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Benchmarking #129

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tischi opened this issue Oct 28, 2020 · 16 comments
Closed

Benchmarking #129

tischi opened this issue Oct 28, 2020 · 16 comments
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enhancement New feature or request high priority

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@tischi
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tischi commented Oct 28, 2020 •
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@haesleinhuepf @nornil

I think I have everything in place now for some benchmarking. The issue is that there is an exponential number of parameter combinations and we thus have to limit ourselves.

Dataset

For the initial benchmarking I suggest to only use one data set where the xyz dimensions are typical for light-sheet data.

FileType: Hdf5
BitDepth: 16
nX: 2048
nY: 2048
nZ: 101
nC: 1
nT: 10

Readouts

  • Input data set size [GB]:
  • Loading of a single z-plane [ ms ]
  • Loading and processing of a single z-plane [ ms ]
    • Relevant to judge how interactive the application is
    • To judge the pure processing time one can simply subtract the loading time (see above)
  • Loading a single xyz volume [ ms ]
  • LPV: Loading and processing of a single xyz volume [ ms ]
    • Relevant to judge how fast a whole data set could be processed
  • SV: Saving of a single xyz volume [ ms ]
    • Relevant to judge how fast a whole data set could be re-saved
  • M: maximal memory usage during processing [GB]
  • Output data set size [GB]:

To estimate the total processing and saving (TPS) time of a whole data set on a single computer one would have to use the following formula:

TPS = nC * nT * (LPV + SV)

Processing

In order to assess the processing we added a single processing step, namely a 3x3 binning in x&y.
This is a very typical processing step and should be the computationally most expensive one of the currently available.
Note that this significantly reduces the saving times as the data to be saved is 3x3=9 times smaller than the data to be loaded.

My plan would be to measure these numbers for a few different computer and data storage scenarios.
What do you think?
@tischi tischi added enhancement New feature or request high priority labels Oct 28, 2020
@haesleinhuepf
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Hi Tischi,

great! Maybe two or three scenarios are enough. I would definitely love to see some numbers comparing local SSD versus remove fileserver. I'm also curious what RAM your laptop uses. Does it makes sense? Does RAM-generation matter much? If you like, you can have some small tests on different computers and then you do two extreme tests ans talk about it in the manuscript.

Cheers,
Robert

@tischi
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tischi commented Oct 28, 2020 •
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local SSD versus remove fileserver.

Sure thing!

I'm also curious what RAM your laptop uses. Does it makes sense? Does RAM-generation matter much?

Good point!

  • I will add available RAM and maximally used RAM into the table. My application is quite careful about not using too much RAM (using a bounded cache) so usually around 16 GB are enough and thus this should not be an issue for a normal computer. There is just one issue in imglib2 that causes one volume more loaded than actually necessary: CellRandomAccess unexpectedly loads neighboring cells imglib/imglib2#252

@nornil
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nornil commented Oct 28, 2020 •
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Great, I have started making a table for this and adding supplementary text.
we could e.g. compare the options "laptop local", "laptop remote", "workstation", and "cluster"

@tischi
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tischi commented Oct 29, 2020 •
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@nornil Thanks!

I added more measurements:

  • Input data set file type:
  • Input data set size [GB]:
  • M: Maximal memory usage during processing of the full data set [ GB ]: ...
  • Output data set file type:
  • Output data set size [GB]:

Could you put the table somewhere where it is accessible from here and paste a link to it please?

@tischi
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tischi commented Oct 29, 2020 •
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Tischi's Mac

Hardware

  • 2.5 GHz Intel Core i7 (4 cores)
  • 16 GB RAM
  • Loading and saving from and to local SSD
Measurements
  • Input data set
    • type: Luxendo Hdf5 volumes file series (no compression)
    • size on disk: 7.9 GB
  • Loading of a single z-plane [ ms ]: ~2
  • Loading and processing of a single z-plane [ ms ]: ~100
  • Loading a single xyz volume [ ms ]: ~300
  • LPV: Loading and processing of a single xyz volume [ ms ]: ~5000
  • M: Maximal memory usage during processing of the full data set [ GB ]: <2
  • SV: Saving of a single xyz volume [ ms ]: ~800
  • Output data set
    • type: ImageJ Tiff stacks
    • size on disk: 900 MB

Testing different output file types:

@nornil
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nornil commented Oct 29, 2020

I have written it into our SI google doc as it need to go there eventually 

@tischi
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tischi commented Oct 29, 2020

I have written it into our SI google doc as it need to go there eventually

We can copy it there later!
Could you please make for now a publicly accessible G-Doc and paste the link here? It will be much easier to work on it!

@tischi
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tischi commented Oct 29, 2020 •
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Tischi's Mac / Data on network share

Hardware

  • 2.5 GHz Intel Core i7 (4 cores)
  • 16 GB RAM
  • Loading and saving from and to file-server with LAN cable
Measurements
  • Input data set
    • type: Luxendo Hdf5 volumes file series
    • size on disk: 7.9 GB
  • Loading of a single z-plane [ ms ]: ~150
  • Loading and processing of a single z-plane [ ms ]: ~260
  • Loading a single xyz volume [ ms ]: ~ 13000
  • LPV: Loading and processing of a single xyz volume [ ms ]: ~ 13000 + 5000
  • M: Maximal memory usage during processing of the full data set [ GB ]: ~2
  • SV: Saving of a single xyz volume [ ms ]: ~2000
  • Output data set
    • type: ImageJ Tiff stacks
    • size on disk: 900 MB

@haesleinhuepf
Maybe it is confusing that the saving times are faster than the reading times?
This is due to the 3x3 binning. However, if one wants to compare whether reading or writing is faster in general one could just multiply the saving times by 9...

@nornil
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nornil commented Oct 29, 2020

https://docs.google.com/document/d/1nDbOI03osMPy7yZyk7kEQRc8jFeK5r6T8__Lk1U0GQA/edit?usp=sharing

@tischi
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tischi commented Oct 29, 2020

Windows VM

Virtual machine in the data centre

image

numCores = 4

  • Input data set
    • type: Luxendo Hdf5 volumes file series
    • size on disk: 7.9 GB
  • Loading of a single z-plane [ ms ]: ~60
  • Loading and processing of a single z-plane [ ms ]: ~230
  • Loading a single xyz volume [ ms ]: ~ 2000
  • LPV: Loading and processing of a single xyz volume [ ms ]: ~ 6000
  • M: Maximal memory usage during processing of the full data set [ GB ]: ~4
  • SV: Saving of a single xyz volume [ ms ]: ~1400
  • Output data set
    • type: ImageJ Tiff stacks
    • size on disk: 900 MB

@tischi
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tischi commented Oct 29, 2020

@nornil
Thanks for sharing the link ❤️ !
Would you have time to transfer the information that I have posted already into the google doc?

@tischi
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tischi commented Oct 29, 2020 •
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Cluster node

Model name: Intel(R) Xeon(R) Gold 6136 CPU @ 3.00GHz

numCores = 8

All 10 timepoints on same cluster node:

  • Loading a single xyz volume [ ms ]: ~ 2000
  • LPV: Loading and processing of a single xyz volume [ ms ]: ~ 4000
  • M: Maximal memory usage during processing of the full data set [ GB ]: <4
  • SV: Saving of a single xyz volume [ ms ]: ~450
BENCHMARK: Read planes 0-100 from time-point 0 in 233 ms
Saving: /g/cba/exchange/bigdataprocessor/data/benchmark/out/volumes/in-binned
BENCHMARK: Processed volume, using 8 thread(s) in [ ms ]: 2994
BENCHMARK: Saved volume in [ ms ]: 508
Frames saved: 1/10; time ( spent, left, task ) [ s ]: 4, 42, 4.78; memory: 1034MB of 15933MB (6%)
Frames saved: 1/10; time ( spent, left, task ) [ s ]: 4, 42, 4.78; memory: 1034MB of 15933MB (6%)
BENCHMARK: Read planes 0-100 from time-point 1 in 240 ms
BENCHMARK: Processed volume, using 8 thread(s) in [ ms ]: 4906
BENCHMARK: Saved volume in [ ms ]: 417
BENCHMARK: Read planes 0-100 from time-point 0 in 331 ms
Frames saved: 2/10; time ( spent, left, task ) [ s ]: 11, 47, 5.96; memory: 3365MB of 15933MB (21%)
Frames saved: 2/10; time ( spent, left, task ) [ s ]: 11, 47, 5.96; memory: 3365MB of 15933MB (21%)
BENCHMARK: Read planes 0-100 from time-point 2 in 247 ms
BENCHMARK: Processed volume, using 8 thread(s) in [ ms ]: 4790
BENCHMARK: Saved volume in [ ms ]: 413
BENCHMARK: Read planes 0-100 from time-point 0 in 252 ms
Frames saved: 3/10; time ( spent, left, task ) [ s ]: 16, 38, 5.56; memory: 3456MB of 15933MB (21%)
Frames saved: 3/10; time ( spent, left, task ) [ s ]: 16, 38, 5.56; memory: 3456MB of 15933MB (21%)
BENCHMARK: Read planes 0-100 from time-point 3 in 260 ms
BENCHMARK: Processed volume, using 8 thread(s) in [ ms ]: 3860
BENCHMARK: Saved volume in [ ms ]: 477
Frames saved: 4/10; time ( spent, left, task ) [ s ]: 21, 31, 5.28; memory: 1828MB of 15933MB (11%)
Frames saved: 4/10; time ( spent, left, task ) [ s ]: 21, 31, 5.28; memory: 1828MB of 15933MB (11%)
BENCHMARK: Read planes 0-100 from time-point 0 in 138 ms
BENCHMARK: Read planes 0-100 from time-point 4 in 254 ms
BENCHMARK: Processed volume, using 8 thread(s) in [ ms ]: 3763
BENCHMARK: Saved volume in [ ms ]: 491
Frames saved: 5/10; time ( spent, left, task ) [ s ]: 25, 25, 5.17; memory: 2648MB of 15933MB (16%)
Frames saved: 5/10; time ( spent, left, task ) [ s ]: 25, 25, 5.17; memory: 2648MB of 15933MB (16%)
BENCHMARK: Read planes 0-100 from time-point 0 in 157 ms
BENCHMARK: Read planes 0-100 from time-point 5 in 222 ms
BENCHMARK: Processed volume, using 8 thread(s) in [ ms ]: 3512
BENCHMARK: Saved volume in [ ms ]: 493
Frames saved: 6/10; time ( spent, left, task ) [ s ]: 30, 20, 5.01; memory: 1829MB of 15933MB (11%)
Frames saved: 6/10; time ( spent, left, task ) [ s ]: 30, 20, 5.01; memory: 1829MB of 15933MB (11%)
BENCHMARK: Read planes 0-100 from time-point 0 in 227 ms
BENCHMARK: Read planes 0-100 from time-point 6 in 215 ms
BENCHMARK: Processed volume, using 8 thread(s) in [ ms ]: 3563
BENCHMARK: Saved volume in [ ms ]: 577
Frames saved: 7/10; time ( spent, left, task ) [ s ]: 34, 14, 4.95; memory: 1828MB of 15933MB (11%)
Frames saved: 7/10; time ( spent, left, task ) [ s ]: 34, 14, 4.95; memory: 1828MB of 15933MB (11%)
BENCHMARK: Read planes 0-100 from time-point 0 in 138 ms
BENCHMARK: Read planes 0-100 from time-point 7 in 223 ms
BENCHMARK: Processed volume, using 8 thread(s) in [ ms ]: 3754
BENCHMARK: Saved volume in [ ms ]: 506
Frames saved: 8/10; time ( spent, left, task ) [ s ]: 39, 9, 4.91; memory: 1828MB of 15933MB (11%)
Frames saved: 8/10; time ( spent, left, task ) [ s ]: 39, 9, 4.91; memory: 1828MB of 15933MB (11%)
BENCHMARK: Read planes 0-100 from time-point 0 in 152 ms
BENCHMARK: Read planes 0-100 from time-point 8 in 227 ms
BENCHMARK: Processed volume, using 8 thread(s) in [ ms ]: 3383
BENCHMARK: Saved volume in [ ms ]: 419
Frames saved: 9/10; time ( spent, left, task ) [ s ]: 43, 4, 4.82; memory: 1828MB of 15933MB (11%)
Frames saved: 9/10; time ( spent, left, task ) [ s ]: 43, 4, 4.82; memory: 1828MB of 15933MB (11%)
BENCHMARK: Read planes 0-100 from time-point 0 in 242 ms
BENCHMARK: Read planes 0-100 from time-point 9 in 224 ms
BENCHMARK: Processed volume, using 8 thread(s) in [ ms ]: 3673
BENCHMARK: Saved volume in [ ms ]: 372
Frames saved: 10/10; time ( spent, left, task ) [ s ]: 48, 0, 4.81; memory: 1739MB of 15933MB (10%)
Frames saved: 10/10; time ( spent, left, task ) [ s ]: 48, 0, 4.81; memory: 1739MB of 15933MB (10%)
Done: 10 / 10

@tischi
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tischi commented Oct 29, 2020 •
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@nornil

I think I have most of it now.

Missing:

  • Access data via VPN and wireless ("home office setting")

Anything else?

@tischi
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tischi commented Oct 30, 2020 •
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@nornil

Home office with mediocre internet connection

  • Computer: Tischi's Mac at home

  • Data location on file server of the institute

  • Data access through VPN with 9 MB/s download speed

  • Reading single plane ~ 6000 ms (*)

  • Reading and processing single plane ~ 6000 ms

  • Reading single volume ~ 600000 ms

  • Reading and processing single volume ~ 600000 ms

  • Saving single volume ~ 400000 ms

(*) I think we can say that this is on the edge of being bearable as research shows that humans typically have a short term attention span of 5 seconds.

For sure this is not useful to actually process the data, but, if one has no other choice, it may be just OK to use this mode to record a processing macro to be later batch executed, e.g. on a computer cluster in the data centre. However, recommendation for home office scenario is to use a VM in the data centre.

@tischi
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tischi commented Nov 10, 2020

@nornil
Here information that should enable us to answer whether reading from tif is faster than reading from hdf5.

/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/bin/java -Xmx12g "-javaagent:/Applications/IntelliJ IDEA CE.app/Contents/lib/idea_rt.jar=57096:/Applications/IntelliJ IDEA CE.app/Contents/bin" -Dfile.encoding=UTF-8 -classpath /Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/charsets.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/deploy.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/ext/cldrdata.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/ext/dnsns.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/ext/jaccess.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/ext/jfxrt.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/ext/localedata.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/ext/nashorn.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/ext/sunec.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/ext/sunjce_provider.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/ext/sunpkcs11.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/ext/zipfs.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/javaws.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/jce.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/jfr.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/jfxswt.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/jsse.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/management-agent.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/plugin.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/resources.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/jre/lib/rt.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/lib/ant-javafx.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/lib/dt.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/lib/javafx-mx.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/lib/jconsole.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/lib/packager.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/lib/sa-jdi.jar:/Library/Java/JavaVirtualMachines/jdk1.8.0_161.jdk/Contents/Home/lib/tools.jar:/Users/tischer/Documents/bigdataprocessor2/target/test-classes:/Users/tischer/Documents/bigdataprocessor2/target/classes:/Users/tischer/.m2/repository/junit/junit/4.13/junit-4.13.jar:/Users/tischer/.m2/repository/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar:/Users/tischer/.m2/repository/net/imglib2/imglib2/5.10.0/imglib2-5.10.0.jar:/Users/tischer/.m2/repository/sc/fiji/bigdataviewer_fiji/6.2.0/bigdataviewer_fiji-6.2.0.jar:/Users/tischer/.m2/repository/net/imagej/imagej-deprecated/0.1.4/imagej-deprecated-0.1.4.jar:/Users/tischer/.m2/repository/net/imglib2/imglib2-ij/2.0.0-beta-46/imglib2-ij-2.0.0-beta-46.jar:/Users/tischer/.m2/repository/io/scif/scifio/0.41.0/scifio-0.41.0.jar:/Users/tischer/.m2/repository/io/scif/scifio-jai-imageio/1.1.1/scifio-jai-imageio-1.1.1.jar:/Users/tischer/.m2/repository/net/imglib2/imglib2-ui/2.0.1/imglib2-ui-2.0.1.jar:/Users/tischer/.m2/repository/sc/fiji/SPIM_Registration/5.0.21/SPIM_Registration-5.0.21.jar:/Users/tischer/.m2/repository/sc/fiji/Fiji_Plugins/3.1.1/Fiji_Plugins-3.1.1.jar:/Users/tischer/.m2/repository/sc/fiji/SPIM_Opener/2.0.2/SPIM_Opener-2.0.2.jar:/Users/tischer/.m2/repository/sc/fiji/VIB-lib/2.2.0/VIB-lib-2.2.0.jar:/Users/tischer/.m2/repository/sc/fiji/pal-optimization/2.0.1/pal-optimization-2.0.1.jar:/Users/tischer/.m2/repository/sc/fiji/fiji-lib/2.1.2/fiji-lib-2.1.2.jar:/Users/tischer/.m2/repository/sc/fiji/legacy-imglib1/1.1.9/legacy-imglib1-1.1.9.jar:/Users/tischer/.m2/repository/edu/mines/mines-jtk/20151125/mines-jtk-20151125.jar:/Users/tischer/.m2/repository/net/imglib2/imglib2-algorithm-gpl/0.2.4/imglib2-algorithm-gpl-0.2.4.jar:/Users/tischer/.m2/repository/gov/nist/math/jama/1.0.3/jama-1.0.3.jar:/Users/tischer/.m2/repository/mpicbg/mpicbg/1.4.0/mpicbg-1.4.0.jar:/Users/tischer/.m2/repository/net/java/dev/jna/jna/4.5.2/jna-4.5.2.jar:/Users/tischer/.m2/repository/org/jfree/jfreechart/1.5.0/jfreechart-1.5.0.jar:/Users/tischer/.m2/repository/org/scijava/vecmath/1.6.0-scijava-2/vecmath-1.6.0-scijava-2.jar:/Users/tischer/.m2/repository/sc/fiji/bigdataviewer-core/9.0.6/bigdataviewer-core-9.0.6.jar:/Users/tischer/.m2/repository/net/imglib2/imglib2-realtransform/3.0.0/imglib2-realtransform-3.0.0.jar:/Users/tischer/.m2/repository/jitk/jitk-tps/3.0.1/jitk-tps-3.0.1.jar:/Users/tischer/.m2/repository/log4j/log4j/1.2.17/log4j-1.2.17.jar:/Users/tischer/.m2/repository/net/imglib2/imglib2-algorithm/0.11.2/imglib2-algorithm-0.11.2.jar:/Users/tischer/.m2/repository/org/ojalgo/ojalgo/45.1.1/ojalgo-45.1.1.jar:/Users/tischer/.m2/repository/sc/fiji/spim_data/2.2.4/spim_data-2.2.4.jar:/Users/tischer/.m2/repository/cisd/jhdf5/14.12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epository/org/jogamp/jogl/jogl-all/2.3.2/jogl-all-2.3.2.jar:/Users/tischer/.m2/repository/com/fasterxml/jackson/core/jackson-core/2.11.0/jackson-core-2.11.0.jar:/Users/tischer/.m2/repository/com/fasterxml/jackson/core/jackson-databind/2.11.0/jackson-databind-2.11.0.jar:/Users/tischer/.m2/repository/commons-lang/commons-lang/2.6/commons-lang-2.6.jar:/Users/tischer/.m2/repository/org/apache/commons/commons-math3/3.6.1/commons-math3-3.6.1.jar:/Users/tischer/.m2/repository/commons-io/commons-io/2.7/commons-io-2.7.jar:/Users/tischer/.m2/repository/sc/fiji/3D_Viewer/4.0.3/3D_Viewer-4.0.3.jar:/Users/tischer/.m2/repository/org/scijava/j3dutils/1.6.0-scijava-2/j3dutils-1.6.0-scijava-2.jar:/Users/tischer/.m2/repository/sc/fiji/bigwarp_fiji/6.0.0/bigwarp_fiji-6.0.0.jar:/Users/tischer/.m2/repository/com/googlecode/efficient-java-matrix-library/ejml/0.24/ejml-0.24.jar:/Users/tischer/.m2/repository/com/opencsv/opencsv/3.9/opencsv-3.9.jar:/Users/tischer/.m2/repository/commons-beanutils/commons-beanutils/1.9.4/commons-beanutils-1.9.4.jar:/Users/tischer/.m2/repository/commons-collections/commons-collections/3.2.2/commons-collections-3.2.2.jar:/Users/tischer/.m2/repository/com/beust/jcommander/1.48/jcommander-1.48.jar:/Users/tischer/.m2/repository/ome/bio-formats_plugins/6.5.1/bio-formats_plugins-6.5.1.jar:/Users/tischer/.m2/repository/ch/qos/logback/logback-classic/1.2.3/logback-classic-1.2.3.jar:/Users/tischer/.m2/repository/org/itc/image-transform-converters/0.1.3/image-transform-converters-0.1.3.jar:/Users/tischer/.m2/repository/com/github/mcib3d/mcib3d-core/3.96.3/mcib3d-core-3.96.3.jar:/Users/tischer/.m2/repository/com/googlecode/combinatoricslib/combinatoricslib/2.0/combinatoricslib-2.0.jar:/Users/tischer/.m2/repository/com/github/quickhull3d/quickhull3d/1.0.0/quickhull3d-1.0.0.jar:/Users/tischer/.m2/repository/nz/ac/waikato/cms/weka/weka-dev/3.9.4/weka-dev-3.9.4.jar:/Users/tischer/.m2/repository/com/github/vbmacher/java-cup/11b-20160615/java-cup-11b-20160615.jar:/Users/tischer/.m2/repository/nz/ac/waikato/cms/weka/thirdparty/bounce/0.18/bounce-0.18.jar:/Users/tischer/.m2/repository/com/googlecode/matrix-toolkits-java/mtj/1.0.4/mtj-1.0.4.jar:/Users/tischer/.m2/repository/com/github/fracpete/jfilechooser-bookmarks/0.1.6/jfilechooser-bookmarks-0.1.6.jar:/Users/tischer/.m2/repository/com/github/fracpete/jclipboardhelper/0.1.0/jclipboardhelper-0.1.0.jar:/Users/tischer/.m2/repository/com/sun/istack/istack-commons-runtime/3.0.8/istack-commons-runtime-3.0.8.jar:/Users/tischer/.m2/repository/jakarta/activation/jakarta.activation-api/1.2.1/jakarta.activation-api-1.2.1.jar:/Users/tischer/.m2/repository/jakarta/xml/bind/jakarta.xml.bind-api/2.3.2/jakarta.xml.bind-api-2.3.2.jar:/Users/tischer/.m2/repository/org/glassfish/jaxb/jaxb-runtime/2.3.2/jaxb-runtime-2.3.2.jar:/Users/tischer/.m2/repository/org/glassfish/jaxb/txw2/2.3.2/txw2-2.3.2.jar:/Users/tischer/.m2/repository/org/jvnet/staxex/stax-ex/1.8.1/stax-ex-1.8.1.jar:/Users/tischer/.m2/repository/com/sun/xml/fastinfoset/FastInfoset/1.2.16/FastInfoset-1.2.16.jar:/Users/tischer/.m2/repository/fr/inra/ijpb/MorphoLibJ_/1.4.2.1/MorphoLibJ_-1.4.2.1.jar:/Users/tischer/.m2/repository/de/embl/cba/imagej-cluster/0.6.3-SNAPSHPOT/imagej-cluster-0.6.3-SNAPSHPOT.jar:/Users/tischer/.m2/repository/com/jcraft/jsch/0.1.55/jsch-0.1.55.jar:/Users/tischer/.m2/repository/ch/epfl/biop/bigdataviewer-bioformats/0.2.10/bigdataviewer-bioformats-0.2.10.jar:/Users/tischer/.m2/repository/ch/epfl/biop/bigdataviewer-spimdata-extras/0.1.0/bigdataviewer-spimdata-extras-0.1.0.jar benchmark.BenchmarkPublication
Setting logging level to: Benchmark
Directory: /Users/tischer/Desktop/bpd2-benchmark/tif/in
Regular expression: (?<T>.*).tif
Sub-folder name pattern: .*
File name pattern: (?<T>.*).tif
Fetching files in /Users/tischer/Desktop/bpd2-benchmark/tif/in/
Found 10 files in folder: /Users/tischer/Desktop/bpd2-benchmark/tif/in/
Folder: /Users/tischer/Desktop/bpd2-benchmark/tif/in/
FileType: Tiff Stacks
BitDepth: 16
Tiff Compression: None
Tiff Strips: 1
nX: 2048
nY: 2048
nZ: 101
nC: 1
nT: 10
voxelUnit: micrometer
voxelSizeX: 0.10400000665600041
voxelSizeY: 0.10400000665600041
voxelSizeZ: 1.4142135381698608
GB: 8.47249408

Setting cache of image: in
  Cache cell dimensions: [2048, 2048, 1, 1, 1]
  Cache size: 100
  Cache type: BOUNDED
BENCHMARK: Read planes 0-0 from time-point 0 in 333 ms
BENCHMARK: Read planes 50-50 from time-point 0 in 126 ms
BENCHMARK: Read planes 18-18 from time-point 0 in 91 ms
BENCHMARK: Loading and processing of random z-plane #18 [ms]: 2252
Saving started; I/O threads: 1
Configuring volume reader with a cache size of 1 volumes.
Setting cache of image: in
  Cache cell dimensions: [2048, 2048, 101, 1, 1]
  Cache size: 1
  Cache type: BOUNDED
BENCHMARK: Read planes 0-100 from time-point 0 in 3695 ms
Saving: /Users/tischer/Desktop/bpd2-benchmark/tif/out/volumes
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 7693
BENCHMARK: Saved volume in [ ms ]: 7821
Frames saved: 1/10; time ( spent, left, task ) [ s ]: 21, 190, 21.1; memory: 3323MB of 10923MB (30%)
Frames saved: 1/10; time ( spent, left, task ) [ s ]: 21, 190, 21.1; memory: 3323MB of 10923MB (30%)
BENCHMARK: Read planes 0-100 from time-point 1 in 2425 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 13883
BENCHMARK: Saved volume in [ ms ]: 8256
Frames saved: 2/10; time ( spent, left, task ) [ s ]: 47, 191, 24.0; memory: 3313MB of 10923MB (30%)
Frames saved: 2/10; time ( spent, left, task ) [ s ]: 47, 191, 24.0; memory: 3313MB of 10923MB (30%)
BENCHMARK: Read planes 0-100 from time-point 0 in 675 ms
BENCHMARK: Read planes 0-100 from time-point 2 in 10992 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 19853
BENCHMARK: Saved volume in [ ms ]: 10299
Frames saved: 3/10; time ( spent, left, task ) [ s ]: 78, 182, 26.1; memory: 3314MB of 10923MB (30%)
Frames saved: 3/10; time ( spent, left, task ) [ s ]: 78, 182, 26.1; memory: 3314MB of 10923MB (30%)
BENCHMARK: Read planes 0-100 from time-point 0 in 542 ms
BENCHMARK: Read planes 0-100 from time-point 3 in 8244 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 17364
BENCHMARK: Saved volume in [ ms ]: 9599
BENCHMARK: Read planes 0-100 from time-point 0 in 1193 ms
Frames saved: 4/10; time ( spent, left, task ) [ s ]: 108, 162, 27.1; memory: 4934MB of 10923MB (45%)
Frames saved: 4/10; time ( spent, left, task ) [ s ]: 108, 162, 27.1; memory: 4934MB of 10923MB (45%)
BENCHMARK: Read planes 0-100 from time-point 4 in 9313 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 22972
BENCHMARK: Saved volume in [ ms ]: 10117
Frames saved: 5/10; time ( spent, left, task ) [ s ]: 148, 148, 29.6; memory: 3313MB of 10923MB (30%)
Frames saved: 5/10; time ( spent, left, task ) [ s ]: 148, 148, 29.6; memory: 3313MB of 10923MB (30%)
BENCHMARK: Read planes 0-100 from time-point 0 in 2206 ms
BENCHMARK: Read planes 0-100 from time-point 5 in 6396 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 17456
BENCHMARK: Saved volume in [ ms ]: 8132
Frames saved: 6/10; time ( spent, left, task ) [ s ]: 174, 116, 29.1; memory: 4143MB of 10923MB (37%)
Frames saved: 6/10; time ( spent, left, task ) [ s ]: 174, 116, 29.1; memory: 4143MB of 10923MB (37%)
BENCHMARK: Read planes 0-100 from time-point 0 in 143 ms
BENCHMARK: Read planes 0-100 from time-point 6 in 913 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 9505
BENCHMARK: Saved volume in [ ms ]: 6618
Frames saved: 7/10; time ( spent, left, task ) [ min ]: 3, 1, 0.455; memory: 3316MB of 10923MB (30%)
Frames saved: 7/10; time ( spent, left, task ) [ min ]: 3, 1, 0.455; memory: 3316MB of 10923MB (30%)
BENCHMARK: Read planes 0-100 from time-point 0 in 133 ms
BENCHMARK: Read planes 0-100 from time-point 7 in 4268 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 10897
BENCHMARK: Saved volume in [ ms ]: 9523
Frames saved: 8/10; time ( spent, left, task ) [ min ]: 3, 0, 0.444; memory: 4128MB of 10923MB (37%)
Frames saved: 8/10; time ( spent, left, task ) [ min ]: 3, 0, 0.444; memory: 4128MB of 10923MB (37%)
BENCHMARK: Read planes 0-100 from time-point 0 in 121 ms
BENCHMARK: Read planes 0-100 from time-point 8 in 4807 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 22595
BENCHMARK: Saved volume in [ ms ]: 15545
Frames saved: 9/10; time ( spent, left, task ) [ min ]: 4, 0, 0.472; memory: 3312MB of 10923MB (30%)
Frames saved: 9/10; time ( spent, left, task ) [ min ]: 4, 0, 0.472; memory: 3312MB of 10923MB (30%)
BENCHMARK: Read planes 0-100 from time-point 0 in 165 ms
BENCHMARK: Read planes 0-100 from time-point 9 in 3870 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 13721
BENCHMARK: Saved volume in [ ms ]: 10992
Frames saved: 10/10; time ( spent, left, task ) [ min ]: 4, 0, 0.469; memory: 2501MB of 10923MB (22%)
Frames saved: 10/10; time ( spent, left, task ) [ min ]: 4, 0, 0.469; memory: 2501MB of 10923MB (22%)
Done: 10 / 10
Saving: Done.

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tischi commented Nov 13, 2020

Read Tif / Write Tif: I/O threads: 1 ; process threads 4 (Tischi's Mac)

Setting logging level to: Benchmark
Directory: /Users/tischer/Desktop/bpd2-benchmark/tif/in
Regular expression: (?<T>.*).tif
Sub-folder name pattern: .*
File name pattern: (?<T>.*).tif
Fetching files in /Users/tischer/Desktop/bpd2-benchmark/tif/in/
Found 10 files in folder: /Users/tischer/Desktop/bpd2-benchmark/tif/in/
Folder: /Users/tischer/Desktop/bpd2-benchmark/tif/in/
FileType: Tiff Stacks
BitDepth: 16
Tiff Compression: None
Tiff Strips: 1
nX: 2048
nY: 2048
nZ: 101
nC: 1
nT: 10
voxelUnit: micrometer
voxelSizeX: 0.10400000665600041
voxelSizeY: 0.10400000665600041
voxelSizeZ: 1.4142135381698608
GB: 8.47249408
 
Setting cache of image: in
  Cache cell dimensions: [2048, 2048, 1, 1, 1]
  Cache size: 100
  Cache type: BOUNDED
# Bin...
Binning: [3, 3, 1, 1, 1]
BENCHMARK: Read planes 0-0 from time-point 0 in 82 ms
BENCHMARK: Read planes 1-1 from time-point 0 in 43 ms
BENCHMARK: Read planes 0-0 from time-point 1 in 55 ms
BENCHMARK: Read planes 50-50 from time-point 0 in 32 ms
BENCHMARK: Loading and processing of random z-plane #50 [ms]: 1005
Saving started; I/O threads: 1
Configuring volume reader with a cache size of 1 volumes.
Setting cache of image: in
  Cache cell dimensions: [2048, 2048, 101, 1, 1]
  Cache size: 1
  Cache type: BOUNDED
BENCHMARK: Read planes 0-100 from time-point 0 in 2394 ms
Saving: /Users/tischer/Desktop/bpd2-benchmark/tif/out/volumes
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 4838
BENCHMARK: Saved volume in [ ms ]: 1410
Frames saved: 1/10; time ( spent, left, task ) [ s ]: 9, 89, 9.98; memory: 1877MB of 10923MB (17%)
BENCHMARK: Read planes 0-100 from time-point 1 in 3926 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 9172
BENCHMARK: Saved volume in [ ms ]: 855
Frames saved: 2/10; time ( spent, left, task ) [ s ]: 20, 81, 10.2; memory: 2682MB of 10923MB (24%)
BENCHMARK: Read planes 0-100 from time-point 0 in 114 ms
BENCHMARK: Read planes 0-100 from time-point 2 in 6266 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 11581
BENCHMARK: Saved volume in [ ms ]: 977
Frames saved: 3/10; time ( spent, left, task ) [ s ]: 33, 78, 11.1; memory: 2696MB of 10923MB (24%)
BENCHMARK: Read planes 0-100 from time-point 0 in 1146 ms
BENCHMARK: Read planes 0-100 from time-point 3 in 2268 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 8820
BENCHMARK: Saved volume in [ ms ]: 992
Frames saved: 4/10; time ( spent, left, task ) [ s ]: 43, 65, 11.0; memory: 1887MB of 10923MB (17%)
BENCHMARK: Read planes 0-100 from time-point 0 in 143 ms
BENCHMARK: Read planes 0-100 from time-point 4 in 2068 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 7137
BENCHMARK: Saved volume in [ ms ]: 960
Frames saved: 5/10; time ( spent, left, task ) [ s ]: 52, 52, 10.4; memory: 1893MB of 10923MB (17%)
BENCHMARK: Read planes 0-100 from time-point 0 in 115 ms
BENCHMARK: Read planes 0-100 from time-point 5 in 3814 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 9004
BENCHMARK: Saved volume in [ ms ]: 933
Frames saved: 6/10; time ( spent, left, task ) [ s ]: 63, 42, 10.6; memory: 1900MB of 10923MB (17%)
BENCHMARK: Read planes 0-100 from time-point 0 in 151 ms
BENCHMARK: Read planes 0-100 from time-point 6 in 3231 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 8365
BENCHMARK: Saved volume in [ ms ]: 932
Frames saved: 7/10; time ( spent, left, task ) [ s ]: 75, 32, 10.8; memory: 1900MB of 10923MB (17%)
BENCHMARK: Read planes 0-100 from time-point 0 in 159 ms
BENCHMARK: Read planes 0-100 from time-point 7 in 2876 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 8294
BENCHMARK: Saved volume in [ ms ]: 819
BENCHMARK: Read planes 0-100 from time-point 0 in 379 ms
Frames saved: 8/10; time ( spent, left, task ) [ s ]: 85, 21, 10.7; memory: 3524MB of 10923MB (32%)
BENCHMARK: Read planes 0-100 from time-point 8 in 2296 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 7591
BENCHMARK: Saved volume in [ ms ]: 927
Frames saved: 9/10; time ( spent, left, task ) [ s ]: 94, 10, 10.6; memory: 1882MB of 10923MB (17%)
BENCHMARK: Read planes 0-100 from time-point 0 in 125 ms
BENCHMARK: Read planes 0-100 from time-point 9 in 1957 ms
BENCHMARK: Processed volume, using 4 thread(s) in [ ms ]: 7032
BENCHMARK: Saved volume in [ ms ]: 989
Frames saved: 10/10; time ( spent, left, task ) [ s ]: 103, 0, 10.4; memory: 1788MB of 10923MB (16%)
Done: 10 / 10
Saving: Done.

@tischi tischi closed this as completed Feb 15, 2021
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@tischi @nornil @haesleinhuepf