From 248f1706bceef014c237cc3edcd8f28d10f2fc4f Mon Sep 17 00:00:00 2001
From: voigta80 <aiko.voigt@univie.ac.at>
Date: Fri, 1 Oct 2021 14:11:47 +0200
Subject: [PATCH] Overhauled benchmarks
---
...benchmark_2d.run.32394761.o_keep4reference | 483 ++++++++++++++++++
...benchmark_2d.run.32398022.o_keep4reference | 183 +++++++
...benchmark_3d.run.32394974.o_keep4reference | 333 ++++++++++++
...benchmark_3d.run.32398032.o_keep4reference | 79 +++
...benchmark_3d.run.32401555.o_keep4reference | 79 +++
...benchmark_3d.run.32401557.o_keep4reference | 79 +++
...-10timesteps.run.32408241.o_keep4reference | 46 ++
...k_cubulation.run.32394751.o_keep4reference | 50 ++
benchmarks/benchmark_2d.py | 1 +
benchmarks/benchmark_2d.run | 20 +-
benchmarks/benchmark_3d.py | 3 +-
benchmarks/benchmark_3d.run | 14 +-
.../benchmark_3d_R10000m-10timesteps.py | 75 +++
.../benchmark_3d_R10000m-10timesteps.run | 21 +
.../benchmark_3d_R10000m-singletimestep.py | 72 +++
.../benchmark_3d_R10000m-singletimestep.run | 21 +
benchmarks/benchmark_cubulation.run | 28 +-
17 files changed, 1557 insertions(+), 30 deletions(-)
create mode 100644 benchmarks/LOG.benchmark_2d.run.32394761.o_keep4reference
create mode 100644 benchmarks/LOG.benchmark_2d.run.32398022.o_keep4reference
create mode 100644 benchmarks/LOG.benchmark_3d.run.32394974.o_keep4reference
create mode 100644 benchmarks/LOG.benchmark_3d.run.32398032.o_keep4reference
create mode 100644 benchmarks/LOG.benchmark_3d.run.32401555.o_keep4reference
create mode 100644 benchmarks/LOG.benchmark_3d.run.32401557.o_keep4reference
create mode 100644 benchmarks/LOG.benchmark_3d_R10000m-10timesteps.run.32408241.o_keep4reference
create mode 100644 benchmarks/LOG.benchmark_cubulation.run.32394751.o_keep4reference
create mode 100644 benchmarks/benchmark_3d_R10000m-10timesteps.py
create mode 100755 benchmarks/benchmark_3d_R10000m-10timesteps.run
create mode 100644 benchmarks/benchmark_3d_R10000m-singletimestep.py
create mode 100755 benchmarks/benchmark_3d_R10000m-singletimestep.run
diff --git a/benchmarks/LOG.benchmark_2d.run.32394761.o_keep4reference b/benchmarks/LOG.benchmark_2d.run.32394761.o_keep4reference
new file mode 100644
index 0000000..d5ee24f
--- /dev/null
+++ b/benchmarks/LOG.benchmark_2d.run.32394761.o_keep4reference
@@ -0,0 +1,483 @@
+Working with /pf/b/b380459/conda-envs/Nawdex-Hackathon/bin/python3.8
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.091548 Min: 0:00:00.073320 Max: 0:00:00.195747
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.022585 Min: 0:00:00.022165 Max: 0:00:00.023405
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.022472 Min: 0:00:00.022012 Max: 0:00:00.023221
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.043345 Min: 0:00:00.041738 Max: 0:00:00.086057
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.024109 Min: 0:00:00.023598 Max: 0:00:00.024889
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.024014 Min: 0:00:00.023460 Max: 0:00:00.024621
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.046223 Min: 0:00:00.044324 Max: 0:00:00.089315
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.027650 Min: 0:00:00.027067 Max: 0:00:00.028171
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.027702 Min: 0:00:00.027020 Max: 0:00:00.028221
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.046094 Min: 0:00:00.043885 Max: 0:00:00.081229
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.025465 Min: 0:00:00.024713 Max: 0:00:00.038073
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.025120 Min: 0:00:00.024684 Max: 0:00:00.026566
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.044324 Min: 0:00:00.042587 Max: 0:00:00.081086
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.023174 Min: 0:00:00.022782 Max: 0:00:00.023769
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.023128 Min: 0:00:00.022625 Max: 0:00:00.024711
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.044376 Min: 0:00:00.042250 Max: 0:00:00.089396
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.023025 Min: 0:00:00.022593 Max: 0:00:00.023827
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.022933 Min: 0:00:00.022552 Max: 0:00:00.023380
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.043113 Min: 0:00:00.041698 Max: 0:00:00.087215
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.022524 Min: 0:00:00.022187 Max: 0:00:00.023050
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.022446 Min: 0:00:00.022127 Max: 0:00:00.022800
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.046294 Min: 0:00:00.042847 Max: 0:00:00.125940
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.024332 Min: 0:00:00.023979 Max: 0:00:00.024959
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.024267 Min: 0:00:00.023933 Max: 0:00:00.024783
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.044507 Min: 0:00:00.042587 Max: 0:00:00.099443
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.024200 Min: 0:00:00.023734 Max: 0:00:00.024779
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.024148 Min: 0:00:00.023737 Max: 0:00:00.024589
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.043602 Min: 0:00:00.041826 Max: 0:00:00.090542
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.023848 Min: 0:00:00.023308 Max: 0:00:00.025302
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.023743 Min: 0:00:00.023410 Max: 0:00:00.024471
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.160846 Min: 0:00:00.111491 Max: 0:00:00.391311
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.106263 Min: 0:00:00.104591 Max: 0:00:00.109506
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.105908 Min: 0:00:00.104468 Max: 0:00:00.109577
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.088686 Min: 0:00:00.086085 Max: 0:00:00.169074
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.117156 Min: 0:00:00.115673 Max: 0:00:00.120187
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.116967 Min: 0:00:00.115425 Max: 0:00:00.120136
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.084595 Min: 0:00:00.082806 Max: 0:00:00.117518
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.106080 Min: 0:00:00.104335 Max: 0:00:00.110090
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.105838 Min: 0:00:00.104399 Max: 0:00:00.108251
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.084749 Min: 0:00:00.083041 Max: 0:00:00.115526
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.106344 Min: 0:00:00.104815 Max: 0:00:00.110307
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.106173 Min: 0:00:00.104649 Max: 0:00:00.108949
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.085238 Min: 0:00:00.082886 Max: 0:00:00.131454
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.106936 Min: 0:00:00.105412 Max: 0:00:00.110505
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.106887 Min: 0:00:00.105577 Max: 0:00:00.109416
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.085478 Min: 0:00:00.084144 Max: 0:00:00.123536
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.105747 Min: 0:00:00.104044 Max: 0:00:00.109831
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.105499 Min: 0:00:00.104097 Max: 0:00:00.108184
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.085233 Min: 0:00:00.083084 Max: 0:00:00.156474
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.107501 Min: 0:00:00.105502 Max: 0:00:00.110556
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.107416 Min: 0:00:00.105578 Max: 0:00:00.109514
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.084743 Min: 0:00:00.082913 Max: 0:00:00.130098
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.107107 Min: 0:00:00.105694 Max: 0:00:00.112273
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.107284 Min: 0:00:00.105888 Max: 0:00:00.110773
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.086071 Min: 0:00:00.082956 Max: 0:00:00.137728
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.105126 Min: 0:00:00.103154 Max: 0:00:00.109758
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.104919 Min: 0:00:00.103079 Max: 0:00:00.108444
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.085041 Min: 0:00:00.083473 Max: 0:00:00.133082
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.108759 Min: 0:00:00.107396 Max: 0:00:00.111874
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.108661 Min: 0:00:00.106734 Max: 0:00:00.111517
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.345799 Min: 0:00:00.297422 Max: 0:00:00.463883
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.517681 Min: 0:00:00.508005 Max: 0:00:00.524430
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.512884 Min: 0:00:00.504172 Max: 0:00:00.519644
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.253063 Min: 0:00:00.247483 Max: 0:00:00.316465
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.514580 Min: 0:00:00.507629 Max: 0:00:00.521464
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.508636 Min: 0:00:00.500982 Max: 0:00:00.522027
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.250970 Min: 0:00:00.246888 Max: 0:00:00.281887
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.522587 Min: 0:00:00.515268 Max: 0:00:00.530972
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.517051 Min: 0:00:00.510642 Max: 0:00:00.527864
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.251323 Min: 0:00:00.246454 Max: 0:00:00.286386
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.513437 Min: 0:00:00.507322 Max: 0:00:00.522297
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.509095 Min: 0:00:00.502533 Max: 0:00:00.516856
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.250744 Min: 0:00:00.245760 Max: 0:00:00.293796
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.516474 Min: 0:00:00.510681 Max: 0:00:00.526819
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.510960 Min: 0:00:00.503869 Max: 0:00:00.522315
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.251378 Min: 0:00:00.246866 Max: 0:00:00.303383
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.529910 Min: 0:00:00.521074 Max: 0:00:00.596735
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.525699 Min: 0:00:00.516668 Max: 0:00:00.596678
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.253959 Min: 0:00:00.246717 Max: 0:00:00.316101
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.518736 Min: 0:00:00.512864 Max: 0:00:00.538839
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.514332 Min: 0:00:00.507810 Max: 0:00:00.521378
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.253252 Min: 0:00:00.248086 Max: 0:00:00.355445
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.547182 Min: 0:00:00.538335 Max: 0:00:00.599083
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.541867 Min: 0:00:00.532159 Max: 0:00:00.572193
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.257788 Min: 0:00:00.248459 Max: 0:00:00.469712
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.567738 Min: 0:00:00.560448 Max: 0:00:00.577117
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.564010 Min: 0:00:00.556407 Max: 0:00:00.584363
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.259379 Min: 0:00:00.247110 Max: 0:00:00.644029
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:00.530274 Min: 0:00:00.522906 Max: 0:00:00.569211
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:00.526057 Min: 0:00:00.518378 Max: 0:00:00.558648
+-----------------------------------------
+
+
+********************************************************************************
+* *
+* This is the automated job summary provided by DKRZ. *
+* If you encounter problems, need assistance or have any suggestion, please *
+* write an email to *
+* *
+* -- beratung@dkrz.de -- *
+* *
+* We hope you enjoyed the DKRZ supercomputer MISTRAL ... *
+*
+* JobID : 32394761
+* JobName : benchmark_2d.run
+* Account : bb1152
+* User : b380459 (24400), bb1018 (1306)
+* Partition : compute
+* QOS : normal
+* Nodelist : m10967 (1)
+* AvgCommBlocking : 0.0000 (in [0,4] less is better)
+* Submit date : 2021-09-17T09:21:55
+* Start time : 2021-09-17T09:21:55
+* End time : 2021-09-17T09:38:05
+* Elapsed time : 00:16:10 (Timelimit=08:00:00)
+* Command : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks/
+* benchmark_2d.run
+* WorkDir : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks
+*
+* StepID | JobName NodeHours MaxRSS [Byte] (@task) ReqCPUFreq [Hz]
+* ------------------------------------------------------------------------------
+* batch | batch 0.27
+* ------------------------------------------------------------------------------
+
diff --git a/benchmarks/LOG.benchmark_2d.run.32398022.o_keep4reference b/benchmarks/LOG.benchmark_2d.run.32398022.o_keep4reference
new file mode 100644
index 0000000..5ccbd32
--- /dev/null
+++ b/benchmarks/LOG.benchmark_2d.run.32398022.o_keep4reference
@@ -0,0 +1,183 @@
+Working with /pf/b/b380459/conda-envs/Nawdex-Hackathon/bin/python3.8
+
+-----------------------------------------
+Working on resolution of R10000m
+Start cell: 264617 Search radius: 851
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:01.122533 Min: 0:00:01.082971 Max: 0:00:01.180265
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.028973 Min: 0:00:02.949858 Max: 0:00:03.209488
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:02.980422 Min: 0:00:02.907899 Max: 0:00:03.215241
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R10000m
+Start cell: 264617 Search radius: 851
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.980489 Min: 0:00:00.959198 Max: 0:00:01.008540
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.217155 Min: 0:00:03.184321 Max: 0:00:03.245573
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:03.176766 Min: 0:00:03.136307 Max: 0:00:03.237251
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R10000m
+Start cell: 264617 Search radius: 851
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.976083 Min: 0:00:00.957103 Max: 0:00:01.002795
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.211835 Min: 0:00:02.949531 Max: 0:00:03.376240
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:03.164140 Min: 0:00:02.908105 Max: 0:00:03.301057
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R10000m
+Start cell: 264617 Search radius: 851
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.976190 Min: 0:00:00.952402 Max: 0:00:01.178692
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.177969 Min: 0:00:03.134447 Max: 0:00:03.210132
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:03.139672 Min: 0:00:03.096136 Max: 0:00:03.231999
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R10000m
+Start cell: 264617 Search radius: 851
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.971076 Min: 0:00:00.954440 Max: 0:00:00.997154
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.040224 Min: 0:00:03.011487 Max: 0:00:03.112464
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:02.993555 Min: 0:00:02.967547 Max: 0:00:03.066382
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R10000m
+Start cell: 264617 Search radius: 851
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.969204 Min: 0:00:00.950165 Max: 0:00:01.007214
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.125401 Min: 0:00:03.101272 Max: 0:00:03.226769
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:03.078770 Min: 0:00:03.052064 Max: 0:00:03.102985
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R10000m
+Start cell: 264617 Search radius: 851
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.973069 Min: 0:00:00.951478 Max: 0:00:01.173814
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.034643 Min: 0:00:03.002625 Max: 0:00:03.100835
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:02.988785 Min: 0:00:02.958435 Max: 0:00:03.034659
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R10000m
+Start cell: 264617 Search radius: 851
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.968911 Min: 0:00:00.951157 Max: 0:00:00.994571
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.212755 Min: 0:00:03.181001 Max: 0:00:03.266346
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:03.164812 Min: 0:00:03.135873 Max: 0:00:03.201813
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R10000m
+Start cell: 264617 Search radius: 851
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.970356 Min: 0:00:00.952445 Max: 0:00:01.004632
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.033230 Min: 0:00:03.010075 Max: 0:00:03.069333
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:02.987272 Min: 0:00:02.961729 Max: 0:00:03.012065
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R10000m
+Start cell: 264617 Search radius: 851
+
+Time to read in 1 time step of data, including moving it onto the 3d cubulated grid; done for 48 time steps
+Mean: 0:00:00.968900 Min: 0:00:00.953680 Max: 0:00:00.995985
+
+Time to do 2d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.242496 Min: 0:00:03.196506 Max: 0:00:03.300305
+
+Time to do 2d connected component labeling with edge connectivity for 1 time step: done for 48 time steps
+Mean: 0:00:03.195363 Min: 0:00:03.160038 Max: 0:00:03.239219
+-----------------------------------------
+
+
+********************************************************************************
+* *
+* This is the automated job summary provided by DKRZ. *
+* If you encounter problems, need assistance or have any suggestion, please *
+* write an email to *
+* *
+* -- beratung@dkrz.de -- *
+* *
+* We hope you enjoyed the DKRZ supercomputer MISTRAL ... *
+*
+* JobID : 32398022
+* JobName : benchmark_2d.run
+* Account : bb1152
+* User : b380459 (24400), bb1018 (1306)
+* Partition : compute
+* QOS : normal
+* Nodelist : m10393 (1)
+* AvgCommBlocking : 0.0000 (in [0,4] less is better)
+* Submit date : 2021-09-17T15:45:56
+* Start time : 2021-09-17T15:46:08
+* End time : 2021-09-17T16:46:21
+* Elapsed time : 01:00:13 (Timelimit=08:00:00)
+* Command : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks/
+* benchmark_2d.run
+* WorkDir : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks
+*
+* StepID | JobName NodeHours MaxRSS [Byte] (@task) ReqCPUFreq [Hz]
+* ------------------------------------------------------------------------------
+* batch | batch 1.0
+* ------------------------------------------------------------------------------
+
diff --git a/benchmarks/LOG.benchmark_3d.run.32394974.o_keep4reference b/benchmarks/LOG.benchmark_3d.run.32394974.o_keep4reference
new file mode 100644
index 0000000..65482bf
--- /dev/null
+++ b/benchmarks/LOG.benchmark_3d.run.32394974.o_keep4reference
@@ -0,0 +1,333 @@
+Working with /pf/b/b380459/conda-envs/Nawdex-Hackathon/bin/python3.8
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:00.547920 Min: 0:00:00.521746 Max: 0:00:00.812113
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:02.253553 Min: 0:00:01.900518 Max: 0:00:09.153602
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.043660 Min: 0:00:02.570211 Max: 0:00:03.513131
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:00.505552 Min: 0:00:00.495893 Max: 0:00:00.536224
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:02.177766 Min: 0:00:01.987205 Max: 0:00:03.866668
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.040872 Min: 0:00:02.663239 Max: 0:00:03.367700
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:00.501560 Min: 0:00:00.497747 Max: 0:00:00.527050
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:02.226258 Min: 0:00:01.999319 Max: 0:00:02.707778
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.165396 Min: 0:00:02.700684 Max: 0:00:03.677924
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:00.503134 Min: 0:00:00.497702 Max: 0:00:00.571902
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:02.296571 Min: 0:00:02.101828 Max: 0:00:03.036468
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.179466 Min: 0:00:02.729514 Max: 0:00:03.641466
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:00.508664 Min: 0:00:00.498304 Max: 0:00:00.710148
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:02.412688 Min: 0:00:02.178746 Max: 0:00:03.006521
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.410031 Min: 0:00:02.911633 Max: 0:00:03.924547
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:00.509750 Min: 0:00:00.501357 Max: 0:00:00.547547
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:02.058428 Min: 0:00:01.886932 Max: 0:00:02.692476
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:02.910747 Min: 0:00:02.471161 Max: 0:00:03.341449
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:00.503007 Min: 0:00:00.497403 Max: 0:00:00.546580
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:02.198209 Min: 0:00:01.980264 Max: 0:00:02.889980
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.074715 Min: 0:00:02.642041 Max: 0:00:03.495916
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:00.502630 Min: 0:00:00.498475 Max: 0:00:00.547539
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:02.246103 Min: 0:00:02.006156 Max: 0:00:02.836574
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.216582 Min: 0:00:02.730957 Max: 0:00:03.698317
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:00.529665 Min: 0:00:00.519062 Max: 0:00:00.734195
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:02.367222 Min: 0:00:02.106152 Max: 0:00:03.095347
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:03.465130 Min: 0:00:02.901796 Max: 0:00:04.025593
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R80000m
+Start cell: 5570 Search radius: 104
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:00.501724 Min: 0:00:00.495631 Max: 0:00:00.532398
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:02.111408 Min: 0:00:01.956011 Max: 0:00:03.270615
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:02.979274 Min: 0:00:02.606359 Max: 0:00:03.391860
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:02.195352 Min: 0:00:02.114504 Max: 0:00:02.407121
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:11.316965 Min: 0:00:10.698491 Max: 0:00:12.459105
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:18.624973 Min: 0:00:16.556972 Max: 0:00:21.462922
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:02.008276 Min: 0:00:01.983720 Max: 0:00:02.230014
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:12.162376 Min: 0:00:11.523418 Max: 0:00:13.373402
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:20.190965 Min: 0:00:18.078734 Max: 0:00:22.927350
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:02.047022 Min: 0:00:01.982691 Max: 0:00:02.308734
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:12.946112 Min: 0:00:11.814331 Max: 0:00:14.295008
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:22.093137 Min: 0:00:19.645776 Max: 0:00:25.043956
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:02.029775 Min: 0:00:01.980258 Max: 0:00:02.309999
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:11.394544 Min: 0:00:10.770702 Max: 0:00:12.671147
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:18.653575 Min: 0:00:16.583412 Max: 0:00:21.019151
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:02.074734 Min: 0:00:02.033848 Max: 0:00:02.276020
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:11.766859 Min: 0:00:11.081453 Max: 0:00:13.041559
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:19.459896 Min: 0:00:17.301897 Max: 0:00:21.982608
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:02.019308 Min: 0:00:01.992588 Max: 0:00:02.260682
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:12.233045 Min: 0:00:11.586644 Max: 0:00:13.378630
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:20.298715 Min: 0:00:18.011464 Max: 0:00:23.015106
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:02.000010 Min: 0:00:01.977968 Max: 0:00:02.217223
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:12.442972 Min: 0:00:11.740573 Max: 0:00:13.576397
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:20.648605 Min: 0:00:18.292522 Max: 0:00:23.316816
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:02.017099 Min: 0:00:01.987846 Max: 0:00:02.226981
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:12.031495 Min: 0:00:11.376853 Max: 0:00:13.264922
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:19.807995 Min: 0:00:17.672700 Max: 0:00:22.254903
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:02.057529 Min: 0:00:02.035336 Max: 0:00:02.253611
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:11.809704 Min: 0:00:11.256231 Max: 0:00:13.133614
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:19.935506 Min: 0:00:17.742626 Max: 0:00:22.474842
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R40000m
+Start cell: 18494 Search radius: 210
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:02.124032 Min: 0:00:01.990088 Max: 0:00:02.554170
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:12.515024 Min: 0:00:11.087728 Max: 0:00:13.812997
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:00:20.732071 Min: 0:00:18.453473 Max: 0:00:23.434702
+-----------------------------------------
+
+
+********************************************************************************
+* *
+* This is the automated job summary provided by DKRZ. *
+* If you encounter problems, need assistance or have any suggestion, please *
+* write an email to *
+* *
+* -- beratung@dkrz.de -- *
+* *
+* We hope you enjoyed the DKRZ supercomputer MISTRAL ... *
+*
+* JobID : 32394974
+* JobName : benchmark_3d.run
+* Account : bb1152
+* User : b380459 (24400), bb1018 (1306)
+* Partition : compute
+* QOS : normal
+* Nodelist : m11354 (1)
+* AvgCommBlocking : 0.0000 (in [0,4] less is better)
+* Submit date : 2021-09-17T09:32:33
+* Start time : 2021-09-17T09:32:39
+* End time : 2021-09-17T15:01:48
+* Elapsed time : 05:29:09 (Timelimit=08:00:00)
+* Command : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks/
+* benchmark_3d.run
+* WorkDir : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks
+*
+* StepID | JobName NodeHours MaxRSS [Byte] (@task) ReqCPUFreq [Hz]
+* ------------------------------------------------------------------------------
+* batch | batch 5.5
+* ------------------------------------------------------------------------------
+
diff --git a/benchmarks/LOG.benchmark_3d.run.32398032.o_keep4reference b/benchmarks/LOG.benchmark_3d.run.32398032.o_keep4reference
new file mode 100644
index 0000000..5faba40
--- /dev/null
+++ b/benchmarks/LOG.benchmark_3d.run.32398032.o_keep4reference
@@ -0,0 +1,79 @@
+Working with /pf/b/b380459/conda-envs/Nawdex-Hackathon/bin/python3.8
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:10.008605 Min: 0:00:09.790976 Max: 0:00:11.921761
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:04.768806 Min: 0:01:00.422163 Max: 0:01:17.948993
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:51.919203 Min: 0:01:40.373851 Max: 0:02:04.333835
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:09.432662 Min: 0:00:09.215789 Max: 0:00:10.819003
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:01.446904 Min: 0:00:57.166310 Max: 0:01:09.574191
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:45.296409 Min: 0:01:34.062472 Max: 0:01:56.076570
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:09.555653 Min: 0:00:09.242180 Max: 0:00:12.821637
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:01.570400 Min: 0:00:57.357266 Max: 0:01:11.275231
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:45.399674 Min: 0:01:34.437822 Max: 0:01:57.540696
+-----------------------------------------
+
+slurmstepd: error: *** JOB 32398032 ON m10067 CANCELLED AT 2021-09-17T23:46:52 DUE TO TIME LIMIT ***
+
+********************************************************************************
+* *
+* This is the automated job summary provided by DKRZ. *
+* If you encounter problems, need assistance or have any suggestion, please *
+* write an email to *
+* *
+* -- beratung@dkrz.de -- *
+* *
+* We hope you enjoyed the DKRZ supercomputer MISTRAL ... *
+*
+* JobID : 32398032
+* JobName : benchmark_3d.run
+* Account : bb1152
+* User : b380459 (24400), bb1018 (1306)
+* Partition : compute
+* QOS : normal
+* Nodelist : m10067 (1)
+* AvgCommBlocking : 0.0000 (in [0,4] less is better)
+* Submit date : 2021-09-17T15:46:28
+* Start time : 2021-09-17T15:46:28
+* End time : 2021-09-17T23:46:52
+* Elapsed time : 08:00:24 (Timelimit=08:00:00)
+* Command : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks/
+* benchmark_3d.run
+* WorkDir : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks
+*
+* StepID | JobName NodeHours MaxRSS [Byte] (@task) ReqCPUFreq [Hz]
+* ------------------------------------------------------------------------------
+* batch | batch 8.0
+* ------------------------------------------------------------------------------
+
diff --git a/benchmarks/LOG.benchmark_3d.run.32401555.o_keep4reference b/benchmarks/LOG.benchmark_3d.run.32401555.o_keep4reference
new file mode 100644
index 0000000..856f328
--- /dev/null
+++ b/benchmarks/LOG.benchmark_3d.run.32401555.o_keep4reference
@@ -0,0 +1,79 @@
+Working with /pf/b/b380459/conda-envs/Nawdex-Hackathon/bin/python3.8
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:09.360930 Min: 0:00:09.207526 Max: 0:00:11.075794
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:01.338977 Min: 0:00:57.205782 Max: 0:01:09.585245
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:46.178032 Min: 0:01:35.034355 Max: 0:01:56.753805
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:09.445592 Min: 0:00:09.224632 Max: 0:00:11.580352
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:02.959299 Min: 0:00:58.846526 Max: 0:01:10.498983
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:48.001010 Min: 0:01:37.260396 Max: 0:02:00.315408
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:09.299384 Min: 0:00:09.027239 Max: 0:00:10.891607
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:03.690287 Min: 0:00:59.287796 Max: 0:01:12.777613
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:50.097236 Min: 0:01:38.366525 Max: 0:02:04.419237
+-----------------------------------------
+
+slurmstepd: error: *** JOB 32401555 ON m10067 CANCELLED AT 2021-09-18T07:57:12 DUE TO TIME LIMIT ***
+
+********************************************************************************
+* *
+* This is the automated job summary provided by DKRZ. *
+* If you encounter problems, need assistance or have any suggestion, please *
+* write an email to *
+* *
+* -- beratung@dkrz.de -- *
+* *
+* We hope you enjoyed the DKRZ supercomputer MISTRAL ... *
+*
+* JobID : 32401555
+* JobName : benchmark_3d.run
+* Account : bb1152
+* User : b380459 (24400), bb1018 (1306)
+* Partition : compute
+* QOS : normal
+* Nodelist : m10067 (1)
+* AvgCommBlocking : 0.0000 (in [0,4] less is better)
+* Submit date : 2021-09-17T23:56:41
+* Start time : 2021-09-17T23:56:42
+* End time : 2021-09-18T07:57:12
+* Elapsed time : 08:00:30 (Timelimit=08:00:00)
+* Command : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks/
+* benchmark_3d.run
+* WorkDir : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks
+*
+* StepID | JobName NodeHours MaxRSS [Byte] (@task) ReqCPUFreq [Hz]
+* ------------------------------------------------------------------------------
+* batch | batch 8.0
+* ------------------------------------------------------------------------------
+
diff --git a/benchmarks/LOG.benchmark_3d.run.32401557.o_keep4reference b/benchmarks/LOG.benchmark_3d.run.32401557.o_keep4reference
new file mode 100644
index 0000000..ade1d5d
--- /dev/null
+++ b/benchmarks/LOG.benchmark_3d.run.32401557.o_keep4reference
@@ -0,0 +1,79 @@
+Working with /pf/b/b380459/conda-envs/Nawdex-Hackathon/bin/python3.8
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:09.634852 Min: 0:00:09.047769 Max: 0:00:10.953744
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:04.435747 Min: 0:00:59.993378 Max: 0:01:08.937020
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:52.532289 Min: 0:01:41.046803 Max: 0:02:05.321025
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:09.384456 Min: 0:00:09.069670 Max: 0:00:11.377304
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:00.572237 Min: 0:00:56.528654 Max: 0:01:07.353440
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:43.948019 Min: 0:01:32.965232 Max: 0:01:55.618110
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R20000m
+Start cell: 69220 Search radius: 423
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid; done for 48 time steps
+Mean: 0:00:09.290946 Min: 0:00:09.027348 Max: 0:00:10.849972
+
+Time to do 3d connected component labeling with vertex connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:00.767570 Min: 0:00:57.012836 Max: 0:01:07.688275
+
+Time to do 3d connected component labeling with edge connectivity for 1 time step; done for 48 time steps
+Mean: 0:01:44.522334 Min: 0:01:34.334333 Max: 0:01:55.514610
+-----------------------------------------
+
+slurmstepd: error: *** JOB 32401557 ON m10593 CANCELLED AT 2021-09-18T07:57:44 DUE TO TIME LIMIT ***
+
+********************************************************************************
+* *
+* This is the automated job summary provided by DKRZ. *
+* If you encounter problems, need assistance or have any suggestion, please *
+* write an email to *
+* *
+* -- beratung@dkrz.de -- *
+* *
+* We hope you enjoyed the DKRZ supercomputer MISTRAL ... *
+*
+* JobID : 32401557
+* JobName : benchmark_3d.run
+* Account : bb1152
+* User : b380459 (24400), bb1018 (1306)
+* Partition : compute
+* QOS : normal
+* Nodelist : m10593 (1)
+* AvgCommBlocking : 0.0000 (in [0,4] less is better)
+* Submit date : 2021-09-17T23:56:53
+* Start time : 2021-09-17T23:57:24
+* End time : 2021-09-18T07:57:44
+* Elapsed time : 08:00:20 (Timelimit=08:00:00)
+* Command : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks/
+* benchmark_3d.run
+* WorkDir : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks
+*
+* StepID | JobName NodeHours MaxRSS [Byte] (@task) ReqCPUFreq [Hz]
+* ------------------------------------------------------------------------------
+* batch | batch 8.0
+* ------------------------------------------------------------------------------
+
diff --git a/benchmarks/LOG.benchmark_3d_R10000m-10timesteps.run.32408241.o_keep4reference b/benchmarks/LOG.benchmark_3d_R10000m-10timesteps.run.32408241.o_keep4reference
new file mode 100644
index 0000000..e7287a1
--- /dev/null
+++ b/benchmarks/LOG.benchmark_3d_R10000m-10timesteps.run.32408241.o_keep4reference
@@ -0,0 +1,46 @@
+Working with /pf/b/b380459/conda-envs/Nawdex-Hackathon/bin/python3.8
+
+-----------------------------------------
+Working on resolution of R10000m
+Start cell: 264617 Search radius: 851
+
+Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid (done for only 10 time steps)
+Mean: 0:00:41.651714 Min: 0:00:40.975602 Max: 0:00:43.392161
+Time to do 3d connected component labeling with vertex connectivity for 1 time step (done for only 10 time steps)
+Mean: 0:05:25.646071 Min: 0:05:09.921350 Max: 0:05:50.240210
+Time to do 3d connected component labeling with edge connectivity for 1 time step (done for only 10 time steps)
+Mean: 0:08:39.642932 Min: 0:08:04.947828 Max: 0:09:20.541529
+-----------------------------------------
+
+
+********************************************************************************
+* *
+* This is the automated job summary provided by DKRZ. *
+* If you encounter problems, need assistance or have any suggestion, please *
+* write an email to *
+* *
+* -- beratung@dkrz.de -- *
+* *
+* We hope you enjoyed the DKRZ supercomputer MISTRAL ... *
+*
+* JobID : 32408241
+* JobName : benchmark_3d_R10000m-10timesteps.run
+* Account : bb1152
+* User : b380459 (24400), bb1018 (1306)
+* Partition : compute
+* QOS : normal
+* Nodelist : m11205 (1)
+* AvgCommBlocking : 0.0000 (in [0,4] less is better)
+* Submit date : 2021-09-19T08:06:09
+* Start time : 2021-09-19T08:06:09
+* End time : 2021-09-19T10:49:41
+* Elapsed time : 02:43:32 (Timelimit=08:00:00)
+* Command : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks/
+* benchmark_3d_R10000m-10timesteps.run
+* WorkDir : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks
+*
+* StepID | JobName NodeHours MaxRSS [Byte] (@task) ReqCPUFreq [Hz]
+* ------------------------------------------------------------------------------
+* batch | batch 2.7
+* ------------------------------------------------------------------------------
+
diff --git a/benchmarks/LOG.benchmark_cubulation.run.32394751.o_keep4reference b/benchmarks/LOG.benchmark_cubulation.run.32394751.o_keep4reference
new file mode 100644
index 0000000..3f03b1a
--- /dev/null
+++ b/benchmarks/LOG.benchmark_cubulation.run.32394751.o_keep4reference
@@ -0,0 +1,50 @@
+Working with /pf/b/b380459/conda-envs/Nawdex-Hackathon/bin/python3.8
+
+-----------------------------------------
+Working on resolution of R10000m
+Start cell: 264617 Search radius: 851 Save cubulation: 1
+Time to read the grid: 0:00:00.728484
+Time to compute cubulation: 2:54:14.426374
+-----------------------------------------
+
+
+-----------------------------------------
+Working on resolution of R10000m
+Start cell: 264617 Search radius: 851 Save cubulation: 1
+Time to read the grid: 0:00:00.467574
+Time to compute cubulation: 3:07:35.355663
+-----------------------------------------
+
+slurmstepd: error: *** JOB 32394751 ON m10179 CANCELLED AT 2021-09-17T17:16:09 DUE TO TIME LIMIT ***
+
+********************************************************************************
+* *
+* This is the automated job summary provided by DKRZ. *
+* If you encounter problems, need assistance or have any suggestion, please *
+* write an email to *
+* *
+* -- beratung@dkrz.de -- *
+* *
+* We hope you enjoyed the DKRZ supercomputer MISTRAL ... *
+*
+* JobID : 32394751
+* JobName : benchmark_cubulation.run
+* Account : bb1152
+* User : b380459 (24400), bb1018 (1306)
+* Partition : compute
+* QOS : normal
+* Nodelist : m10179 (1)
+* AvgCommBlocking : 0.0000 (in [0,4] less is better)
+* Submit date : 2021-09-17T09:15:45
+* Start time : 2021-09-17T09:15:45
+* End time : 2021-09-17T17:16:09
+* Elapsed time : 08:00:24 (Timelimit=08:00:00)
+* Command : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks/
+* benchmark_cubulation.run
+* WorkDir : /mnt/lustre01/pf/b/b380459/BigDataClouds/tricco/benchmarks
+*
+* StepID | JobName NodeHours MaxRSS [Byte] (@task) ReqCPUFreq [Hz]
+* ------------------------------------------------------------------------------
+* batch | batch 8.0
+* ------------------------------------------------------------------------------
+
diff --git a/benchmarks/benchmark_2d.py b/benchmarks/benchmark_2d.py
index 7e45a2a..d79039c 100644
--- a/benchmarks/benchmark_2d.py
+++ b/benchmarks/benchmark_2d.py
@@ -18,6 +18,7 @@ import datetime
print(' ')
print('-----------------------------------------')
print('Working on resolution of', resol)
+print('Start cell:', startcell, 'Search radius:', searchrad)
# load previously computed cubulation
import numpy as np
diff --git a/benchmarks/benchmark_2d.run b/benchmarks/benchmark_2d.run
index 14d0cea..ffbd087 100755
--- a/benchmarks/benchmark_2d.run
+++ b/benchmarks/benchmark_2d.run
@@ -17,18 +17,18 @@ cd /pf/b/b380459/BigDataClouds/tricco/benchmarks
MYPYTHON="/pf/b/b380459/conda-envs/Nawdex-Hackathon/bin/python3.8"
echo "Working with" ${MYPYTHON}
-for i in {1..10}; do
- $MYPYTHON benchmark_2d.py R80000m 5738 102
-done
+#for i in {1..10}; do
+# $MYPYTHON benchmark_2d.py R80000m 5570 104
+#done
-for i in {1..10}; do
- $MYPYTHON benchmark_2d.py R40000m 18538 230
-done
+#for i in {1..10}; do
+# $MYPYTHON benchmark_2d.py R40000m 18494 210
+#done
-for i in {1..10}; do
- $MYPYTHON benchmark_2d.py R20000m 69309 460
-done
+#for i in {1..10}; do
+# $MYPYTHON benchmark_2d.py R20000m 69220 423
+#done
for i in {1..10}; do
- $MYPYTHON benchmark_2d.py R10000m 264792 2000
+ $MYPYTHON benchmark_2d.py R10000m 264617 851
done
diff --git a/benchmarks/benchmark_3d.py b/benchmarks/benchmark_3d.py
index 7687eb8..d9cca02 100644
--- a/benchmarks/benchmark_3d.py
+++ b/benchmarks/benchmark_3d.py
@@ -18,6 +18,7 @@ import datetime
print(' ')
print('-----------------------------------------')
print('Working on resolution of', resol)
+print('Start cell:', startcell, 'Search radius:', searchrad)
# load previously computed cubulation
import numpy as np
@@ -40,7 +41,7 @@ datafile={'R80000m': 'nawdexnwp-80km-mis-0001_2016092200_3dcloud_DOM01_ML_',
dtime_dat = list()
dtime_ver = list()
dtime_edg = list()
-# loop over 1 day of 30-min output data --> 48 timesteps
+# loop over 2 days of 1-hour output data --> 48 timesteps
for time in range(10,59):
# read in data
begin_time = datetime.datetime.now()
diff --git a/benchmarks/benchmark_3d.run b/benchmarks/benchmark_3d.run
index 85bfc33..e70abf4 100755
--- a/benchmarks/benchmark_3d.run
+++ b/benchmarks/benchmark_3d.run
@@ -18,17 +18,17 @@ MYPYTHON="/pf/b/b380459/conda-envs/Nawdex-Hackathon/bin/python3.8"
echo "Working with" ${MYPYTHON}
#for i in {1..10}; do
-# $MYPYTHON benchmark_3d.py R80000m 5738 102
+# $MYPYTHON benchmark_3d.py R80000m 5570 104
#done
#for i in {1..10}; do
-# $MYPYTHON benchmark_3d.py R40000m 18538 230
-#done
-
-#for i in {1..10}; do
-# $MYPYTHON benchmark_3d.py R20000m 69309 460
+# $MYPYTHON benchmark_3d.py R40000m 18494 210
#done
for i in {1..10}; do
- $MYPYTHON benchmark_3d.py R10000m 264792 2000
+ $MYPYTHON benchmark_3d.py R20000m 69220 423
done
+
+#for i in {1..1}; do
+# $MYPYTHON benchmark_3d.py R10000m 264617 851
+#done
diff --git a/benchmarks/benchmark_3d_R10000m-10timesteps.py b/benchmarks/benchmark_3d_R10000m-10timesteps.py
new file mode 100644
index 0000000..cb3315f
--- /dev/null
+++ b/benchmarks/benchmark_3d_R10000m-10timesteps.py
@@ -0,0 +1,75 @@
+# Perform benchmarking of 3d cloud data given a previously computed cubulation
+
+# special case for resolution R10000m, which is very slow and so only 10 time steps are analyzed
+
+# parse command line parameters
+import sys
+resol = sys.argv[1]
+startcell = int(sys.argv[2])
+searchrad = int(sys.argv[3])
+
+# gridfile including path
+gridfile = '/work/bb1018/b380459/NAWDEX/grids/icon-grid_nawdex_78w40e23n80n_'+resol+'.nc'
+
+# load other needed packages
+sys.path.append('/pf/b/b380459/connected-components-3d/')
+sys.path.append('/pf/b/b380459/tricco/')
+import tricco
+import datetime
+
+print(' ')
+print('-----------------------------------------')
+print('Working on resolution of', resol)
+print('Start cell:', startcell, 'Search radius:', searchrad)
+
+# load previously computed cubulation
+import numpy as np
+cubulpath = '/scratch/b/b380459/tricco_output/'
+cubulfile = cubulpath+'/icon-grid_nawdex_78w40e23n80n_'+resol+'_cubulation_start'+str(startcell)+'_radius'+str(searchrad)+'.npy'
+cubulation = np.load(cubulfile, allow_pickle=True)
+
+# read in cloud data
+
+# cloud file depends on resolution
+datapath={'R80000m': '/work/bb1018/b380459/NAWDEX/ICON_OUTPUT_NWP/nawdexnwp-80km-mis-0001/',
+ 'R40000m': '/work/bb1018/b380459/NAWDEX/ICON_OUTPUT_NWP/nawdexnwp-40km-mis-0001/',
+ 'R20000m': '/work/bb1018/b380459/NAWDEX/ICON_OUTPUT_NWP/nawdexnwp-20km-mis-0001/',
+ 'R10000m': '/work/bb1018/b380459/NAWDEX/ICON_OUTPUT_NWP/nawdexnwp-10km-mis-0001/'}
+datafile={'R80000m': 'nawdexnwp-80km-mis-0001_2016092200_3dcloud_DOM01_ML_',
+ 'R40000m': 'nawdexnwp-40km-mis-0001_2016092200_3dcloud_DOM01_ML_',
+ 'R20000m': 'nawdexnwp-20km-mis-0001_2016092200_3dcloud_DOM01_ML_',
+ 'R10000m': 'nawdexnwp-10km-mis-0001_2016092200_3dcloud_DOM01_ML_'}
+
+dtime_dat = list()
+dtime_ver = list()
+dtime_edg = list()
+# consider only 10 time steps
+for time in range(10,21):
+ # read in data
+ begin_time = datetime.datetime.now()
+ field, field_cube = tricco.prepare_field_lev(model='ICON', path=datapath[resol],
+ file=datafile[resol]+'00'+str(time)+'.nc',
+ var='clc', threshold=85.0, cubulation=cubulation)
+ end_time = datetime.datetime.now()
+ dtime_dat.append(end_time-begin_time)
+ # perform connected component analysis for vertex connectivity
+ begin_time = datetime.datetime.now()
+ _ = tricco.compute_connected_components_3d(cubulation, field_cube, connectivity = 'vertex')
+ end_time = datetime.datetime.now()
+ dtime_ver.append(end_time-begin_time)
+ # perform connected component analysis for edge connectivity
+ begin_time = datetime.datetime.now()
+ _ = tricco.compute_connected_components_3d(cubulation, field_cube, connectivity = 'edge')
+ end_time = datetime.datetime.now()
+ dtime_edg.append(end_time-begin_time)
+
+print(' ')
+print('Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid (done for only 10 time steps)')
+print('Mean:', np.mean(dtime_dat), 'Min:', np.min(dtime_dat), 'Max:', np.max(dtime_dat))
+print('Time to do 3d connected component labeling with vertex connectivity for 1 time step (done for only 10 time steps)')
+print('Mean:', np.mean(dtime_ver), 'Min:', np.min(dtime_ver), 'Max:', np.max(dtime_ver))
+print('Time to do 3d connected component labeling with edge connectivity for 1 time step (done for only 10 time steps)')
+print('Mean:', np.mean(dtime_edg), 'Min:', np.min(dtime_edg), 'Max:', np.max(dtime_edg))
+
+print('-----------------------------------------')
+print(' ')
diff --git a/benchmarks/benchmark_3d_R10000m-10timesteps.run b/benchmarks/benchmark_3d_R10000m-10timesteps.run
new file mode 100755
index 0000000..c40fff5
--- /dev/null
+++ b/benchmarks/benchmark_3d_R10000m-10timesteps.run
@@ -0,0 +1,21 @@
+#!/bin/bash
+#=============================================================================
+# mistral batch job parameters
+#-----------------------------------------------------------------------------
+#SBATCH --account=bb1152
+#SBATCH --job-name=benchmark_3d_R10000m-10timesteps.run
+#SBATCH --partition=compute
+#SBATCH --nodes=1
+#SBATCH --threads-per-core=1
+#SBATCH --output=/pf/b/b380459/BigDataClouds/tricco/benchmarks/LOG.benchmark_3d_R10000m-10timesteps.run.%j.o
+#SBATCH --error=/pf/b/b380459/BigDataClouds/tricco/benchmarks/LOG.benchmark_3d_R10000m-10timesteps.run.%j.o
+#SBATCH --exclusive
+#SBATCH --time=08:00:00
+
+cd /pf/b/b380459/BigDataClouds/tricco/benchmarks
+
+MYPYTHON="/pf/b/b380459/conda-envs/Nawdex-Hackathon/bin/python3.8"
+echo "Working with" ${MYPYTHON}
+
+$MYPYTHON benchmark_3d_R10000m-10timesteps.py R10000m 264617 851
+
diff --git a/benchmarks/benchmark_3d_R10000m-singletimestep.py b/benchmarks/benchmark_3d_R10000m-singletimestep.py
new file mode 100644
index 0000000..91c2dd4
--- /dev/null
+++ b/benchmarks/benchmark_3d_R10000m-singletimestep.py
@@ -0,0 +1,72 @@
+# Perform benchmarking of 3d cloud data given a previously computed cubulation
+
+# special case for resolution R10000m, which is very slow and so only 1 time step is analyzed
+
+# parse command line parameters
+import sys
+resol = sys.argv[1]
+startcell = int(sys.argv[2])
+searchrad = int(sys.argv[3])
+
+# gridfile including path
+gridfile = '/work/bb1018/b380459/NAWDEX/grids/icon-grid_nawdex_78w40e23n80n_'+resol+'.nc'
+
+# load other needed packages
+sys.path.append('/pf/b/b380459/connected-components-3d/')
+sys.path.append('/pf/b/b380459/tricco/')
+import tricco
+import datetime
+
+print(' ')
+print('-----------------------------------------')
+print('Working on resolution of', resol)
+print('Start cell:', startcell, 'Search radius:', searchrad)
+
+# load previously computed cubulation
+import numpy as np
+cubulpath = '/scratch/b/b380459/tricco_output/'
+cubulfile = cubulpath+'/icon-grid_nawdex_78w40e23n80n_'+resol+'_cubulation_start'+str(startcell)+'_radius'+str(searchrad)+'.npy'
+cubulation = np.load(cubulfile, allow_pickle=True)
+
+# read in cloud data
+
+# cloud file depends on resolution
+datapath={'R80000m': '/work/bb1018/b380459/NAWDEX/ICON_OUTPUT_NWP/nawdexnwp-80km-mis-0001/',
+ 'R40000m': '/work/bb1018/b380459/NAWDEX/ICON_OUTPUT_NWP/nawdexnwp-40km-mis-0001/',
+ 'R20000m': '/work/bb1018/b380459/NAWDEX/ICON_OUTPUT_NWP/nawdexnwp-20km-mis-0001/',
+ 'R10000m': '/work/bb1018/b380459/NAWDEX/ICON_OUTPUT_NWP/nawdexnwp-10km-mis-0001/'}
+datafile={'R80000m': 'nawdexnwp-80km-mis-0001_2016092200_3dcloud_DOM01_ML_',
+ 'R40000m': 'nawdexnwp-40km-mis-0001_2016092200_3dcloud_DOM01_ML_',
+ 'R20000m': 'nawdexnwp-20km-mis-0001_2016092200_3dcloud_DOM01_ML_',
+ 'R10000m': 'nawdexnwp-10km-mis-0001_2016092200_3dcloud_DOM01_ML_'}
+
+dtime_dat = list()
+dtime_ver = list()
+dtime_edg = list()
+# consider only one time step
+for time in range(10,11):
+ # read in data
+ begin_time = datetime.datetime.now()
+ field, field_cube = tricco.prepare_field_lev(model='ICON', path=datapath[resol],
+ file=datafile[resol]+'00'+str(time)+'.nc',
+ var='clc', threshold=85.0, cubulation=cubulation)
+ end_time = datetime.datetime.now()
+ dtime_dat.append(end_time-begin_time)
+ # perform connected component analysis for vertex connectivity
+ begin_time = datetime.datetime.now()
+ _ = tricco.compute_connected_components_3d(cubulation, field_cube, connectivity = 'vertex')
+ end_time = datetime.datetime.now()
+ dtime_ver.append(end_time-begin_time)
+ # perform connected component analysis for edge connectivity
+ begin_time = datetime.datetime.now()
+ _ = tricco.compute_connected_components_3d(cubulation, field_cube, connectivity = 'edge')
+ end_time = datetime.datetime.now()
+ dtime_edg.append(end_time-begin_time)
+
+print(' ')
+print('Time to read in 1 time step of data, including moving it onto the 3d x lev cubulated grid (done for only 1 time step):' , dtime_dat)
+print('Time to do 3d connected component labeling with vertex connectivity for 1 time step (done for only 1 time step):', dtime_ver)
+print('Time to do 3d connected component labeling with edge connectivity for 1 time step (done for only 1 time step):', dtime_edg)
+
+print('-----------------------------------------')
+print(' ')
diff --git a/benchmarks/benchmark_3d_R10000m-singletimestep.run b/benchmarks/benchmark_3d_R10000m-singletimestep.run
new file mode 100755
index 0000000..a77418d
--- /dev/null
+++ b/benchmarks/benchmark_3d_R10000m-singletimestep.run
@@ -0,0 +1,21 @@
+#!/bin/bash
+#=============================================================================
+# mistral batch job parameters
+#-----------------------------------------------------------------------------
+#SBATCH --account=bb1152
+#SBATCH --job-name=benchmark_3d_R10000m-singletimestep.run
+#SBATCH --partition=compute
+#SBATCH --nodes=1
+#SBATCH --threads-per-core=1
+#SBATCH --output=/pf/b/b380459/BigDataClouds/tricco/benchmarks/LOG.benchmark_3d_R10000m-singletimestep.run.%j.o
+#SBATCH --error=/pf/b/b380459/BigDataClouds/tricco/benchmarks/LOG.benchmark_3d_R10000m-singletimestep.run.%j.o
+#SBATCH --exclusive
+#SBATCH --time=08:00:00
+
+cd /pf/b/b380459/BigDataClouds/tricco/benchmarks
+
+MYPYTHON="/pf/b/b380459/conda-envs/Nawdex-Hackathon/bin/python3.8"
+echo "Working with" ${MYPYTHON}
+
+$MYPYTHON benchmark_3d_R10000m-singletimestep.py R10000m 264617 851
+
diff --git a/benchmarks/benchmark_cubulation.run b/benchmarks/benchmark_cubulation.run
index 9e0da59..0a21a23 100755
--- a/benchmarks/benchmark_cubulation.run
+++ b/benchmarks/benchmark_cubulation.run
@@ -17,20 +17,24 @@ cd /pf/b/b380459/BigDataClouds/tricco/benchmarks
MYPYTHON="/pf/b/b380459/conda-envs/Nawdex-Hackathon/bin/python3.8"
echo "Working with" ${MYPYTHON}
-for i in {1..10}; do
-# $MYPYTHON benchmark_cubulation.py R80000m 5738 102 1
- $MYPYTHON benchmark_cubulation.py R80000m 5568 200 1
-done
+# parameters given to benchmark_cubulation.py:
+# resolution, e.g., R80000m
+# start cell
+# radius
+# save cubulation by setting 4ht parameter to 1
-for i in {1..10}; do
-# $MYPYTHON benchmark_cubulation.py R40000m 18538 230 1
- $MYPYTHON benchmark_cubulation.py R40000m 18493 400 1
-done
+#for i in {1..1}; do
+# $MYPYTHON benchmark_cubulation.py R80000m 5570 104 1
+#done
-#for i in {1..10}; do
-# $MYPYTHON benchmark_cubulation.py R20000m 69309 460 1
+#for i in {1..1}; do
+# $MYPYTHON benchmark_cubulation.py R40000m 18494 210 1
#done
-#for i in {1..10}; do
-# $MYPYTHON benchmark_cubulation.py R10000m 264792 2000 1
+#for i in {1..1}; do
+# $MYPYTHON benchmark_cubulation.py R20000m 69220 423 1
#done
+
+for i in {1..10}; do
+ $MYPYTHON benchmark_cubulation.py R10000m 264617 851 1
+done
--
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