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perf: remove unused parameters from paramlist and parameter structure
doc: update doc to latest changes data: update benchmarks to latest changes
This commit is contained in:
Max Luebke
parent
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37ee74faaf
71
README.md
71
README.md
@ -1,5 +1,5 @@
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<!--
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Time-stamp: "Last modified 2023-07-20 11:30:44 delucia"
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Time-stamp: "Last modified 2023-08-02 13:55:11 mluebke"
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-->
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# POET
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@ -69,6 +69,9 @@ following available options:
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DHT usage. Defaults to _OFF_.
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- **POET_ENABLE_TESTING**=_boolean_ - enables small set of unit tests (more to
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come). Defaults to _OFF_.
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- **POET_PHT_ADDITIONAL_INFO**=_boolean_ - enabling the count of accesses to one
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PHT bucket. Use with caution, as things will get slowed down significantly.
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Defaults to _OFF_.
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### Example: Build from scratch
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@ -109,15 +112,24 @@ poet
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│ └── kin_r_library.R
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└── share
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└── poet
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├── bench
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│ ├── dolo_diffu_inner_large.R
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│ ├── dolo_diffu_inner.R
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│ └── dolo_inner.pqi
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└── examples
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├── dol.pqi
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├── phreeqc_kin.dat
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├── SimDol1D_diffu.R
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└── SimDol2D_diffu.R
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└── bench
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├── barite
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│ ├── barite_interp_eval.R
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│ ├── barite.pqi
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│ ├── barite.R
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│ └── db_barite.dat
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├── dolo
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│ ├── dolo_diffu_inner_large.R
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│ ├── dolo_diffu_inner.R
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│ ├── dolo_inner.pqi
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│ ├── dolo_interp_long.R
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│ └── phreeqc_kin.dat
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└── surfex
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├── ExBase.pqi
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├── ex.R
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├── SMILE_2021_11_01_TH.dat
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├── SurfExBase.pqi
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└── surfex.R
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```
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The R libraries will be loaded at runtime and the paths are hardcoded
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@ -125,6 +137,10 @@ absolute paths inside `poet.cpp`. So, if you consider to move
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`bin/poet` either change paths of the R source files and recompile
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POET or also move `R_lib/*` relative to the binary.
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The benchmarks consist of input scripts, which are provided as .R files.
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Additionally, Phreeqc scripts and their corresponding databases are required,
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stored as .pqi and .dat files, respectively.
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## Running
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Run POET by `mpirun ./poet <OPTIONS> <SIMFILE> <OUTPUT_DIRECTORY>`
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@ -132,28 +148,25 @@ where:
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- **OPTIONS** - runtime parameters (explained below)
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- **SIMFILE** - simulation described as R script (e.g.
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`<POET_INSTALL_DIR>/share/examples/SimDol2D_diffu.R`)
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`<POET_INSTALL_DIR>/share/poet/bench/dolo/dolo_interp_long.R`)
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- **OUTPUT_DIRECTORY** - path, where all output of POET should be stored
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### Runtime options
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The following parameters can be set:
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| Option | Value | Description |
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|--------------------------|--------------|--------------------------------------------------------------------------------------------------------------------------|
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| **--work-package-size=** | _1..n_ | size of work packages (defaults to _5_) |
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| **--ignore-result** | | disables store of simulation resuls |
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| **--dht** | | enabling DHT usage (defaults to _OFF_) |
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| **--dht-signif=** | _1..n_ | set rounding to number of significant digits (defaults to _5_) (it is recommended to use `signif_vec` in R input script) |
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| **--dht-strategy=** | _0-1_ | change DHT strategy. **NOT IMPLEMENTED YET** (Defaults to _0_) |
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| **--dht-size=** | _1-n_ | size of DHT per process involved in megabyte (defaults to _1000 MByte_) |
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| **--dht-snaps=** | _0-2_ | disable or enable storage of DHT snapshots |
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| **--dht-file=** | `<SNAPSHOT>` | initializes DHT with the given snapshot file |
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#### Additions to `dht-signif`
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Only used if no vector is given in setup file. For individual values
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per column use R vector `signif_vector` in `SIMFILE`.
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| Option | Value | Description |
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|-----------------------------|--------------|--------------------------------------------------------------------------------------------------------------------------|
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| **--work-package-size=** | _1..n_ | size of work packages (defaults to _5_) |
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| **--ignore-result** | | disables store of simulation resuls |
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| **--dht** | | enabling DHT usage (defaults to _OFF_) |
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| **--dht-strategy=** | _0-1_ | change DHT strategy. **NOT IMPLEMENTED YET** (Defaults to _0_) |
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| **--dht-size=** | _1-n_ | size of DHT per process involved in megabyte (defaults to _1000 MByte_) |
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| **--dht-snaps=** | _0-2_ | disable or enable storage of DHT snapshots |
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| **--dht-file=** | `<SNAPSHOT>` | initializes DHT with the given snapshot file |
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| **--interp-size** | _1-n_ | size of PHT (interpolation) per process in megabyte |
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| **--interp-bucket-entries** | _1-n_ | number of entries to store at maximum in one PHT bucket |
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| **--interp-min** | _1-n_ | number of entries in PHT bucket needed to start interpolation |
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#### Additions to `dht-snaps`
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@ -168,13 +181,13 @@ Following values can be set:
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### Example: Running from scratch
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We will continue the above example and start a simulation with
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`SimDol2D_diffu.R`. As transport a simple fixed-coefficient diffusion is used.
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`dolo_diffu_inner.R`. As transport a simple fixed-coefficient diffusion is used.
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It's a 2D, 100x100 grid, simulating 10 time steps. To start the simulation with
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4 processes `cd` into your previously installed POET-dir
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`<POET_INSTALL_DIR>/bin` and run:
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```sh
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mpirun -n 4 ./poet ../share/poet/examples/SimDol2D_diffu.R output
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mpirun -n 4 ./poet ../share/poet/bench/dolo/dolo_diffu_inner.R/ output
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```
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After a finished simulation all data generated by POET will be found
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@ -187,7 +200,7 @@ produced. This is done by appending the `--dht-snaps=<value>` option. The
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resulting call would look like this:
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```sh
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mpirun -n 4 ./poet --dht --dht-snaps=2 ../share/poet/examples/SimDol2D_diffu.R output
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mpirun -n 4 ./poet --dht --dht-snaps=2 ../share/poet/bench/dolo/dolo_diffu_inner.R/ output
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```
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## About the usage of MPI_Wtime()
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@ -1,4 +1,4 @@
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## Time-stamp: "Last modified 2023-04-24 16:51:23 mluebke"
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## Time-stamp: "Last modified 2023-08-02 13:59:22 mluebke"
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database <- normalizePath("../share/poet/bench/barite/db_barite.dat")
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input_script <- normalizePath("../share/poet/bench/barite/barite.pqi")
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@ -28,11 +28,7 @@ init_cell <- list(
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grid <- list(
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n_cells = c(n, m),
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s_cells = c(1, 1),
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type = types[1],
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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database = database,
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input_script = input_script
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type = types[1]
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)
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@ -1,4 +1,4 @@
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## Time-stamp: "Last modified 2023-07-28 16:57:40 mluebke"
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## Time-stamp: "Last modified 2023-08-02 13:59:02 mluebke"
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database <- normalizePath("../share/poet/bench/dolo/phreeqc_kin.dat")
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input_script <- normalizePath("../share/poet/bench/dolo/dolo_inner.pqi")
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@ -29,11 +29,7 @@ init_cell <- list(
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grid <- list(
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n_cells = c(n, m),
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s_cells = c(1, 1),
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type = types[1],
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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database = database,
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input_script = input_script
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type = types[1]
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)
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@ -1,4 +1,4 @@
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## Time-stamp: "Last modified 2023-07-28 16:57:40 mluebke"
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## Time-stamp: "Last modified 2023-08-02 13:59:12 mluebke"
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database <- normalizePath("../share/poet/bench/dolo/phreeqc_kin.dat")
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input_script <- normalizePath("../share/poet/bench/dolo/dolo_inner.pqi")
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@ -29,11 +29,7 @@ init_cell <- list(
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grid <- list(
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n_cells = c(n, m),
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s_cells = c(2, 1),
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type = types[1],
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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database = database,
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input_script = input_script
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type = types[1]
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)
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@ -1,4 +1,4 @@
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## Time-stamp: "Last modified 2023-08-01 18:34:47 mluebke"
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## Time-stamp: "Last modified 2023-08-02 13:47:06 mluebke"
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database <- normalizePath("../share/poet/bench/dolo/phreeqc_kin.dat")
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input_script <- normalizePath("../share/poet/bench/dolo/dolo_inner.pqi")
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@ -29,11 +29,7 @@ init_cell <- list(
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grid <- list(
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n_cells = c(n, m),
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s_cells = c(5, 2.5),
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type = types[1],
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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database = database,
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input_script = input_script
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type = types[1]
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)
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@ -1,4 +1,4 @@
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## Time-stamp: "Last modified 2023-04-17 12:29:27 mluebke"
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## Time-stamp: "Last modified 2023-08-02 13:59:35 mluebke"
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database <- normalizePath("./SMILE_2021_11_01_TH.dat")
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input_script <- normalizePath("./ExBase.pqi")
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@ -40,11 +40,7 @@ init_cell <- list(H = 1.476571028625e-01,
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grid <- list(
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n_cells = c(n, m),
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s_cells = c(1, 1),
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type = "scratch",
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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database = database,
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input_script = input_script
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type = "scratch"
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)
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@ -1,4 +1,4 @@
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## Time-stamp: "Last modified 2023-04-17 15:48:21 mluebke"
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## Time-stamp: "Last modified 2023-08-02 13:59:44 mluebke"
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database <- normalizePath("../share/poet/bench/surfex/SMILE_2021_11_01_TH.dat")
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input_script <- normalizePath("../share/poet/bench/surfex/SurfExBase.pqi")
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@ -40,11 +40,7 @@ init_cell <- list(H = 1.476571028625e-01,
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grid <- list(
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n_cells = c(n, m),
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s_cells = c(1, 1),
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type = "scratch",
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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database = database,
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input_script = input_script
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type = "scratch"
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)
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@ -13,10 +13,6 @@ by POET.
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| `n_cells` | Numeric Vector | Number of cells in each direction |
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| `s_cells` | Numeric Vector | Spatial resolution of grid in each direction |
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| `type` | String | Type of initialization, can be set to *scratch*, *phreeqc* or *rds* |
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| `init_cell` | Data Frame | Containing all exactly one value per species to initialize the field. |
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| `props` | String Vector | Names of all species |
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| `database` | String | Path to Phreeqc database |
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| `input_script` | String | Path to Phreeqc initial script |
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## Diffusion parameters
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@ -70,10 +66,12 @@ vecinj_index <- list(
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## Chemistry parameters
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| name | type | description |
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|----------------|--------|-----------------------------------|
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| `database` | String | Path to the Phreeqc database |
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| `input_script` | String | Path the the Phreeqc input script |
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| name | type | description |
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|----------------|--------------|----------------------------------------------------------------------------------|
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| `database` | String | Path to the Phreeqc database |
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| `input_script` | String | Path the the Phreeqc input script |
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| `dht_species` | Named Vector | Indicates significant digits to use for each species for DHT rounding. |
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| `pht_species` | Named Vector | Indicates significant digits to use for each species for Interpolation rounding. |
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## Final setup
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@ -86,10 +84,3 @@ vecinj_index <- list(
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| `timesteps` | Numeric Vector | $\Delta t$ to use for specific iteration |
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| `store_result` | Boolean | Indicates if results should be stored |
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| `out_save` | Numeric Vector | *optional:* At which iteration the states should be stored |
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### DHT setup
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| name | type | description |
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|-----------------|----------------|---------------------------------------------------------------------------------|
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| `signif_vector` | Numeric Vector | Indicates significant digits to use for DHT rounding. Order of `props` vector. |
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| `prop_type` | String Vector | Set type of species for rounding, can be left blank or set to *act* or *ignore* |
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@ -240,11 +240,12 @@ private:
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std::list<std::string> validateOptions(argh::parser cmdl);
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const std::set<std::string> flaglist{
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"ignore-result", "dht", "dht-nolog", "P", "progress", "interp"};
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"ignore-result", "dht", "P", "progress", "interp"};
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const std::set<std::string> paramlist{
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"work-package-size", "dht-signif", "dht-strategy",
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"dht-size", "dht-snaps", "dht-file",
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"interp-size", "interp-min", "interp-bucket-entries"};
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"work-package-size", "dht-strategy",
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"dht-size", "dht-snaps",
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"dht-file", "interp-size",
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"interp-min", "interp-bucket-entries"};
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t_simparams simparams;
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@ -56,14 +56,6 @@ poet::GridParams::s_GridParams(RInside &R) {
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(dim == 1 ? this->n_cells[0] : this->n_cells[0] * this->n_cells[1]);
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this->type = Rcpp::as<std::string>(R.parseEval("mysetup$grid$type"));
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this->init_df =
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Rcpp::as<Rcpp::DataFrame>(R.parseEval("mysetup$grid$init_cell"));
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this->props =
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Rcpp::as<std::vector<std::string>>(R.parseEval("mysetup$grid$props"));
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this->input_script =
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Rcpp::as<std::string>(R.parseEval("mysetup$grid$input_script"));
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this->database_path =
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Rcpp::as<std::string>(R.parseEval("mysetup$grid$database"));
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}
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poet::DiffusionParams::s_DiffusionParams(RInside &R) {
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