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Merge branch 'mdl/fgcsbench' into 'main'

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Mdl/fgcsbench

See merge request naaice/poet!43
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Max Lübke 2024-12-13 12:19:57 +01:00
commit 9d7fa5457d
7 changed files with 136 additions and 109 deletions
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37
README.md
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@ -9,7 +9,7 @@ original MPI-based Distributed Hash Table.
## Parsed code documentiation
A parsed version of POET's documentation can be found at [Gitlab
pages](https://naaice.git-pages.gfz-potsdam.de/poet).
pages](https://naaice.git-pages.gfz.de/poet).
## External Libraries
@ -18,8 +18,8 @@ The following external libraries are shipped with POET:
- **CLI11** - <https://github.com/CLIUtils/CLI11>
- **IPhreeqc** with patches from GFZ/UP -
<https://github.com/usgs-coupled/iphreeqc> -
<https://git.gfz-potsdam.de/naaice/iphreeqc>
- **tug** - <https://git.gfz-potsdam.de/naaice/tug>
<https://git.gfz.de/naaice/iphreeqc>
- **tug** - <https://git.gfz.de/naaice/tug>
## Installation
@ -41,7 +41,7 @@ installed:
- [Rcpp](https://cran.r-project.org/web/packages/Rcpp/index.html)
- [RInside](https://cran.r-project.org/web/packages/RInside/index.html)
- [qs](https://cran.r-project.org/web/packages/qs/index.html)
- [qs2](https://cran.r-project.org/web/packages/qs2/index.html)
This can be simply achieved by issuing the following commands:
```sh
@ -49,7 +49,7 @@ This can be simply achieved by issuing the following commands:
$ R
# install R dependencies (case sensitive!)
> install.packages(c("Rcpp", "RInside","qs"))
> install.packages(c("Rcpp", "RInside","qs","qs2"))
> q(save="no")
```
@ -59,7 +59,7 @@ POET can be anonimously cloned from this repo over https. Make sure to
also download the submodules:
```sh
git clone --recurse-submodules https://git.gfz-potsdam.de/naaice/poet.git
git clone --recurse-submodules https://git.gfz.de/naaice/poet.git
```
The `--recurse-submodules` option is a shorthand for:
```sh
@ -110,7 +110,7 @@ follows:
$ R
# install R dependencies
> install.packages(c("Rcpp", "RInside","qs"))
> install.packages(c("Rcpp", "RInside","qs","qs2"))
> q(save="no")
# cd into POET project root
@ -138,17 +138,17 @@ poet
└── share
└── poet
├── barite
│   ├── barite_200.rds
│   ├── barite_200.qs2
│   ├── barite_200_rt.R
│   ├── barite_het.rds
│   ├── barite_het.qs2
│   └── barite_het_rt.R
├── dolo
│   ├── dolo_inner_large.rds
│   ├── dolo_inner_large.qs2
│   ├── dolo_inner_large_rt.R
│   ├── dolo_interp.rds
│   ├── dolo_interp.qs2
│   └── dolo_interp_rt.R
└── surfex
├── PoetEGU_surfex_500.rds
├── PoetEGU_surfex_500.qs2
└── PoetEGU_surfex_500_rt.R
```
@ -182,7 +182,8 @@ The following parameters can be set:
| **-P, --progress** | | show progress bar |
| **--ai-surrogate** | | activates the AI surrogate chemistry model (defaults to _OFF_) |
| **--dht** | | enabling DHT usage (defaults to _OFF_) |
| **--qs** | | store results using qs::qsave() (.qs extension) instead of default RDS (.rds) |
| **--qs** | | store results using qs::qsave() (.qs extension) instead of default qs2 (.qs2) |
| **--rds** | | store results using saveRDS() (.rds extension) instead of default qs2 (.qs2) |
| **--dht-strategy=** | _0-1_ | change DHT strategy. **NOT IMPLEMENTED YET** (Defaults to _0_) |
| **--dht-size=** | _1-n_ | size of DHT per process involved in megabyte (defaults to _1000 MByte_) |
| **--dht-snaps=** | _0-2_ | disable or enable storage of DHT snapshots |
@ -213,7 +214,7 @@ installed POET-dir `<POET_INSTALL_DIR>/bin` and run:
```sh
cp ../share/poet/barite/barite_het* .
mpirun -n 4 ./poet barite_het_rt.R barite_het.rds output
mpirun -n 4 ./poet barite_het_rt.R barite_het.qs2 output
```
After a finished simulation all data generated by POET will be found
@ -226,7 +227,7 @@ DHT snapshot shall be produced. This is done by appending the
`--dht-snaps=<value>` option. The resulting call would look like this:
```sh
mpirun -n 4 ./poet --dht --dht-snaps=2 barite_het_rt.R barite_het.rds output
mpirun -n 4 ./poet --dht --dht-snaps=2 barite_het_rt.R barite_het.qs2 output
```
### Example: Preparing Environment and Running with AI surrogate
@ -273,7 +274,7 @@ cp <project_root_dir>/bench/barite/{barite_50ai*,db_barite.dat,barite.pqi} .
./poet_init barite_50ai.R
# run POET with AI surrogate and GPU utilization
srun --gres=gpu -N 1 -n 12 ./poet --ai-surrogate barite_50ai_rt.R barite_50ai.rds output
srun --gres=gpu -N 1 -n 12 ./poet --ai-surrogate barite_50ai_rt.R barite_50ai.qs2 output
```
Keep in mind that the AI surrogate is currently not stable or might also not
@ -284,7 +285,7 @@ produce any valid predictions.
In order to provide a model to POET, you need to setup a R script
which can then be used by `poet_init` to generate the simulation
input. Which parameters are required can be found in the
[Wiki](https://git.gfz-potsdam.de/naaice/poet/-/wikis/Initialization).
[Wiki](https://git.gfz.de/naaice/poet/-/wikis/Initialization).
We try to keep the document up-to-date. However, if you encounter
missing information or need help, please get in touch with us via the
issue tracker or E-Mail.
@ -298,7 +299,7 @@ issue tracker or E-Mail.
where:
- **output** - name of the output file (defaults to the input file
name with the extension `.rds`)
name with the extension `.qs2`)
- **setwd** - set the working directory to the directory of the input
file (e.g. to allow relative paths in the input script). However,
the output file will be stored in the directory from which

141
R_lib/kin_r_library.R
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@ -94,7 +94,7 @@ master_iteration_end <- function(setup, state_T, state_C) {
## Add last time step to simulation time
setup$simulation_time <- setup$simulation_time + setup$timesteps[iter]
msgm("done iteration", iter, "/", length(setup$timesteps))
## msgm("done iteration", iter, "/", length(setup$timesteps))
setup$iter <- setup$iter + 1
return(setup)
}
@ -109,69 +109,6 @@ msgm <- function(...) {
}
## Function called by master R process to store on disk all relevant
## parameters for the simulation
StoreSetup <- function(setup, filesim, out_dir) {
to_store <- vector(mode = "list", length = 4)
## names(to_store) <- c("Sim", "Flow", "Transport", "Chemistry", "DHT")
names(to_store) <- c("Sim", "Transport", "DHT", "Cmdline")
## read the setup R file, which is sourced in kin.cpp
tmpbuff <- file(filesim, "r")
setupfile <- readLines(tmpbuff)
close.connection(tmpbuff)
to_store$Sim <- setupfile
## to_store$Flow <- list(
## snapshots = setup$snapshots,
## gridfile = setup$gridfile,
## phase = setup$phase,
## density = setup$density,
## dt_differ = setup$dt_differ,
## prolong = setup$prolong,
## maxiter = setup$maxiter,
## saved_iter = setup$iter_output,
## out_save = setup$out_save )
to_store$Transport <- setup$diffusion
## to_store$Chemistry <- list(
## nprocs = n_procs,
## wp_size = work_package_size,
## base = setup$base,
## first = setup$first,
## init = setup$initsim,
## db = db,
## kin = setup$kin,
## ann = setup$ann)
if (dht_enabled) {
to_store$DHT <- list(
enabled = dht_enabled,
log = dht_log
## signif = dht_final_signif,
## proptype = dht_final_proptype
)
} else {
to_store$DHT <- FALSE
}
if (dht_enabled) {
to_store$DHT <- list(
enabled = dht_enabled,
log = dht_log
# signif = dht_final_signif,
# proptype = dht_final_proptype
)
} else {
to_store$DHT <- FALSE
}
saveRDS(to_store, file = paste0(fileout, "/setup.rds"))
msgm("initialization stored in ", paste0(fileout, "/setup.rds"))
}
GetWorkPackageSizesVector <- function(n_packages, package_size, len) {
ids <- rep(1:n_packages, times = package_size, each = 1)[1:len]
return(as.integer(table(ids)))
@ -179,7 +116,7 @@ GetWorkPackageSizesVector <- function(n_packages, package_size, len) {
## Handler to read R objs from binary files using either builtin
## readRDS() or qs::qread() based on file extension
## readRDS(), qs::qread() or qs2::qs_read() based on file extension
ReadRObj <- function(path) {
## code borrowed from tools::file_ext()
pos <- regexpr("\\.([[:alnum:]]+)$", path)
@ -187,20 +124,88 @@ ReadRObj <- function(path) {
switch(extension,
rds = readRDS(path),
qs = qs::qread(path)
qs = qs::qread(path),
qs2 = qs2::qs_read(path)
)
}
## Handler to store R objs to binary files using either builtin
## saveRDS() or qs::qsave() based on file extension
SaveRObj <- function(x, path) {
msgm("Storing to", path)
## msgm("Storing to", path)
## code borrowed from tools::file_ext()
pos <- regexpr("\\.([[:alnum:]]+)$", path)
extension <- ifelse(pos > -1L, substring(path, pos + 1L), "")
switch(extension,
rds = saveRDS(object = x, file = path),
qs = qs::qsave(x = x, file = path)
qs = qs::qsave(x = x, file = path),
qs2 = qs2::qs_save(object = x, file = path)
)
}
######## Old relic code
## ## Function called by master R process to store on disk all relevant
## ## parameters for the simulation
## StoreSetup <- function(setup, filesim, out_dir) {
## to_store <- vector(mode = "list", length = 4)
## ## names(to_store) <- c("Sim", "Flow", "Transport", "Chemistry", "DHT")
## names(to_store) <- c("Sim", "Transport", "DHT", "Cmdline")
## ## read the setup R file, which is sourced in kin.cpp
## tmpbuff <- file(filesim, "r")
## setupfile <- readLines(tmpbuff)
## close.connection(tmpbuff)
## to_store$Sim <- setupfile
## ## to_store$Flow <- list(
## ## snapshots = setup$snapshots,
## ## gridfile = setup$gridfile,
## ## phase = setup$phase,
## ## density = setup$density,
## ## dt_differ = setup$dt_differ,
## ## prolong = setup$prolong,
## ## maxiter = setup$maxiter,
## ## saved_iter = setup$iter_output,
## ## out_save = setup$out_save )
## to_store$Transport <- setup$diffusion
## ## to_store$Chemistry <- list(
## ## nprocs = n_procs,
## ## wp_size = work_package_size,
## ## base = setup$base,
## ## first = setup$first,
## ## init = setup$initsim,
## ## db = db,
## ## kin = setup$kin,
## ## ann = setup$ann)
## if (dht_enabled) {
## to_store$DHT <- list(
## enabled = dht_enabled,
## log = dht_log
## ## signif = dht_final_signif,
## ## proptype = dht_final_proptype
## )
## } else {
## to_store$DHT <- FALSE
## }
## if (dht_enabled) {
## to_store$DHT <- list(
## enabled = dht_enabled,
## log = dht_log
## # signif = dht_final_signif,
## # proptype = dht_final_proptype
## )
## } else {
## to_store$DHT <- FALSE
## }
## saveRDS(to_store, file = paste0(fileout, "/setup.rds"))
## msgm("initialization stored in ", paste0(fileout, "/setup.rds"))
## }

2
bench/CMakeLists.txt
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@ -7,7 +7,7 @@ function(ADD_BENCH_TARGET TARGET POET_BENCH_LIST RT_FILES OUT_PATH)
foreach(BENCH_FILE ${${POET_BENCH_LIST}})
get_filename_component(BENCH_NAME ${BENCH_FILE} NAME_WE)
set(OUT_FILE ${CMAKE_CURRENT_BINARY_DIR}/${BENCH_NAME})
set(OUT_FILE_EXT ${OUT_FILE}.qs)
set(OUT_FILE_EXT ${OUT_FILE}.qs2)
add_custom_command(
OUTPUT ${OUT_FILE_EXT}

2
src/Transport/DiffusionModule.cpp
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@ -70,7 +70,7 @@ VecToMatrix(const std::vector<TugType> &vec, std::uint32_t n_rows,
// static constexpr double ZERO_MULTIPLICATOR = 10E-14;
void DiffusionModule::simulate(double requested_dt) {
MSG("Starting diffusion ...");
// MSG("Starting diffusion ...");
const auto start_diffusion_t = std::chrono::high_resolution_clock::now();
const auto &n_rows = this->param_list.n_rows;

16
src/initializer.cpp
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@ -35,7 +35,11 @@ int main(int argc, char **argv) {
->default_val(false);
bool asRDS;
app.add_flag("-r, --rds", asRDS, "Save output as .rds file instead of .qs")
app.add_flag("-r, --rds", asRDS, "Save output as .rds")
->default_val(false);
bool asQS;
app.add_flag("-q, --qs", asQS, "Save output as .qs")
->default_val(false);
CLI11_PARSE(app, argc, argv);
@ -69,8 +73,14 @@ int main(int argc, char **argv) {
}
// append the correct file extension
output_file += asRDS ? ".rds" : ".qs";
if (asRDS) {
output_file += ".rds";
} else if (asQS) {
output_file += ".qs";
} else {
output_file += ".qs2";
}
// set working directory to the directory of the input script
if (setwd) {
const std::string dir_path = Rcpp::as<std::string>(

43
src/poet.cpp
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@ -45,7 +45,7 @@
#include <poet.hpp>
#include <vector>
using namespace std;
// using namespace std;
using namespace poet;
using namespace Rcpp;
@ -57,7 +57,7 @@ static std::unique_ptr<Rcpp::List> global_rt_setup;
// before the R runtime is initialized
static poet::DEFunc master_init_R;
static poet::DEFunc master_iteration_end_R;
static poet::DEFunc store_setup_R;
// MDL: unused -> static poet::DEFunc store_setup_R;
static poet::DEFunc ReadRObj_R;
static poet::DEFunc SaveRObj_R;
static poet::DEFunc source_R;
@ -66,7 +66,7 @@ static void init_global_functions(RInside &R) {
R.parseEval(kin_r_library);
master_init_R = DEFunc("master_init");
master_iteration_end_R = DEFunc("master_iteration_end");
store_setup_R = DEFunc("StoreSetup");
// MDL: unused -> store_setup_R = DEFunc("StoreSetup");
source_R = DEFunc("source");
ReadRObj_R = DEFunc("ReadRObj");
SaveRObj_R = DEFunc("SaveRObj");
@ -146,8 +146,11 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
"Enable AI surrogate for chemistry module");
app.add_flag("--rds", params.as_rds,
"Save output as .rds file instead of .qs");
"Save output as .rds file instead of default .qs2");
app.add_flag("--qs", params.as_qs,
"Save output as .qs file instead of default .qs2");
std::string init_file;
std::string runtime_file;
@ -174,7 +177,9 @@ int parseInitValues(int argc, char **argv, RuntimeParameters &params) {
}
// set the output extension
params.out_ext = params.as_rds ? "rds" : "qs";
params.out_ext = "qs2";
if (params.as_rds) params.out_ext = "rds";
if (params.as_qs) params.out_ext = "qs";
if (MY_RANK == 0) {
// MSG("Complete results storage is " + BOOL_PRINT(simparams.store_result));
@ -287,18 +292,20 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters &params,
const double &dt = params.timesteps[iter - 1];
// cout << "CPP: Next time step is " << dt << "[s]" << endl;
MSG("Next time step is " + std::to_string(dt) + " [s]");
std::cout << std::endl;
/* displaying iteration number, with C++ and R iterator */
MSG("Going through iteration " + std::to_string(iter));
MSG("Going through iteration " + std::to_string(iter) + "/" +
std::to_string(maxiter));
MSG("Current time step is " + std::to_string(dt));
/* run transport */
diffusion.simulate(dt);
chem.getField().update(diffusion.getField());
MSG("Chemistry step");
// MSG("Chemistry start");
if (params.use_ai_surrogate) {
double ai_start_t = MPI_Wtime();
// Save current values from the tug field as predictor for the ai step
@ -314,16 +321,16 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters &params,
R.parseEval("predictors_scaled <- preprocess(predictors)");
// Predict
MSG("AI Predict");
MSG("AI Prediction");
R.parseEval(
"aipreds_scaled <- prediction_step(model, predictors_scaled)");
// Apply postprocessing
MSG("AI Postprocesing");
MSG("AI Postprocessing");
R.parseEval("aipreds <- postprocess(aipreds_scaled)");
// Validate prediction and write valid predictions to chem field
MSG("AI Validate");
MSG("AI Validation");
R.parseEval(
"validity_vector <- validate_predictions(predictors, aipreds)");
@ -333,8 +340,8 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters &params,
MSG("AI TempField");
std::vector<std::vector<double>> RTempField =
R.parseEval("set_valid_predictions(predictors,\
aipreds,\
validity_vector)");
aipreds,\
validity_vector)");
MSG("AI Set Field");
Field predictions_field =
@ -385,9 +392,11 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, const RuntimeParameters &params,
MSG("End of *coupling* iteration " + std::to_string(iter) + "/" +
std::to_string(maxiter));
MSG();
// MSG();
} // END SIMULATION LOOP
std::cout << std::endl;
Rcpp::List chem_profiling;
chem_profiling["simtime"] = chem.GetChemistryTime();
chem_profiling["loop"] = chem.GetMasterLoopTime();
@ -583,7 +592,7 @@ int main(int argc, char *argv[]) {
R["setup"] = *global_rt_setup;
R["setup$out_ext"] = run_params.out_ext;
string r_vis_code;
std::string r_vis_code;
r_vis_code = "SaveRObj(x = profiling, path = paste0(out_dir, "
"'/timings.', setup$out_ext));";
R.parseEval(r_vis_code);

4
src/poet.hpp.in
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@ -45,8 +45,10 @@ struct RuntimeParameters {
Rcpp::List init_params;
// MDL added to accomodate for qs::qsave/qread
bool as_rds = false;
std::string out_ext; // MDL added to accomodate for qs::qsave/qread
bool as_qs = false;
std::string out_ext;
bool print_progress = false;