Critical Flags, Variables, and Other Important ALCF Minutiae Jini Ramprakash Technical Support Specialist Argonne Leadership Computing Facility

Presentation outline  It’s all about your job! –Job management –Job basics Submission Queuing Execution Termination  Software environment  Optimization for beginners  ALCF resources, outlined Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 2

Job management  Cobalt (the ALCF resource scheduler) is used on all ALCF systems –Similar to PBS but not the same –Find more information at  Job management commands: –qsub: submit a job –qstat: query a job status –qdel: delete a job –qalter: alter batched job parameters –qmove: move job to different queue –qhold: place queued (non-running) job on hold –qrls: release hold on job –showres: show current and future reservations Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 3

Job basics – submission  Two modes of submitting jobs –Basic –Script mode  Get all flags and options by running ‘man qsub’  For example:  qsub -A alchemy -n mode c1 -t env “OMP_NUM_THREADS=4” lead_to_gold –In English: Charge project “Alchemy” for this job. Run on nodes, with one MPI rank per node. Run for 720 minutes. Set the “OMP_NUM_THREADS” environment variable to 4. Run the “lead_to_gold” binary. Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 4

qsub checks your submission for sanity  Did you specify a nodecount and walltime? Are they legal?  Is the mode you specified valid?  Did you ask for more than the minimum runtime?  Are you a member of the project you specified? Does that project have a usable allocation?  If so … all systems go! Get a JOBID, and put it in the queue Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 5

Not there yet! Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 6

Job basics - life in the queue  Periodically, your job’s score will increase  Periodically, the scheduler will decide if there are any jobs it wants to run  Check current state with qstat  At some point, your score will be high enough, and it will be YOUR TURN! Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 7

Score accrual  Large jobs are prioritized  Jobs that have been waiting long are prioritized  INCITE/ALCC projects are prioritized  Negative allocations have a score cap lower than the starting score of other jobs Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 8

Job basics - execution  Book-keeping –Put a start record in the database. Output a log file start record. Send of job start if –notify was requested. Start job timers  Fire up to execute the job –Cobalt boots partition –runjob starts executable Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 9

Script mode jobs  All jobs launch via runjob on the service nodes  Script mode jobs launch your script on a special login node  That script is responsible for calling runjob to launch the actual compute-node job  You are charged for the duration of the script Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 10

Job basics – termination aka are we there yet?  Your requested wall-time ticks down. Either your runjob returns, or you run out of wall-time and your job is forcibly removed  Job-end cleanup happens –If your partition wasn’t cleaned up, that happens now  Job-end book-keeping happens –Database, log file, notify if requested Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 11

Job basics – Termination, life after your job  If you had a job depending on you, it can be released to run. If you had a non-zero exit code, it moves to dep_fail instead  That night, the log files will be fed into clusterbank (the ALCF accounting system) to create charges Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 12

Non-standard job events  Reservations and/or draining  qsub rejection  Job holds  Job redefinition (qalter)  Job removal (qdel)  Abnormal job failure  Why isn’t this job running? Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 13

Software environment - SoftEnv  A tool for managing your environment –Sets your PATH to access desired front-end tools –Your compiler version can be changed here  Settings: –Maintained in the file ~/.soft –Add/remove keywords from ~/.soft to change environment –Make is at the very end  Commands: –softenv a list of all keywords defined on the systems –resoft reloads initial environment from ~/.soft file –soft add|remove keyword Temporarily modify environment by adding/removing keywords  Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 14

Software libraries  ALCF Supports two sets of libraries: –IBM system and provided libraries: /bgsys/drivers/ppcfloor glibc mpi –Site supported libraries and programs: /soft/ PETSc ESSL –And many others See Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 15

Compiler wrappers Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 16  MPI wrappers for IBM XL cross-compilers:  MPI wrappers for GNU cross-compilers: WrapperThread-Safe Wrapper Underlying Compiler Description mpixlcmpixlc_rbgxlcIBM BG C Compiler mpixlcxxmpixlcxx_rbgxlCIBM BG C++ Compiler mpixlf77mpixlf77_rbgxlfIBM BG Fortran 77 Compiler mpixlf90mpixlf90_rbgxlf90IBM BG Fortran 90 Compiler mpixlf95mpixlf95_rbgxlf95IBM BG Fortran 95 Compiler mpixlf2003mpixlf2003_rbgxlf2003IBM BG Fortran 2003 Compiler WrapperUnderlying CompilerDescription mpiccpowerpc-bgp-linux-gccGNU BG C Compiler mpicxxpowerpc-bgp-linux-g++GNU BG C++ Compiler mpif77powerpc-bgp-linux-gfortranGNU BG Fortran 77 Compiler mpif90powerpc-bgp-linux-gfortranGNU BG Fortran 90 Compiler

Optimization for beginners  Suggested set of optimization levels from least to most optimization:  -O0 # best level for use with a debugger  -O2 # good level for verifying correctness, baseline perf  -O2 -qmaxmem=-1 -qhot=level=0  -O3 -qstrict (preserves program semantics)  -O3  -O3 -qhot=level=1  -O4  -O5 Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 17

Optimization tips  -qlistopt generates a listing with all flags used in compilation  -qreport produces a listing, shows how code was optimized  Performance can decrease at higher levels of optimization, especially at -O4 or -O5  May specify different optimization levels for different routines/files Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 18

ALCF Resources – BG/Q systems  Mira – BG/Q system –49,152 nodes / 786,432 cores –786 TB of memory –Peak flop rate: 10 PF –Linpack flop rate: 8.1 PF  Cetus (T&D) – BG/Q system –1024 nodes / 16,384 cores –16 TB of memory –Peak flop rate: 208 TF  Vesta (T&D) -­‐ BG/Q systems –2,048 nodes / 32,768 cores –32 TB of memory –Peak flop rate: 416 TF Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 19

ALCF Resources – supporting systems  Tukey –Nvidia system –100 nodes / 1600 x86 cores/ 200 M2070 GPUs –6.4 TB x86 memory / 1.2 TB GPU memory –Peak flop rate: 220 TF  Storage –Scratch: 28.8 PB raw capacity, 240 GB/s bw (GPFS) –Home: 1.8 PB raw capacity, 45 GB/s bw (GPFS) –Storage upgrade planned in 2015 Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 20

ALCF Resources Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 21 Mira 48 racks/768K cores 10 PF Cetus (Dev) 1 rack/16K cores 208 TF Tukey (Viz) 100 nodes/1600 cores 200 NVIDIA GPUs 220 TF Networks 100Gb (via Esnet, internet2 UltraScienceNet) Vesta (Dev) 2 racks/32K cores 416 TF

Coming up next…  Data Transfers in the ALCF - Robert Scott, ALCF Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 22

Thank You!  Questions? Argonne Leadership Computing Facility - supported by the Office of Science of the U.S. Department of Energy 23