I am getting the below error on an AWS EC2 instance (I specifically say that as I don't have an issue with this on my Mac):
Error: Command failed: gm convert: No decode delegate for this image format (/tmp/5c5830319d29e4678e8691cd-1549705844271.jpg)
The file does exist just in case that looks to be the suspect.
My config for gm is as follows:
[mw-user#mwServer ~]$ gm version
GraphicsMagick 1.3.31 2018-11-17 Q8 http://www.GraphicsMagick.org/
Copyright (C) 2002-2018 GraphicsMagick Group.
Additional copyrights and licenses apply to this software.
See http://www.GraphicsMagick.org/www/Copyright.html for details.
Feature Support:
Native Thread Safe yes
Large Files (> 32 bit) yes
Large Memory (> 32 bit) yes
BZIP no
DPS no
FlashPix no
FreeType no
Ghostscript (Library) no
JBIG no
JPEG-2000 no
JPEG no
Little CMS no
Loadable Modules no
OpenMP yes (201511)
PNG no
TIFF no
TRIO no
UMEM no
WebP no
WMF no
X11 no
XML no
ZLIB yes
Host type: x86_64-pc-linux-gnu
Configured using the command:
./configure
Final Build Parameters:
CC = gcc
CFLAGS = -fopenmp -g -O2 -Wall -pthread
CPPFLAGS =
CXX = g++
CXXFLAGS = -pthread
LDFLAGS =
LIBS = -lz -lm -lpthread
I am using the Node module:
var gm = require('gm');
gm("/tmp/5c5830319d29e4678e8691cd-1549705844271.jpg")
.resize(450, null)
.write("/tmp/5c5830319d29e4678e8691cd-1549705844271-Resized.jpg", (function(err){
if (err) {
console.log(err);
}
}));
I don't know enough about gm to go anywhere from here. The problem seems like I don't have a "converter" for JPEG. Question is - how does one set this up so it supports most image formats like: jpg, png etc?
Thanks in advance!
You don't say what OS your instance is running, but basically you don't seem to have JPEG support in GraphicsMagick.
So you need to work out what package manager your instance uses and then use that to install libjpeg and libjpeg-dev packages and then probably re-install GraphicsMagick.
Your comment seems to imply your question is broader than the JPEG-support you mention, but the answer is the same. You need to install
libTIFF, libTIFF-dev
libPNG, libPNG-dev
...
and then re-install GraphicsMagick.
Related
I'm trying to use packages that require Rcpp in R on my M1 Mac, which I was never able to get up and running after purchasing this computer. I updated it to Monterey in the hope that this would fix some installation issues but it hasn't. I tried running the Rcpp check from this page but I get the following error:
> Rcpp::sourceCpp("~/github/helloworld.cpp")
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0'
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sourceCpp_4.so] Error 1
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/RcppArmadillo/include" -I"/Users/afredston/github" -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c helloworld.cpp -o helloworld.o
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o sourceCpp_4.so helloworld.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in Rcpp::sourceCpp("~/github/helloworld.cpp") :
Error 1 occurred building shared library.
I get that it can't "find" gfortran. I installed this release of gfortran for Monterey. When I type which gfortran into Terminal, it returns /opt/homebrew/bin/gfortran. (Maybe this version of gfortran requires Xcode tools that are too new—it says something about 13.2 and when I run clang --version it says 13.0—but I don't see another release of gfortran for Monterey?)
I also appended /opt/homebrew/bin: to PATH in R so it looks like this now:
> Sys.getenv("PATH")
[1] "/opt/homebrew/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:/Applications/RStudio.app/Contents/MacOS/postback"
Other things I checked:
Xcode command line tools is installed (which clang returns /usr/bin/clang).
Files ~/.R/Makevars and ~/.Renviron don't exist.
Here's my session info:
R version 4.1.1 (2021-08-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.1 tools_4.1.1 RcppArmadillo_0.10.7.5.0
[4] Rcpp_1.0.7
Background
Currently (2023-02-20), CRAN builds R 4.2 binaries for Apple silicon using Apple clang from Command Line Tools for Xcode 13.1 and using an experimental fork of GNU Fortran 12.
If you obtain R from CRAN (i.e., here), then you need to replicate CRAN's compiler setup on your system before building R packages that contain C/C++/Fortran code from their sources (and before using Rcpp, etc.). This requirement ensures that your package builds are compatible with R itself.
A further complication is the fact that Apple clang doesn't support OpenMP, so you need to do even more work to compile programs that make use of multithreading. You could circumvent the issue by building R itself and all R packages from sources with LLVM clang, which does support OpenMP, but that approach is onerous and "for experts only".
There is another approach that has been tested by a few people, including Simon Urbanek, the maintainer of R for macOS. It is experimental and also "for experts only", but it works on my machine and is much simpler than learning to build R yourself.
Instructions for obtaining a working toolchain
Warning: These come with no warranty and could break at any time. Some level of familiarity with C/C++/Fortran program compilation, Makefile syntax, and Unix shells is assumed. Everyone is encouraged to consult official documentation, which is more likely to be maintained than answers on SO. As usual, sudo at your own risk.
I will try to address compilers and OpenMP support at the same time. I am going to assume that you are starting from nothing. Feel free to skip steps you've already taken, though you might find a fresh start helpful.
I've tested these instructions on a machine running Big Sur, and at least one person has tested them on a machine running Monterey. I would be glad to hear from others.
Download an R 4.2 binary from CRAN here and install. Be sure to select the binary built for Apple silicon.
Run
$ sudo xcode-select --install
in Terminal to install the latest release version of Apple's Command Line Tools for Xcode, which includes Apple clang. You can obtain earlier versions from your browser here. However, the version that you install should not be older than the one that CRAN used to build your R binary.
Download the gfortran binary recommended here and install by unpacking to root:
$ curl -LO https://mac.r-project.org/tools/gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz
$ sudo tar xvf gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz -C /
$ sudo ln -sfn $(xcrun --show-sdk-path) /opt/R/arm64/gfortran/SDK
The last command updates a symlink inside of the gfortran installation so that it points to the SDK inside of your Command Line Tools installation.
Download an OpenMP runtime suitable for your Apple clang version here and install by unpacking to root. You can query your Apple clang version with clang --version. For example, I have version 1300.0.29.3, so I did:
$ curl -LO https://mac.r-project.org/openmp/openmp-12.0.1-darwin20-Release.tar.gz
$ sudo tar xvf openmp-12.0.1-darwin20-Release.tar.gz -C /
After unpacking, you should find these files on your system:
/usr/local/lib/libomp.dylib
/usr/local/include/ompt.h
/usr/local/include/omp.h
/usr/local/include/omp-tools.h
Add the following lines to $(HOME)/.R/Makevars, creating the file if necessary.
CPPFLAGS += -I/usr/local/include -Xclang -fopenmp
LDFLAGS += -L/usr/local/lib -lomp
Run R and test that you can compile a program with OpenMP support. For example:
if (!requireNamespace("RcppArmadillo", quietly = TRUE))
install.packages("RcppArmadillo")
Rcpp::sourceCpp(code = '
#include <RcppArmadillo.h>
#ifdef _OPENMP
# include <omp.h>
#endif
// [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::export]]
void omp_test()
{
#ifdef _OPENMP
Rprintf("OpenMP threads available: %d\\n", omp_get_max_threads());
#else
Rprintf("OpenMP not supported\\n");
#endif
}
')
omp_test()
OpenMP threads available: 8
If the C++ code fails to compile, or if it compiles without error but you get linker warnings or you find that OpenMP is not supported, then one of us has probably made a mistake. Please report any issues.
References
Everything is a bit scattered:
R Installation and Administration manual [link]
R for macOS Developers page [link]
I resolved this issue by adding a path to the homebrew installation of gfortran to my ~/.R/Makevars following these instructions: https://pat-s.me/transitioning-from-x86-to-arm64-on-macos-experiences-of-an-r-user/#gfortran
I just avoided the issue until MacOS had things working more smoothly. so I either Windows Developer Virtual Machine (VM) or run my code development in another environment. I'm not too impressed with the updated and "faster" chipset, but that it doesn't work with much. Slow to implement and work-a-rounds often are a must.
Tested the following process for making multithread data.table work in a M2 MacBook Pro (macOS Monterey)
Steps are mostly the same with this answer by the user inferator.
Download and install R from CRAN
Download and install RStudio with developer tools
Run the following commands in terminal to install OpenMP
curl -O https://mac.r-project.org/openmp/openmp-12.0.1-darwin20-Release.tar.gz
sudo tar fvxz openmp-12.0.1-darwin20-Release.tar.gz -C /
Add compiler flags to connect clan w/ OpenMP. In terminal, write the following:
cd ~
mkdir .R
nano .R/Makevars
Inside the opened Makevars file paste the following lines. Once finished, hit command+O and then Enter to save. Do a command+X to close the editor.
CPPFLAGS += -Xclang -fopenmp
LDFLAGS += -lomp
Download and run the installer for gfortran by downloading gfortran-ARM-12.1-Monterey.dmg from the respective GitHub repo
This concludes the steps regarding enabling OpenMP and (hopefully) Rcpp in R under a M2 chip system.
Now, for testing that everything works with data.table I did the following
Open RStudio and run
install.packages("data.table", type = "source")
If everything is done correctly, the package should compile without any errors and return the following when running getDTthreads(verbose = TRUE):
OpenMP version (_OPENMP) 201811
omp_get_num_procs() 8
R_DATATABLE_NUM_PROCS_PERCENT unset (default 50)
R_DATATABLE_NUM_THREADS unset
R_DATATABLE_THROTTLE unset (default 1024)
omp_get_thread_limit() 2147483647
omp_get_max_threads() 8
OMP_THREAD_LIMIT unset
OMP_NUM_THREADS unset
RestoreAfterFork true
data.table is using 4 threads with throttle==1024. See ?setDTthreads.
[1] 4
I'm trying to use packages that require Rcpp in R on my M1 Mac, which I was never able to get up and running after purchasing this computer. I updated it to Monterey in the hope that this would fix some installation issues but it hasn't. I tried running the Rcpp check from this page but I get the following error:
> Rcpp::sourceCpp("~/github/helloworld.cpp")
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0'
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sourceCpp_4.so] Error 1
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/RcppArmadillo/include" -I"/Users/afredston/github" -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c helloworld.cpp -o helloworld.o
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o sourceCpp_4.so helloworld.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in Rcpp::sourceCpp("~/github/helloworld.cpp") :
Error 1 occurred building shared library.
I get that it can't "find" gfortran. I installed this release of gfortran for Monterey. When I type which gfortran into Terminal, it returns /opt/homebrew/bin/gfortran. (Maybe this version of gfortran requires Xcode tools that are too new—it says something about 13.2 and when I run clang --version it says 13.0—but I don't see another release of gfortran for Monterey?)
I also appended /opt/homebrew/bin: to PATH in R so it looks like this now:
> Sys.getenv("PATH")
[1] "/opt/homebrew/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:/Applications/RStudio.app/Contents/MacOS/postback"
Other things I checked:
Xcode command line tools is installed (which clang returns /usr/bin/clang).
Files ~/.R/Makevars and ~/.Renviron don't exist.
Here's my session info:
R version 4.1.1 (2021-08-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.1 tools_4.1.1 RcppArmadillo_0.10.7.5.0
[4] Rcpp_1.0.7
Background
Currently (2023-02-20), CRAN builds R 4.2 binaries for Apple silicon using Apple Clang from Command Line Tools for Xcode 13.1 and using an experimental fork of GNU Fortran 12.
If you obtain R from CRAN (i.e., here), then you need to replicate CRAN's compiler setup on your system before building R packages that contain C/C++/Fortran code from their sources (and before using Rcpp, etc.). This requirement ensures that your package builds are compatible with R itself.
A further complication is the fact that Apple Clang doesn't support OpenMP, so you need to do even more work to compile programs that make use of multithreading. You could circumvent the issue by building R itself, all R packages, and all external libraries from sources with LLVM Clang, which does support OpenMP, but that approach is onerous and "for experts only".
There is another approach that has been tested by a few people, including Simon Urbanek, the maintainer of R for macOS. It is experimental and also "for experts only", but it works on my machine and is much simpler than learning to build R and other libraries yourself.
Instructions for obtaining a working toolchain
Warning: These come with no warranty and could break at any time. Some level of familiarity with C/C++/Fortran program compilation, Makefile syntax, and Unix shells is assumed. Everyone is encouraged to consult official documentation, which is more likely to be maintained than answers on SO. As usual, sudo at your own risk.
I will try to address compilers and OpenMP support at the same time. I am going to assume that you are starting from nothing. Feel free to skip steps you've already taken, though you might find a fresh start helpful.
I've tested these instructions on a machine running Big Sur, but they should also work on Monterey and Ventura.
Download an R 4.2 binary from CRAN here and install. Be sure to select the binary built for Apple silicon.
Run
$ sudo xcode-select --install
in Terminal to install the latest release version of Apple's Command Line Tools for Xcode, which includes Apple Clang. You can obtain earlier versions from your browser here. However, the version that you install should not be older than the one that CRAN used to build your R binary.
Download the GNU Fortran binary provided here and install by unpacking to root:
$ curl -LO https://mac.r-project.org/tools/gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz
$ sudo tar xvf gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz -C /
$ sudo ln -sfn $(xcrun --show-sdk-path) /opt/R/arm64/gfortran/SDK
The last command updates a symlink inside of the installation so that it points to the SDK inside of your Command Line Tools installation.
Download an OpenMP runtime suitable for your Apple Clang version here and install by unpacking to root. You can query your Apple Clang version with clang --version. For example, I have version 1300.0.29.3, so I did:
$ curl -LO https://mac.r-project.org/openmp/openmp-12.0.1-darwin20-Release.tar.gz
$ sudo tar xvf openmp-12.0.1-darwin20-Release.tar.gz -C /
After unpacking, you should find these files on your system:
/usr/local/lib/libomp.dylib
/usr/local/include/ompt.h
/usr/local/include/omp.h
/usr/local/include/omp-tools.h
Add the following lines to $(HOME)/.R/Makevars, creating the file if necessary.
CPPFLAGS += -I/usr/local/include -Xclang -fopenmp
LDFLAGS += -L/usr/local/lib -lomp
Test that you are able to use R to compile a C or C++ program with OpenMP support while linking relevant libraries from the GNU Fortran installation (indicated by the -l flags in the output of R CMD CONFIG FLIBS).
The most transparent approach is to use R CMD SHLIB directly. In a temporary directory, create an empty source file omp_test.c and add the following lines:
#ifdef _OPENMP
# include <omp.h>
#endif
#include <Rinternals.h>
SEXP omp_test(void)
{
#ifdef _OPENMP
Rprintf("OpenMP threads available: %d\n", omp_get_max_threads());
#else
Rprintf("OpenMP not supported\n");
#endif
return R_NilValue;
}
Compile it:
$ R CMD SHLIB omp_test.c $(R CMD CONFIG FLIBS)
Then call the compiled C function from R:
$ R -e 'dyn.load("omp_test.so"); invisible(.Call("omp_test"))'
OpenMP threads available: 8
If the compiler or linker throws an error, or if you find that OpenMP is still not supported, then one of us has made a mistake. Please report any issues.
Note that you can implement the same test using Rcpp, if you don't mind installing it:
library(Rcpp)
registerPlugin("flibs", Rcpp.plugin.maker(libs = "$(FLIBS)"))
sourceCpp(code = '
#ifdef _OPENMP
# include <omp.h>
#endif
#include <Rcpp.h>
// [[Rcpp::plugins(flibs)]]
// [[Rcpp::export]]
void omp_test()
{
#ifdef _OPENMP
Rprintf("OpenMP threads available: %d\\n", omp_get_max_threads());
#else
Rprintf("OpenMP not supported\\n");
#endif
return;
}
')
omp_test()
OpenMP threads available: 8
References
Everything is a bit scattered:
R Installation and Administration manual [link]
Writing R Extensions manual [link]
R for macOS Developers web page [link]
I resolved this issue by adding a path to the homebrew installation of gfortran to my ~/.R/Makevars following these instructions: https://pat-s.me/transitioning-from-x86-to-arm64-on-macos-experiences-of-an-r-user/#gfortran
I just avoided the issue until MacOS had things working more smoothly. so I either Windows Developer Virtual Machine (VM) or run my code development in another environment. I'm not too impressed with the updated and "faster" chipset, but that it doesn't work with much. Slow to implement and work-a-rounds often are a must.
Tested the following process for making multithread data.table work in a M2 MacBook Pro (macOS Monterey)
Steps are mostly the same with this answer by the user inferator.
Download and install R from CRAN
Download and install RStudio with developer tools
Run the following commands in terminal to install OpenMP
curl -O https://mac.r-project.org/openmp/openmp-12.0.1-darwin20-Release.tar.gz
sudo tar fvxz openmp-12.0.1-darwin20-Release.tar.gz -C /
Add compiler flags to connect clan w/ OpenMP. In terminal, write the following:
cd ~
mkdir .R
nano .R/Makevars
Inside the opened Makevars file paste the following lines. Once finished, hit command+O and then Enter to save. Do a command+X to close the editor.
CPPFLAGS += -Xclang -fopenmp
LDFLAGS += -lomp
Download and run the installer for gfortran by downloading gfortran-ARM-12.1-Monterey.dmg from the respective GitHub repo
This concludes the steps regarding enabling OpenMP and (hopefully) Rcpp in R under a M2 chip system.
Now, for testing that everything works with data.table I did the following
Open RStudio and run
install.packages("data.table", type = "source")
If everything is done correctly, the package should compile without any errors and return the following when running getDTthreads(verbose = TRUE):
OpenMP version (_OPENMP) 201811
omp_get_num_procs() 8
R_DATATABLE_NUM_PROCS_PERCENT unset (default 50)
R_DATATABLE_NUM_THREADS unset
R_DATATABLE_THROTTLE unset (default 1024)
omp_get_thread_limit() 2147483647
omp_get_max_threads() 8
OMP_THREAD_LIMIT unset
OMP_NUM_THREADS unset
RestoreAfterFork true
data.table is using 4 threads with throttle==1024. See ?setDTthreads.
[1] 4
There's probably a gazillion threads on OSX+Rcpp+openMP, but the bottom line right now appears to be this (per coatless):
Unfortunately, with R 4.0.0 the CRAN distributed version of R loses
the ability to use OpenMP without a custom setup.
I came across other ideas, including compiling llvm yourself, using homebrew or macports to install R and/or llvm and/or gcc, and then figuring out how to use the right compiler and/or flags with (R)cpp. However, I find this all very confusing.
I am not a mac user, but it seems to me that setting up a mac to compile Rcpp packages or code snippets with openMP seems to be too difficult for most mac users. However, I would like my R package on github to be used by more users, and since it relies on openMP, I am losing that audience.
Can someone provide the necessary steps to set up R on mac in a way that it can compile Rcpp code with openMP? I'd like to turn that into a quick tutorial.
EDIT: I should have added - on Apple Silicon, because there are some extra confusions where things go - /usr/local vs /opt
I spent a day figuring this out (original post here); here are the steps I used to compile R packages from source with openMP:
Install xcode from the app store (instructions for installing xcode) then install/reinstall the xcode command line tools from the terminal:
# To delete an existing command line tools installation:
sudo rm -rf /Library/Developer/CommandLineTools
# To install the command line tools
sudo xcode-select --install
Install gcc via Homebrew (instructions for installing Homebrew) or, if you already have gcc installed, skip to step 3.
# WARNING: This can take several hours
brew install gcc
To avoid "legacy" version issues:
brew cleanup
brew update
brew upgrade
brew reinstall gcc
Link some headers into /usr/local/include
sudo ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/* /usr/local/include/
# You can ignore warnings like this:
#ln: /usr/local/include//tcl.h: File exists
#ln: /usr/local/include//tclDecls.h: File exists
#ln: /usr/local/include//tclPlatDecls.h: File exists
#ln: /usr/local/include//tclTomMath.h: File exists
#ln: /usr/local/include//tclTomMathDecls.h: File exists
#ln: /usr/local/include//tk.h: File exists
#ln: /usr/local/include//tkDecls.h: File exists
#ln: /usr/local/include//tkPlatDecls.h: File exists
Check your version of gfortran (cd /usr/local/gfortran/lib/gcc/x86_64-apple-darwin19/; ls) then edit your ~/.R/Makevars file (if you don't have a file called Makevars in your ~/.R/ directory) and include only these lines:
LOC = /usr/local/gfortran
CC=$(LOC)/bin/gcc -fopenmp
CXX=$(LOC)/bin/g++ -fopenmp
CXX11 = $(LOC)/bin/g++ -fopenmp
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L$(LOC)/lib -Wl,-rpath,$(LOC)/lib
CPPFLAGS=-I$(LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
# (check that the version of gfortran - in this case 10.2.0 - matches the version specified in FLIBS)
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++
Open R and install a package to test that it compiles with openMP enabled (when asked, compile from source = "Yes"):
install.packages("data.table", type = "source")
Unfortunately, I do not believe a more "simple" setup exists.
Eventually, I found a process that works on a M1 mac with Big Sur.
Head over to https://mac.r-project.org/, it contains most things you will need
Download and install R via R-4.1-branch.pkg. The CRAN version might also work, but I used the installer from mac.r-project.org, which required opening the osx security settings to allow the installation.
Install RStudio, start it, and let it install the developer tools. Alternatively, run sudo xcode-select --install in Terminal.
Head to https://mac.r-project.org/openmp/. Download openmp-11.0.1-darwin20-Release.tar.gz and install it (see Terminal commands below).
curl -O https://mac.r-project.org/openmp/openmp-11.0.1-darwin20-Release.tar.gz
sudo tar fvx openmp-11.0.1-darwin20-Release.tar.gz -C /
Now we need to add compiler flags so that clan uses openMP. In Terminal, create the Makevars file.
cd ~
mkdir .R
nano .R/Makevars
in nano, paste these additional compiler flags into the Makevars file:
CPPFLAGS += -Xclang -fopenmp
LDFLAGS += -lomp
Hit Control+O, Control+X to save and close
Head over to the gfortran page: https://github.com/fxcoudert/gfortran-for-macOS/releases
Use the installer gfortran-ARM-11.0-BigSur.pkg to install gfortran.
For some reason it appears to install in /usr/local/gfortran, but R expects it in /opt. The mac-R team likes to separate arm64 and intel related files. We could go and fix paths, or simply also install gfortran under /opt. Download the tar file gfortran-ARM-11.0-BigSur.tar.xz. You can use curl, or just download it and point tar in the command line to it.
cd /opt/R/arm64/
sudo mkdir gfortran
sudo tar -xzyf gfortran-ARM-11.0-BigSur.tar.xz -C /opt/R/arm64/
(replace gfortran-ARM-11.0-BigSur.tar.xz with /users/YOURUSERNAME/downloads/gfortran-ARM-11.0-BigSur.tar.xz)
Now it should work.
Not an expert in OSX, but doing this so others can figure out how to use my R package. I'd like to streamline the process some more, but wiping the mac, reinstalling osx and testing it takes so much time.
I am new with CDO, and wanted to use it to merge several netcdf files on the time variable with
cdo mergetime pr_Amon_IITM-ESM_historical_r1i1p1f1_gn_199001-199912.nc pr_Amon_IITM-ESM_historical_r1i1p1f1_gn_201001-201412.nc output.nc
I just installed CDO on Mac following the instructions given here: https://thiagodossantos.com/post/1-mac-science-software/.
I have Version 1.9.9 and it seems to work fine, however it can't open any .nc file I have tried so far.
This is the error message I got:
cdo mergetime: Open failed on >pr_Amon_IITM-ESM_historical_r1i1p1f1_gn_199001-199912.nc<
No such file or directory
This is the Version I am using:
Climate Data Operators version 1.9.9 (https://mpimet.mpg.de/cdo)
System: x86_64-apple-darwin20.1.0
CXX Compiler: /opt/local/bin/g++-mp-10 -pipe -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk -arch x86_64 -pthread
CXX version : g++-mp-10 (MacPorts gcc10 10.2.0_4) 10.2.0
C Compiler: /opt/local/bin/gcc-mp-10 -pipe -Os -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX11.0.sdk -arch x86_64 -pthread -pthread
C version : gcc-mp-10 (MacPorts gcc10 10.2.0_4) 10.2.0
F77 Compiler: gfortran -pipe -Os -m64
F77 version : GNU Fortran (MacPorts gcc10 10.2.0_4) 10.2.0
Features: 8GB 4threads C++14 Fortran PTHREADS HDF5 NC4/HDF5 OPeNDAP SZ UDUNITS2 PROJ CURL FFTW3 SSE3
Libraries: HDF5/1.12.0 proj/5.2.0 curl/7.74.0
Filetypes: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5
CDI library version : 1.9.9
ecCodes library version : 2.19.1
NetCDF library version : 4.7.4 of Jan 28 2021 10:09:27 $
hdf5 library version : 1.12.0
exse library version : 1.4.1
FILE library version : 1.9.1
I've also tried to reinstall it, but it didn't help. Any help is much appreciated!
P.S: I am also new with stack overflow, so please excuse me if I didn't ask the question correctly.
I was experiencing a similar problem, and I fixed it by closing that .nc by calling nc_close("file")-file after performing my calculations.
RcppArmadillo 0.8.400.0.0 works just fine on my computer, both from sourceCpp and cxxfunction. Now I want to upgrade to 0.8.500.0, which requires compilation from source. Then I got the error
ccache /usr/local/clang6/bin/clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -I/Applications/CPLEX_Studio128/cplex/include -I/Applications/CPLEX_Studio128/concert/include -DIL_STD -fPIC -Wall -g -O2 -c RcppArmadillo.cpp -o RcppArmadillo.o
RcppArmadillo.cpp:22:10: fatal error: 'RcppArmadillo.h' file not found
#include <RcppArmadillo.h>
^~~~~~~~~~~~~~~~~
1 error generated.
I got this error whether I ran install.packages("RcppArmadillo") in RStudio or in R console outside RStudio. My compiler is clang4, and I have no problem installing RcppParallel or compiling my own Rcpp code that uses RcppArmadillo and RcppParallel. R version: 3.5.0, MacOS High Sierra.
Edit: I looked at https://github.com/RcppCore/RcppArmadillo/issues/143, which is very relevant. I did install clang6 and gfortran 6.1, both downloaded from the CRAN website. I also changed the .R/Makevars file to reflect the changes to clang6. I have also installed ccache as suggested, to make compilation faster. Here's my Makevars:
F77 = /usr/local/gfortran/bin/gfortran
FC = $F77
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=ccache /usr/local/clang6/bin/clang
SHLIB_CXXLD=ccache /usr/local/clang6/bin/clang++
CXX= ccache /usr/local/clang6/bin/clang++ -Wall
CXX1X= ccache /usr/local/clang6/bin/clang++
CXX98= ccache /usr/local/clang6/bin/clang++
CXX11= ccache /usr/local/clang6/bin/clang++
CXX14= ccache /usr/local/clang6/bin/clang++
CXX17= ccache /usr/local/clang6/bin/clang++
LDFLAGS=-L/usr/local/clang6/lib
From the outputs in the R console when I was installing the package (added to the error message above), I can tell that clang6 was used for compilation. I also found the downloaded RcppArmadillo tarball, unpacked it, and ran ./configure from the command line. Nothing seemed wrong there; no config.log file was generated. This doesn't seem to be a configuration problem. Then I still got the exact same error when trying to install the package in R, after configuration, in libs. I also didn't get any message about -fopenmp. It seems that my problem is a bit different from that in the GitHub ticket.
R 3.5.x requires clang6 and adding clang6 to your system PATH variable.
Steps:
x Download and install the clang-6.0.0.pkg official package from CRAN.
x Delete your ~/.R/Makevars as it is likely set to use clang4. To do this, open Terminal and type:
sudo rm ~/.R/Makevars
x Then add to your ~/.bash_profile the following:
if [ -d "/usr/local/clang6/bin" ] ; then
export PATH="/usr/local/clang6/bin:$PATH"
fi
Note: If you are using a shell other than bash you will need to add the above into the appropriate file, e.g. for zsh add to ~/.zshrc, as this was not implemented in the official installer.
I should have a few cycles to finish writing a new unofficial Rtools installer a bit later. See: https://github.com/coatless/r-macos-rtools/issues/7
Note: Alternatively, you can remove the paths individual with
sudo vi ~/.R/Makevars
Pressing I to enter insert mode, deleting lines with clang4 in the path, and then pressing ESC + :wq to write changes to file.
Never mind, this problem went away with version 0.8.600. Later, this problem appeared again when I upgraded to RcppArmadillo 0.9.100.5.0. Somehow I only got this error when building from source; I downloaded the binary manually from the CRAN website, and used R CMD INSTALL to install the prebuilt version, and it worked; somehow R doesn't seem to know that there is a binary available for the newest version.
I did install clang6 and modified .R/Makevars to use clang6, but the same problem persisted; probably something else caused the problem.