUAL: 2 MPI tasks per CPU. 2GB available for each task –VN: 4 MPI tasks per CPU. 1GB available for each task Shaheen LoadLeveler job management system to be used –2 queues (12hr production and 30min development) –Users do not need to specify partition id Pre/Post-processing work to be ran on linux cluster –Shared filesystems allow easy data transfer

Available IBM Linux Clusters KAUST SL Orientation Session October 13, 2009

IBM Linux clusters - overview KAUST researchers have access to two clusters WATSONlinux (32-node NY, USA) Shaheen (96-node KAUST) 16 these systems are primarily intended to be used as auxiliary computational resources for pre/post-processing, and initial x86 code tests prior to their enablement on Shaheen NOTE:

IBM Linux clusters – overview continued 17

Accessing the linux clusters Need to ssh/sftp into a front-end machine kstxfen1.watson.ibm.com kstxfen2.watson.ibm.com shaheenx.hpc.kaust.edu.sa KAUST King Abdullah University of Science and Technology18

IBM Linux clusters - Modules a simple mechanism to update a user's environment such as PATH, MANPATH, NLSPATH, LD_LIBRARY_PATH, etc. module list -> to show currently loaded modules module avail -> to show available modules module what-is -> to describe module module load -> to load module KAUST King Abdullah University of Science and Technology19 ~]$ module avail /opt/modules Loadleveler hdf5 postprocessing/nccmp compilers/GNU netcdf postprocessing/ncl compilers/INTEL netcdf4 totalview fftw2 postprocessing/ferret wien2k fftw3 postprocessing/grads

IBM Linux clusters – Programming Environment Compilers GNU and Intel compilers (C, C++ and FORTRAN) available PGI has been ordered MPI Support3 MPICH2 is default MPICH1 and OpenMPI are available as well It is strongly encouraged that Modules be used for compiling and linking KAUST King Abdullah University of Science and Technology20

IBM Linux clusters – Compiling serial codes Intel compilers: module load compilers/INTEL ifort -> calls the Intel Fortran compiler icc -> calls the Intel C compiler icpc -> calls the Intel C++ compiler GNU compilers: module load compilers/GNU gfortran -> calls the GNU Fortran compiler gcc -> calls the GNU C compiler g++ -> calls the GNU C++ compiler KAUST King Abdullah University of Science and Technology21

IBM Linux clusters – Compiling MPI codes Intel compilers: module load compilers/INTEL mpicc -> calls the Intel C compiler with MPI support enabled mpic++-> calls the Intel C++ compiler with MPI support enabled mpif77 -> calls the Intel F77 compiler with MPI support enabled mpif90 -> calls the Intel F90 compiler with MPI support enabled GNU compilers: module load compilers/GNU mpicc -> calls the GNU C compiler with MPI support enabled mpic++ -> calls the GNU C++ compiler with MPI support enabled mpif77 -> calls the GNU F77 compiler with MPI support enabled mpif90 -> calls the GNU F90 compiler with MPI support enabled 22

IBM Linux clusters – INTEL MKL The following Intel Math Kernel Libraries are available BLAS LAPACK BLACS SCALAPACK KAUST King Abdullah University of Science and Technology23

IBM Linux clusters – INTEL MKL Linking codes with Intel MKL BLAS and LAPACK Static, sequential, 64-bit integer $MKLPATH/libmkl_solver_ilp64_sequential.a -Wl,--start-group $MKLPATH/libmkl_intel_ilp64.a $MKLPATH/libmkl_sequential.a $MKLPATH/libmkl_core.a - Wl,--end-group -lpthread Dynamic, multi-threaded, 64-bit integer -L$MKLPATH $MKLPATH/libmkl_solver_ilp64.a -Wl,--start-group -lmkl_intel_ilp64 - lmkl_intel_thread -lmkl_core -Wl,--end-group -openmp -lpthread KAUST King Abdullah University of Science and Technology24

IBM Linux clusters – INTEL MKL Linking codes with Intel MKL SCALAPACK and BLACS SCALAPACK: Static, sequential, 64-bit integer, MPICH2 $MKLPATH/libmkl_scalapack_ilp64.a $MKLPATH/libmkl_solver_ilp64.a -Wl,--start-group $MKLPATH/libmkl_intel_ilp64.a $MKLPATH/libmkl_intel_thread.a $MKLPATH/libmkl_core.a $MKLPATH/libmkl_blacs_intelmpi_ilp64.a -Wl,--end-group -openmp -lpthread BLACS: Dynamic, multi-threaded, 64-bit integer, MPICH2 -L$MKLPATH $MKLPATH/libmkl_solver_ilp64.a -Wl,--start-group -lmkl_intel_ilp64 - lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_ilp64 -Wl,--end-group -openmp -lpthread KAUST King Abdullah University of Science and Technology25

IBM Linux clusters – running a job LoadLeveler job management and queuing system present Useful LoadLeveler commands llsubmit submit a job to LoadLeveler llq show queued and running jobs llcancel delete queued or running job llstatus display system information 26 ~]$ module load compilers/INTEL ~]$ module load Loadleveler ~]$ llsubmit jobscript llsubmit: The job "n1.linux32.watson.ibm.com.96" has been submitted. ~]$ llq Id Owner Submitted ST PRI Class Running On n xxxxx 10/13 03:42 R 50 No_Class n1 1 job step(s) in queue, 0 waiting, 0 pending, 1 running, 0 held, 0 preempted

IBM Linux clusters – constructing a jobfile EXAMPLE: parallel job with only MPI tasks #! /bin/csh -f output = out error = err job_type = parallel node = 1 notification = never environment = COPY_ALL queue cd $LOADL_STEP_INITDIR mpdboot -n 1 -f ${LOADL_HOSTFILE} mpiexec -n 8./hello_intel mpdallexit **Here 8 MPI tasks are spawned a single (2 quadcore Xeon) compute node KAUST King Abdullah University of Science and Technology27

IBM Linux clusters – constructing a jobfile EXAMPLE: parallel job with only OpenMP threads #! /bin/csh -f output = out error = err job_type = parallel node = 1 notification = never environment = COPY_ALL queue setenv OMP_NUM_THREADS 8 cd $LOADL_STEP_INITDIR./hello_omp_gnu **Here 8 OpenMP threads are spawned a single (2 quadcore Xeon) compute node KAUST King Abdullah University of Science and Technology28

IBM Linux clusters – constructing a jobfile EXAMPLE: parallel job with 2 MPI tasks that each spawn 8 OpenMP threads #! /bin/csh -f output = out error = err job_type = parallel node = 2 notification = never environment = COPY_ALL queue setenv OMP_NUM_THREADS 8 cd $LOADL_STEP_INITDIR mpdboot -n 2 -f ${LOADL_HOSTFILE} mpiexec -np 2./hello_mpi_omp_intel mpdallexit KAUST King Abdullah University of Science and Technology29 **Here 8 OpenMP threads are spawned a single (2 quadcore Xeon) compute node

IBM Linux clusters – 3 rd party software Installation/support of 3 rd party software is based on the mutual agreement between the requesting PI and KAUST SL KAUST King Abdullah University of Science and Technology30 applications gaussian schrodinger wien2k math libraries blas/lapack boost INTEL MKL fftw GSL IO libraries hdf5 netcdf pnetcdf debugging gdb Totalview (Shaheen only) Supported software: located under /opt Control by MODULES Please allow some time for supported software stack to be built Post- processing ferret grads ncl ncview udunits

Available Texas A&M Linux Clusters KAUST SL Orientation Session October 13, 2009

Resources Available in the “Near Future” KAUST SL Orientation Session October 13, 2009

More resources are on the way… Shaheen installation continues Expansion from 8 to 16 racks Full 1.9PB shared disk space Archive not built yet Other HPC systems are being shipped 256 node x86 linux cluster 4 SMP nodes 16 TESLA GPGPU nodes 1 PB shared disk KAUST King Abdullah University of Science and Technology33

Project & Account Creation Procedures KAUST SL Orientation Session October 13, 2009

Accessing Shaheen Organization application Terms and conditions acknowledgement Funding authorization Project proposal Scientific description Authorized researchers Individual application Personal information KAUST King Abdullah University of Science and Technology35

Accessing Shaheen (restrictions) Nationals of “group E” countries Cuba Iran North Korea Sudan Syria KAUST King Abdullah University of Science and Technology36

Accessing Shaheen (restrictions) Unauthorized research Weapons Rockets Unmanned aerial vehicles Nuclear fuel facilities (except by treaty) Heavy water production facilities (except by treaty) KAUST King Abdullah University of Science and Technology37

Contacting Us Our internal wiki/website is available to KAUST users For HPC Support Queries Or drop by and see us in person Level 0, Building 1(across from the cafeteria) Offices KAUST King Abdullah University of Science and Technology38

Thank you for your attention Questions?