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Jobs/job_lumi.slrum Normal file
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#!/bin/bash -e
#SBATCH --job-name=lumi
#SBATCH --account=project_4650000xx
#SBATCH --time=00:10:00
#SBATCH --partition=dev-g
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --gpus=2
#SBATCH --gpus-per-node=2
#SBATCH -o %x-%j.out
#
N=$SLURM_JOB_NUM_NODES
echo "--nbr of nodes:", $N
echo "--total nbr of gpus:", $SLURM_NTASKS
Mydir=/project/project_4650000xx
Myapplication=${Mydir}/FiniteVolumeGPU_hip/mpiTesting.py
#modules
ml LUMI/23.03 partition/G
ml lumi-container-wrapper
ml cray-python/3.9.13.1
ml rocm/5.2.3
ml craype-accel-amd-gfx90a
ml cray-mpich/8.1.27
#Enable GPU-aware MPI
export MPICH_GPU_SUPPORT_ENABLED=1
export PATH="/project/project_4650000xx/FiniteVolumeGPU_hip/MyCondaEnv/bin:$PATH"
srun python ${Myapplication} -nx 1024 -ny 1024 --profile

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LICENSE Normal file
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(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
<program> Copyright (C) <year> <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<https://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<https://www.gnu.org/licenses/why-not-lgpl.html>.

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# FiniteVolumeGPU
This is a HIP version of the [FiniteVolume code](https://github.com/babrodtk/FiniteVolumeGPU) (work in progress). It is a Python software package that implements several finite volume discretizations on Cartesian grids for the shallow water equations and the Euler equations.
## Setup
A good place to start exploring this codebase is the notebooks. Complete the following steps to run the notebooks:
1. Install conda (see e.g. Miniconda or Anaconda)
2. Change directory to the repository root and run the following commands
3. conda env create -f conda_environment.yml
4. conda activate ShallowWaterGPU
5. jupyter notebook
Make sure you are running the correct kernel ("conda:ShallowWaterGPU"). If not, change kernel using the "Kernel"-menu in the notebook.
If you do not need to run notebooks you may use the conda environment found in conda_environment_hpc.yml
## Troubleshooting
Have a look at the conda documentation and https://towardsdatascience.com/how-to-set-up-anaconda-and-jupyter-notebook-the-right-way-de3b7623ea4a
## Setup on LUMI-G
Here is a step-by-step guide on installing packages on LUMI-G
### Step 0: load modules
```
ml LUMI/23.03
ml lumi-container-wrapper
ml cray-python/3.9.13.1
```
### Step 1: run conda-container
Installation via conda can be done as:
```
conda-containerize new --prefix MyCondaEnv conda_environment_lumi.yml
```
where the file `conda_environment_lumi.yml` contains packages to be installed.
### Step 2: Set the env. variable to search for binaries
```
export the bin path: export PATH="$PWD/MyCondaEnv/bin:$PATH"
```
### An alternative: Convert to a singularity container with cotainr
```
cotainr build my_container.sif --system=lumi-g --conda-env=conda_environment_lumi.yml
```

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# Assumes that conda, pip, build-essentials and cuda are installed
---
name: ShallowWaterGPU_HPC
channels:
- conda-forge
dependencies:
- python=3.9
- numpy
- mpi4py
- six
- pytools
- netcdf4
- scipy
- pip:
- hip-python
- hip-python-as-cuda
- -i https://test.pypi.org/simple/
#On LUMI-G
#module load LUMI/23.03
#module load lumi-container-wrapper
#ml cray-python/3.9.13.1
#conda-containerize new --prefix MyCondaEnv conda_environment_lumi.yml
# export the bin path: export PATH="$PWD/MyCondaEnv/bin:$PATH"
#
#
#
# Install conda environment (one-time operation):
# $ conda env create -f conda_environment_hpc.yml
# Activate environment and install the following packages using pip:
# $ conda activate ShallowWaterGPU_HPC
# - pycuda: $ pip3 install --no-deps -U pycuda
# on Windows: make sure your visual studio c++ compiler is available in PATH
# PATH should have something like C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\bin\

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# -*- coding: utf-8 -*-
"""
This python module implements MPI simulations for benchmarking
Copyright (C) 2018 SINTEF ICT
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
import numpy as np
import gc
import time
import json
import logging
import os
#GPU-aware MPI
from os import environ
if environ.get("MPICH_GPU_SUPPORT_ENABLED", False):
from ctypes import CDLL, RTLD_GLOBAL
CDLL(f"{environ.get('CRAY_MPICH_ROOTDIR')}/gtl/lib/libmpi_gtl_hsa.so", mode=RTLD_GLOBAL)
# MPI
from mpi4py import MPI
# CUDA
#import pycuda.driver as cuda
from hip import hip
# Simulator engine etc
from GPUSimulators import MPISimulator, Common, CudaContext
from GPUSimulators import EE2D_KP07_dimsplit
from GPUSimulators.helpers import InitialConditions as IC
from GPUSimulators.Simulator import BoundaryCondition as BC
import argparse
parser = argparse.ArgumentParser(description='Strong and weak scaling experiments.')
parser.add_argument('-nx', type=int, default=128)
parser.add_argument('-ny', type=int, default=128)
parser.add_argument('--profile', action='store_true') # default: False
def hip_check(call_result):
err = call_result[0]
result = call_result[1:]
if len(result) == 1:
result = result[0]
if isinstance(err, hip.hipError_t) and err != hip.hipError_t.hipSuccess:
raise RuntimeError(str(err))
elif (
isinstance(err, hiprtc.hiprtcResult)
and err != hiprtc.hiprtcResult.HIPRTC_SUCCESS
):
raise RuntimeError(str(err))
return result
args = parser.parse_args()
if(args.profile):
profiling_data = {}
# profiling: total run time
t_total_start = time.time()
t_init_start = time.time()
# Get MPI COMM to use
comm = MPI.COMM_WORLD
####
# Initialize logging
####
log_level_console = 20
log_level_file = 10
log_filename = 'mpi_' + str(comm.rank) + '.log'
logger = logging.getLogger('GPUSimulators')
logger.setLevel(min(log_level_console, log_level_file))
ch = logging.StreamHandler()
ch.setLevel(log_level_console)
logger.addHandler(ch)
logger.info("Console logger using level %s",
logging.getLevelName(log_level_console))
fh = logging.FileHandler(log_filename)
formatter = logging.Formatter(
'%(asctime)s:%(name)s:%(levelname)s: %(message)s')
fh.setFormatter(formatter)
fh.setLevel(log_level_file)
logger.addHandler(fh)
logger.info("File logger using level %s to %s",
logging.getLevelName(log_level_file), log_filename)
####
# Initialize MPI grid etc
####
logger.info("Creating MPI grid")
grid = MPISimulator.MPIGrid(MPI.COMM_WORLD)
####
# Initialize CUDA
####
#cuda.init(flags=0)
#logger.info("Initializing CUDA")
local_rank = grid.getLocalRank()
#num_cuda_devices = cuda.Device.count()
num_cuda_devices = hip_check(hip.hipGetDeviceCount())
cuda_device = local_rank % num_cuda_devices
logger.info("Process %s using CUDA device %s", str(local_rank), str(cuda_device))
cuda_context = CudaContext.CudaContext(device=cuda_device, autotuning=False)
####
# Set initial conditions
####
# DEBUGGING - setting random seed
np.random.seed(42)
logger.info("Generating initial conditions")
nx = args.nx
ny = args.ny
dt = 0.000001
gamma = 1.4
#save_times = np.linspace(0, 0.000009, 2)
#save_times = np.linspace(0, 0.000099, 11)
#save_times = np.linspace(0, 0.000099, 2)
save_times = np.linspace(0, 0.0000999, 2)
outfile = "mpi_out_" + str(MPI.COMM_WORLD.rank) + ".nc"
save_var_names = ['rho', 'rho_u', 'rho_v', 'E']
arguments = IC.genKelvinHelmholtz(nx, ny, gamma, grid=grid)
arguments['context'] = cuda_context
arguments['theta'] = 1.2
arguments['grid'] = grid
if(args.profile):
t_init_end = time.time()
t_init = t_init_end - t_init_start
profiling_data["t_init"] = t_init
####
# Run simulation
####
logger.info("Running simulation")
# Helper function to create MPI simulator
def genSim(grid, **kwargs):
local_sim = EE2D_KP07_dimsplit.EE2D_KP07_dimsplit(**kwargs)
sim = MPISimulator.MPISimulator(local_sim, grid)
return sim
outfile, sim_runner_profiling_data, sim_profiling_data = Common.runSimulation(
genSim, arguments, outfile, save_times, save_var_names, dt)
if(args.profile):
t_total_end = time.time()
t_total = t_total_end - t_total_start
profiling_data["t_total"] = t_total
print("Total run time on rank " + str(MPI.COMM_WORLD.rank) + " is " + str(t_total) + " s")
# write profiling to json file
if(args.profile and MPI.COMM_WORLD.rank == 0):
job_id = ""
if "SLURM_JOB_ID" in os.environ:
job_id = int(os.environ["SLURM_JOB_ID"])
allocated_nodes = int(os.environ["SLURM_JOB_NUM_NODES"])
allocated_gpus = int(os.environ["HIP_VISIBLE_DEVICES"].count(",") + 1)
# allocated_gpus = int(os.environ["CUDA_VISIBLE_DEVICES"].count(",") + 1)
profiling_file = "MPI_jobid_" + \
str(job_id) + "_" + str(allocated_nodes) + "_nodes_and_" + str(allocated_gpus) + "_GPUs_profiling.json"
profiling_data["outfile"] = outfile
else:
profiling_file = "MPI_" + str(MPI.COMM_WORLD.size) + "_procs_and_" + str(num_cuda_devices) + "_GPUs_profiling.json"
for stage in sim_runner_profiling_data["start"].keys():
profiling_data[stage] = sim_runner_profiling_data["end"][stage] - sim_runner_profiling_data["start"][stage]
for stage in sim_profiling_data["start"].keys():
profiling_data[stage] = sim_profiling_data["end"][stage] - sim_profiling_data["start"][stage]
profiling_data["nx"] = nx
profiling_data["ny"] = ny
profiling_data["dt"] = dt
profiling_data["n_time_steps"] = sim_profiling_data["n_time_steps"]
profiling_data["slurm_job_id"] = job_id
profiling_data["n_cuda_devices"] = str(num_cuda_devices)
profiling_data["n_processes"] = str(MPI.COMM_WORLD.size)
profiling_data["git_hash"] = Common.getGitHash()
profiling_data["git_status"] = Common.getGitStatus()
with open(profiling_file, "w") as write_file:
json.dump(profiling_data, write_file)
####
# Clean shutdown
####
sim = None
local_sim = None
cuda_context = None
arguments = None
logging.shutdown()
gc.collect()
####
# Print completion and exit
####
print("Completed!")
exit(0)

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##############################################################################
# Generated by SWASHES version 1.03.00, 2016-01-29
##############################################################################
# Dimension: 1
# Type: 3 (=Dam break)
# Domain: 1
# Choice: 1 (=on a wet domain without friction (Stoker's solution))
##############################################################################
# PARAMETERS OF THE SOLUTION
#
# Length of the domain: 10 meters
# Space step: 0.078125 meters
# Number of cells: 128
# Position of the dam: x=5 meters
# Time value: 6 seconds
##############################################################################
#
#(i-0.5)*dx h[i] u[i] topo[i] q[i] topo[i]+h[i] Fr[i]=Froude topo[i]+hc[i]
0.0390625 0.005 0 0 0 0.005 0 0
0.117188 0.005 0 0 0 0.005 0 0
0.195312 0.005 0 0 0 0.005 0 0
0.273438 0.005 0 0 0 0.005 0 0
0.351562 0.005 0 0 0 0.005 0 0
0.429688 0.005 0 0 0 0.005 0 0
0.507812 0.005 0 0 0 0.005 0 0
0.585938 0.005 0 0 0 0.005 0 0
0.664062 0.005 0 0 0 0.005 0 0
0.742188 0.005 0 0 0 0.005 0 0
0.820312 0.005 0 0 0 0.005 0 0
0.898438 0.005 0 0 0 0.005 0 0
0.976562 0.005 0 0 0 0.005 0 0
1.05469 0.005 0 0 0 0.005 0 0
1.13281 0.005 0 0 0 0.005 0 0
1.21094 0.005 0 0 0 0.005 0 0
1.28906 0.005 0 0 0 0.005 0 0
1.36719 0.005 0 0 0 0.005 0 0
1.44531 0.005 0 0 0 0.005 0 0
1.52344 0.005 0 0 0 0.005 0 0
1.60156 0.005 0 0 0 0.005 0 0
1.67969 0.005 0 0 0 0.005 0 0
1.75781 0.005 0 0 0 0.005 0 0
1.83594 0.005 0 0 0 0.005 0 0
1.91406 0.005 0 0 0 0.005 0 0
1.99219 0.005 0 0 0 0.005 0 0
2.07031 0.005 0 0 0 0.005 0 0
2.14844 0.005 0 0 0 0.005 0 0
2.22656 0.005 0 0 0 0.005 0 0
2.30469 0.005 0 0 0 0.005 0 0
2.38281 0.005 0 0 0 0.005 0 0
2.46094 0.005 0 0 0 0.005 0 0
2.53906 0.005 0 0 0 0.005 0 0
2.61719 0.005 0 0 0 0.005 0 0
2.69531 0.005 0 0 0 0.005 0 0
2.77344 0.005 0 0 0 0.005 0 0
2.85156 0.005 0 0 0 0.005 0 0
2.92969 0.005 0 0 0 0.005 0 0
3.00781 0.005 0 0 0 0.005 0 0
3.08594 0.005 0 0 0 0.005 0 0
3.16406 0.005 0 0 0 0.005 0 0
3.24219 0.005 0 0 0 0.005 0 0
3.32031 0.005 0 0 0 0.005 0 0
3.39844 0.005 0 0 0 0.005 0 0
3.47656 0.005 0 0 0 0.005 0 0
3.55469 0.005 0 0 0 0.005 0 0
3.63281 0.005 0 0 0 0.005 0 0
3.71094 0.00490073 0.00441906 0 2.16566e-005 0.00490073 0.0201542 0.000362943
3.78906 0.00470863 0.0130996 0 6.16813e-005 0.00470863 0.0609504 0.000729255
3.86719 0.00452038 0.0217802 0 9.84546e-005 0.00452038 0.103428 0.000996019
3.94531 0.00433596 0.0304607 0 0.000132076 0.00433596 0.147694 0.00121151
4.02344 0.00415538 0.0391413 0 0.000162647 0.00415538 0.193863 0.0013919
4.10156 0.00397865 0.0478218 0 0.000190266 0.00397865 0.242061 0.00154532
4.17969 0.00380575 0.0565024 0 0.000215034 0.00380575 0.292423 0.00167667
4.25781 0.0036367 0.065183 0 0.000237051 0.0036367 0.345101 0.00178925
4.33594 0.00347148 0.0738635 0 0.000256416 0.00347148 0.400256 0.00188541
4.41406 0.00331011 0.0825441 0 0.00027323 0.00331011 0.458068 0.00196696
4.49219 0.00315257 0.0912246 0 0.000287592 0.00315257 0.518734 0.0020353
4.57031 0.00299888 0.0999052 0 0.000299604 0.00299888 0.58247 0.00209158
4.64844 0.00284903 0.108586 0 0.000309364 0.00284903 0.649516 0.00213677
4.72656 0.00270302 0.117266 0 0.000316973 0.00270302 0.720135 0.00217166
4.80469 0.00256085 0.125947 0 0.000322531 0.00256085 0.794623 0.00219697
4.88281 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
4.96094 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
5.03906 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
5.11719 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
5.19531 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
5.27344 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
5.35156 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
5.42969 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
5.50781 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
5.58594 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
5.66406 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
5.74219 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
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Can't render this file because it has a wrong number of fields in line 18.

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reference/swashes_1_nx=256.csv Normal file
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@ -0,0 +1,274 @@
##############################################################################
# Generated by SWASHES version 1.03.00, 2016-01-29
##############################################################################
# Dimension: 1
# Type: 3 (=Dam break)
# Domain: 1
# Choice: 1 (=on a wet domain without friction (Stoker's solution))
##############################################################################
# PARAMETERS OF THE SOLUTION
#
# Length of the domain: 10 meters
# Space step: 0.0390625 meters
# Number of cells: 256
# Position of the dam: x=5 meters
# Time value: 6 seconds
##############################################################################
#
#(i-0.5)*dx h[i] u[i] topo[i] q[i] topo[i]+h[i] Fr[i]=Froude topo[i]+hc[i]
0.0195312 0.005 0 0 0 0.005 0 0
0.0585938 0.005 0 0 0 0.005 0 0
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3.69141 0.00494936 0.00224893 0 1.11307e-005 0.00494936 0.0102062 0.000232877
3.73047 0.00485235 0.0065892 0 3.19731e-005 0.00485235 0.0302011 0.00047058
3.76953 0.0047563 0.0109295 0 5.19839e-005 0.0047563 0.0505977 0.000650663
3.80859 0.00466121 0.0152698 0 7.11755e-005 0.00466121 0.0714082 0.000802289
3.84766 0.00456708 0.01961 0 8.95606e-005 0.00456708 0.0926456 0.000935093
3.88672 0.00447391 0.0239503 0 0.000107152 0.00447391 0.114323 0.00105384
3.92578 0.0043817 0.0282906 0 0.000123961 0.0043817 0.136454 0.00116136
3.96484 0.00429045 0.0326309 0 0.000140001 0.00429045 0.159053 0.0012595
4.00391 0.00420017 0.0369711 0 0.000155285 0.00420017 0.182136 0.00134957
4.04297 0.00411084 0.0413114 0 0.000169825 0.00411084 0.205717 0.00143255
4.08203 0.00402247 0.0456517 0 0.000183633 0.00402247 0.229814 0.00150919
4.12109 0.00393506 0.049992 0 0.000196722 0.00393506 0.254443 0.00158008
4.16016 0.00384861 0.0543323 0 0.000209104 0.00384861 0.279622 0.0016457
4.19922 0.00376313 0.0586725 0 0.000220792 0.00376313 0.30537 0.00170647
4.23828 0.0036786 0.0630128 0 0.000231799 0.0036786 0.331706 0.00176272
4.27734 0.00359503 0.0673531 0 0.000242137 0.00359503 0.358651 0.00181475
4.31641 0.00351242 0.0716934 0 0.000251818 0.00351242 0.386226 0.00186281
4.35547 0.00343078 0.0760336 0 0.000260855 0.00343078 0.414453 0.00190711
4.39453 0.00335009 0.0803739 0 0.00026926 0.00335009 0.443356 0.00194786
4.43359 0.00327036 0.0847142 0 0.000277046 0.00327036 0.472959 0.00198523
4.47266 0.0031916 0.0890545 0 0.000284226 0.0031916 0.503289 0.00201939
4.51172 0.00311379 0.0933948 0 0.000290812 0.00311379 0.534371 0.00205046
4.55078 0.00303694 0.097735 0 0.000296816 0.00303694 0.566236 0.00207859
4.58984 0.00296106 0.102075 0 0.000302251 0.00296106 0.598912 0.00210389
4.62891 0.00288613 0.106416 0 0.000307129 0.00288613 0.63243 0.00212646
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4.74609 0.00266712 0.119436 0 0.000318551 0.00266712 0.738383 0.00217886
4.78516 0.00259603 0.123777 0 0.000321328 0.00259603 0.775621 0.00219151
4.82422 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
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5.01953 0.00253936 0.127279 0 0.000323208 0.00253936 0.806419 0.00220005
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6.26953 0.001 0 0 0 0.001 0 0
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Can't render this file because it has a wrong number of fields in line 18.

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reference/swashes_1_nx=512.csv Normal file
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@ -0,0 +1,530 @@
##############################################################################
# Generated by SWASHES version 1.03.00, 2016-01-29
##############################################################################
# Dimension: 1
# Type: 3 (=Dam break)
# Domain: 1
# Choice: 1 (=on a wet domain without friction (Stoker's solution))
##############################################################################
# PARAMETERS OF THE SOLUTION
#
# Length of the domain: 10 meters
# Space step: 0.0195312 meters
# Number of cells: 512
# Position of the dam: x=5 meters
# Time value: 6 seconds
##############################################################################
#
#(i-0.5)*dx h[i] u[i] topo[i] q[i] topo[i]+h[i] Fr[i]=Froude topo[i]+hc[i]
0.00976562 0.005 0 0 0 0.005 0 0
0.0292969 0.005 0 0 0 0.005 0 0
0.0488281 0.005 0 0 0 0.005 0 0
0.0683594 0.005 0 0 0 0.005 0 0
0.0878906 0.005 0 0 0 0.005 0 0
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