I'm using the JuliaCall library to use Julia code in R. I'm trying to increase the number of threads but I can't seem to succeed.
I'm using Windows 10 and RStudio version 1.4.1103
Thank you so much!
Simply run
Sys.setenv(JULIA_NUM_THREADS = "8")
before calling library(JuliaCall).
Here is a full console output on my machine:
> Sys.setenv(JULIA_NUM_THREADS = "8")
> library(JuliaCall)
> julia_command("Threads.nthreads()")
Julia version 1.6.0 at location C:\JULIA-~1.0\bin will be used.
Loading setup script for JuliaCall...
Finish loading setup script for JuliaCall.
8
Related
Problem
RStudio keeps crashing when I use this code tutorial from 'R for Data Science':
library(tidyverse)
library(nycflights13)
filter(flights, month == 1, day == 1).
I would appreciate it if anyone knows how I can solve this.
When I run RStudio via anaconda-navigator from the terminal, I get the following error message (home directory edited to ~ for privacy):
~/.anaconda/navigator/scripts/rstudio.sh: line 3: 19137 Segmentation fault
~/anaconda3/bin/rstudio > ~/.anaconda/navigator/scripts/rstudio-out-1.txt
~/.anaconda/navigator/scripts/rstudio-err-1.txt
I'm new to R, but have some background in python, so I have tried the following:
RStudio presents and reads the 'flights' dataframe without problems.
Assigning the filter to an object (jan1 <- filter(flights, month == 1, day == 1)) works, but calling the object jan1 then crashes RStudio again.
filtering only by month or day alone causes no problems.
I can perform this task using the R interpreter on the terminal without problem.
I am using RStudio v1.1.383, installed using conda 4.4.11, on Linux Mint - Linux version 4.4.0-92-generic (buildd#lcy01-17) (gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4).
I can't get the h2o to work in my R. It shows the following error. Have no clue what it means. Previously it gave me an error because I didn't have Java 64 bit version. I downloaded the 64bit - restarted my pc - and started the process again and now it gives me this error.
Any suggestions?
library(h2o)
----------------------------------------------------------------------
Your next step is to start H2O:
> h2o.init()
For H2O package documentation, ask for help:
> ??h2o
After starting H2O, you can use the Web UI at http://localhost:54321
For more information visit http://docs.h2o.ai
----------------------------------------------------------------------
Attaching package: ‘h2o’
The following objects are masked from ‘package:stats’:
cor, sd, var
The following objects are masked from ‘package:base’:
%*%, %in%, &&, ||, apply, as.factor, as.numeric, colnames, colnames<-, ifelse,
is.character, is.factor, is.numeric, log, log10, log1p, log2, round, signif, trunc
> h2o.init(nthreads = -1)
H2O is not running yet, starting it now...
Note: In case of errors look at the following log files:
C:\Users\ADM_MA~1\AppData\Local\Temp\RtmpygK1EJ/h2o_Adm_Mayur_started_from_r.out
C:\Users\ADM_MA~1\AppData\Local\Temp\RtmpygK1EJ/h2o_Adm_Mayur_started_from_r.err
java version "9"
Java(TM) SE Runtime Environment (build 9+181)
Java HotSpot(TM) 64-Bit Server VM (build 9+181, mixed mode)
Starting H2O JVM and connecting: ............................................................
[1] "localhost"
[1] 54321
[1] TRUE
[1] -1
[1] "Failed to connect to localhost port 54321: Connection refused"
[1] 127
Error in h2o.init(nthreads = -1) :
H2O failed to start, stopping execution.
In addition: Warning message:
running command 'curl 'http://localhost:54321'' had status 127
Screenshot for h2o error in R
Based on the error message and the troubleshooting we carried out in the comments, it seems that you are using a version of Java (Java 1.9) which is too new for your version of H2O.
Your 2 options seem to be:
Verify that your version of H2O is up to date. If not, update it.
Download a compatible version of Java, i.e. Java 1.8 (you can just use it for this 1 task rather than for everything, if you prefer)
Note that on the main documentation page of H2O v3 it says:
Java 7 or later. Note: Java 9 is not yet released and is not currently
supported.
But at the same time they usually have several Beta and Alpha development branches going, so you might find one of those that works with Java 9.
So if anyone else is facing the same issue.
My recommendation (after spending about over 10 hours trying to figure this out (worth mentioning)) is check your version of java.
If it's higher than 8 then either keep it remove it.
I removed it because I didn't want to deal with setting the JAVA Home function in R and to reduce work.
Make sure you install Java 7 or 8 but a 64 bit version. h2o doesn't work if you have 32 bit.
Then voila! Just go ahead and type install.package('h2o') in your rstudio.
I wanted to be extra careful in my final attempt of this so unloaded and uninstalled the library because I had installed it before and then installed it again and then loaded it using library(h2o) and then h20.init() worked just fine.
I've recently converted my windows R code to a Linux installation for running DEoptim on a function. On my windows system it all worked fine using:
ans <- DEoptim1(Calibrate,lower,upper,
DEoptim.control(trace=TRUE,parallelType=1,parVAr=parVarnames3,
packages=c("hydromad","maptools","compiler","tcltk","raster")))
where the function 'Calibrate' consisted of multiple functions. On the windows system I simply downloaded the various packages needed into the R library. The option paralleType=1 ran the code across a series of cores.
However, now I want to put this code onto a Linux based computing cluster - the function 'Calibrate' works fine when stand alone, as does DEoptim if I want to run the code on one core. However, when I specify the parelleType=1, the code fails and returns:
Error in checkForRemoteErrors(lapply(cl, recvResult)) :
7 nodes produced errors; first error: there is no package called ‘raster’
This error is reproduced whatever package I try and recall, even though the
library(raster)
command worked fine and 'raster' is clearly shown as okay when I call all the libraries using:
library()
So, my gut feeling is, is that even though all the packages and libraries are loaded okay, it is because I have used a personal library and the packages element of DEoptim.control is looking in a different space. An example of how the packages were installed is below:
install.packages("/home/antony/R/Pkges/raster_2.4-15.tar.gz",rpeo=NULL,target="source",lib="/home/antony/R/library")
I also set the lib paths option as below:
.libPaths('/home/antony/R/library')
Has anybody any idea of what I am doing wrong and how to set the 'packages' option in DEoptim control so I can run DEoptim across multiple cores in parallel?
Many thanks, Antony
I would like to build a simple webserver using Rook, however I am having strange errors when trying it in R-Studio:
The code
library(Rook)
s <- Rhttpd$new()
s$start()
print(s)
returns the rather useless error
"Error in listenPort > 0 :
comparison (6) is possible only for atomic and list types".
When trying the same code in a simple R-Console,everything works - so I would like to understand why that happens and how I can fix it.
RStudio is Version 0.99.484 and R is R 3.2.2
I've experienced same thing.
TLDR: This pull request solves the problem: https://github.com/jeffreyhorner/Rook/pull/31
RStudio is treated in different way and Rook port is same as tools:::httpdPort value. The problem is that in current Rook master tools:::httpdPort is assigned directly. It's a function that's why we need to evaluate it first.
If you want to have it solved right now, without waiting for merge into master: install devtools and load package from my fork #github.
install.packages("devtools")
library(devtools)
install_github("filipstachura/Rook")
My R script worked fine in RStudio (Version 0.98.1091) on Windows 7. Then I restarted my laptop, entered again in RStudio and now it provides the following error messages each time I want to execute my code:
cl <- makeCluster(mc); # build the cluster
Error: could not find function "makeCluster"
> registerDoParallel(cl)
Error: could not find function "registerDoParallel"
> fileIdndexes <- gsub("\\.[^.]*","",basename(SF))
Error in basename(SF) : object 'SF' not found
These error messages are slightly different each time I run the code. It seems that RStudio cannot find any function that is used in the code.
I restarted R Session, cleaned Workspace, restarted RStudio. Nothing helps.
It must be noticed that after many attempts to execute the code, it finally was initialized. However, after 100 iterations, it crashed with the message related to unavailability of localhost.
Add library(*the package needed/where the function is*) for each of the packages you're using.