thr3ads.net - R SIG Fedora - [R-sig-Fedora] R code works on Fedora 32, but not since Fedora 33 [Nov 2021]

If this information is useful, please help other people find it:
Share via:

René Genz

2021-Nov-04 17:23 UTC

[R-sig-Fedora] R code works on Fedora 32, but not since Fedora 33

Hi,

the other day I was asked to investigate a problem regarding R. The R 
code works on Fedora 32, but not since Fedora 33. I am stuck and need 
help. I can test and provide more information if needed.

On Fedora 32 the code produces a PDF file (397 KiB) containing 6 pages. 
It can be viewed.
Since Fedora 33 the R calculation stalls after a second. The PDF file 
(3.5 KiB) cannot be viewed.

I tested with virtual machines with Fedora 32 to 35. I installed with 
the netinstall ISO the "Xfce Desktop" group. After installation was
done
I ran as root:
# dnf update -y --refresh ; dnf install -y R ; reboot

After reboot I logged in as user, received the CSV file and ran:
$ cd 2021-11-02-R-F32-F34 ; R
and copy-pasted the R code. The R package "plotly" requires the R 
package "httr" which requires:
# dnf install -y curl-devel openssl-devel
Maybe you need to quit and re-run that R package installation command.


Attached is the execution log for F32 and F33. If you compare them 
(`diff` or `meld`), you will notice different compiler options and some 
different compiler messages. I do not know if they are related.


Attached is the R code. I added the print commands at the end (not 
included in the logs). The command 'print("a")' results in
output '[1]
"a"'. On F32 the output a to f repeats 6 times (matches page
number). In
`top` during PDF creation you can see 3 rsession processes during most 
of calculation. Calculation takes approximately 30 seconds.

Since F33 you see only this output:
[1] "a"
[1] "b"
That means the problem is at "cvm[[i]] <- cvrisk(model[[i]])" line.
It
is part of the R package mboost.
In `top` you see only 1 rsession process for a second. Calculcation 
stalls. You must abort with Ctrl+c. The PDF file cannot be viewed.

You can leave the R environment (prompt ">") with either:
- Ctrl+d
- quit()
No need to save the workspace image (press n and enter).



Additional information:

Fedora 32:
 > sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 32 (Thirty Two)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.12.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=en_US.UTF-8
  [7] LC_PAPER=C.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  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GGally_2.1.2  stringi_1.7.5 plotly_4.10.0 Amelia_1.8.0  Rcpp_1.0.7
[6] ggplot2_3.3.5 mboost_2.9-5  stabs_0.6-4

loaded via a namespace (and not attached):
  [1] tidyselect_1.1.1   inum_1.0-4         purrr_0.3.4 
splines_4.0.5
  [5] lattice_0.20-41    colorspace_2.0-2   vctrs_0.3.8 
generics_0.1.1
  [9] htmltools_0.5.2    viridisLite_0.4.0  utf8_1.2.2 
survival_3.2-10
[13] rlang_0.4.12       pillar_1.6.4       foreign_0.8-81     glue_1.4.2 

[17] withr_2.4.2        RColorBrewer_1.1-2 plyr_1.8.6 
lifecycle_1.0.1
[21] munsell_0.5.0      gtable_0.3.0       htmlwidgets_1.5.4 
mvtnorm_1.1-3
[25] fastmap_1.1.0      fansi_0.5.0        scales_1.1.1 
jsonlite_1.7.2
[29] digest_0.6.28      dplyr_1.0.7        grid_4.0.5 
quadprog_1.5-8
[33] tools_4.0.5        magrittr_2.0.1     lazyeval_0.2.2 
tibble_3.1.5
[37] Formula_1.2-4      crayon_1.4.2       tidyr_1.1.4 
pkgconfig_2.0.3
[41] partykit_1.2-15    ellipsis_0.3.2     libcoin_1.0-9 
Matrix_1.3-2
[45] data.table_1.14.2  nnls_1.4           reshape_0.8.8      httr_1.4.2 

[49] R6_2.5.1           rpart_4.1-15       compiler_4.0.5
 > Sys.getlocale()
[1] 
"LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=C.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C"



Fedora 33:
 > sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 33 (Thirty Three)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libflexiblas.so.3.0

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=en_US.UTF-8
  [7] LC_PAPER=C.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  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GGally_2.1.2  stringi_1.7.5 plotly_4.10.0 Amelia_1.8.0  Rcpp_1.0.7
[6] ggplot2_3.3.5 mboost_2.9-5  stabs_0.6-4

loaded via a namespace (and not attached):
  [1] tidyselect_1.1.1   inum_1.0-4         purrr_0.3.4 
splines_4.0.5
  [5] lattice_0.20-41    colorspace_2.0-2   vctrs_0.3.8 
generics_0.1.1
  [9] htmltools_0.5.2    viridisLite_0.4.0  utf8_1.2.2 
survival_3.2-10
[13] rlang_0.4.12       pillar_1.6.4       foreign_0.8-81     glue_1.4.2 

[17] withr_2.4.2        RColorBrewer_1.1-2 plyr_1.8.6 
lifecycle_1.0.1
[21] munsell_0.5.0      gtable_0.3.0       htmlwidgets_1.5.4 
mvtnorm_1.1-3
[25] fastmap_1.1.0      fansi_0.5.0        scales_1.1.1 
jsonlite_1.7.2
[29] digest_0.6.28      dplyr_1.0.7        grid_4.0.5 
quadprog_1.5-8
[33] tools_4.0.5        magrittr_2.0.1     lazyeval_0.2.2 
tibble_3.1.5
[37] Formula_1.2-4      crayon_1.4.2       tidyr_1.1.4 
pkgconfig_2.0.3
[41] partykit_1.2-15    ellipsis_0.3.2     libcoin_1.0-9 
Matrix_1.3-2
[45] data.table_1.14.2  nnls_1.4           reshape_0.8.8      httr_1.4.2 

[49] R6_2.5.1           rpart_4.1-15       compiler_4.0.5
 > Sys.getlocale()
[1] 
"LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=C.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C"

Thank you for your help.
-- 
Best regards,
Ren?
-------------- next part --------------
A non-text attachment was scrubbed...
Name: R_CSV_TXT.7z
Type: application/x-7z-compressed
Size: 117189 bytes
Desc: not available
URL:
<https://stat.ethz.ch/pipermail/r-sig-fedora/attachments/20211104/86c2b432/attachment-0001.bin>

Iñaki Ucar

2021-Nov-04 20:02 UTC

head link

[R-sig-Fedora] R code works on Fedora 32, but not since Fedora 33

Hi,

Since F33, openblas-openmp is the default BLAS implementation in
Fedora. I see that mboost::cvrisk uses parallelization via mclapply by
default, which may not play well with OpenMP. So you have 3 options
here:

Option 1. Force mboost::cvrisk to run sequentially by providing
papply=lapply as an argument.

Option 2. Limit the number of OpenMP threads to 1:

$ sudo dnf -y install R-flexiblas
$ R> flexiblas::flexiblas_set_num_threads(1)
> # then, run your script
or simply:

$ OMP_NUM_THREADS=1 R
$ # then, run your script

Option 3. Switch to sequential OpenBLAS:

$ sudo dnf -y install flexiblas-openblas-serial R-flexiblas
$ R>
flexiblas::flexiblas_switch(flexiblas::flexiblas_load_backend("openblas-serial"))
> # then, run your script
or simply:

$ sudo dnf -y install flexiblas-openblas-serial
$ FLEXIBLAS=openblas-serial R> # then, run your script
See [1] for more info. Hope it helps.

I?aki

[1] https://cran.r-project.org/bin/linux/fedora/#blaslapack-switching

On Thu, 4 Nov 2021 at 18:47, Ren? Genz <liebundartig at freenet.de>
wrote:>
> Hi,
>
> the other day I was asked to investigate a problem regarding R. The R
> code works on Fedora 32, but not since Fedora 33. I am stuck and need
> help. I can test and provide more information if needed.
>
> On Fedora 32 the code produces a PDF file (397 KiB) containing 6 pages.
> It can be viewed.
> Since Fedora 33 the R calculation stalls after a second. The PDF file
> (3.5 KiB) cannot be viewed.
>
> I tested with virtual machines with Fedora 32 to 35. I installed with
> the netinstall ISO the "Xfce Desktop" group. After installation
was done
> I ran as root:
> # dnf update -y --refresh ; dnf install -y R ; reboot
>
> After reboot I logged in as user, received the CSV file and ran:
> $ cd 2021-11-02-R-F32-F34 ; R
> and copy-pasted the R code. The R package "plotly" requires the R
> package "httr" which requires:
> # dnf install -y curl-devel openssl-devel
> Maybe you need to quit and re-run that R package installation command.
>
>
> Attached is the execution log for F32 and F33. If you compare them
> (`diff` or `meld`), you will notice different compiler options and some
> different compiler messages. I do not know if they are related.
>
>
> Attached is the R code. I added the print commands at the end (not
> included in the logs). The command 'print("a")' results
in output '[1]
> "a"'. On F32 the output a to f repeats 6 times (matches page
number). In
> `top` during PDF creation you can see 3 rsession processes during most
> of calculation. Calculation takes approximately 30 seconds.
>
> Since F33 you see only this output:
> [1] "a"
> [1] "b"
> That means the problem is at "cvm[[i]] <- cvrisk(model[[i]])"
line. It
> is part of the R package mboost.
> In `top` you see only 1 rsession process for a second. Calculcation
> stalls. You must abort with Ctrl+c. The PDF file cannot be viewed.
>
> You can leave the R environment (prompt ">") with either:
> - Ctrl+d
> - quit()
> No need to save the workspace image (press n and enter).
>
>
>
> Additional information:
>
> Fedora 32:
>  > sessionInfo()
> R version 4.0.5 (2021-03-31)
> Platform: x86_64-redhat-linux-gnu (64-bit)
> Running under: Fedora 32 (Thirty Two)
>
> Matrix products: default
> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.12.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=en_US.UTF-8
>   [7] LC_PAPER=C.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  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] GGally_2.1.2  stringi_1.7.5 plotly_4.10.0 Amelia_1.8.0  Rcpp_1.0.7
> [6] ggplot2_3.3.5 mboost_2.9-5  stabs_0.6-4
>
> loaded via a namespace (and not attached):
>   [1] tidyselect_1.1.1   inum_1.0-4         purrr_0.3.4
> splines_4.0.5
>   [5] lattice_0.20-41    colorspace_2.0-2   vctrs_0.3.8
> generics_0.1.1
>   [9] htmltools_0.5.2    viridisLite_0.4.0  utf8_1.2.2
> survival_3.2-10
> [13] rlang_0.4.12       pillar_1.6.4       foreign_0.8-81     glue_1.4.2
>
> [17] withr_2.4.2        RColorBrewer_1.1-2 plyr_1.8.6
> lifecycle_1.0.1
> [21] munsell_0.5.0      gtable_0.3.0       htmlwidgets_1.5.4
> mvtnorm_1.1-3
> [25] fastmap_1.1.0      fansi_0.5.0        scales_1.1.1
> jsonlite_1.7.2
> [29] digest_0.6.28      dplyr_1.0.7        grid_4.0.5
> quadprog_1.5-8
> [33] tools_4.0.5        magrittr_2.0.1     lazyeval_0.2.2
> tibble_3.1.5
> [37] Formula_1.2-4      crayon_1.4.2       tidyr_1.1.4
> pkgconfig_2.0.3
> [41] partykit_1.2-15    ellipsis_0.3.2     libcoin_1.0-9
> Matrix_1.3-2
> [45] data.table_1.14.2  nnls_1.4           reshape_0.8.8      httr_1.4.2
>
> [49] R6_2.5.1           rpart_4.1-15       compiler_4.0.5
>  > Sys.getlocale()
> [1]
>
"LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=C.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C"
>
>
>
> Fedora 33:
>  > sessionInfo()
> R version 4.0.5 (2021-03-31)
> Platform: x86_64-redhat-linux-gnu (64-bit)
> Running under: Fedora 33 (Thirty Three)
>
> Matrix products: default
> BLAS/LAPACK: /usr/lib64/libflexiblas.so.3.0
>
> 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=en_US.UTF-8
>   [7] LC_PAPER=C.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  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] GGally_2.1.2  stringi_1.7.5 plotly_4.10.0 Amelia_1.8.0  Rcpp_1.0.7
> [6] ggplot2_3.3.5 mboost_2.9-5  stabs_0.6-4
>
> loaded via a namespace (and not attached):
>   [1] tidyselect_1.1.1   inum_1.0-4         purrr_0.3.4
> splines_4.0.5
>   [5] lattice_0.20-41    colorspace_2.0-2   vctrs_0.3.8
> generics_0.1.1
>   [9] htmltools_0.5.2    viridisLite_0.4.0  utf8_1.2.2
> survival_3.2-10
> [13] rlang_0.4.12       pillar_1.6.4       foreign_0.8-81     glue_1.4.2
>
> [17] withr_2.4.2        RColorBrewer_1.1-2 plyr_1.8.6
> lifecycle_1.0.1
> [21] munsell_0.5.0      gtable_0.3.0       htmlwidgets_1.5.4
> mvtnorm_1.1-3
> [25] fastmap_1.1.0      fansi_0.5.0        scales_1.1.1
> jsonlite_1.7.2
> [29] digest_0.6.28      dplyr_1.0.7        grid_4.0.5
> quadprog_1.5-8
> [33] tools_4.0.5        magrittr_2.0.1     lazyeval_0.2.2
> tibble_3.1.5
> [37] Formula_1.2-4      crayon_1.4.2       tidyr_1.1.4
> pkgconfig_2.0.3
> [41] partykit_1.2-15    ellipsis_0.3.2     libcoin_1.0-9
> Matrix_1.3-2
> [45] data.table_1.14.2  nnls_1.4           reshape_0.8.8      httr_1.4.2
>
> [49] R6_2.5.1           rpart_4.1-15       compiler_4.0.5
>  > Sys.getlocale()
> [1]
>
"LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=C.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C"
>
> Thank you for your help.
> --
> Best regards,
> Ren?_______________________________________________
> R-SIG-Fedora mailing list
> R-SIG-Fedora at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora


-- 
I?aki ?car

R SIG Fedora - Nov 2021 - R code works on Fedora 32, but not since Fedora 33

[R-sig-Fedora] R code works on Fedora 32, but not since Fedora 33

[R-sig-Fedora] R code works on Fedora 32, but not since Fedora 33