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qsbase · Jun 10, 2024 · 54d5790 · 54d5790
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Showing 21 changed files with 823 additions and 48 deletions.
diff --git a/configure b/configure
@@ -2793,47 +2793,6 @@ RELEASE=`echo $VERSION_STRING | cut -d. -f3`
 echo $(($MAJOR*100000+$MINOR*100+$RELEASE))
 }
 
-########################################################
-#### Compiler specific flags
-
-# Check if simple C++ program using atomic header can compile using AC_COMPILE_IFELSE
-
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h.  */
-
-#include <atomic>
-#include <cstdint>
-std::atomic<std::uint64_t> x1{0};
-std::atomic<std::uint8_t> x2{0};
-std::atomic<char*> x3{nullptr};
-std::atomic<bool> x4{false};
-int main() {
-  x1.fetch_add(1);
-  x2.fetch_add(1);
-  char temp = 'a';
-  x3.store(&temp);
-  x4.store(true);
-  return 0;
-}
-
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"
-then :
-  NEED_LIBATOMIC="no"
-else case e in #(
-  e) NEED_LIBATOMIC="yes" ;;
-esac
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
-
-if test xx$NEED_LIBATOMIC = "xxyes"; then
-  echo "Requires -latomic flag"
-  COMPILER_SPECIFIC_LIBS="-latomic"
-else
-  echo "Does not require -latomic flag"
-  COMPILER_SPECIFIC_LIBS=""
-fi
-
 ########################################################
 #### Compile ZSTD checks
 
@@ -2890,6 +2849,51 @@ else
   TBB_FLAG="-DRCPP_PARALLEL_USE_TBB=0"
 fi
 
+########################################################
+#### Check if -latomic flag is needed, only necessary if using TBB
+
+if test xx$using_tbb = "xxtrue"; then
+  # Check if simple C++ program using atomic header can compile using AC_COMPILE_IFELSE
+
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+  #include <atomic>
+  #include <cstdint>
+  std::atomic<std::uint64_t> x1{0};
+  std::atomic<std::uint8_t> x2{0};
+  std::atomic<char*> x3{nullptr};
+  std::atomic<bool> x4{false};
+  int main() {
+    x1.fetch_add(1);
+    x2.fetch_add(1);
+    char temp = 'a';
+    x3.store(&temp);
+    x4.store(true);
+    return 0;
+  }
+
+_ACEOF
+if ac_fn_cxx_try_compile "$LINENO"
+then :
+  NEED_LIBATOMIC="no"
+else case e in #(
+  e) NEED_LIBATOMIC="yes" ;;
+esac
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.beam conftest.$ac_ext
+
+  if test xx$NEED_LIBATOMIC = "xxyes"; then
+    echo "Requires -latomic flag"
+    COMPILER_SPECIFIC_LIBS="-latomic"
+  else
+    echo "Does not require -latomic flag"
+    COMPILER_SPECIFIC_LIBS=""
+  fi
+else
+  COMPILER_SPECIFIC_LIBS=""
+fi
+
 ########################################################
 #### Compile SIMD checks
 
@@ -2909,7 +2913,7 @@ fi
 QSBLOCKSIZE=""
 
 if test xx$with_qsblocksize != "xx"; then
-echo "Using blocksize ${QSBLOCKSIZE}"
+echo "Using blocksize ${with_qsblocksize}"
   QSBLOCKSIZE=-DQS2_BLOCKSIZE_TESTING_ONLY_DO_NOT_USE=${with_qsblocksize}
 fi
 

diff --git a/inst/benchmarks/plot_benchmark_results.R b/inst/benchmarks/plot_benchmark_results.R
@@ -7,18 +7,16 @@ library(this.path)
 library(stringplus)
 set_string_ops("&", "|")
 
-
+PLATFORM <- "mac"
 algo_subset <- c("qs-legacy", "qs2", "qdata")
 for(DATASET in c("enwik8", "gaia", "mnist", "tcell")) {
-df <- fread("~/GoogleDrive/qs2/inst/benchmarks/results/ubuntu_serialization_benchmarks_%s.csv" | DATASET) %>%
+df <- fread("%s/results/%s_serialization_benchmarks_%s.csv" | c(this.dir(), PLATFORM, DATASET)) %>%
   filter(algo %in% algo_subset)
 df$algo <- factor(df$algo, levels = algo_subset)
 
 dfs <- df %>% group_by(algo, nthreads, compress_level) %>%
   summarize(file_size = unique(file_size), save_time = median(save_time), read_time = median(read_time))
 
-filter(dfs, sapply(file_size, length) > 1) %>% as.data.frame
-
 g1 <- ggplot(df, aes(x = file_size, y = save_time, color = algo, shape = factor(nthreads))) + 
   geom_point() + 
   geom_line(data = dfs, aes(lty = factor(nthreads))) + 
@@ -47,6 +45,55 @@ g2 <- ggplot(df, aes(x = save_time, y = read_time, color = algo, shape = factor(
 
 g <- g1 + g2 + patchwork::plot_layout(guides = "collect")
 
-ggsave(g, file = "%s/plots/%s_benchmark_plot.png" | c(this.dir(), DATASET), width = 8, height = 3.75)
+ggsave(g, file = "%s/plots/%s_%s_benchmark_plot.png" | c(this.dir(), PLATFORM, DATASET), width = 8, height = 3.75)
 
 }
+
+################################################################################
+# total across 4 datasets
+df <- lapply(c("enwik8", "gaia", "mnist", "tcell"), function(DATASET) {
+  fread("%s/results/%s_serialization_benchmarks_%s.csv" | c(this.dir(), PLATFORM, DATASET)) %>%
+    filter(algo %in% algo_subset) %>%
+    mutate(dataset = DATASET)
+}) %>% rbindlist
+df$algo <- factor(df$algo, levels = algo_subset)
+
+df <- df %>% 
+  group_by(algo, nthreads, compress_level, rep) %>%
+  summarize(file_size = sum(file_size), save_time = sum(save_time), read_time = sum(read_time))
+
+dfs <- df %>%
+  group_by(algo, nthreads, compress_level) %>%
+  summarize(file_size = unique(file_size), save_time = median(save_time), read_time = median(read_time))
+
+
+g1 <- ggplot(df, aes(x = file_size, y = save_time, color = algo, shape = factor(nthreads))) + 
+  geom_point() + 
+  geom_line(data = dfs, aes(lty = factor(nthreads))) + 
+  # scale_x_log10() + 
+  scale_y_log10() + 
+  scale_color_manual(values = palette.colors(palette = "Okabe-Ito")) +
+  labs(color = "Format", lty = "Threads", pch = "Threads",
+       x = "File Size (MB)", y = "Save Time (s)") + 
+  theme_bw(base_size=11) + 
+  guides(color = guide_legend(order = 1), 
+         pch = guide_legend(order = 2),
+         lty = guide_legend(order = 2))
+
+
+g2 <- ggplot(df, aes(x = save_time, y = read_time, color = algo, shape = factor(nthreads))) + 
+  geom_point() + 
+  geom_line(data = dfs, aes(lty = factor(nthreads))) + 
+  scale_x_log10() + scale_y_log10() +
+  scale_color_manual(values = palette.colors(palette = "Okabe-Ito")) +
+  labs(color = "Format", lty = "Threads", pch = "Threads",
+       y = "Read Time (s)", x = "Save Time (s)") + 
+  theme_bw(base_size=11) + 
+  guides(color = guide_legend(order = 1),
+         pch = guide_legend(order = 2),
+         lty = guide_legend(order = 2))
+
+g <- g1 + g2 + patchwork::plot_layout(guides = "collect")
+
+ggsave(g, file = "%s/plots/%s_combined_benchmark_plot.png" | c(this.dir(), PLATFORM), width = 8, height = 3.75)
+
diff --git a/inst/benchmarks/plots/enwik8_benchmark_plot.png b/inst/benchmarks/plots/enwik8_benchmark_plot.png
diff --git a/inst/benchmarks/plots/gaia_benchmark_plot.png b/inst/benchmarks/plots/gaia_benchmark_plot.png
diff --git a/inst/benchmarks/plots/mac_combined_benchmark_plot.png b/inst/benchmarks/plots/mac_combined_benchmark_plot.png
diff --git a/inst/benchmarks/plots/mac_enwik8_benchmark_plot.png b/inst/benchmarks/plots/mac_enwik8_benchmark_plot.png
diff --git a/inst/benchmarks/plots/mac_gaia_benchmark_plot.png b/inst/benchmarks/plots/mac_gaia_benchmark_plot.png
diff --git a/inst/benchmarks/plots/mac_mnist_benchmark_plot.png b/inst/benchmarks/plots/mac_mnist_benchmark_plot.png
diff --git a/inst/benchmarks/plots/mac_tcell_benchmark_plot.png b/inst/benchmarks/plots/mac_tcell_benchmark_plot.png
diff --git a/inst/benchmarks/plots/mnist_benchmark_plot.png b/inst/benchmarks/plots/mnist_benchmark_plot.png
diff --git a/inst/benchmarks/plots/tcell_benchmark_plot.png b/inst/benchmarks/plots/tcell_benchmark_plot.png
diff --git a/inst/benchmarks/plots/ubuntu_combined_benchmark_plot.png b/inst/benchmarks/plots/ubuntu_combined_benchmark_plot.png
diff --git a/inst/benchmarks/plots/ubuntu_enwik8_benchmark_plot.png b/inst/benchmarks/plots/ubuntu_enwik8_benchmark_plot.png
diff --git a/inst/benchmarks/plots/ubuntu_gaia_benchmark_plot.png b/inst/benchmarks/plots/ubuntu_gaia_benchmark_plot.png
diff --git a/inst/benchmarks/plots/ubuntu_mnist_benchmark_plot.png b/inst/benchmarks/plots/ubuntu_mnist_benchmark_plot.png
diff --git a/inst/benchmarks/plots/ubuntu_tcell_benchmark_plot.png b/inst/benchmarks/plots/ubuntu_tcell_benchmark_plot.png
diff --git a/inst/benchmarks/results/mac_serialization_benchmarks_enwik8.csv b/inst/benchmarks/results/mac_serialization_benchmarks_enwik8.csv
@@ -0,0 +1,181 @@
+algo,compress_level,nthreads,rep,save_time,read_time,file_size
+qdata,3,4,2,0.218180179595947,0.920108079910278,35.8806943893433
+qs-legacy,7,1,3,1.66920113563538,0.975362062454224,33.9900665283203
+qdata,11,1,3,3.17094302177429,0.981371879577637,32.992488861084
+qs-legacy,9,1,3,1.96937203407288,0.964427947998047,33.7422189712524
+qs2,9,1,3,2.2372670173645,1.02592086791992,33.8121643066406
+qdata,1,4,3,0.140744209289551,0.908569097518921,40.5108032226563
+qs-legacy,7,4,2,0.665509939193726,0.969509840011597,33.9900665283203
+qs2,3,4,5,0.23112416267395,0.929660081863403,36.735668182373
+qdata,1,4,5,0.143319129943848,0.916823148727417,40.5108032226563
+qs2,5,4,5,0.393964052200317,0.923666954040527,35.3520374298096
+qdata,7,4,2,0.608901977539063,0.923305988311768,33.4590539932251
+qs2,7,1,1,1.77460908889771,1.04013204574585,34.1244297027588
+qdata,9,4,3,0.729050159454346,0.922981023788452,33.1589050292969
+qdata,7,1,5,1.5693302154541,0.995135068893433,33.4590539932251
+qs2,11,1,1,3.36194896697998,1.00719714164734,33.6027097702026
+qdata,7,4,5,0.57516622543335,0.918521881103516,33.4590539932251
+qdata,11,1,5,3.19080805778503,1.01104688644409,32.992488861084
+qs-legacy,11,4,5,1.15806412696838,0.972970962524414,33.6047334671021
+qs2,3,1,3,0.748267889022827,1.01729989051819,36.735668182373
+qs2,7,4,3,0.603024005889893,0.932165145874023,34.1244297027588
+qs2,11,1,4,3.43799185752869,1.02130699157715,33.6027097702026
+qs-legacy,7,4,1,0.658999919891357,0.969995021820068,33.9900665283203
+qs-legacy,5,4,4,0.42157506942749,0.987696170806885,34.931432723999
+qdata,11,4,5,1.30510592460632,0.928042888641357,32.992488861084
+qdata,7,1,1,1.65986084938049,0.9896399974823,33.4590539932251
+qs-legacy,1,4,1,0.139781951904297,0.9719078540802,40.5963258743286
+qs2,9,4,5,0.756778955459595,0.924296855926514,33.8121643066406
+qs-legacy,7,4,5,0.642716884613037,0.971292018890381,33.9900665283203
+qs-legacy,11,1,5,2.6232898235321,0.993521213531494,33.6047334671021
+qdata,1,1,5,0.442862987518311,1.00880694389343,40.5108032226563
+qs-legacy,9,1,2,2.1741509437561,0.973517179489136,33.7422189712524
+qs-legacy,5,1,4,1.12675404548645,1.18350505828857,34.931432723999
+qs2,11,1,3,3.44373798370361,1.01490211486816,33.6027097702026
+qs2,5,4,4,0.395595073699951,0.924275875091553,35.3520374298096
+qs-legacy,7,1,5,1.72590589523315,0.980098962783813,33.9900665283203
+qdata,1,1,4,0.487936019897461,1.02848696708679,40.5108032226563
+qdata,7,4,1,0.582828044891357,0.935718059539795,33.4590539932251
+qs-legacy,5,4,5,0.408643960952759,0.968690156936646,34.931432723999
+qs2,11,4,2,1.39893007278442,0.951234102249146,33.6027097702026
+qdata,1,1,2,0.469209909439087,0.990387916564941,40.5108032226563
+qdata,3,4,5,0.249212980270386,0.934927940368652,35.8806943893433
+qs2,9,4,1,0.764551162719727,0.921451091766357,33.8121643066406
+qdata,9,1,1,2.17393803596497,0.991391897201538,33.1589050292969
+qs-legacy,9,4,1,0.767686128616333,0.982846975326538,33.7422189712524
+qs2,1,1,3,0.553164005279541,1.00831604003906,41.5029220581055
+qdata,7,4,4,0.576091051101685,0.927416086196899,33.4590539932251
+qs2,1,4,4,0.152478933334351,0.928745031356812,41.5029220581055
+qs-legacy,9,1,1,1.94528198242188,1.01645994186401,33.7422189712524
+qs-legacy,11,4,4,1.18209290504456,0.978740930557251,33.6047334671021
+qs-legacy,9,4,3,0.762059926986694,0.972508907318115,33.7422189712524
+qdata,9,1,3,2.15405201911926,0.990767002105713,33.1589050292969
+qs-legacy,1,1,2,0.441058874130249,1.00203609466553,40.5963258743286
+qs-legacy,3,4,4,0.247656106948853,0.986696004867554,36.216139793396
+qdata,7,1,3,1.64061999320984,1.00061893463135,33.4590539932251
+qs2,1,4,1,0.152202129364014,0.929331064224243,41.5029220581055
+qs-legacy,9,1,4,1.97670102119446,0.975831985473633,33.7422189712524
+qs-legacy,9,1,5,1.95155787467957,0.976623058319092,33.7422189712524
+qs-legacy,11,4,1,1.14159989356995,0.966847896575928,33.6047334671021
+qdata,1,4,1,0.14001202583313,0.923097133636475,40.5108032226563
+qs2,5,4,1,0.393970966339111,0.924370050430298,35.3520374298096
+qdata,9,1,5,2.12500691413879,1.05019617080688,33.1589050292969
+qdata,5,1,4,1.12527513504028,1.0418529510498,34.5112924575806
+qdata,11,4,3,1.33813905715942,0.929855108261108,32.992488861084
+qdata,3,4,1,0.225500106811523,0.919832944869995,35.8806943893433
+qs-legacy,5,4,1,0.413792133331299,1.00252294540405,34.931432723999
+qs2,3,4,2,0.234230041503906,0.921794891357422,36.735668182373
+qs-legacy,1,4,2,0.139997005462646,0.989223957061768,40.5963258743286
+qdata,5,1,5,1.07970714569092,1.00178003311157,34.5112924575806
+qdata,3,1,4,0.689329862594605,1.00757193565369,35.8806943893433
+qs-legacy,11,1,4,2.64494895935059,1.02183794975281,33.6047334671021
+qs-legacy,7,4,4,0.637389898300171,0.970676898956299,33.9900665283203
+qs2,1,1,1,0.489444017410278,1.06297993659973,41.5029220581055
+qs2,7,4,5,0.610751152038574,0.931798934936523,34.1244297027588
+qdata,11,4,4,1.33432602882385,0.955682992935181,32.992488861084
+qs2,7,4,1,0.617357969284058,0.921568870544434,34.1244297027588
+qdata,1,4,2,0.141404867172241,0.923961162567139,40.5108032226563
+qs2,9,1,1,2.30394005775452,1.00606894493103,33.8121643066406
+qs-legacy,9,4,5,0.775880813598633,0.970836162567139,33.7422189712524
+qs-legacy,1,1,1,0.416102886199951,0.976650953292847,40.5963258743286
+qs2,3,4,4,0.228637933731079,0.949862003326416,36.735668182373
+qs2,3,4,3,0.230727910995483,0.92956805229187,36.735668182373
+qs2,3,1,2,0.753386974334717,1.06122803688049,36.735668182373
+qdata,5,1,3,1.09429597854614,1.0095272064209,34.5112924575806
+qs-legacy,1,1,4,0.433292865753174,0.975621938705444,40.5963258743286
+qs2,5,1,1,1.16068196296692,1.02248287200928,35.3520374298096
+qs-legacy,5,1,1,1.04505181312561,1.0166609287262,34.931432723999
+qdata,5,1,1,1.05780291557312,1.00861597061157,34.5112924575806
+qdata,9,4,1,0.740909099578857,0.926774024963379,33.1589050292969
+qs2,7,4,4,0.604793071746826,0.930402994155884,34.1244297027588
+qs-legacy,7,1,4,1.68970799446106,0.985357999801636,33.9900665283203
+qs-legacy,11,1,2,2.62518286705017,0.98632287979126,33.6047334671021
+qdata,3,4,4,0.219121932983398,1.03751397132874,35.8806943893433
+qdata,5,4,3,0.439361095428467,1.03325796127319,34.5112924575806
+qs-legacy,3,4,3,0.282451868057251,0.970804929733276,36.216139793396
+qs2,5,1,2,1.15880012512207,1.01839804649353,35.3520374298096
+qs2,1,4,2,0.151521921157837,0.935590028762817,41.5029220581055
+qdata,1,1,3,0.448063135147095,0.986173868179321,40.5108032226563
+qdata,7,1,4,1.67981100082397,1.00332880020142,33.4590539932251
+qdata,5,4,1,0.379070043563843,0.924031972885132,34.5112924575806
+qdata,3,1,3,0.729329824447632,0.998731851577759,35.8806943893433
+qs2,11,1,5,3.44166898727417,1.00454711914062,33.6027097702026
+qdata,5,4,4,0.379226922988892,0.916393995285034,34.5112924575806
+qs-legacy,5,1,3,1.08338904380798,0.982345104217529,34.931432723999
+qs2,7,1,4,1.71839714050293,1.03905701637268,34.1244297027588
+qs2,5,4,3,0.392080068588257,0.933168888092041,35.3520374298096
+qdata,5,1,2,1.08088397979736,1.02697610855103,34.5112924575806
+qs-legacy,5,1,5,1.05624318122864,0.997048139572144,34.931432723999
+qdata,3,4,3,0.241533994674683,0.985894918441772,35.8806943893433
+qs2,3,1,4,0.744220018386841,1.01184797286987,36.735668182373
+qs-legacy,3,4,5,0.248114109039307,0.973035097122192,36.216139793396
+qdata,5,4,2,0.374050140380859,0.924262046813965,34.5112924575806
+qdata,5,4,5,0.37542986869812,0.925734043121338,34.5112924575806
+qs2,1,1,4,0.551736116409302,1.04864096641541,41.5029220581055
+qs-legacy,11,1,1,2.60514187812805,0.97241997718811,33.6047334671021
+qs2,9,4,3,0.779651165008545,0.919161796569824,33.8121643066406
+qs-legacy,7,1,1,1.69791412353516,1.0160768032074,33.9900665283203
+qs2,5,1,3,1.14140605926514,1.04013800621033,35.3520374298096
+qdata,9,1,4,2.11513805389404,0.987239122390747,33.1589050292969
+qs-legacy,3,1,2,0.737931966781616,1.01202297210693,36.216139793396
+qdata,3,1,1,0.704370975494385,0.992788076400757,35.8806943893433
+qs2,7,1,5,1.74576187133789,1.04564189910889,34.1244297027588
+qs-legacy,5,1,2,1.07217812538147,0.983603000640869,34.931432723999
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