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Benchmark with h5 package #92
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Hi, no you are not doing anything wrong. It is a known issue that I recently unfortunately didn't have time to dig into. |
Hi Hans-Peter, Rprof("issue-92-hdf5r.out", line.profiling=TRUE)
h5file <- hdf5r::H5File$new("testdata.h5", "r")
sets <- h5file$ls()$name
result <- lapply(sets, function(i) h5file[[i]][])
h5file$close_all()
Rprof(NULL)
summaryRprof("issue-92-hdf5r.out", lines = "show")
|
Yes exactly. When I commented out (Spurred by #86 I tried with a hdf5r branch where |
Yep, I observed similar issues and posted issue #85. I put up some benchmarks in that issues too. |
This is an old issue I know but I found similar results about I removed that line in I don't fully understand what the |
I noticed that reading hdf5 files with the
hdf5r
package is much slower than with the deprecatedh5
package (16 times slower in example below).Am I doing something wrong?
MWE:
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