RStudio session aborted when executing keras_model_sequential(): invalid pointer

jerryji1993 commented 5 years ago

Hi,

My RStudio session aborts every time I run keras_model_sequential() function on a computing cluster. However, when I load a saved hdf5 file with load_model_hdf5() (previously trained elsewhere), I am able to proceed with evaluate(), predict() and keras_model() functions. Also the same code runs without any problem in a regular R session (not RStudio).

What I did to install and load the packages:

> devtools::install_github("rstudio/keras")
> library(keras)

From here, I tried both install_keras(method = "conda", conda = "...") in R (since I found install_keras() only installs conda env with python 3.7) and also custom installation $ conda create -n r-tensorflow python=3.6, then specifying the environment with use_condaenv("r-tensorflow", conda = "..."). Neither seems to solve the problem.

The traceback I had (followed by long memory map info, which is not pasted here):

*** Error in `/hpc/software/RStudio-desk/1.1.383/bin/rsession': free(): invalid pointer: 0x000000000316cbd8 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x2b4447471489]
/home/xxx/R/x86_64-pc-linux-gnu-library/3.6/reticulate/libs/reticulate.so(_Z31exception_to_condition_templateIN4Rcpp9exceptionEEP7SEXPRECRKT_b+0x329)[0x2b445fd48229]
/home/xxx/R/x86_64-pc-linux-gnu-library/3.6/reticulate/libs/reticulate.so(_reticulate_py_call_impl+0x2c2)[0x2b445fd42472]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1380b6)[0x2b44459c60b6]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b44459d30c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b44459d46fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b44459d5417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b44459c3974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b44459d30c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b44459d46fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b44459d5417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b44459c3974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b44459d30c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b44459d46fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b44459d5417]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x2fc)[0x2b44459d307c]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_ReplIteration+0x232)[0x2b4445a038d2]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x175c31)[0x2b4445a03c31]
/software/R/3.6.0/lib64/R/lib/libR.so(run_Rmainloop+0x4f)[0x2b4445a03ccf]
/hpc/software/RStudio-desk/1.1.383/bin/rsession(_ZN7rstudio1r7session12runEmbeddedRERKNS_4core8FilePathES5_bb7SA_TYPERKNS1_9CallbacksEPNS1_17InternalCallbacksE+0x1aa)[0xd514aa]
/hpc/software/RStudio-desk/1.1.383/bin/rsession(_ZN7rstudio1r7session3runERKNS1_8ROptionsERKNS1_10RCallbacksE+0xd57)[0xd35317]
/hpc/software/RStudio-desk/1.1.383/bin/rsession(main+0x2acd)[0x6f87ad]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b44474123d5]
/hpc/software/RStudio-desk/1.1.383/bin/rsession[0x709ce5]
======= Memory map: ========
(omitted)

I also tried adding export RETICULATE_PYTHON = "..." to my bash_profile, but that also didn't seem to help.

My reticulate::py_config():

python:         /home/xxx/.conda/envs/r-tensorflow/bin/python
libpython:      /home/xxx/.conda/envs/r-tensorflow/lib/libpython3.6m.so
pythonhome:     /home/xxx/.conda/envs/r-tensorflow:/home/xxx/.conda/envs/r-tensorflow
version:        3.6.8 |Anaconda, Inc.| (default, Dec 30 2018, 01:22:34)  [GCC 7.3.0]
numpy:          /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/site-packages/numpy
numpy_version:  1.16.4
tensorflow:     /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/site-packages/tensorflow

NOTE: Python version was forced by RETICULATE_PYTHON

tf_config():

TensorFlow v1.14.0 (~/.conda/envs/r-tensorflow/lib/python3.6/site-packages/tensorflow)
Python v3.6 (~/.conda/envs/r-tensorflow/bin/python)

sessionInfo():

R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.5 (Maipo)

Matrix products: default
BLAS:   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
LAPACK: /home/xxx/.conda/envs/r-tensorflow/lib/libmkl_rt.so

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

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

other attached packages:
[1] tensorflow_1.13.1  caret_6.0-84       ggplot2_3.1.1      lattice_0.20-38    keras_2.2.4.1.9001

loaded via a namespace (and not attached):
 [1] reticulate_1.12    tidyselect_0.2.5   purrr_0.3.2        reshape2_1.4.3     splines_3.6.0      colorspace_1.4-1   generics_0.0.2     stats4_3.6.0      
 [9] yaml_2.2.0         base64enc_0.1-3    survival_2.44-1.1  prodlim_2018.04.18 rlang_0.4.0        ModelMetrics_1.2.2 pillar_1.4.0       glue_1.3.1        
[17] withr_2.1.2        foreach_1.4.4      plyr_1.8.4         lava_1.6.5         stringr_1.4.0      timeDate_3043.102  munsell_0.5.0      gtable_0.3.0      
[25] recipes_0.1.5      codetools_0.2-16   tfruns_1.4         class_7.3-15       Rcpp_1.0.1         scales_1.0.0       ipred_0.9-9        jsonlite_1.6      
[33] stringi_1.4.3      dplyr_0.8.1        grid_3.6.0         tools_3.6.0        magrittr_1.5       lazyeval_0.2.2     tibble_2.1.1       crayon_1.3.4      
[41] whisker_0.3-2      pkgconfig_2.0.2    zeallot_0.1.0      MASS_7.3-51.4      Matrix_1.2-17      data.table_1.12.2  lubridate_1.7.4    gower_0.2.1       
[49] assertthat_0.2.1   rstudioapi_0.10    iterators_1.0.10   R6_2.4.0           rpart_4.1-15       nnet_7.3-12        nlme_3.1-139       compiler_3.6.0

Besides, running reticulate::repl_python() also crashes the session.

Any help is sincerely appreciated!

skeydan commented 5 years ago

Perhaps it's easiest to start from the last thing you're reporting (reticulate::repl_python() crashing).

Assuming you do this as the very first thing in a freshly restarted session, - does this happen

1) only in RStudio or or also from R?

2) with both reticulate from CRAN as well as from github?

3) in both the base and the r-tensorflow environments?

Also, can you report the complete output from the crash?

jerryji1993 commented 5 years ago

Perhaps it's easiest to start from the last thing you're reporting (reticulate::repl_python() crashing).

Assuming you do this as the very first thing in a freshly restarted session, - does this happen

only in RStudio or or also from R?

with both reticulate from CRAN as well as from github?

in both the base and the r-tensorflow environments?

Also, can you report the complete output from the crash?

Hi skeydan,

Thank you very much for your useful instructions. I tried as you suggested and indeed reticulate::repl_python() fails in all situations above (i.e. also crashes R).

When I ran reticulate::repl_python():

Python 3.6.8 (/home/yjq6148/.conda/envs/r-tensorflow/bin/python)
Reticulate 1.12.0.9003 REPL -- A Python interpreter in R.
>>> import os

and it gave me the invalid pointer error and crashed everything, in all cases.

And sorry about the crash messages--the complete output is shown below.

In R (r-tensorflow environment):

*** Error in `/software/R/3.6.0/lib64/R/bin/exec/R': free(): invalid pointer: 0x000000000697c138 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x2abea9744489]
/home/xxx/R/x86_64-pc-linux-gnu-library/3.6/reticulate/libs/reticulate.so(_Z31exception_to_condition_templateIN4Rcpp9exceptionEEP7SEXPRECRKT_b+0x329)[0x2abeb662d689]
/home/xxx/R/x86_64-pc-linux-gnu-library/3.6/reticulate/libs/reticulate.so(_reticulate_py_eval_impl+0x282)[0x2abeb6629792]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1380b6)[0x2abea8b010b6]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2abea8b0f6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2abea8b10417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2abea8afe974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2abea8b0f6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2abea8b10417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2abea8afe974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2abea8b0e826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2abea8b0dcb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2abea8b0e826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2abea8b0dcb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2abea8b0e826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2abea8b0dcb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2abea8b0e826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2abea8b0dcb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2abea8b0f6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2abea8b10417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2abea8afe974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2abea8b0f6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2abea8b10417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2abea8afe974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2abea8b0f6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2abea8b10417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2abea8afe974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2abea8b0f6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2abea8b10417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2abea8afe974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2abea8b0f6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2abea8b10417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2abea8afe974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2abea8b0f6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2abea8b10417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2abea8afe974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2abea8b0e826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2abea8b0dcb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2abea8b0e826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2abea8b0dcb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2abea8b0e826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2abea8b0dcb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2abea8b0e826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2abea8b0dcb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2abea8b0e0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2abea8b0f6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2abea8b10417]
======= Memory map: ========
00400000-00401000 r-xp 00000000 00:28 29957074                           /hpc/software/R/3.6.0/lib64/R/bin/exec/R
00600000-00601000 r--p 00000000 00:28 29957074                           /hpc/software/R/3.6.0/lib64/R/bin/exec/R
00601000-00602000 rw-p 00001000 00:28 29957074                           /hpc/software/R/3.6.0/lib64/R/bin/exec/R
008c3000-0a849000 rw-p 00000000 00:00 0                                  [heap]
2abea87a5000-2abea87c7000 r-xp 00000000 fd:00 83887133                   /usr/lib64/ld-2.17.so
2abea87c7000-2abea87ca000 rw-p 00000000 00:00 0 
2abea87ca000-2abea87cb000 r--p 00000000 00:28 29957971                   /hpc/software/R/3.6.0/lib64/R/library/translations/en/LC_MESSAGES/R.mo
2abea87cb000-2abea87d2000 r--s 00000000 fd:00 67172538                   /usr/lib64/gconv/gconv-modules.cache
2abea87d2000-2abea87d3000 r--p 00000000 00:2b 102652674                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2abea87d3000-2abea87d5000 r-xp 00001000 00:2b 102652674                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2abea87d5000-2abea87d6000 r--p 00003000 00:2b 102652674                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2abea87d6000-2abea87d7000 r--p 00003000 00:2b 102652674                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2abea87d7000-2abea87d9000 rw-p 00004000 00:2b 102652674                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2abea87d9000-2abea87dc000 r--p 00000000 00:2b 102652692                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
2abea87dc000-2abea87e2000 r-xp 00003000 00:2b 102652692                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
2abea87e2000-2abea87e4000 r--p 00009000 00:2b 102652692                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
2abea87e4000-2abea87e5000 ---p 0000b000 00:2b 102652692                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
2abea87e5000-2abea87e6000 r--p 0000b000 00:2b 102652692                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
2abea87e6000-2abea87e8000 rw-p 0000c000 00:2b 102652692                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
2abea87e8000-2abea87e9000 rwxp 00000000 00:00 0 
2abea87e9000-2abea87ea000 r--p 00000000 00:2b 86153141                   /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/site-packages/numpy/_mklinit.cpython-36m-x86_64-linux-gnu.so
2abea87ea000-2abea87eb000 r-xp 00001000 00:2b 86153141                   /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/site-packages/numpy/_mklinit.cpython-36m-x86_64-linux-gnu.so
2abea87eb000-2abea87ec000 r--p 00002000 00:2b 86153141                   /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/site-packages/numpy/_mklinit.cpython-36m-x86_64-linux-gnu.so
2abea87ec000-2abea87ed000 r--p 00002000 00:2b 86153141                   /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/site-packages/numpy/_mklinit.cpython-36m-x86_64-linux-gnu.so
2abea87ed000-2abea87ee000 rw-p 00003000 00:2b 86153141                   /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/site-packages/numpy/_mklinit.cpython-36m-x86_64-linux-gnu.so
2abea87ee000-2abea87ef000 rw-p 00000000 00:00 0 
2abea87f1000-2abea89c2000 rw-p 00000000 00:00 0 
2abea89c6000-2abea89c7000 r--p 00021000 fd:00 83887133                   /usr/lib64/ld-2.17.so
2abea89c7000-2abea89c8000 rw-p 00022000 fd:00 83887133                   /usr/lib64/ld-2.17.so
2abea89c8000-2abea89c9000 rw-p 00000000 00:00 0 
2abea89c9000-2abea8cd1000 r-xp 00000000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2abea8cd1000-2abea8ed0000 ---p 00308000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2abea8ed0000-2abea8eee000 r--p 00307000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2abea8eee000-2abea8efa000 rw-p 00325000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2abea8efa000-2abea904c000 rw-p 00000000 00:00 0 
2abea904c000-2abea9078000 r-xp 00000000 00:28 29957067                   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
2abea9078000-2abea9277000 ---p 0002c000 00:28 29957067                   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
2abea9277000-2abea9278000 r--p 0002b000 00:28 29957067                   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
2abea9278000-2abea9279000 rw-p 0002c000 00:28 29957067                   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
2abea9279000-2abea92a5000 r-xp 00000000 00:28 3292602                    /hpc/software/gcc/6.4.0/lib64/libgomp.so.1.0.0
2abea92a5000-2abea94a5000 ---p 0002c000 00:28 3292602                    /hpc/software/gcc/6.4.0/lib64/libgomp.so.1.0.0
2abea94a5000-2abea94a6000 r--p 0002c000 00:28 3292602                    /hpc/software/gcc/6.4.0/lib64/libgomp.so.1.0.0
2abea94a6000-2abea94a7000 rw-p 0002d000 00:28 3292602                    /hpc/software/gcc/6.4.0/lib64/libgomp.so.1.0.0
2abea94a7000-2abea94be000 r-xp 00000000 fd:00 87526431                   /usr/lib64/libpthread-2.17.so
2abea94be000-2abea96bd000 ---p 00017000 fd:00 87526431                   /usr/lib64/libpthread-2.17.so
2abea96bd000-2abea96be000 r--p 00016000 fd:00 87526431                   /usr/lib64/libpthread-2.17.so
2abea96be000-2abea96bf000 rw-p 00017000 fd:00 87526431                   /usr/lib64/libpthread-2.17.so
2abea96bf000-2abea96c3000 rw-p 00000000 00:00 0 
Aborted

In R (base R environment):

*** Error in `/software/R/3.6.0/lib64/R/bin/exec/R': free(): invalid pointer: 0x000000000aa70bb8 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x2b877e927489]
/home/xxx/R/x86_64-pc-linux-gnu-library/3.6/reticulate/libs/reticulate.so(_Z31exception_to_condition_templateIN4Rcpp9exceptionEEP7SEXPRECRKT_b+0x329)[0x2b8790739689]
/home/xxx/R/x86_64-pc-linux-gnu-library/3.6/reticulate/libs/reticulate.so(_reticulate_py_eval_impl+0x282)[0x2b8790735792]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1380b6)[0x2b877dce40b6]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b877dcf26fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b877dcf3417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b877dce1974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b877dcf26fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b877dcf3417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b877dce1974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b877dcf1826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b877dcf0cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b877dcf1826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b877dcf0cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b877dcf1826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b877dcf0cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b877dcf1826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b877dcf0cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b877dcf26fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b877dcf3417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b877dce1974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b877dcf26fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b877dcf3417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b877dce1974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b877dcf26fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b877dcf3417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b877dce1974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b877dcf26fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b877dcf3417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b877dce1974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b877dcf26fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b877dcf3417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b877dce1974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b877dcf26fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b877dcf3417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b877dce1974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b877dcf1826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b877dcf0cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b877dcf1826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b877dcf0cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b877dcf1826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b877dcf0cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b877dcf1826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b877dcf0cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b877dcf10c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b877dcf26fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b877dcf3417]
======= Memory map: ========
00400000-00401000 r-xp 00000000 00:28 29957074                           /hpc/software/R/3.6.0/lib64/R/bin/exec/R
00600000-00601000 r--p 00000000 00:28 29957074                           /hpc/software/R/3.6.0/lib64/R/bin/exec/R
00601000-00602000 rw-p 00001000 00:28 29957074                           /hpc/software/R/3.6.0/lib64/R/bin/exec/R
00cd3000-0b849000 rw-p 00000000 00:00 0                                  [heap]
2b877d988000-2b877d9aa000 r-xp 00000000 fd:00 83887133                   /usr/lib64/ld-2.17.so
2b877d9aa000-2b877d9ad000 rw-p 00000000 00:00 0 
2b877d9ad000-2b877d9ae000 r--p 00000000 00:28 29957971                   /hpc/software/R/3.6.0/lib64/R/library/translations/en/LC_MESSAGES/R.mo
2b877d9ae000-2b877d9b5000 r--s 00000000 fd:00 67172538                   /usr/lib64/gconv/gconv-modules.cache
2b877d9b5000-2b877d9b6000 rwxp 00000000 00:00 0 
2b877d9b6000-2b877d9b7000 rw-p 00000000 00:00 0 
2b877d9d4000-2b877dba5000 rw-p 00000000 00:00 0 
2b877dba9000-2b877dbaa000 r--p 00021000 fd:00 83887133                   /usr/lib64/ld-2.17.so
2b877dbaa000-2b877dbab000 rw-p 00022000 fd:00 83887133                   /usr/lib64/ld-2.17.so
2b877dbab000-2b877dbac000 rw-p 00000000 00:00 0 
2b877dbac000-2b877deb4000 r-xp 00000000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2b877deb4000-2b877e0b3000 ---p 00308000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2b877e0b3000-2b877e0d1000 r--p 00307000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2b877e0d1000-2b877e0dd000 rw-p 00325000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2b877e0dd000-2b877e22f000 rw-p 00000000 00:00 0 
2b877e22f000-2b877e25b000 r-xp 00000000 00:28 29957067                   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
2b877e25b000-2b877e45a000 ---p 0002c000 00:28 29957067                   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
2b877e45a000-2b877e45b000 r--p 0002b000 00:28 29957067                   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
2b877e45b000-2b877e45c000 rw-p 0002c000 00:28 29957067                   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
2b877e45c000-2b877e488000 r-xp 00000000 00:28 3292602                    /hpc/software/gcc/6.4.0/lib64/libgomp.so.1.0.0
2b877e488000-2b877e688000 ---p 0002c000 00:28 3292602                    /hpc/software/gcc/6.4.0/lib64/libgomp.so.1.0.0
2b877e688000-2b877e689000 r--p 0002c000 00:28 3292602                    /hpc/software/gcc/6.4.0/lib64/libgomp.so.1.0.0
2b877e689000-2b877e68a000 rw-p 0002d000 00:28 3292602                    /hpc/software/gcc/6.4.0/lib64/libgomp.so.1.0.0
2b877e68a000-2b877e6a1000 r-xp 00000000 fd:00 87526431                   /usr/lib64/libpthread-2.17.so
2b877e6a1000-2b877e8a0000 ---p 00017000 fd:00 87526431                   /usr/lib64/libpthread-2.17.so
2b877e8a0000-2b877e8a1000 r--p 00016000 fd:00 87526431                   /usr/lib64/libpthread-2.17.so
2b877e8a1000-2b877e8a2000 rw-p 00017000 fd:00 87526431                   /usr/lib64/libpthread-2.17.so
2b877e8a2000-2b877e8a6000 rw-p 00000000 00:00 0 
2b877e8a6000-2b877ea68000 r-xp 00000000 fd:00 85715731                   /usr/lib64/libc-2.17.so
2b877ea68000-2b877ec68000 ---p 001c2000 fd:00 85715731                   /usr/lib64/libc-2.17.so
2b877ec68000-2b877ec6c000 r--p 001c2000 fd:00 85715731                   /usr/lib64/libc-2.17.so
2b877ec6c000-2b877ec6e000 rw-p 001c6000 fd:00 85715731                   /usr/lib64/libc-2.17.so
2b877ec6e000-2b877ec73000 rw-p 00000000 00:00 0 
2b877ec73000-2b877ed97000 r-xp 00000000 00:28 2239929                    /hpc/software/gcc/6.4.0/lib64/libgfortran.so.3.0.0
2b877ed97000-2b877ef96000 ---p 00124000 00:28 2239929                    /hpc/software/gcc/6.4.0/lib64/libgfortran.so.3.0.0
2b877ef96000-2b877ef97000 r--p 00123000 00:28 2239929                    /hpc/software/gcc/6.4.0/lib64/libgfortran.so.3.0.0
2b877ef97000-2b877ef99000 rw-p 00124000 00:28 2239929                    /hpc/software/gcc/6.4.0/lib64/libgfortran.so.3.0.0
2b877ef99000-2b877f09a000 r-xp 00000000 fd:00 84541978                   /usr/lib64/libm-2.17.so
2b877f09a000-2b877f299000 ---p 00101000 fd:00 84541978                   /usr/lib64/libm-2.17.so
2b877f299000-2b877f29a000 r--p 00100000 fd:00 84541978                   /usr/lib64/libm-2.17.so
2b877f29a000-2b877f29b000 rw-p 00101000 fd:00 84541978                   /usr/lib64/libm-2.17.so
2b877f29b000-2b877f2d9000 r-xp 00000000 00:28 2239917                    /hpc/software/gcc/6.4.0/lib64/libquadmath.so.0.0.0
2b877f2d9000-2b877f4d8000 ---p 0003e000 00:28 2239917                    /hpc/software/gcc/6.4.0/lib64/libquadmath.so.0.0.0
2b877f4d8000-2b877f4d9000 r--p 0003d000 00:28 2239917                    /hpc/software/gcc/6.4.0/lib64/libquadmath.so.0.0.0
2b877f4d9000-2b877f4da000 rw-p 0003e000 00:28 2239917                    /hpc/software/gcc/6.4.0/lib64/libquadmath.so.0.0.0
2b877f4da000-2b877f516000 r-xp 00000000 fd:00 83887372                   /usr/lib64/libreadline.so.6.2
2b877f516000-2b877f716000 ---p 0003c000 fd:00 83887372                   /usr/lib64/libreadline.so.6.2
2b877f716000-2b877f718000 r--p 0003c000 fd:00 83887372                   /usr/lib64/libreadline.so.6.2
2b877f718000-2b877f71e000 rw-p 0003e000 fd:00 83887372                   /usr/lib64/libreadline.so.6.2
2b877f71e000-2b877f720000 rw-p 00000000 00:00 0 
2b877f720000-2b877f75f000 r-xp 00000000 00:28 24606380                   /hpc/software/pcre/8.32/lib/libpcre.so.1.2.0
2b877f75f000-2b877f95f000 ---p 0003f000 00:28 24606380                   /hpc/software/pcre/8.32/lib/libpcre.so.1.2.0
2b877f95f000-2b877f960000 rw-p 0003f000 00:28 24606380                   /hpc/software/pcre/8.32/lib/libpcre.so.1.2.0
2b877f960000-2b877f985000 r-xp 00000000 fd:00 83887197                   /usr/lib64/liblzma.so.5.2.2
2b877f985000-2b877fb84000 ---p 00025000 fd:00 83887197                   /usr/lib64/liblzma.so.5.2.2
2b877fb84000-2b877fb85000 r--p 00024000 fd:00 83887197                   /usr/lib64/liblzma.so.5.2.2
2b877fb85000-2b877fb86000 rw-p 00025000 fd:00 83887197                   /usr/lib64/liblzma.so.5.2.2
2b877fb86000-2b877fb95000 r-xp 00000000 fd:00 83887391                   /usr/lib64/libbz2.so.1.0.6
2b877fb95000-2b877fd94000 ---p 0000f000 fd:00 83887391                   /usr/lib64/libbz2.so.1.0.6
2b877fd94000-2b877fd95000 r--p 0000e000 fd:00 83887391                   /usr/lib64/libbz2.so.1.0.6
2b877fd95000-2b877fd96000 rw-p 0000f000 fd:00 83887391                   /usr/lib64/libbz2.so.1.0.6
Aborted

In RStudio (base R environment):

*** Error in `/hpc/software/RStudio-desk/1.1.383/bin/rsession': free(): invalid pointer: 0x00000000059b09a8 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x2b47295e8489]
/home/xxx/R/x86_64-pc-linux-gnu-library/3.6/reticulate/libs/reticulate.so(_Z31exception_to_condition_templateIN4Rcpp9exceptionEEP7SEXPRECRKT_b+0x329)[0x2b4737a43689]
/home/xxx/R/x86_64-pc-linux-gnu-library/3.6/reticulate/libs/reticulate.so(_reticulate_py_eval_impl+0x282)[0x2b4737a3f792]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1380b6)[0x2b4727b3d0b6]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b4727b4b6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b4727b4c417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b4727b3a974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b4727b4b6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b4727b4c417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b4727b3a974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b4727b4a826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b4727b49cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b4727b4a826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b4727b49cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b4727b4a826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b4727b49cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b4727b4a826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b4727b49cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b4727b4b6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b4727b4c417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b4727b3a974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b4727b4b6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b4727b4c417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b4727b3a974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b4727b4b6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b4727b4c417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b4727b3a974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b4727b4b6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b4727b4c417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b4727b3a974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b4727b4b6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b4727b4c417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b4727b3a974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b4727b4b6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b4727b4c417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2b4727b3a974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b4727b4a826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b4727b49cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b4727b4a826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b4727b49cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b4727b4a826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b4727b49cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2b4727b4a826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2b4727b49cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2b4727b4a0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2b4727b4b6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2b4727b4c417]
======= Memory map: ========
00400000-011a3000 r-xp 00000000 00:28 1909741                            /hpc/software/RStudio-desk/1.1.383/bin/rsession
013a2000-013be000 r--p 00da2000 00:28 1909741                            /hpc/software/RStudio-desk/1.1.383/bin/rsession
013be000-013c3000 rw-p 00dbe000 00:28 1909741                            /hpc/software/RStudio-desk/1.1.383/bin/rsession
013c3000-013cc000 rw-p 00000000 00:00 0 
01aa5000-0ee1b000 rw-p 00000000 00:00 0                                  [heap]
2b47277e1000-2b4727803000 r-xp 00000000 fd:00 83887133                   /usr/lib64/ld-2.17.so
2b4727803000-2b4727805000 rw-p 00000000 00:00 0 
2b4727805000-2b4727806000 r--p 00000000 00:28 29957971                   /hpc/software/R/3.6.0/lib64/R/library/translations/en/LC_MESSAGES/R.mo
2b4727806000-2b4727807000 rwxp 00000000 00:00 0 
2b4727807000-2b472780e000 r--s 00000000 fd:00 67172538                   /usr/lib64/gconv/gconv-modules.cache
2b472780e000-2b472780f000 rw-p 00000000 00:00 0 
2b472782d000-2b47279ff000 rw-p 00000000 00:00 0 
2b4727a02000-2b4727a03000 r--p 00021000 fd:00 83887133                   /usr/lib64/ld-2.17.so
2b4727a03000-2b4727a04000 rw-p 00022000 fd:00 83887133                   /usr/lib64/ld-2.17.so
2b4727a04000-2b4727a05000 rw-p 00000000 00:00 0 
2b4727a05000-2b4727d0d000 r-xp 00000000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2b4727d0d000-2b4727f0c000 ---p 00308000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2b4727f0c000-2b4727f2a000 r--p 00307000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2b4727f2a000-2b4727f36000 rw-p 00325000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2b4727f36000-2b4728088000 rw-p 00000000 00:00 0 
2b4728088000-2b472808a000 r-xp 00000000 fd:00 84541976                   /usr/lib64/libdl-2.17.so
2b472808a000-2b472828a000 ---p 00002000 fd:00 84541976                   /usr/lib64/libdl-2.17.so
2b472828a000-2b472828b000 r--p 00002000 fd:00 84541976                   /usr/lib64/libdl-2.17.so
2b472828b000-2b472828c000 rw-p 00003000 fd:00 84541976                   /usr/lib64/libdl-2.17.so
2b472828c000-2b47282a3000 r-xp 00000000 fd:00 87526431                   /usr/lib64/libpthread-2.17.so
2b47282a3000-2b47284a2000 ---p 00017000 fd:00 87526431                   /usr/lib64/libpthread-2.17.so
2b47284a2000-2b47284a3000 r--p 00016000 fd:00 87526431                   /usr/lib64/libpthread-2.17.so
2b47284a3000-2b47284a4000 rw-p 00017000 fd:00 87526431                   /usr/lib64/libpthread-2.17.so
2b47284a4000-2b47284a8000 rw-p 00000000 00:00 0 
2b47284a8000-2b47284aa000 r-xp 00000000 fd:00 87526439                   /usr/lib64/libutil-2.17.so
2b47284aa000-2b47286a9000 ---p 00002000 fd:00 87526439                   /usr/lib64/libutil-2.17.so
2b47286a9000-2b47286aa000 r--p 00001000 fd:00 87526439                   /usr/lib64/libutil-2.17.so
2b47286aa000-2b47286ab000 rw-p 00002000 fd:00 87526439                   /usr/lib64/libutil-2.17.so
2b47286ab000-2b47286af000 r-xp 00000000 fd:00 83913832                   /usr/lib64/libuuid.so.1.3.0
2b47286af000-2b47288ae000 ---p 00004000 fd:00 83913832                   /usr/lib64/libuuid.so.1.3.0
2b47288ae000-2b47288af000 r--p 00003000 fd:00 83913832                   /usr/lib64/libuuid.so.1.3.0
2b47288af000-2b47288b0000 rw-p 00004000 fd:00 83913832                   /usr/lib64/libuuid.so.1.3.0
2b47288b0000-2b47288b7000 r-xp 00000000 fd:00 87526435                   /usr/lib64/librt-2.17.so
2b47288b7000-2b4728ab6000 ---p 00007000 fd:00 87526435                   /usr/lib64/librt-2.17.so
2b4728ab6000-2b4728ab7000 r--p 00006000 fd:00 87526435                   /usr/lib64/librt-2.17.so
2b4728ab7000-2b4728ab8000 rw-p 00007000 fd:00 87526435                   /usr/lib64/librt-2.17.so
2b4728ab8000-2b4728acd000 r-xp 00000000 fd:00 85715747                   /usr/lib64/libz.so.1.2.7
2b4728acd000-2b4728ccc000 ---p 00015000 fd:00 85715747                   /usr/lib64/libz.so.1.2.7
2b4728ccc000-2b4728ccd000 r--p 00014000 fd:00 85715747                   /usr/lib64/libz.so.1.2.7
2b4728ccd000-2b4728cce000 rw-p 00015000 fd:00 85715747                   /usr/lib64/libz.so.1.2.7
2b4728cce000-2b4728e3f000 r-xp 00000000 00:28 2239813                    /hpc/software/gcc/6.4.0/lib64/libstdc++.so.6.0.22
2b4728e3f000-2b472903e000 ---p 00171000 00:28 2239813                    /hpc/software/gcc/6.4.0/lib64/libstdc++.so.6.0.22
2b472903e000-2b4729048000 r--p 00170000 00:28 2239813                    /hpc/software/gcc/6.4.0/lib64/libstdc++.so.6.0.22
2b4729048000-2b472904a000 rw-p 0017a000 00:28 2239813                    /hpc/software/gcc/6.4.0/lib64/libstdc++.so.6.0.22
2b472904a000-2b472904e000 rw-p 00000000 00:00 0 
2b472904e000-2b472914f000 r-xp 00000000 fd:00 84541978                   /usr/lib64/libm-2.17.so
2b472914f000-2b472934e000 ---p 00101000 fd:00 84541978                   /usr/lib64/libm-2.17.so
2b472934e000-2b472934f000 r--p 00100000 fd:00 84541978                   /usr/lib64/libm-2.17.so
2b472934f000-2b4729350000 rw-p 00101000 fd:00 84541978                   /usr/lib64/libm-2.17.so
2b4729350000-2b4729366000 r-xp 00000000 00:28 2239040                    /hpc/software/gcc/6.4.0/lib64/libgcc_s.so.1
2b4729366000-2b4729565000 ---p 00016000 00:28 2239040                    /hpc/software/gcc/6.4.0/lib64/libgcc_s.so.1
2b4729565000-2b4729566000 r--p 00015000 00:28 2239040                    /hpc/software/gcc/6.4.0/lib64/libgcc_s.so.1
2b4729566000-2b4729567000 rw-p 00016000 00:28 2239040                    /hpc/software/gcc/6.4.0/lib64/libgcc_s.so.1
2b4729567000-2b4729729000 r-xp 00000000 fd:00 85715731                   /usr/lib64/libc-2.17.so
2b4729729000-2b4729929000 ---p 001c2000 fd:00 85715731                   /usr/lib64/libc-2.17.so
2b4729929000-2b472992d000 r--p 001c2000 fd:00 85715731                   /usr/lib64/libc-2.17.so
2b472992d000-2b472992f000 rw-p 001c6000 fd:00 85715731                   /usr/lib64/libc-2.17.so
2b472992f000-2b4729934000 rw-p 00000000 00:00 0 
2b4729934000-2b4729960000 r-xp 00000000 00:28 29957067                   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
2b4729960000-2b4729b5f000 ---p 0002c000 00:28 29957067                   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
2b4729b5f000-2b4729b60000 r--p 0002b000 00:28 29957067                   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
2b4729b60000-2b4729b61000 rw-p 0002c000 00:28 29957067                   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
2b4729b61000-2b4729c85000 r-xp 00000000 00:28 2239929                    /hpc/software/gcc/6.4.0/lib64/libgfortran.so.3.0.0
2b4729c85000-2b4729e84000 ---p 00124000 00:28 2239929                    /hpc/software/gcc/6.4.0/lib64/libgfortran.so.3.0.0
2b4729e84000-2b4729e85000 r--p 00123000 00:28 2239929                    /hpc/software/gcc/6.4.0/lib64/libgfortran.so.3.0.0
2b4729e85000-2b4729e87000 rw-p 00124000 00:28 2239929                    /hpc/software/gcc/6.4.0/lib64/libgfortran.so.3.0.0
2b4729e87000-2b4729ec5000 r-xp 00000000 00:28 2239917                    /hpc/software/gcc/6.4.0/lib64/libquadmath.so.0.0.0
2b4729ec5000-2b472a0c4000 ---p 0003e000 00:28 2239917                    /hpc/software/gcc/6.4.0/lib64/libquadmath.so.0.0.0
2b472a0c4000-2b472a0c5000 r--p 0003d000 00:28 2239917                    /hpc/software/gcc/6.4.0/lib64/libquadmath.so.0.0.0
2b472a0c5000-2b472a0c6000 rw-p 0003e000 00:28 2239917                    /hpc/software/gcc/6.4.0/lib64/libquadmath.so.0.0.0
2b472a0c6000-2b472a102000 r-xp 00000000 fd:00 83887372                   /usr/lib64/libreadline.so.6.2
2b472a102000-2b472a302000 ---p 0003c000 fd:00 83887372                   /usr/lib64/libreadline.so.6.2
2b472a302000-2b472a304000 r--p 0003c000 fd:00 83887372                   /usr/lib64/libreadline.so.6.2

In RStudio (r-tensorflow environment)

*** Error in `/hpc/software/RStudio-desk/1.1.383/bin/rsession': free(): invalid pointer: 0x0000000001d4ce38 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x2aeaf9e0f489]
/home/xxx/R/x86_64-pc-linux-gnu-library/3.6/reticulate/libs/reticulate.so(_Z31exception_to_condition_templateIN4Rcpp9exceptionEEP7SEXPRECRKT_b+0x329)[0x2aeb1aa4b689]
/home/xxx/R/x86_64-pc-linux-gnu-library/3.6/reticulate/libs/reticulate.so(_reticulate_py_eval_impl+0x282)[0x2aeb1aa47792]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1380b6)[0x2aeaf83640b6]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2aeaf83726fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2aeaf8373417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2aeaf8361974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2aeaf83726fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2aeaf8373417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2aeaf8361974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2aeaf8371826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2aeaf8370cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2aeaf8371826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2aeaf8370cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2aeaf8371826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2aeaf8370cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2aeaf8371826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2aeaf8370cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2aeaf83726fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2aeaf8373417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2aeaf8361974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2aeaf83726fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2aeaf8373417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2aeaf8361974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2aeaf83726fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2aeaf8373417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2aeaf8361974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2aeaf83726fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2aeaf8373417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2aeaf8361974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2aeaf83726fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2aeaf8373417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2aeaf8361974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2aeaf83726fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2aeaf8373417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2aeaf8361974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2aeaf8371826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2aeaf8370cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2aeaf8371826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2aeaf8370cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2aeaf8371826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2aeaf8370cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2aeaf8371826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2aeaf8370cb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2aeaf83710c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2aeaf83726fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2aeaf8373417]
======= Memory map: ========
00400000-011a3000 r-xp 00000000 00:28 1909741                            /hpc/software/RStudio-desk/1.1.383/bin/rsession
013a2000-013be000 r--p 00da2000 00:28 1909741                            /hpc/software/RStudio-desk/1.1.383/bin/rsession
013be000-013c3000 rw-p 00dbe000 00:28 1909741                            /hpc/software/RStudio-desk/1.1.383/bin/rsession
013c3000-013cc000 rw-p 00000000 00:00 0 
0199d000-0effd000 rw-p 00000000 00:00 0                                  [heap]
2aeaf8008000-2aeaf802a000 r-xp 00000000 fd:00 83887133                   /usr/lib64/ld-2.17.so
2aeaf802a000-2aeaf802c000 rw-p 00000000 00:00 0 
2aeaf802c000-2aeaf802d000 r--p 00000000 00:28 29957971                   /hpc/software/R/3.6.0/lib64/R/library/translations/en/LC_MESSAGES/R.mo
2aeaf802d000-2aeaf802e000 rwxp 00000000 00:00 0 
2aeaf802e000-2aeaf8035000 r--s 00000000 fd:00 67172538                   /usr/lib64/gconv/gconv-modules.cache
2aeaf8035000-2aeaf8036000 r--p 00000000 00:2b 102652674                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2aeaf8036000-2aeaf8038000 r-xp 00001000 00:2b 102652674                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2aeaf8038000-2aeaf8039000 r--p 00003000 00:2b 102652674                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2aeaf8039000-2aeaf803a000 r--p 00003000 00:2b 102652674                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2aeaf803a000-2aeaf803c000 rw-p 00004000 00:2b 102652674                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
2aeaf803c000-2aeaf803f000 r--p 00000000 00:2b 102652692                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
2aeaf803f000-2aeaf8045000 r-xp 00003000 00:2b 102652692                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
2aeaf8045000-2aeaf8047000 r--p 00009000 00:2b 102652692                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
2aeaf8047000-2aeaf8048000 ---p 0000b000 00:2b 102652692                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
2aeaf8048000-2aeaf8049000 r--p 0000b000 00:2b 102652692                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
2aeaf8049000-2aeaf804b000 rw-p 0000c000 00:2b 102652692                  /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
2aeaf804b000-2aeaf804c000 r--p 00000000 00:2b 86153141                   /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/site-packages/numpy/_mklinit.cpython-36m-x86_64-linux-gnu.so
2aeaf804c000-2aeaf804d000 r-xp 00001000 00:2b 86153141                   /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/site-packages/numpy/_mklinit.cpython-36m-x86_64-linux-gnu.so
2aeaf804d000-2aeaf804e000 r--p 00002000 00:2b 86153141                   /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/site-packages/numpy/_mklinit.cpython-36m-x86_64-linux-gnu.so
2aeaf804e000-2aeaf804f000 r--p 00002000 00:2b 86153141                   /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/site-packages/numpy/_mklinit.cpython-36m-x86_64-linux-gnu.so
2aeaf804f000-2aeaf8050000 rw-p 00003000 00:2b 86153141                   /home/xxx/.conda/envs/r-tensorflow/lib/python3.6/site-packages/numpy/_mklinit.cpython-36m-x86_64-linux-gnu.so
2aeaf8050000-2aeaf8051000 rw-p 00000000 00:00 0 
2aeaf8054000-2aeaf8226000 rw-p 00000000 00:00 0 
2aeaf8229000-2aeaf822a000 r--p 00021000 fd:00 83887133                   /usr/lib64/ld-2.17.so
2aeaf822a000-2aeaf822b000 rw-p 00022000 fd:00 83887133                   /usr/lib64/ld-2.17.so
2aeaf822b000-2aeaf822c000 rw-p 00000000 00:00 0 
2aeaf822c000-2aeaf8534000 r-xp 00000000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2aeaf8534000-2aeaf8733000 ---p 00308000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2aeaf8733000-2aeaf8751000 r--p 00307000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
2aeaf8751000-2aeaf875d000 rw-p 00325000 00:28 29957076                   /hpc/software/R/3.6.0/lib64/R/lib/libR.so
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2aeaf8ccb000-2aeaf8ccf000 rw-p 00000000 00:00 0 
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2aeaf8cd1000-2aeaf8ed0000 ---p 00002000 fd:00 87526439                   /usr/lib64/libutil-2.17.so
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2aeaf8ed2000-2aeaf8ed6000 r-xp 00000000 fd:00 83913832                   /usr/lib64/libuuid.so.1.3.0
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2aeaf90d7000-2aeaf90de000 r-xp 00000000 fd:00 87526435                   /usr/lib64/librt-2.17.so
2aeaf90de000-2aeaf92dd000 ---p 00007000 fd:00 87526435                   /usr/lib64/librt-2.17.so
2aeaf92dd000-2aeaf92de000 r--p 00006000 fd:00 87526435                   /usr/lib64/librt-2.17.so

skeydan commented 5 years ago

Thanks! So it seems like tensorflow is not really involved (and notreticulate either I guess).

Could you try using the virtualenv method instead of conda, to see if it's due to the Python installed by conda (in interaction with other things on this system)? Please get the current tensorflow from github and do

install_tensorflow(method = "virtualenv")

and then try again.

If that doesn't help, can you install an older version of R (3.5)?

jerryji1993 commented 5 years ago

Hi skeydan,

Thanks--unfortunately I was also not able to install via virtualenv method. When I tried to do this in a clear R (version 3.6) session, without any conda environment activated, it gives me the following error:

Creating  r-tensorflow  virtualenv environment... 
Creating virtual environment 'r-tensorflow' ...
Using python: /hpc/software/anaconda3.6/bin/python3.6
Error: Command '['/home/xxx/.virtualenvs/r-tensorflow/bin/python3.6', '-Im', 'ensurepip', '--upgrade', '--default-pip']' returned non-zero exit status 1.
Error: Error creating virtual environment 'r-tensorflow' [error code 1]

It seems that it is related to pip on my system. Since I'm running on a high performance computing cluster, the way this system works is that I'm not allowed to install/modify softwares globally. Based on the error message, my guess is that the program crashes when it attempts to globally upgrade my pip?

That being said, I actually need to run two commands every time before I use python/R to load the specific python/R version previously installed on our system:

$module load python/anaconda3.6
$module load R/3.6.0

However, I can create conda environment locally and install anything I want in there, which was why I used the conda method initially.

Also, this time when I removed tensorflow, keras and reticulate R packages and reinstall them (this time I installed tensorflow first and then keras both from github, following your instruction, while previously I only installed keras without explicitly installing tensorflow), simply loading keras package (library(keras)) crashes the system.

In R 3.5.1: I installed everything and ran model <- keras_model_sequential() in both base and r-tensorflow conda environment. In either cases, I was given the following error:

Base environment:

Error: Python module tensorflow.python.keras was not found.

Detected Python configuration:

python:         /software/anaconda3.6/bin/python
libpython:      /software/anaconda3.6/lib/libpython3.6m.so
pythonhome:     /software/anaconda3.6:/software/anaconda3.6
version:        3.6.0 |Anaconda 4.3.0 (64-bit)| (default, Dec 23 2016, 12:22:00)  [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
numpy:          /home/xxx/.local/lib/python3.6/site-packages/numpy
numpy_version:  1.16.4
tensorflow:     /software/anaconda3.6/lib/python3.6/site-packages/tensorflow

python versions found: 
 /software/anaconda3.6/bin/python
 /usr/bin/python

r-tensorflow environment:

Error: Python module tensorflow.python.keras was not found.

Detected Python configuration:

python:         /home/xxx/.conda/envs/r-tensorflow/bin/python
libpython:      /home/xxx/.conda/envs/r-tensorflow/lib/libpython3.7m.so
pythonhome:     /home/xxx/.conda/envs/r-tensorflow:/home/yjq6148/.conda/envs/r-tensorflow
version:        3.7.3 (default, Mar 27 2019, 22:11:17)  [GCC 7.3.0]
numpy:          /home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/numpy
numpy_version:  1.16.4
tensorflow:     /home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow

python versions found: 
 /home/xxx/.conda/envs/r-tensorflow/bin/python
 /usr/bin/python

Haven't tried in RStudio yet.

dfalbel commented 5 years ago

Just to be sure it works from python... Can you try importing tensorflow directly in python?

You can run in your terminal:

/home/xxx/.conda/envs/r-tensorflow/bin/python

And then run import tensorflow as tf

jerryji1993 commented 5 years ago

Just to be sure it works from python... Can you try importing tensorflow directly in python?

You can run in your terminal:
/home/xxx/.conda/envs/r-tensorflow/bin/python
And then run import tensorflow as tf

Hi dfalbel,

Importing tensorflow failed inside the conda environment.

>>> import tensorflow as tf
Traceback (most recent call last):
  File "/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
    from tensorflow.python.pywrap_tensorflow_internal import *
  File "/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
    _pywrap_tensorflow_internal = swig_import_helper()
  File "/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
    _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
  File "/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/imp.py", line 242, in load_module
    return load_dynamic(name, filename, file)
  File "/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/imp.py", line 342, in load_dynamic
    return _load(spec)
ImportError: /lib64/libm.so.6: version `GLIBC_2.23' not found (required by /home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow/__init__.py", line 24, in <module>
    from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
  File "/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow/python/__init__.py", line 49, in <module>
    from tensorflow.python import pywrap_tensorflow
  File "/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
    raise ImportError(msg)
ImportError: Traceback (most recent call last):
  File "/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
    from tensorflow.python.pywrap_tensorflow_internal import *
  File "/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
    _pywrap_tensorflow_internal = swig_import_helper()
  File "/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
    _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
  File "/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/imp.py", line 242, in load_module
    return load_dynamic(name, filename, file)
  File "/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/imp.py", line 342, in load_dynamic
    return _load(spec)
ImportError: /lib64/libm.so.6: version `GLIBC_2.23' not found (required by /home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so)

Failed to load the native TensorFlow runtime.

See https://www.tensorflow.org/install/errors

for some common reasons and solutions.  Include the entire stack trace
above this error message when asking for help.

However, importing in base environment was successful. Yet, in either case the R package fails.

Thanks!

skeydan commented 5 years ago

I was going to ask what you meant by "base environment" and scrolling up, I found something I actually had missed somehow, namely, that you have 2 Anaconda installations of TensorFlow (leaving aside any virtualenvs):

/software/anaconda3.6/lib/python3.6/site-packages/tensorflow with Python 3.6
/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow with Python 3.7

Googling for the glibc - related error yielded e.g. https://github.com/tensorflow/tensorflow/issues/28660 which indicates that people running into this error on CentOS seem to have been able to solve it by using Python 3.6 instead of Python 3.7. This matches what you're reporting, that you can import TensorFlow in the base env.

So let's focus on this one for now. What happens if you call repl_python in command line R?

jerryji1993 commented 5 years ago

I was going to ask what you meant by "base environment" and scrolling up, I found something I actually had missed somehow, namely, that you have 2 Anaconda installations of TensorFlow (leaving aside any virtualenvs):

/software/anaconda3.6/lib/python3.6/site-packages/tensorflow with Python 3.6

/home/xxx/.conda/envs/r-tensorflow/lib/python3.7/site-packages/tensorflow with Python 3.7

Googling for the glibc - related error yielded e.g. tensorflow/tensorflow#28660 which indicates that people running into this error on CentOS seem to have been able to solve it by using Python 3.6 instead of Python 3.7. This matches what you're reporting, that you can import TensorFlow in the base env.

So let's focus on this one for now. What happens if you call repl_python in command line R?

Hi skeydan,

Thanks for your response and so sorry about the confusion.

What I meant by "base" is just no activated conda environments i.e. using the python and anaconda globally installed on our cluster, not the ones I install in my conda environment (essentially, i tried both source activate r-tensorflow and then command line R, and without activating the r-tensorflow environment, but neither worked--please see earlier post).

Calling repl_python() works fine in R 3.5.1.

In 3.6.0:

*** Error in `/software/R/3.6.0/lib64/R/bin/exec/R': free(): invalid pointer: 0x000000000c321b78 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7c503)[0x2ae95558c503]
/home/xxx/R/x86_64-pc-linux-gnu-library/3.6/reticulate/libs/reticulate.so(_Z31exception_to_condition_templateIN4Rcpp9exceptionEEP7SEXPRECRKT_b+0x329)[0x2ae961082229]
/home/xxx/R/x86_64-pc-linux-gnu-library/3.6/reticulate/libs/reticulate.so(_reticulate_py_eval_impl+0x282)[0x2ae96107e362]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1380b6)[0x2ae95494e0b6]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2ae95495c6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2ae95495d417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2ae95494b974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2ae95495c6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2ae95495d417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2ae95494b974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2ae95495b826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2ae95495acb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2ae95495b826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2ae95495acb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2ae95495b826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2ae95495acb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2ae95495b826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2ae95495acb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2ae95495c6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2ae95495d417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2ae95494b974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2ae95495c6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2ae95495d417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2ae95494b974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2ae95495c6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2ae95495d417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2ae95494b974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2ae95495c6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2ae95495d417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2ae95494b974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2ae95495c6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2ae95495d417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2ae95494b974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2ae95495c6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2ae95495d417]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x135974)[0x2ae95494b974]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2ae95495b826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2ae95495acb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2ae95495b826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2ae95495acb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2ae95495b826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2ae95495acb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x145826)[0x2ae95495b826]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x144cb1)[0x2ae95495acb1]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_eval+0x348)[0x2ae95495b0c8]
/software/R/3.6.0/lib64/R/lib/libR.so(+0x1466fb)[0x2ae95495c6fb]
/software/R/3.6.0/lib64/R/lib/libR.so(Rf_applyClosure+0x187)[0x2ae95495d417]
======= Memory map: ========
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2ae9a79c5000-2ae9a79c8000 r-xp 00000000 00:28 27108960                   /hpc/software/anaconda3.6/lib/python3.6/lib-dynload/_random.cpython-36m-x86_64-linux-gnu.so
2ae9a79c8000-2ae9a7bc7000 ---p 00003000 00:28 27108960                   /hpc/software/anaconda3.6/lib/python3.6/lib-dynload/_random.cpython-36m-x86_64-linux-gnu.so
2ae9a7bc7000-2ae9a7bc8000 rw-p 00002000 00:28 27108960                   /hpc/software/anaconda3.6/lib/python3.6/lib-dynload/_random.cpython-36m-x86_64-linux-gnu.so
2ae9a7bc8000-2ae9a7bc9000 ---p 00000000 00:00 0 
2ae9a7bc9000-2ae9a7e09000 rw-p 00000000 00:00 0                          [stack:21175]
2ae9a7e09000-2ae9a7e0a000 r-xp 00000000 00:28 27108957                   /hpc/software/anaconda3.6/lib/python3.6/lib-dynload/_opcode.cpython-36m-x86_64-linux-gnu.so
2ae9a7e0a000-2ae9a8009000 ---p 00001000 00:28 27108957                   /hpc/software/anaconda3.6/lib/python3.6/lib-dynload/_opcode.cpython-36m-x86_64-linux-gnu.so
2ae9a8009000-2ae9a800a000 rw-p 00000000 00:28 27108957                   /hpc/software/anaconda3.6/lib/python3.6/lib-dynload/_opcode.cpython-36m-x86_64-linux-gnu.so
7ffc37a13000-7ffc37a5d000 rw-p 00000000 00:00 0                          [stack]
7ffc37a90000-7ffc37a92000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)

skeydan commented 5 years ago

Calling repl_python() works fine in R 3.5.1.

Would working in the base environment, under R 3.5.1, be an option for you then? Given the little control you have in an environment others are managing, I'd go for the first thing that works.

jerryji1993 commented 5 years ago

UPDATE: I reinstalled my tensorflow with the following command:

python3 -m pip install --upgrade --user https://storage.googleapis.com/tensorflow/linux/cpu/tensorflow-1.14.0-cp36-cp36m-linux_x86_64.whl

and now it works in R/3.5.1 (both in command line R and RStudio).

jerryji1993 commented 5 years ago

Calling repl_python() works fine in R 3.5.1.

Would working in the base environment, under R 3.5.1, be an option for you then? Given the little control you have in an environment others are managing, I'd go for the first thing that works.

Hi skeydan,

Thanks for all your help! Preferably, I would like to work in R 3.6.0 since some of my other packages requires 3.6.0. I haven't tried running in 3.6.0 with my reinstalled tensorflow yet, will try that in a minute.

However, are you suggesting that the problem may be due to the installation of R/python in our system? I should be able to contact our system administrator for a fix, but I need to know where the problem is.

Thanks!

skeydan commented 5 years ago

No, I didn't mean to imply that - just that the whole software stack involved is pretty big, and that on enterprise systems like RedHat options may sometimes be restricted due to compatibility issues :-)

jerryji1993 commented 5 years ago

No, I didn't mean to imply that - just that the whole software stack involved is pretty big, and that on enterprise systems like RedHat options may sometimes be restricted due to compatibility issues :-)

Hi skeydan,

Got it!

Good news--everything also works in R 3.6.0 now. It seems weird, but reinstalling tensorflow this time seems to have solved everything (although I have tried a couple of times eariler using different commands for reinstallation).

Again, thanks for all the help :-)!!

skeydan commented 5 years ago

You're welcome! I'm happy to hear that it worked!

rstudio / keras3

RStudio session aborted when executing keras_model_sequential(): invalid pointer #824