Added qs2 as new default format

R_lib/kin_r_library.R

@@ -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)
@@ -187,7 +124,8 @@ ReadRObj <- function(path) {
 
     switch(extension,
         rds = readRDS(path),
-        qs  = qs::qread(path)
+        qs  = qs::qread(path),
+        qs2 = qs2::qs_read(path)
     )
 }
 
@@ -201,6 +139,73 @@ SaveRObj <- function(x, path) {
 
     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"))
+## }

bench/CMakeLists.txt

@@ -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}

src/initializer.cpp

@@ -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>(

src/poet.cpp

@@ -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));

src/poet.hpp.in

@@ -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;