Error: C stack usage of HDF5Array
1
0
Entering edit mode
Koki • 0
@koki-7888
Last seen 2 hours ago
Japan

I tried to create a very huge three-dimensional array.

It cannot be created by standard array due to the out-of-memory error, so I used HDF5Array but the writing step stopped because of C stack error.

Is this because that I have to set something special setting when using HDF5Array?

I changed the setting of the C stack size by ulimit -s but the situation remains the same.

Thank you in advance.

library("HDF5Array")

# cf. https://rdrr.io/bioc/DelayedArray/man/write_block.html
.sarray <- function(dim){
    dim <- as.integer(dim)
    setAutoRealizationBackend("HDF5Array")
    sink <- AutoRealizationSink(dim, as.sparse=TRUE)
    close(sink)
    as(sink, "DelayedArray")
}

human <- array(runif(13889*1977), dim=c(13889, 1977))
mouse <- array(runif(13889*1907), dim=c(13889, 1907))

new_modes <- c(ncol(human), ncol(mouse), nrow(human))
darr <- .sarray(new_modes)
for(i in seq(dim(darr)[3])){
    print(paste0(i, " / ", dim(darr)[3]))
    darr[,,i] <- outer(human[i,], mouse[i,])
}

# After several step (e.g. 90 / 13889)
# This calculation stops by the following error.
# Error: C stack usage  1947092 is too close to the limit

I'm using the devel version of R and Biconductor.

sessionInfo()
R Under development (unstable) (2021-03-18 r80099)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] rTensor_1.4.1        testthat_3.0.2       BiocSingular_1.7.2
 [4] HDF5Array_1.19.15    rhdf5_2.35.2         DelayedArray_0.17.11
 [7] IRanges_2.25.10      S4Vectors_0.29.17    MatrixGenerics_1.3.1
[10] matrixStats_0.58.0   BiocGenerics_0.37.4  Matrix_1.3-2
[13] BiocManager_1.30.12

loaded via a namespace (and not attached):
 [1] rprojroot_2.0.2     compiler_4.1.0      tools_4.1.0
 [4] rsvd_1.0.5          Rcpp_1.0.6          rhdf5filters_1.3.4
 [7] beachmat_2.7.7      irlba_2.3.3         desc_1.3.0
[10] ScaledMatrix_0.99.2 BiocParallel_1.25.5 rlang_0.4.10
[13] lattice_0.20-41     Rhdf5lib_1.13.4     magrittr_2.0.1
[16] R6_2.5.0            withr_2.4.2         crayon_1.4.1
[19] grid_4.1.0
DelayedArray HDF5Array • 84 views
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1
Entering edit mode
@herve-pages-1542
Last seen 3 hours ago
Seattle, WA, United States

Hi,

You never wrote anything to your RealizationSink object!

Here is why:

  • Your .sarray() function creates the RealizationSink object, then immediately closes it (without writing anything to it), and finally turns the sink object into a DelayedArray object.
  • Then you try to modify the DelayedArray in a loop with darr[,,i] <- .... But it's too late! These modifications are treated as delayed operations that are piling up on the DelayedArray object, and not as write operations to the HDF5 file.
  • It's important to keep in mind that a DelayedArray object always treats the file that it's pointing at as read-only. In other words, you can never modify the file by operating on the DelayedArray object.

As explained in the man page for write_block and RealizationSink objects, things must be done in the following order:

  1. Create the realization sink.

  2. Write blocks of array data to the realization sink with one or several calls to write_block().

  3. Close the realization sink with close().

  4. Coerce the realization sink to DelayedArray.

Note that you must use write_block() to write data to the realization sink.

Please check the examples in the man page. They have plenty of comments that cover many details.

Best,

H.

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0
Entering edit mode

Ok, I didn't really understand the documentation because it was a little technical for me, but I think I finally got it.

I see that I need to align the block of the on-memory object with the block to be written to HDF5.

library("HDF5Array")

human <- as(array(runif(13889*1977), dim=c(13889, 1977)), "HDF5Array")
mouse <- as(array(runif(13889*1907), dim=c(13889, 1907)), "HDF5Array")

new_modes <- as.integer(c(1977, 1907, 13889))
human_grid <- rowAutoGrid(human, nrow=30)
mouse_grid <- rowAutoGrid(mouse, nrow=30)

setAutoRealizationBackend("HDF5Array")
sink <- AutoRealizationSink(new_modes)
sink_grid <- RegularArrayGrid(dim(sink), spacings=c(1977, 1907, 30))

stopifnot(length(sink_grid) == length(human_grid))
stopifnot(length(sink_grid) == length(mouse_grid))

block_outer <- function(A, B){
    stopifnot(nrow(A) == nrow(B))
    arr <- array(0, dim=c(ncol(A), ncol(B), nrow(A)))
    for(i in seq(dim(arr)[3])){
        arr[,,i] <- outer(A[i,], B[i, ])
    }
    arr
}

FUN <- function(viewport, sink) {
    bid <- currentBlockId()
    human_block <- read_block(human, human_grid[[bid]])
    mouse_block <- read_block(mouse, mouse_grid[[bid]])
    block <- block_outer(human_block, mouse_block)
    write_block(sink, viewport, block)
}
system.time(sink <- gridReduce(FUN, sink_grid, sink, verbose=TRUE))

close(sink)
M <- as(sink, "DelayedArray")
dim(M)
M[1:2,1:2,1:2]
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