vsc4Recap from previous exercises:

cd ~/HY-LRZ/he-hy                             #   change into your he-hy directory


job_*.sh                                                #   job-scripts to run the provided tools, 2 x job_*_exercise.sh

*.[c|f90]                                               #   various codes (hello world & tests) - NO need to look into these!

coolmuc2/coolmuc2_slurm.out_*     #   coolmuc2 output files --> sorted (note: physical cores via modulo 48)

IN THE ONLINE COURSE he-hy shall be done in two parts:
    first exercise            =   1. + 2. + 3. + 4. (already done before)

    second exercise   =   5. + 6. + 7.   (after the talk on pinning)

vsc4 - compute node - topology4. Recap from previous exercise: get to know the hardware

    → Find out about the hardware of compute nodes:

    → solution.out =  coolmuc2/coolmuc2_slurm.out_check-hw_solution

5. MPI-pure MPI:      compile and run the MPI "Hello world!" program (pinning)

    job_he-mpi_[default|ordered].sh,  he-mpi.[c|f90],  help_fortran_find_core_id.c    

vsc-4 - job-script - pinning pure MPI    compile he-mpi - either C or Fortran - precompiled version = C: 
    C:             mpiicc -o he-mpi he-mpi.c
    Fortran:   icc -c help_fortran_find_core_id.c
    Fortran:   mpiifort -o he-mpi he-mpi.f90 help_fortran_find_core_id.o

    submit he-mpi to a compute node (mpirun):
    sbatch job_he-mpi_default.sh   # CoolMUC2 --> okay (pinned to cores, but not to hw-thread; i.e., physical cores modulo 28)
    sbatch job_he-mpi_ordered.sh # CoolMUC2 --> pinning to cores & hw-thread (T1); i.e., to physical cores 0-27 --> perfect smile

    ? Why is the output (most of the time) unsorted ? ==> here (he-mpi) you can use: ... | sort -n

    ? Can you rely on the defaults for pinning ? ==> Always take care of & check correct pinning yourself !

vsc-4 - job script - hybrid exercise

6. MPI+OpenMP: :TODO: compile and run the Hybrid "Hello world!" program

    job_he-hy_exercise.sh,  he-hy.[c|f90],  help_fortran_find_core_id.c

    compile he-hy - either C or Fortran - precompiled version = C:
    C:             mpiicc -qopenmp -o he-hy he-hy.c
    Fortran:   icc -c help_fortran_find_core_id.c
    Fortran:   mpiifort -qopenmp -o he-hy he-hy.f90 help_fortran_find_core_id.o


     Run he-hy on a compute node, i.e.:  sbatch job_he-hy_exercise.sh

    ? Why is the output (most of the time) unsorted ? ==> here (he-hy) you can use: ... | sort -n

vsc-4 - solution - hybrid pinning    → Find out what's the default pinning with mpirun !
        # CoolMUC2 --> the default is already perfect --> but let's do it explicitly !

    → Look into: job_he-hy_exercise.sh 

    → Do NOT YET do the pinning exercise, see below 7.

vsc-4 - result - hybrid pinning    ? Can you rely on the defaults for pinning ? ==> Always take care of & check correct pinning yourself !

7. MPI+OpenMP: :TODO: how to do pinning

    job_he-hy_[exercise|solution].sh,  he-hy.[c|f90]

      TODO (see below for info):

    → Do the pinning exercise in:  job_he-hy_exercise.sh

     one possible solution = job_he-hy_solution.sh
        # CoolMUC2 --> explicit pinning of MPI procs & OMP threads done perfectly smile

PINNING: (→ see also slides 72-86)

Pinning depends on:

               batch system    [SLURM*] \
               MPI library [Intel*]  |   interaction between these !
               startup [mpirun*|srun]    /

Always check your pinning !

          → job_he-hy...sh (he-hy.[c|f90] prints core_id)

          → print core_id in your application (see he-hy.*)

          → turn on debugging info & verbose output in job

          → monitor your job → login to nodes: top [1 q]

Intel → PINNING is done via environment variables (valid for Intel-only!):

pure MPI:           I_MPI_PIN_PROCESSOR_LIST=<proclist>   (other possiblities see Web)



                                                                  omp - number of logical cores = OMP_NUM_THREADS

                             I_MPI_PIN_DOMAIN=[m_1,.....m_n] hexadecimal bit mask, [] included!

OpenMP:            KMP_AFFINITY=[<modifier>,...]<type>[,<permute>][,<offset>]

                                    modifier                                             type (required)

                                    granularity=fine|thread|core|tile         compact
                                    proclist={<proc-list>}                          balanced
                                    [no]respect (an OS affinity mask)      scatter
                                    [no]verbose                                          explicit  (no permute,offset)
                                    [no]warnings                                        disabled (no permute,offset)
                                                                                                   none      (no permute,offset)

                                    default: noverbose,respect,granularity=core,none[,0,0]

Debug:              KMP_AFFINITY=verbose

Example from slide 85 (last pinning example in the slides):         

                           1 MPI process per socket, 14 cores per socket, 2 sockets per node:

                         export OMP_NUM_THREADS=14

                         export KMP_AFFINITY=scatter

                         export I_MPI_PIN_DOMAIN=socket

                         mpirun -ppn 2 -np # ./<exe>

                                                           see:  job_he-hy_test-1ps.sh + slurm.out_he-hy_mpirun_test-1ps (note: physical cores via modulo 28)

Last modified: Wednesday, 22 June 2022, 1:00 PM