Rstudio crashing when trying to run xgboost model


#1

Hello,

I've been trying now for two days to get xgboost running with CPU. When I run the model, Rstudio crashes and I get the following error in the logs

26 Nov 2018 16:07:24 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26

Diagnostics Report Below: (I have removed personal info, replaced with [NAME])

[1] "1.1.463"

$R
[1] "C:\PROGRA~1\MIE74D~1\RCLIEN~1\R_SERVER\bin\x64\R.exe"

$pdflatex
[1] ""

$bibtex
[1] ""

$gcc
[1] "C:\Rtools\mingw_64\bin\gcc.exe"

$git
[1] "C:\PROGRA~1\Git\cmd\git.exe"

$svn
[1] ""

R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

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

other attached packages:
[1] RevoUtilsMath_10.0.0 RevoUtils_10.0.2 RevoMods_10.0.0 MicrosoftML_1.0.0 mrsdeploy_1.0 RevoScaleR_9.0.1 lattice_0.20-34
[8] rpart_4.1-10

loaded via a namespace (and not attached):
[1] codetools_0.2-15 CompatibilityAPI_1.1.0 foreach_1.4.3 grid_3.3.2 R6_2.2.0 jsonlite_1.1 curl_2.2
[8] iterators_1.0.8 tools_3.3.2 mrupdate_1.0.0

SysInfo:
sysname release version nodename machine login user effective_user
"Windows" ">= 8 x64" "build 9200" "LONG" "x86-64" "[NAME]" "[NAME]" "[NAME]"

R Version:
_
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 3
minor 3.2
year 2016
month 10
day 31
svn rev 71607
language R
version.string R version 3.3.2 (2016-10-31)
nickname Sincere Pumpkin Patch
$ALLUSERSPROFILE
[1] "C:\ProgramData"

$APPDATA
[1] "C:\Users\[NAME]\AppData\Roaming"

$CHARSET
[1] "cp1252"

$CLICOLOR_FORCE
[1] "1"

$CLIENTNAME
[1] "[NAME]"

$CommonProgramFiles
[1] "C:\Program Files\Common Files"

$CommonProgramFiles(x86)
[1] "C:\Program Files (x86)\Common Files"

$CommonProgramW6432
[1] "C:\Program Files\Common Files"

$COMPUTERNAME
[1] "LONG"

$ComSpec
[1] "C:\WINDOWS\system32\cmd.exe"

$CUDA_PATH
[1] "C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.0"

$CUDA_PATH_V10_0
[1] "C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.0"

$DISPLAY
[1] ":0"

$ERLANG_HOME
[1] "C:\Program Files\erl8.0"

$GFORTRAN_STDERR_UNIT
[1] "-1"

$GFORTRAN_STDOUT_UNIT
[1] "-1"

$HOME
[1] "C:/Users/[NAME]/Documents"

$HOMEDRIVE
[1] "C:"

$HOMEPATH
[1] "\Users\[NAME]"

$LOCALAPPDATA
[1] "C:\Users\[NAME]\AppData\Local"

$LOGONSERVER
[1] "\\S1"

$MSMPI_BIN
[1] "C:\Program Files\Microsoft MPI\Bin\"

$NUMBER_OF_PROCESSORS
[1] "4"

$NVCUDASAMPLES_ROOT
[1] "C:\ProgramData\NVIDIA Corporation\CUDA Samples\v10.0"

$NVCUDASAMPLES10_0_ROOT
[1] "C:\ProgramData\NVIDIA Corporation\CUDA Samples\v10.0"

$NVTOOLSEXT_PATH
[1] "C:\Program Files\NVIDIA Corporation\NvToolsExt\"

$OneDrive
[1] "C:\Users\[NAME]\OneDrive"

$OS
[1] "Windows_NT"

$PATH
[1] "C:\Program Files\Microsoft\R Client\R_SERVER\bin\x64;C:\Rtools\bin;C:\Rtools\mingw_64\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.0\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.0\libnvvp;C:\Program Files\Microsoft MPI\Bin\;C:\Rtools\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Users\[NAME]\.dnx\bin;C:\Program Files\Microsoft DNX\Dnvm\;C:\Program Files\Microsoft SQL Server\130\Tools\Binn\;C:\Program Files (x86)\Microsoft SQL Server\Client SDK\ODBC\130\Tools\Binn\;C:\Program Files (x86)\Microsoft SQL Server\130\Tools\Binn\;C:\Program Files (x86)\Microsoft SQL Server\130\DTS\Binn\;C:\Program Files (x86)\Microsoft SQL Server\130\Tools\Binn\ManagementStudio\;C:\Program Files (x86)\Skype\Phone\;C:\Program Files\dotnet\;C:\Program Files (x86)\Microsoft SQL Server\140\Tools\Binn\;C:\Program Files (x86)\Microsoft SQL Server\140\DTS\Binn\;C:\Program Files (x86)\Microsoft SQL Server\140\Tools\Binn\ManagementStudio\;C:\Program Files\TortoiseGit\bin;C:\Program Files\PuTTY\;C:\Program Files\Microsoft SQL Server\110\Tools\Binn\;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files\Git\cmd;C:\Users\[NAME]\AppData\Local\Microsoft\WindowsApps;C:\Program Files\CMake\bin"

$PATHEXT
[1] ".COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC"

$PROCESSOR_ARCHITECTURE
[1] "AMD64"

$PROCESSOR_IDENTIFIER
[1] "Intel64 Family 6 Model 94 Stepping 3, GenuineIntel"

$PROCESSOR_LEVEL
[1] "6"

$PROCESSOR_REVISION
[1] "5e03"

$ProgramData
[1] "C:\ProgramData"

$ProgramFiles
[1] "C:\Program Files"

$ProgramFiles(x86)
[1] "C:\Program Files (x86)"

$ProgramW6432
[1] "C:\Program Files"

$PSModulePath
[1] "C:\Program Files\WindowsPowerShell\Modules;C:\WINDOWS\system32\WindowsPowerShell\v1.0\Modules;C:\Program Files (x86)\Microsoft SQL Server\130\Tools\PowerShell\Modules\"

$PUBLIC
[1] "C:\Users\Public"

$R_ARCH
[1] "/x64"

$R_COMPILED_BY
[1] "gcc 4.9.3"

$R_DOC_DIR
[1] "C:/PROGRA~1/MIE74D~1/RCLIEN~1/R_SERVER/doc"

$R_HOME
[1] "C:/PROGRA~1/MIE74D~1/RCLIEN~1/R_SERVER"

$R_LIBS_USER
[1] "C:/Users/[NAME]/Documents/R/win-library/3.3"

$R_USER
[1] "C:/Users/[NAME]/Documents"

$RMARKDOWN_MATHJAX_PATH
[1] "C:/Program Files/RStudio/resources/mathjax-26"

$RS_LOCAL_PEER
[1] "\\.\pipe\13249-rsession"

$RS_RPOSTBACK_PATH
[1] "C:/Program Files/RStudio/bin/rpostback"

$RS_SHARED_SECRET
[1] "63341846741"

$RSTUDIO
[1] "1"

$RSTUDIO_CONSOLE_COLOR
[1] "256"

$RSTUDIO_CONSOLE_WIDTH
[1] "80"

$RSTUDIO_MSYS_SSH
[1] "C:/Program Files/RStudio/bin/msys-ssh-1000-18"

$RSTUDIO_PANDOC
[1] "C:/Program Files/RStudio/bin/pandoc"

$RSTUDIO_SESSION_PORT
[1] "13249"

$RSTUDIO_USER_IDENTITY
[1] "[NAME]"

$RSTUDIO_WINUTILS
[1] "C:/Program Files/RStudio/bin/winutils"

$SESSIONNAME
[1] "RDP-Tcp#0"

$SystemDrive
[1] "C:"

$SystemRoot
[1] "C:\WINDOWS"

$TEMP
[1] "C:\Users\[NAME]~1\AppData\Local\Temp"

$TERM
[1] "xterm-256color"

$TMP
[1] "C:\Users\[NAME]~1\AppData\Local\Temp"

$USERDNSDOMAIN
[1] "SDL.OFFICE"

$USERDOMAIN
[1] "sdloffice"

$USERDOMAIN_ROAMINGPROFILE
[1] "sdloffice"

$USERNAME
[1] "[NAME]"

$USERPROFILE
[1] "C:\Users\[NAME]"

$VS140COMNTOOLS
[1] "C:\Program Files (x86)\Microsoft Visual Studio 14.0\Common7\Tools\"

$windir
[1] "C:\WINDOWS"

[1] ".GlobalEnv" "tools:rstudio" "package:RevoUtilsMath" "package:RevoUtils" "package:RevoMods" "package:MicrosoftML"
[7] "package:mrsdeploy" "package:RevoScaleR" "package:lattice" "package:rpart" "package:stats" "package:graphics"
[13] "package:grDevices" "package:utils" "package:datasets" "package:methods" "Autoloads" "package:base"
Log file: rdesktop.log

26 Nov 2018 16:07:24 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26 Nov 2018 16:07:34 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26 Nov 2018 16:07:44 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26 Nov 2018 16:07:54 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26 Nov 2018 16:10:15 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26 Nov 2018 16:10:25 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26 Nov 2018 16:10:35 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26 Nov 2018 16:10:45 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26 Nov 2018 16:10:55 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26 Nov 2018 16:22:35 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26 Nov 2018 16:23:30 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26 Nov 2018 16:23:30 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26 Nov 2018 16:24:50 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288
26 Nov 2018 16:24:51 [rdesktop] ERROR system error 2 (The system cannot find the file specified); OCCURRED AT: virtual void rstudio::core::http::NamedPipeAsyncClient::connectAndWriteRequest() C:/Users/Administrator/rstudio/src/cpp/core/include/core/http/NamedPipeAsyncClient.hpp:84; LOGGED FROM: void rstudio::desktop::NetworkReply::onError(const rstudio::core::Error&) C:\Users\Administrator\rstudio\src\cpp\desktop\DesktopNetworkReply.cpp:288

Log file: rsession-[NAME].log

(Empty)


#2

Could you please provide us with a self-contained reprex (short for reproducible example)? It will help us help you if we can be sure we're all working with/looking at the same stuff.

install.packages("reprex")

If you've never heard of a reprex before, you might want to start by reading the tidyverse.org help page. The reprex dos and don'ts are also useful.

What to do if you run into clipboard problems

If you run into problems with access to your clipboard, you can specify an outfile for the reprex, and then copy and paste the contents into the forum.

reprex::reprex(input = "fruits_stringdist.R", outfile = "fruits_stringdist.md")

For pointers specific to the community site, check out the reprex FAQ.


#3

Hi,

When I try to create a reprex of the entire code:

require(xgboost)

data(agaricus.train, package='xgboost')
data(agaricus.test, package='xgboost')
train <- agaricus.train
test <- agaricus.test

bstSparse <- xgboost(data = train$data, label = train$label, max.depth = 2, eta = 1, nthread = 2, nrounds = 2, objective = "binary:logistic")

I get the following error: "Error: callr failed, could not start R, exited with non-zero status, has crashed or was killed " but if I don't include the xgboost command the reprex command runs fine. I'm not sure how to share the html file on this website.

Regarding the step by step of the xgboost compilation with GPU support:

  1. I download cmake
  2. I download git for windows
  3. I download and install visual studio 2015 with c++ libraries.
  4. I download and install cuda 9.
  5. I then run the following commands in git for windows:

git submodule init
git submodule update
git clone --recursive https://github.com/dmlc/xgboost
cd xgboost
mkdir build
cd build
cmake .. -G"Visual Studio 14 2015 Win64" -DUSE_CUDA=ON -DR_LIB=ON
cmake --build . --target install --config Release


#4

Do you see the same error when you run this in e.g. RGui or within an R session launched from the terminal?


#5

Yes.

If I run it in the RGui, after I run the xgboost command I get "R for Windows terminal front-end has stopped working".


#6

I just wanted to note that when I run the last command in the installation (i.e. cmake --build . --target install --config Release)

It finishes installing with 0 errors, but 1597 warnings including the last one:

logging.obj : warning LNK4221: This object file does not define any previously undefined public symbols, so it will not be used by any link operation that consumes this library [C:\Users[NAME]\xgboost\build\objxgboost.vcxproj]


#7

If the crash also exists in RGui, there must be something else going on -- e.g. something went wrong during xgboost compilation, or there's some incompatibility with the GPU / GPU drivers you have installed, or something more nebulous. Unfortunately, debugging this will likely be challenging.