General exercise instructions

Working with the summerschool repository

We recommend that you work with your own personal fork of the summerschool git-repository. That way you can easily commit and push your own solutions to exercises.

Before starting out, synchronize your fork with "Sync fork" in the github web-GUI.

We also recommend that you create a separate branch for your own work, see "Using local workstation" or "Using supercomputers" below for details.

Once forked to yourself, you can sync with the original repository (in case of updates) by running:

git pull https://github.com/csc-training/summerschool.git

Repository structure

The exercise assignments are provided in various README.mds. For most of the exercises, skeleton codes are provided both for Fortran and C/C++ in the corresponding subdirectory. Some exercise skeletons have sections marked with “TODO” for completing the exercises. In addition, all of the exercises have exemplary full codes (that can be compiled and run) in the solutions folder. Note that these are seldom the only or even the best way to solve the problem.

Using local workstation

In case you have working parallel program development environment in your laptop (Fortran or C/C++ compiler, MPI development library, etc.) you may use that for exercises. Note, however, that no support for installing MPI environment can be provided during the course. Otherwise, you can use CSC supercomputers for carrying out the exercises.

Clone your personal fork in appropriate directory:

git clone git@github.com:<my-github-id>/summerschool.git

Create a branch:

git checkout -b hpcss23

Using supercomputers

Exercises can be carried out using the LUMI supercomputer.

LUMI can be accessed via ssh using the provided username and ssh key pair:

ssh -i <path-to-private-key> <username>@lumi.csc.fi

Disk areas

All the exercises in the supercomputers should be carried out in the scratch disk area. The name of the scratch directory can be queried with the command lumi-workspaces. As the base directory is shared between members of the project, you should create your own directory:

cd /scratch/project_465000536/
mkdir -p $USER
cd $USER

Working with git

In order to push code to your own fork, you need to add your SSH public key in LUMI to your github account. The SSH key can be added via "Settings"->"SSH and GPG keys"->"New SSH key", by copy-pasting output of the following command:

cat $HOME/.ssh/id_rsa.pub

Once succesfull, make sure you in your personal workspace in scratch area /scratch/project_465000536/$USER, clone the repository, and a create a branch:

git clone git@github.com:<my-github-id>/summerschool.git
git checkout -b hpcss23

If you haven't used git before in LUMI, you need to add also your identity:

git config --global user.email "you@example.com"
git config --global user.name "Your Name"

Default editor for commit messages is vim, if you prefer something else you can add to the file $HOME/.bashrc e.g.

export EDITOR=nano

Editors

For editing program source files you can use e.g. nano editor:

nano prog.f90

(^ in nano's shortcuts refer to Ctrl key, i.e. in order to save file and exit editor press Ctrl+X) Also other popular editors such as emacs and vim are available.

Compilation

LUMI has several programming environments. For summerschool, we recommend that you use the special summerschool modules:

module use /project/project_465000536/modules

For CPU programming use:

module load hpcss/cpu

For GPU programming use:

module load hpcss/gpu

MPI

Compilation of the MPI programs can be performed with the CC, cc, or ftn wrapper commands:

CC -o my_mpi_exe test.cpp

or

cc -o my_mpi_exe test.c

or

ftn -o my_mpi_exe test.f90

The wrapper commands include automatically all the flags needed for building MPI programs.

OpenMP (threading with CPUs)

Pure OpenMP (as well as serial) programs can also be compiled with the CC, cc, and ftn wrapper commands. OpenMP is enabled with the -fopenmp flag:

CC -o my_exe test.cpp -fopenmp

or

cc -o my_exe test.c -fopenmp

or

ftn -o my_exe test.f90 -fopenmp

When code uses also MPI, the wrapper commands include automatically all the flags needed for building MPI programs.

HDF5

In order to use HDF5 in CSC supercomputers, you need the load the HDF5 module with MPI I/O support. The appropriate module in Lumi is

module load cray-hdf5-parallel/1.12.2.1

No special flags are needed for compiling and linking, the compiler wrappers take care of them automatically.

Usage in local workstation may vary.

OpenMP offloading

On Lumi, the following modules are required:

module load LUMI/22.08
module load partition/G 
module load cce/15.0.1
module load rocm/5.3.3

On Lumi, to compile your program, use

CC -fopenmp <source.cpp>

HIP

Use the following modules :

module load LUMI/22.08
module load partition/G
module load cce/15.0.1
module load rocm/5.3.3

To compile your program, use:

CC -xhip <source.cpp>

HIPFORT

The following modules are required:

module load LUMI/22.08
module load partition/G
module load cce/15.0.1
module load rocm/5.3.3

Because the default HIPFORT installation only supports gfortran, we use a custom installation prepared in the summer school project. This package provide Fortran modules compatible with the Cray Fortran compiler as well as direct use of hipfort with the Fortran Cray Compiler wrapper (ftn).

The package was installed via:

git clone https://github.com/ROCmSoftwarePlatform/hipfort.git
cd hipfort;
mkdir build;
cd build;
cmake -DHIPFORT_INSTALL_DIR=<path-to>/HIPFORT -DHIPFORT_COMPILER_FLAGS="-ffree -eZ" -DHIPFORT_COMPILER=ftn -DHIPFORT_AR=${CRAY_BINUTILS_BIN_X86_64}/ar -DHIPFORT_RANLIB=${CRAY_BINUTILS_BIN_X86_64}/ranlib  ..
make -j 64 
make install

We will use the Cray 'ftn' compiler wrapper as you would do to compile any fortran code plus some additional flags:

export HIPFORT_HOME=/project/project_465000536/appl/HIPFORT
ftn -I$HIPFORT_HOME/include/hipfort/amdgcn "-DHIPFORT_ARCH=\"amd\"" -L$HIPFORT_HOME/lib -lhipfort-amdgcn $LIB_FLAGS -c <fortran_code>.f90 
CC -xhip -c <hip_kernels>.cpp
ftn  -I$HIPFORT_HOME/include/hipfort/amdgcn "-DHIPFORT_ARCH=\"amd\"" -L$HIPFORT_HOME/lib -lhipfort-amdgcn $LIB_FLAGS -o main <fortran_code>.o hip_kernels.o

This option gives enough flexibility for calling HIP libraries from Fortran or for a mix of OpenMP/OpenACC offloading to GPUs and HIP kernels/libraries.

Running in LUMI

Pure MPI

Programs need to be executed via the batch job system. Simple job running with 4 MPI tasks can be submitted with the following batch job script:

#!/bin/bash
#SBATCH --job-name=example
#SBATCH --account=project_465000536
#SBATCH --partition=standard
#SBATCH --reservation=summerschool_standard
#SBATCH --time=00:05:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=1  

srun my_mpi_exe

Save the script e.g. as job.sh and submit it with sbatch job.sh. The output of job will be in file slurm-xxxxx.out. You can check the status of your jobs with squeue -u $USER and kill possible hanging applications with scancel JOBID.

The reservation summerschool is available during the course days and it is accessible only with the training user accounts.

Pure OpenMP

For pure OpenMP programs one should use only one node and one MPI task per nodesingle tasks and specify the number of cores reserved for threading with --cpus-per-task:

#!/bin/bash
#SBATCH --job-name=example
#SBATCH --account=project_465000536
#SBATCH --partition=standard
#SBATCH --reservation=summerschool_standard
#SBATCH --time=00:05:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=4

# Set the number of threads based on --cpus-per-task
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
srun my_omp_exe

Hybrid MPI+OpenMP

For hybrid MPI+OpenMP programs it is recommended to specify explicitly number of nodes, number of MPI tasks per node (pure OpenMP programs as special case with one node and one task per node), and number of cores reserved for threading. The number of nodes is specified with --nodes (for most of the exercises you should use only a single node), number of MPI tasks per node with --ntasks-per-node, and number of cores reserved for threading with --cpus-per-task. The actual number of threads is specified with OMP_NUM_THREADS environment variable. Simple job running with 4 MPI tasks and 4 OpenMP threads per MPI task can be submitted with the following batch job script:

#!/bin/bash
#SBATCH --job-name=example
#SBATCH --account=project_465000536
#SBATCH --partition=standard
#SBATCH --reservation=summerschool_standard
#SBATCH --time=00:05:00
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=32
#SBATCH --cpus-per-task=4
# Set the number of threads based on --cpus-per-task
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
srun my_exe

GPU programs

When running GPU programs, few changes need to made to the batch job script. The partition is are now different, and one must also request explicitly given number of GPUs per node with the --gpus-per-node=8 option. As an example, in order to use a single GPU with single MPI task and a single thread use:

#!/bin/bash
#SBATCH --job-name=example
#SBATCH --account=project_465000536
#SBATCH --partition=standard-g
#SBATCH --reservation=summerschool_standard-g
#SBATCH --gpus-per-node=8
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --time=00:05:00

srun my_gpu_exe

Running in local workstation

In most MPI implementations parallel program can be started with the mpiexec launcher:

mpiexec -n 4 ./my_mpi_exe

In most workstations, programs build with OpenMP use as many threads as there are CPU cores (note that this might include also "logical" cores with simultaneous multithreading). A pure OpenMP program can be normally started with specific number of threads with

OMP_NUM_THREADS=4 ./my_exe

and a hybrid MPI+OpenMP program e.g. with

OMP_NUM_THREADS=4 mpiexec -n 2 ./my_exe

Debugging

See the MPI debugging exercise, CSC user guide, and LUMI documentation for possible debugging options.

Performance analysis with TAU and Omniperf

TAU and Omniperf can be used to do performance analysis. In order to use TAU one only has to load the modules needed to run the application be ran and set the paths to the TAU install folder:

export TAU=/project/project_465000536/appl/tau/2.32/craycnl
export PATH=$TAU/bin:$PATH

In order to use omniperf load the follwoing modules:

module use /project/project_465000536/Omni/omniperf/modulefiles
module load omniperf
module load cray-python

More information about TAU can be found in TAU User Documentation, while for Omniperf at Omniperf User Documentation

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exercise-instructions.md

exercise-instructions.md

General exercise instructions

Working with the summerschool repository

Repository structure

Using local workstation

Using supercomputers

Disk areas

Working with git

Editors

Compilation

MPI

OpenMP (threading with CPUs)

HDF5

OpenMP offloading

HIP

HIPFORT

Running in LUMI

Pure MPI

Pure OpenMP

Hybrid MPI+OpenMP

GPU programs

Running in local workstation

Debugging

Performance analysis with TAU and Omniperf

Files

exercise-instructions.md

Latest commit

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exercise-instructions.md

File metadata and controls

General exercise instructions

Working with the summerschool repository

Repository structure

Using local workstation

Using supercomputers

Disk areas

Working with git

Editors

Compilation

MPI

OpenMP (threading with CPUs)

HDF5

OpenMP offloading

HIP

HIPFORT

Running in LUMI

Pure MPI

Pure OpenMP

Hybrid MPI+OpenMP

GPU programs

Running in local workstation

Debugging

Performance analysis with TAU and Omniperf