M1 Mac appears to abort when running `reticulate::py_module_available("tensorflow")` #465

njtierney · 2021-05-10T08:36:36Z

I wasn't able to reproduce this running reprex as this crashes R, but when using the CRAN version of greta, when I run reticulate::py_module_available("tensorflow"), I get

This reprex appears to crash R.
See standard output and standard error for more details.

Standard output and error

 *** caught illegal operation ***
address 0x189ddd024, cause 'illegal trap'

Traceback:
 1: py_module_import(module, convert = convert)
 2: import(module)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch({    import(module)    TRUE}, error = clear_error_handler(FALSE))
 7: reticulate::py_module_available("tensorflow")
 8: eval(expr, envir, enclos)
 9: eval(expr, envir, enclos)
10: withVisible(eval(expr, envir, enclos))
11: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,     error = eHandler, message = mHandler)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
16: try(f, silent = TRUE)
17: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,     enclos)), warning = wHandler, error = eHandler, message = mHandler))
18: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
19: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     output_handler = output_handler, include_timing = include_timing)
20: evaluate::evaluate(...)
21: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),     keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options))
22: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),     stop_on_error = if (is.numeric(options$error)) options$error else {        if (options$error && options$include)             0L        else 2L    }, output_handler = knit_handlers(options$render, options)))
23: eng_r(options)
24: block_exec(params)
25: call_block(x)
26: process_group.block(group)
27: process_group(group)
28: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        setwd(wd)        cat(res, sep = "\n", file = output %n% "")        message("Quitting from lines ", paste(current_lines(i),             collapse = "-"), " (", knit_concord$get("infile"),             ") ")    })
29: process_file(text, output)
30: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
31: rmarkdown::render(input, quiet = TRUE, envir = globalenv(), encoding = "UTF-8")
32: (function (input) {    rmarkdown::render(input, quiet = TRUE, envir = globalenv(),         encoding = "UTF-8")})(input = base::quote("soot-cub_reprex.R"))
33: (function (what, args, quote = FALSE, envir = parent.frame()) {    if (!is.list(args))         stop("second argument must be a list")    if (quote)         args <- lapply(args, enquote)    .Internal(do.call(what, args, envir))})(base::quote(function (input) {    rmarkdown::render(input, quiet = TRUE, envir = globalenv(),         encoding = "UTF-8")}), base::quote(list(input = "soot-cub_reprex.R")), envir = base::quote(<environment>),     quote = base::quote(TRUE))
34: do.call(do.call, c(readRDS("/var/folders/fs/clgy1jd123b6cjk9ffx51tgdv5kdzr/T//Rtmpzkt86P/callr-fun-9387fb88307"),     list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv,     quote = TRUE)
35: saveRDS(do.call(do.call, c(readRDS("/var/folders/fs/clgy1jd123b6cjk9ffx51tgdv5kdzr/T//Rtmpzkt86P/callr-fun-9387fb88307"),     list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv,     quote = TRUE), file = "/var/folders/fs/clgy1jd123b6cjk9ffx51tgdv5kdzr/T//Rtmpzkt86P/callr-res-93871aa248a1")
36: withCallingHandlers({    NULL    saveRDS(do.call(do.call, c(readRDS("/var/folders/fs/clgy1jd123b6cjk9ffx51tgdv5kdzr/T//Rtmpzkt86P/callr-fun-9387fb88307"),         list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv,         quote = TRUE), file = "/var/folders/fs/clgy1jd123b6cjk9ffx51tgdv5kdzr/T//Rtmpzkt86P/callr-res-93871aa248a1")    flush(stdout())    flush(stderr())    NULL    invisible()}, error = function(e) {    {        callr_data <- as.environment("tools:callr")$`__callr_data__`        err <- callr_data$err        assign(".Traceback", .traceback(4), envir = callr_data)        dump.frames("__callr_dump__")        assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data)        rm("__callr_dump__", envir = .GlobalEnv)        e$call <- deparse(conditionCall(e), nlines = 6)        e2 <- err$new_error(conditionMessage(e), call. = conditionCall(e))        class(e2) <- c("callr_remote_error", class(e2))        e2$error <- e        calls <- sys.calls()        dcframe <- which(vapply(calls, function(x) length(x) >=             1 && identical(x[[1]], quote(do.call)), logical(1)))[1]        if (!is.na(dcframe))             e2$`_ignore` <- list(c(1, dcframe + 1L))        e2$`_pid` <- Sys.getpid()        e2$`_timestamp` <- Sys.time()        if (inherits(e, "rlib_error_2_0"))             e2$parent <- e$parent        e2 <- err$add_trace_back(e2, embed = FALSE)        saveRDS(list("error", e2), file = paste0("/var/folders/fs/clgy1jd123b6cjk9ffx51tgdv5kdzr/T//Rtmpzkt86P/callr-res-93871aa248a1",             ".error"))    }}, interrupt = function(e) {    {        callr_data <- as.environment("tools:callr")$`__callr_data__`        err <- callr_data$err        assign(".Traceback", .traceback(4), envir = callr_data)        dump.frames("__callr_dump__")        assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data)        rm("__callr_dump__", envir = .GlobalEnv)        e$call <- deparse(conditionCall(e), nlines = 6)        e2 <- err$new_error(conditionMessage(e), call. = conditionCall(e))        class(e2) <- c("callr_remote_error", class(e2))        e2$error <- e        calls <- sys.calls()        dcframe <- which(vapply(calls, function(x) length(x) >=             1 && identical(x[[1]], quote(do.call)), logical(1)))[1]        if (!is.na(dcframe))             e2$`_ignore` <- list(c(1, dcframe + 1L))        e2$`_pid` <- Sys.getpid()        e2$`_timestamp` <- Sys.time()        if (inherits(e, "rlib_error_2_0"))             e2$parent <- e$parent        e2 <- err$add_trace_back(e2, embed = FALSE)        saveRDS(list("error", e2), file = paste0("/var/folders/fs/clgy1jd123b6cjk9ffx51tgdv5kdzr/T//Rtmpzkt86P/callr-res-93871aa248a1",             ".error"))    }}, callr_message = function(e) {    try(signalCondition(e))})
37: doTryCatch(return(expr), name, parentenv, handler)
38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
39: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
40: doTryCatch(return(expr), name, parentenv, handler)
41: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
42: tryCatchList(expr, classes, parentenv, handlers)
43: tryCatch(withCallingHandlers({    NULL    saveRDS(do.call(do.call, c(readRDS("/var/folders/fs/clgy1jd123b6cjk9ffx51tgdv5kdzr/T//Rtmpzkt86P/callr-fun-9387fb88307"),         list(envir = .GlobalEnv, quote = TRUE)), envir = .GlobalEnv,         quote = TRUE), file = "/var/folders/fs/clgy1jd123b6cjk9ffx51tgdv5kdzr/T//Rtmpzkt86P/callr-res-93871aa248a1")    flush(stdout())    flush(stderr())    NULL    invisible()}, error = function(e) {    {        callr_data <- as.environment("tools:callr")$`__callr_data__`        err <- callr_data$err        assign(".Traceback", .traceback(4), envir = callr_data)        dump.frames("__callr_dump__")        assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data)        rm("__callr_dump__", envir = .GlobalEnv)        e$call <- deparse(conditionCall(e), nlines = 6)        e2 <- err$new_error(conditionMessage(e), call. = conditionCall(e))        class(e2) <- c("callr_remote_error", class(e2))        e2$error <- e        calls <- sys.calls()        dcframe <- which(vapply(calls, function(x) length(x) >=             1 && identical(x[[1]], quote(do.call)), logical(1)))[1]        if (!is.na(dcframe))             e2$`_ignore` <- list(c(1, dcframe + 1L))        e2$`_pid` <- Sys.getpid()        e2$`_timestamp` <- Sys.time()        if (inherits(e, "rlib_error_2_0"))             e2$parent <- e$parent        e2 <- err$add_trace_back(e2, embed = FALSE)        saveRDS(list("error", e2), file = paste0("/var/folders/fs/clgy1jd123b6cjk9ffx51tgdv5kdzr/T//Rtmpzkt86P/callr-res-93871aa248a1",             ".error"))    }}, interrupt = function(e) {    {        callr_data <- as.environment("tools:callr")$`__callr_data__`        err <- callr_data$err        assign(".Traceback", .traceback(4), envir = callr_data)        dump.frames("__callr_dump__")        assign(".Last.dump", .GlobalEnv$`__callr_dump__`, envir = callr_data)        rm("__callr_dump__", envir = .GlobalEnv)        e$call <- deparse(conditionCall(e), nlines = 6)        e2 <- err$new_error(conditionMessage(e), call. = conditionCall(e))        class(e2) <- c("callr_remote_error", class(e2))        e2$error <- e        calls <- sys.calls()        dcframe <- which(vapply(calls, function(x) length(x) >=             1 && identical(x[[1]], quote(do.call)), logical(1)))[1]        if (!is.na(dcframe))             e2$`_ignore` <- list(c(1, dcframe + 1L))        e2$`_pid` <- Sys.getpid()        e2$`_timestamp` <- Sys.time()        if (inherits(e, "rlib_error_2_0"))             e2$parent <- e$parent        e2 <- err$add_trace_back(e2, embed = FALSE)        saveRDS(list("error", e2), file = paste0("/var/folders/fs/clgy1jd123b6cjk9ffx51tgdv5kdzr/T//Rtmpzkt86P/callr-res-93871aa248a1",             ".error"))    }}, callr_message = function(e) {    try(signalCondition(e))}), error = function(e) {    NULL    try(stop(e))}, interrupt = function(e) {    NULL    e})
An irrecoverable exception occurred. R is aborting now ...

This is also a laptop that (currently, at least), does not let me have administrator access, so it is possible that perhaps that is causing other issues?

system info is below:

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 4.0.5 (2021-03-31)
#>  os       macOS Big Sur 10.16         
#>  system   x86_64, darwin17.0          
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_AU.UTF-8                 
#>  ctype    en_AU.UTF-8                 
#>  tz       Australia/Perth             
#>  date     2021-05-10                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date       lib source        
#>  backports     1.2.1   2020-12-09 [1] CRAN (R 4.0.2)
#>  cli           2.5.0   2021-04-26 [1] CRAN (R 4.0.2)
#>  crayon        1.4.1   2021-02-08 [1] CRAN (R 4.0.2)
#>  digest        0.6.27  2020-10-24 [1] CRAN (R 4.0.2)
#>  ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.0.2)
#>  evaluate      0.14    2019-05-28 [1] CRAN (R 4.0.1)
#>  fansi         0.4.2   2021-01-15 [1] CRAN (R 4.0.2)
#>  fs            1.5.0   2020-07-31 [1] CRAN (R 4.0.2)
#>  glue          1.4.2   2020-08-27 [1] CRAN (R 4.0.2)
#>  highr         0.9     2021-04-16 [1] CRAN (R 4.0.2)
#>  htmltools     0.5.1.1 2021-01-22 [1] CRAN (R 4.0.2)
#>  knitr         1.33    2021-04-24 [1] CRAN (R 4.0.2)
#>  lifecycle     1.0.0   2021-02-15 [1] CRAN (R 4.0.2)
#>  magrittr      2.0.1   2020-11-17 [1] CRAN (R 4.0.2)
#>  pillar        1.6.0   2021-04-13 [1] CRAN (R 4.0.2)
#>  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.0.2)
#>  purrr         0.3.4   2020-04-17 [1] CRAN (R 4.0.2)
#>  reprex        2.0.0   2021-04-02 [1] CRAN (R 4.0.2)
#>  rlang         0.4.11  2021-04-30 [1] CRAN (R 4.0.2)
#>  rmarkdown     2.8     2021-05-07 [1] CRAN (R 4.0.2)
#>  sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 4.0.2)
#>  stringi       1.5.3   2020-09-09 [1] CRAN (R 4.0.2)
#>  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.0.2)
#>  styler        1.4.1   2021-03-30 [1] CRAN (R 4.0.2)
#>  tibble        3.1.1   2021-04-18 [1] CRAN (R 4.0.2)
#>  utf8          1.2.1   2021-03-12 [1] CRAN (R 4.0.2)
#>  vctrs         0.3.8   2021-04-29 [1] CRAN (R 4.0.2)
#>  withr         2.4.2   2021-04-18 [1] CRAN (R 4.0.2)
#>  xfun          0.22    2021-03-11 [1] CRAN (R 4.0.2)
#>  yaml          2.2.1   2020-02-01 [1] CRAN (R 4.0.2)
#> 
#> [1] /Users/ntierney/Library/R/4.0/library
#> [2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

The text was updated successfully, but these errors were encountered:

dfalbel · 2021-05-10T12:40:55Z

See also rstudio/keras3#1210 and rstudio/keras3#1165

juliasilge · 2021-05-26T15:14:07Z

@njtierney I was having the same problem! 😩

@dfalbel pointed me to this blog post where someone got TensorFlow up and running using pre-release binaries from Apple + the ARM release of R + the new preview release of RStudio. This worked for me!

library(keras)
library(tensorflow)
use_python("~/miniforge3/bin/python")
use_condaenv("tf_env")
reticulate::py_discover_config("tensorflow")
#> python:         /Users/juliasilge/miniforge3/envs/tf_env/bin/python
#> libpython:      /Users/juliasilge/miniforge3/envs/tf_env/lib/libpython3.8.dylib
#> pythonhome:     /Users/juliasilge/miniforge3/envs/tf_env:/Users/juliasilge/miniforge3/envs/tf_env
#> version:        3.8.10 | packaged by conda-forge | (default, May 11 2021, 06:27:18)  [Clang 11.1.0 ]
#> numpy:          /Users/juliasilge/miniforge3/envs/tf_env/lib/python3.8/site-packages/numpy
#> numpy_version:  1.20.3
#> tensorflow:     /Users/juliasilge/miniforge3/envs/tf_env/lib/python3.8/site-packages/tensorflow
#> 
#> python versions found: 
#>  /Users/juliasilge/miniforge3/bin/python
#>  /Users/juliasilge/miniforge3/envs/tf_env/bin/python
#>  /Users/juliasilge/miniforge3/envs/tf_env/bin/python3
#>  /usr/bin/python3
#>  /usr/bin/python

^{Created on 2021-05-26 by the reprex package (v2.0.0)}

Here is some proof:

What I have tried so far (mostly models from SMLTAR) has worked, but a few things seem weird. For example, tensorflow::tf$random$set_seed(1234) gives an error.

njtierney · 2021-05-27T11:24:31Z

Hi @juliasilge - thanks! I'll try this out and let you know how I go.

t-kalinowski · 2021-12-06T21:13:41Z

The development version of tensorflow::install_tensorflow() (and keras::install_keras()) now has support for Arm Macs.
This should setup a working Tensorflow installation:

remotes::install_github("rstudio/tensorflow")
reticulate::install_miniconda()
tensorflow::install_tensorflow()

Please file an issue if you encounter errors!

njtierney · 2021-12-06T22:50:07Z

OK! Will let you know how we go :)

ginxyang · 2022-04-14T23:47:43Z

Hi there, I am still having issues with having tensorflow working in my R studio.
I did the above

remotes::install_github("rstudio/tensorflow")
reticulate::install_miniconda()
tensorflow::install_tensorflow()

when I run

> library(tensorflow)
> tf$constant("Hellow Tensorflow")

the following is the trace:

 *** caught illegal operation ***
address 0x120170489, cause 'illegal opcode'

Traceback:
 1: py_module_import(module, convert = convert)
 2: import(module)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch(import(module), error = clear_error_handler())
 7: py_resolve_module_proxy(x)
 8: `$.python.builtin.module`(tf, constant)
 9: tf$constant

t-kalinowski · 2022-04-15T12:51:55Z

@ginxyang Can you please file a new issue? The "Installation Issue" template has some instructions for collecting information that is useful for troubleshooting these types of issues.

ginxyang · 2022-04-15T14:18:25Z

@ginxyang Can you please file a new issue? The "Installation Issue" template has some instructions for collecting information that is useful for troubleshooting these types of issues.

Thanks, I have opened new issues: #527

t-kalinowski mentioned this issue Jun 16, 2021

TensorFlow with GPU acceleration on Mac #474

Closed

t-kalinowski added the apple silicon label Jul 27, 2021

t-kalinowski mentioned this issue Jul 27, 2021

Refactor installation #476

Merged

t-kalinowski closed this as completed Dec 6, 2021

njtierney mentioned this issue Dec 7, 2021

Issues installing tensorflow on M1 mac #493

Closed

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M1 Mac appears to abort when running `reticulate::py_module_available("tensorflow")` #465

M1 Mac appears to abort when running `reticulate::py_module_available("tensorflow")` #465

njtierney commented May 10, 2021

dfalbel commented May 10, 2021 •

edited

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juliasilge commented May 26, 2021

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njtierney commented May 27, 2021

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t-kalinowski commented Dec 6, 2021

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njtierney commented Dec 6, 2021

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ginxyang commented Apr 14, 2022

Uh oh!

t-kalinowski commented Apr 15, 2022

Uh oh!

ginxyang commented Apr 15, 2022

Uh oh!

M1 Mac appears to abort when running reticulate::py_module_available("tensorflow") #465

M1 Mac appears to abort when running reticulate::py_module_available("tensorflow") #465

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njtierney commented May 10, 2021

Standard output and error

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juliasilge commented May 26, 2021

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njtierney commented May 27, 2021

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t-kalinowski commented Dec 6, 2021

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njtierney commented Dec 6, 2021

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ginxyang commented Apr 14, 2022

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t-kalinowski commented Apr 15, 2022

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ginxyang commented Apr 15, 2022

Uh oh!

M1 Mac appears to abort when running `reticulate::py_module_available("tensorflow")` #465

M1 Mac appears to abort when running `reticulate::py_module_available("tensorflow")` #465

dfalbel commented May 10, 2021 •

edited

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