Project Documentation

Backend: Quickly build basic restful style API with echo.
Network Server Framework: Implement data reception using the gnet network framework.
API Documentation: Build automated documentation with Swagger.
Configuration File: Parse configuration files using viper.
CLI: Implement command line parameters with cobra.

Software description

SPARTA is an acronym for Stochastic PArallel Rarefied-gas Time-accurate Analyzer.

SPARTA is a parallel DSMC or Direct Simulation Monte Carlo code for performing simulations of low-density gases in 2d or 3d. Particles advect through a hierarchical Cartesian grid that overlays the simulation box. The grid is used to group particles by grid cell for purposes of performing collisions and chemistry. Physical objects with triangulated surfaces can be embedded in the grid, creating cut and split grid cells. The grid is also used to efficiently find particle/surface collisions.

Start

Configuration File

vim sparta_backend.toml

[service]
data_dir = "/{your workspace dir}/sparta_backend/data"                      # generate all file 
sparta_python_tools = "/{your workspace dir}/sparta_backend/sparta/pizza"   # export SPARTA_PYTHON_TOOLS=/this path
script_dir = "/{your workspace dir}/sparta_backend/sparta"                  # python script path
spa_exec = "/{your workspace dir}/sparta_backend/bin/spa_"                  # sparta executable file

./sparta_backend run

view api

http://localhost:8000/api/swagger

eg.:

view sparta configuration

http://localhost:8000/api/static/in.circle

################################################################################
# 2d flow around a circle
#
# Note:
#  - The "comm/sort” option to the “global” command is used to match MPI runs.
#  - The “twopass” option is used to match Kokkos runs.
# The "comm/sort" and "twopass" options should not be used for production runs.
################################################################################

seed			 12345
dimension        3
global           gridcut 0.0 comm/sort yes

boundary         oo oo oo
create_box       -0.5 0.5 -0.6 0.6 -0.1 0.2
create_grid      100 100 100
balance_grid     rcb cell

global           nrho 6.83e8 fnum 3.28e10

species          co2.species CO2
mixture          air N2 CO2  vstream 4900 0 0 temp 180

read_surf        h.surf scale 0.001 0.001 0.001
surf_collide     1 diffuse 10000 1
surf_modify      all collide 1

collide          vss air co2.vss

compute          1 grid all species u v w 
fix              1 ave/grid all 10 100 1000 c_1[*]

compute          2 eflux/grid all species heatx heaty heatz 
fix              2 ave/grid all 10 100 1000 c_2[*]

compute          3 thermal/grid all species temp press 
fix              3 ave/grid all 10 100 1000 c_3[*]

dump             1 grid all 1000 tmp.grid.* id xc yc zc f_1[*] f_3[*]

write_grid       data.grid 

timestep         5.102e-7

dump                2 image all 100 h.surf.*.ppm type type pdiam 0.001 &
			surf proc 0.01 size 1024 1024 zoom 1.75 &
			gline no 0.005
dump_modify	    2 pad 4

stats            100
stats_style      step cpu np nattempt ncoll nscoll nscheck

run              1000

Manually verify the configuration parameters

Go to the /home/workspace/project/sparta_backend/data directory

cd /home/workspace/project/sparta_backend/data

executive program

../bin/spa_ < in.circle

Software running environment

System:

DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=20.04
DISTRIB_CODENAME=focal
DISTRIB_DESCRIPTION="Ubuntu 20.04.6 LTS"

gcc:

gcc (Ubuntu 10.5.0-1ubuntu1~20.04) 10.5.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

g++

g++ (Ubuntu 10.5.0-1ubuntu1~20.04) 10.5.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

pytho3:

Python 3.8.10

Reference:

https://sparta.github.io/doc/dump.html

Please refer to the following for development and debugging

Environment configuration

Ubuntu 20.04 Sources

/etc/apt/sources.list

deb http://mirrors.aliyun.com/ubuntu/ focal main restricted universe multiverse
deb-src http://mirrors.aliyun.com/ubuntu/ focal main restricted universe multiverse
 
deb http://mirrors.aliyun.com/ubuntu/ focal-security main restricted universe multiverse
deb-src http://mirrors.aliyun.com/ubuntu/ focal-security main restricted universe multiverse
 
deb http://mirrors.aliyun.com/ubuntu/ focal-updates main restricted universe multiverse
deb-src http://mirrors.aliyun.com/ubuntu/ focal-updates main restricted universe multiverse
 
deb http://mirrors.aliyun.com/ubuntu/ focal-proposed main restricted universe multiverse
deb-src http://mirrors.aliyun.com/ubuntu/ focal-proposed main restricted universe multiverse
 
deb http://mirrors.aliyun.com/ubuntu/ focal-backports main restricted universe multiverse
deb-src http://mirrors.aliyun.com/ubuntu/ focal-backports main restricted universe multiverse

Update

sudo apt-get update
sudo apt-get install paraview

Installation Instructions

golang version >= v1.20

Install go

reference:

https://kiga.top/docs/install-golang/

2. Source Code Compilation

# Using go.mod

# Install go dependency packages
go list (go mod tidy)

# Compile
./build.sh sparta_backend sparta_backend

firewall

firewall-cmd --zone=public --add-port=8000/tcp --permanent
firewall-cmd --reload
# netstat -an | grep 8000

third-party library

install cmake: version = 3.16.0

wget https://github.com/Kitware/CMake/releases/download/v3.16.0/cmake-3.16.0.tar.gz

decompress

tar -zxvf cmake-3.16.0.tar.gz

make and install

cd cmake-3.16.0

./bootstrap
make
sudo make install

cmake --version

Install libopenmpi

apt install libopenmpi-dev

Install paraview

# ubuntu
apt install paraview

Install convert command

apt-get install imagemagick

Extract

tar -xvf sparta.tar.gz -C /home

make all component

rm -rf build
mkdir build install
cd build

The output is as follows：

request sparta_backend ws://localhost:8000/api/ws

SPARTA (13 Apr 2023)
Running on 1 MPI task(s)
Created orthogonal box = (-5 -5 -5) to (5 5 5)
Created 1000 child grid cells
  CPU time = 0.00297177 secs
  create/ghost percent = 57.981 42.019
Balance grid migrated 0 cells
  CPU time = 0.00145617 secs
  reassign/sort/migrate/ghost percent = 25.7127 1.05318 8.49537 64.7388
Reading surface file ...
  602 points
  1200 triangles
  -1 1 xlo xhi
  -1 1 ylo yhi
  -1 1 zlo zhi
  0.100631 min triangle edge length
  0.00439601 min triangle area
  32 0 = cells overlapping surfs, overlap cells with unmarked corner pts
  968 0 32 = cells outside/inside/overlapping surfs
  32 = surf cells with 1,2,etc splits
  995.861713454453 995.861713454453 = cell-wise and global flow volume
  CPU time = 0.407375 secs
  read/check/sort/surf2grid/ghost/inout/particle percent = 0.360998 1.0254 0.0390368 8.19112 90.3835 0.0904272 9.75046e-05
  surf2grid time = 0.0333686 secs
  map/comm1/comm2/comm3/comm4/split percent = 4.8971 2.01322 0.830313 0.428894 1.64338 89.5996
Creating particles ...
Created 9551 particles
  CPU time = 0.00749267 secs
WARNING: One or more fix inflow faces oppose streaming velocity (/xxx/src/sparta-13Apr2023/src/fix_emit_face.cpp:195)
Memory usage per proc in Mbytes:
  particles (ave,min,max) = 1.6875 1.6875 1.6875
  grid      (ave,min,max) = 1.66638 1.66638 1.66638
  surf      (ave,min,max) = 0.151062 0.151062 0.151062
  total     (ave,min,max) = 3.51257 3.51257 3.51257
Step CPU Np Natt Ncoll Nscoll c_max 
       0            0     9551        0        0        0           11 
     100   0.13060571     9560        1        1        2           20 
     200   0.29553304     9545        2        2        3           24 
     300   0.48495292     9723        3        3        1           30 
     400    0.6758407     9798        4        3        2           30 
     500   0.87547277     9908        6        5        0           33 
     600    1.0693094    10032        5        5        1           30 
     700    1.2874078     9996        4        4        0           26 
     800    1.5381838     9900        4        3        1           31 
     900    1.7528691     9880        6        6        1           28 
    1000    1.9551728     9902        4        3        2           29 
Loop time of 1.95518 on 1 procs for 1000 steps with 9902 particles

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Move    | 1.5366     | 1.5366     | 1.5366     |   0.0 | 78.59
Coll    | 0.22145    | 0.22145    | 0.22145    |   0.0 | 11.33
Sort    | 0.12458    | 0.12458    | 0.12458    |   0.0 |  6.37
Comm    | 0.0034114  | 0.0034114  | 0.0034114  |   0.0 |  0.17
Modify  | 0.064003   | 0.064003   | 0.064003   |   0.0 |  3.27
Output  | 0.0029384  | 0.0029384  | 0.0029384  |   0.0 |  0.15
Other   |            | 0.002226   |            |       |  0.11

Particle moves    = 9840342 (9.84M)
Cells touched     = 10097748 (10.1M)
Particle comms    = 0 (0K)
Boundary collides = 0 (0K)
Boundary exits    = 27428 (27.4K)
SurfColl checks   = 22610438 (22.6M)
SurfColl occurs   = 1400 (1.4K)
Surf reactions    = 0 (0K)
Collide attempts  = 144009 (0.144M)
Collide occurs    = 110469 (0.11M)
Gas reactions     = 0 (0K)
Particles stuck   = 0
Axisymm bad moves = 0

Particle-moves/CPUsec/proc: 5.03295e+06
Particle-moves/step: 9840.34
Cell-touches/particle/step: 1.02616
Particle comm iterations/step: 1
Particle fraction communicated: 0
Particle fraction colliding with boundary: 0
Particle fraction exiting boundary: 0.0027873
Surface-checks/particle/step: 2.29773
Surface-collisions/particle/step: 0.000142271
Surface-reactions/particle/step: 0
Collision-attempts/particle/step: 0.0146346
Collisions/particle/step: 0.0112261
Gas-reactions/particle/step: 0

Particles: 9902 ave 9902 max 9902 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Cells:     1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
GhostCell: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
EmptyCell: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Surfs:     1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
GhostSurf: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
WARNING: One or more fix inflow faces oppose streaming velocity (/xxx/src/sparta-13Apr2023/src/fix_emit_face.cpp:195)
Memory usage per proc in Mbytes:
  particles (ave,min,max) = 1.6875 1.6875 1.6875
  grid      (ave,min,max) = 1.66638 1.66638 1.66638
  surf      (ave,min,max) = 0.151062 0.151062 0.151062
  total     (ave,min,max) = 3.51257 3.51257 3.51257
Step CPU Np Natt Ncoll Nscoll c_max 
    1000            0     9902        4        3        0           29 
    1100   0.19659224     9920        5        5        1           29 
    1200   0.39655017    10046        5        5        3           28 
    1300   0.63425945     9945        5        5        0           28 
    1400   0.84268371    10042        4        4        1           28 
    1500    1.0254795    10019        5        5        3           30 
    1600    1.2178706    10070        5        5        0           29 
    1700    1.4145789    10120        2        2        0           26 
    1800    1.5863573    10011        2        2        0           27 
    1900    1.7781846     9846        1        1        4           27 
    2000    1.9548043     9791        3        3        2           26 
Loop time of 1.95482 on 1 procs for 1000 steps with 9791 particles

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Move    | 1.542      | 1.542      | 1.542      |   0.0 | 78.88
Coll    | 0.22429    | 0.22429    | 0.22429    |   0.0 | 11.47
Sort    | 0.11932    | 0.11932    | 0.11932    |   0.0 |  6.10
Comm    | 0.0032291  | 0.0032291  | 0.0032291  |   0.0 |  0.17
Modify  | 0.060898   | 0.060898   | 0.060898   |   0.0 |  3.12
Output  | 0.0030458  | 0.0030458  | 0.0030458  |   0.0 |  0.16
Other   |            | 0.002047   |            |       |  0.10

Particle moves    = 10014828 (10M)
Cells touched     = 10277594 (10.3M)
Particle comms    = 0 (0K)
Boundary collides = 0 (0K)
Boundary exits    = 27871 (27.9K)
SurfColl checks   = 23298852 (23.3M)
SurfColl occurs   = 1344 (1.34K)
Surf reactions    = 0 (0K)
Collide attempts  = 153491 (0.153M)
Collide occurs    = 117981 (0.118M)
Gas reactions     = 0 (0K)
Particles stuck   = 0
Axisymm bad moves = 0

Particle-moves/CPUsec/proc: 5.12316e+06
Particle-moves/step: 10014.8
Cell-touches/particle/step: 1.02624
Particle comm iterations/step: 1
Particle fraction communicated: 0
Particle fraction colliding with boundary: 0
Particle fraction exiting boundary: 0.00278297
Surface-checks/particle/step: 2.32644
Surface-collisions/particle/step: 0.000134201
Surface-reactions/particle/step: 0
Collision-attempts/particle/step: 0.0153264
Collisions/particle/step: 0.0117806
Gas-reactions/particle/step: 0

Particles: 9791 ave 9791 max 9791 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Cells:     1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
GhostCell: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
EmptyCell: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Surfs:     1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
GhostSurf: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Docker Installation

# Create docker image
make

# Start
docker run -it --rm -p 8000:8000 --name sparta_backend sparta_backend:dev

script command

# spa command
/home/workspace/project/sparta_backend/bin/spa_  < in.circle

# if need to use python script
# export SPARTA_PYTHON_TOOLS=/home/workspace/project/sparta_backend/sparta/pizza

## convert ppm to gif
convert *.ppm image.gif

## grid2paraview
pvpython grid2paraview.py  /home/workspace/project/sparta_backend/data/in.txt /home/workspace/project/sparta_backend/data/output/  -r /home/workspace/project/sparta_backend/data/tmp.grid.*

## log2txt
python log2txt.py ../examples/circle/log.sparta  data.txt

Using preset file

for i in serial chama openmpi
do 
cmake --log-level=VERBOSE [-C /home/sparta/cmake/presets/$i.cmake] -DBUILD_SHARED_LIBS=ON /home/sparta/cmake
make VERBOSE=1
done

Name		Name	Last commit message	Last commit date
Latest commit History 40 Commits
backup		backup
bin		bin
cmd		cmd
data		data
pkg		pkg
report		report
script		script
sparta		sparta
src		src
swagger		swagger
test		test
web		web
.gitignore		.gitignore
Dockerfile		Dockerfile
Makefile		Makefile
QA		QA
README.md		README.md
api.md		api.md
build.sh		build.sh
example.json		example.json
go.mod		go.mod
go.sum		go.sum
in.circle		in.circle
log.sparta		log.sparta
main.go		main.go
post.json		post.json
screenshot.png		screenshot.png
sparta_backend		sparta_backend
sparta_backend.toml		sparta_backend.toml
version		version

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Project Documentation

Software description

Start

Configuration File

view api

view sparta configuration

Manually verify the configuration parameters

Software running environment

System:

gcc:

g++

pytho3:

Please refer to the following for development and debugging

Environment configuration

Ubuntu 20.04 Sources

Update

Installation Instructions

Install go

2. Source Code Compilation

firewall

third-party library

Install libopenmpi

Install paraview

Install convert command

Extract

make all component

The output is as follows：

Docker Installation

script command

Using preset file

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kiga-hub/sparta_backend

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Repository files navigation

Project Documentation

Software description

Start

Configuration File

view api

view sparta configuration

Manually verify the configuration parameters

Software running environment

System:

gcc:

g++

pytho3:

Please refer to the following for development and debugging

Environment configuration

Ubuntu 20.04 Sources

Update

Installation Instructions

Install go

2. Source Code Compilation

firewall

third-party library

Install libopenmpi

Install paraview

Install convert command

Extract

make all component

The output is as follows：

Docker Installation

script command

Using preset file

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