jean997
commented
5 years ago Thanks for posting! Can you share your sessionInfo()?
Closed jonaszierer closed 4 years ago
jean997
commented
5 years ago Thanks for posting! Can you share your sessionInfo()?
jonaszierer
commented
5 years ago sure! sorry for the tardy response
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/prog/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib/libopenblas_haswellp-r0.2.20.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cause_0.2.0.0161 feather_0.3.3 forcats_0.4.0 stringr_1.4.0
[5] dplyr_0.8.3 purrr_0.3.2 readr_1.3.1 tidyr_0.8.3
[9] tibble_2.1.3 ggplot2_3.2.0 tidyverse_1.2.1 colorout_1.2-1
loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 ashr_2.2-32 haven_2.1.1
[4] lattice_0.20-38 colorspace_1.4-1 vctrs_0.2.0
[7] generics_0.0.2 loo_2.1.0 rlang_0.4.0
[10] mixsqp_0.1-97 pillar_1.4.2 glue_1.3.1
[13] withr_2.1.2 modelr_0.1.4 readxl_1.3.1
[16] matrixStats_0.54.0 foreach_1.4.4 munsell_0.5.0
[19] gtable_0.3.0 cellranger_1.1.0 rvest_0.3.4
[22] codetools_0.2-16 doParallel_1.0.14 pscl_1.5.2
[25] parallel_3.5.0 broom_0.5.2 Rcpp_1.0.1
[28] scales_1.0.0 backports_1.1.4 RcppParallel_4.4.3
[31] jsonlite_1.6 truncnorm_1.0-8 gridExtra_2.3
[34] hms_0.5.0 stringi_1.4.3 numDeriv_2016.8-1.1
[37] grid_3.5.0 cli_1.1.0 tools_3.5.0
[40] magrittr_1.5 lazyeval_0.2.2 crayon_1.3.4
[43] pkgconfig_2.0.2 zeallot_0.1.0 MASS_7.3-51.4
[46] Matrix_1.2-17 SQUAREM_2017.10-1 xml2_1.2.0
[49] lubridate_1.7.4 assertthat_0.2.1 httr_1.4.0
[52] rstudioapi_0.10 iterators_1.0.10 R6_2.4.0
[55] intervals_0.15.1 nlme_3.1-140 compiler_3.5.0
CreRecombinase
commented
5 years ago is it possible that /usr/prog/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib/libopenblas_haswellp-r0.2.20.so as in:
Matrix products: default
BLAS/LAPACK: /usr/prog/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib/libopenblas_haswellp-r0.2.20.soand /usr/prog/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib/libopenblas.so.0 (from the backtrace) are not the same? If you run
ls -l /usr/prog/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib/libopenblas_haswellp-r0.2.20.soand
ls -l /usr/prog/OpenBLAS/0.2.20-GCC-6.4.0-2.28/lib/libopenblas.so.0from the shell, do they point to different files? If that's the case it looks like something might be funny with the way R is linking OpenBLAS. What's the output of R CMD config BLAS_LIBS ?
jonaszierer
commented
5 years ago the libopenblas.so.0 is actually just a symlink to libopenblas_haswellp-r0.2.20.so.
R CMD config BLAS_LIBS gives -lopenblas -lgfortran
However, I noticed that running it in a conda environment solves the problem. So it is probably some funny linking problem with openBlas
I'm trying to get the LDL example (https://jean997.github.io/cause/ldl_cad.html) to work but when i am running
est_cause_paramsi get the following errors:which continues like that for a while and then later on
Any idea where this is coming from...?