User: felicien.meunier

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Posts by felicien.meunier

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Comment: C: HDF5 reading speed
... Ok, I could install it but it did not change much as compared to the optimized solution you suggested above. ...
written 16 months ago by felicien.meunier40
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Comment: C: HDF5 reading speed
... Thanks for the follow up. For sake of exhaustivity, here is the result for the different file types: > library(rhdf5) > library(hdf5) > library(microbenchmark) > > direct = '/home/femeunier/Documents/ED2/ED/run/paracou/analy' > direct2= '/home/femeunier/Documents/ED2_archives/Ma ...
written 16 months ago by felicien.meunier40
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Comment: C: HDF5 reading speed
... As said above, I need to read almost everything in these files. That is why I use hdf5load and h5read. Thanks for the tip, I will try the devel branch version of the rhdf5 package and let you know the potential changes. EDIT: somehow I could not install the develop version: > biocLite('rhdf5_ ...
written 16 months ago by felicien.meunier40
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Comment: C: HDF5 reading speed
... Thank for the reply and the time you dedicate to my problem. Let me know if you find anything. No, I did not create the 1.6.10 version of the package. As it was a while ago, I can remember where exactly by I downloaded it online. Maybe here: https://packages.debian.org/fr/jessie/r-cran-hdf5 ...
written 16 months ago by felicien.meunier40
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Comment: C: HDF5 reading speed
... Yes, sure. I tested the two functions over the full range of file size and types: library(rhdf5) library(hdf5) library(microbenchmark) direct = '/home/femeunier/Documents/ED2/ED/run/paracou/analy/' direct2= '/home/femeunier/Documents/ED2_archives/Marcos/ED2/ED/run/amazon/nolianas/' small_fl = ...
written 16 months ago by felicien.meunier40
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HDF5 reading speed
... For research purposes, I must read a lot of large hdf5 files generated by an environmental model. Right now, I open them in rstudio using the rhdf5 package. I recently noticed that the most time-limiting step was the reading of the hdf5 files and so I wanted to speed up that part of the code. Switch ...
rhdf5 hdf5 written 16 months ago by felicien.meunier40 • updated 16 months ago by Mike Smith3.7k

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