Cluster Computing: Updraft. Charles Reid Scientific Computing Summer Workshop June 29, 2010
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1 Cluster Computing: Updraft Charles Reid Scientific Computing Summer Workshop June 29, 2010
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3 Updraft Cluster: Hardware 256 Dual Quad-Core Nodes 2048 Cores 2.8 GHz Intel Xeon Processors 16 GB memory per node Qlogic Infiniband network interconnect Ethernet network interconnect
4 Updraft Cluster: Hardware 256 Dual Quad-Core Nodes 2048 Cores 2.8 GHz Intel Xeon Processors 16 GB memory per node Qlogic Infiniband network interconnect Ethernet network interconnect
5 Node Networking Networking flavors for nodes: Ethernet Infiniband
6 Node Networking Networking flavors for nodes: Ethernet Infiniband
7 Head Nodes Updraft 1 (updraft1.chpc.utah.edu) Updraft 2 (updraft2.chpc.utah.edu) NOT FOR COMPUTATION!!! Illustrative Example
8 Updraft Cluster: Hardware 256 Dual Quad-Core Nodes 2048 Cores 2.8 GHz Intel Xeon Processors 16 GB memory per node Qlogic Infiniband interconnect Gigabit ethernet interconnect
9 Simple Parallel Example What actually happens when you run programs on multiple cores?
10 Golden Rule: The one with the gold makes the rules
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12 Funding for Updraft: ICSE CSAFE Others
13 Updraft Policies ICSE and CSAFE users: running big jobs Updraft designed for big jobs High throughput vs. High capacity Preemption: some jobs can preempt other jobs QOS: your quality of service determines whether you can pre-empt other jobs
14 Updraft Policies: Allocations Allocation = how much time you get on Updraft Every CPU hour run decreases your allocation Allocations given for each quarter Jan-Mar, Apr-Jun, Jul-Sep, Sep-Dec Allocations distributed/grouped by P.I. (primary investigators), not on individual basis CHPC website: current allocation status
15 Updraft Policies: Preemptors QOS Priority bigrun uintah general +++ (preemptor) ++ (preemptor) ++ (preemptor) NOT FOR SMALL JOBS!!! Jobs > 512 nodes Must be in Uintah group Anyone
16 Updraft Policies: Preemptees QOS Priority preemptable + (preemptable) Charges allocation at 1/4 the rate freecycle 0 (preemptable) Doesn t use/require any allocation
17 Updraft Policies: DATs Dedicated Access Time 48 hours to access 100% of Updraft 1st week of the month - Uintah DAT 3rd week of the month - Uintah DAT 4th week of the month - General DAT How to find out when DATs are?
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19 Updraft Queue System Queue system: schedules and manages jobs and resources Other systems: Moab, Maui, etc. PBS scripts - see CHPC website for examples Submitting jobs - qsub Deleting jobs - qdel Checking on jobs - checkjob Showing entire queue - showq / qstat
20 Updraft Hard Disks When you run a job, where do you put stuff? NFS (Network file system) Uintah disk space Scratch & temp disk space
21 Updraft Hard Disks: NFS Slowest MB/s NOT for dumping simulation output!!! Home directories: /uufs/chpc.utah.edu/common/home CRSim group space: /uufs/chpc.utah.edu/common/home/crsim_grp ICSE group space: /uufs/chpc.utah.edu/common/home/icse_grp
22 Updraft Hard Disks: Uintah Disk Space Faster access... for executables and code NOT for simulation output!!! Limited disk space for code development/ execution Only accessible from updraft2.chpc.utah.edu head node Location: /uufs/updraft.arches/common/uintah/homebrew
23 Updraft Hard Disks: Scratch/Temp Disk Space This IS for simulation output!!! Disk speeds are faster: MB/s WARNING: Cleaned monthly/at random! Uintah scratch space: /scratch/uintah General scratch space: /scratch/general Node scratch space (very small): /tmp
24 Updraft Hard Disks: Getting Disk Info Disk usage summaries are ed weekly to be added to list for disk usage summaries disk usage (for files/folders): du disk free space (for file systems): df
25 Updraft Software Compilers GCC compiler suite (gcc) Intel compiler suite (icc) Pathscale compilers (pathcc) Portland group compilers (pgcc)
26 Updraft Software MPI MPICH MVAPICH/MVAPICH2 OpenMPI Qlogic
27 Updraft Software Linear algebra packages ATLAS BLAS LAPACK/ScaLAPACK IMKL (Intel Math Kernel Library) Hypre PETSc
28 Updraft Software Full list of software: Presentations (many cover software mentioned here): Locations for stuff: /uufs/chpc.utah.edu/sys/pkg /uufs/updraft.arches/sys/pkg Subject of next workshop! Alternatively: build your own stuff $HOME/pkg
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30 $ system_profiler $ cat /proc/cpuinfo $ top $ who $ finger $ showres $ qdel $ checkjob $ qstat $ showq $ du -h $ df -h $ qsub
31 Cluster Hardware: Updraft User s Guide: Queue system: Available Software: Presentations: CHPC Wiki:
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