clang++ can not locate c++ header and library - c++

My OS is OS X 10.10.2 and the default compiler for C is clang.
But this version of clang does not support ubsan (undefined sanitizer) which comes in the 3.4 release of clang. I also want to use KLEE to do some analysis. AFAIK KLEE works well with LLVM-<=3.4. I decided to install
llvm-3.4 and clang-3.4 in my laptop.
After installing clang-3.4 in my system, I encountered a issue that the compiler can not locate the c++ header file. I installed clang-3.4 in /usr/local and I can find the c++ header file in /usr/local/include/c++/4.8.4. How can I add this directory to the search path of clang-3.4 and also the c++ library?
for the following demo code:
#include <iostream>
using namespace std;
int main(){
cout<<"Hellow World\n";
return 0;
}
When I compile it using command clang++ test.cpp, I got the error
test1.cpp:1:10: fatal error: 'iostream' file not found
#include <iostream>
^
1 error generated.
Below is the version of clang I used
clang version 3.4 (tags/RELEASE_34/final)
Target: x86_64-apple-darwin14.1.0
Thread model: posix
I used the following shell command to install llvm-3.4 and clang-3.4:
wget http://llvm.org/releases/3.4/llvm-3.4.src.tar.gz \
http://llvm.org/releases/3.4/clang-3.4.src.tar.gz \
http://llvm.org/releases/3.4/clang-tools-extra-3.4.src.tar.gz \
http://llvm.org/releases/3.4/compiler-rt-3.4.src.tar.gz
tar zxf llvm-3.4.src.tar.gz
tar zxf clang-3.4.src.tar.gz -C llvm-3.4/tools
mv llvm-3.4/tools/clang{-3.4,}
tar zxf clang-tools-extra-3.4.src.tar.gz -C llvm-3.4/tools/clang/tools
mv llvm-3.4/tools/clang/tools/{clang-tools-extra-3.4,extra}
tar zxf compiler-rt-3.4.src.tar.gz -C llvm-3.4/projects
mv llvm-3.4/projects/compiler-rt{-3.4,}
cd llvm-3.4
./configure --enable-cxx11 \
--enable-bindings=none --enable-shared \
--enable-debug-symbols --enable-optimized
make
make install
Now I have two versions of clang in my OS, one is the default one shipped with OSX located in /usr/bin and the other is clang-3.4 located in /usr/local/bin. The previous one can find the C++ header file while the latter can not.

Did you read the user documentation of clang notably the section on command line options ? BTW, current (march 2015) version of clang is 3.6!
For C++ code you should use the clang++ command, not the clang command.
You might pass -I and -L options to clang++ but you might perhaps have misinstalled your clang compiler.
You should be aware of the -v and -H options of clang or clang++ ; they could be useful, at least to understand more your issue.
addenda
BTW, a program reported to work with Clang 3.4 is extremely likely to work with a more modern version, like Clang 3.5 or 3.6
You probably have a PATH issue; you should have configure -d your Clang-3.4 & LLvm-3.4 programs with --program-suffix=-my-3.4 (if you do that, repeat your entire compiler build and installation) and you probably should run /usr/local/bin/clang++-my-3.4 ; maybe you also need some --with-gcc-toolchain additional configure option.
I'm pretty sure that you should be able to try to compile or use your mysterious software requiring Clang-3.4 with a more modern version like 3.5 or 3.6 ; your MacOSX 10.10.2 is rumored to have a Clang-3.5 based system compiler, it very probably is able to compile and work with your mysterious software.

Related

Configuring compilers on Mac M1 (Big Sur, Monterey) for Rcpp and other tools

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

Compile OpenMP programs with gcc compiler on OS X Yosemite

$ gcc 12.c -fopenmp
12.c:9:9: fatal error: 'omp.h' file not found
#include<omp.h>
^
1 error generated.
While compiling openMP programs I get the above error. I am using OS X Yosemite. I first tried by installing native gcc compiler by typing gcc in terminal and later downloaded Xcode too still I got the same error. Then I downloaded gcc through:
$ brew install gcc
Still I'm getting the same error. I did try changing the compiler path too still it shows:
$ which gcc
/usr/bin/gcc
So how do I compile programs with gcc?
EDIT: As of 13 Aug 2017 the --without-multilib option is no longer present in Homebrew and should not be used. The standard installation
brew install gcc
will provide a gcc installation that can be used to compile OpenMP programs. As below it will be installed into /usr/local/bin as gcc-<version>. The current gcc version available from Homebrew (as of writing) will install as gcc-8. You can compile programs with OpenMP support using it via
gcc-8 -fopenmp hello.c
Alternatively you could put an alias in your .bashrcfile as
alias gcc='gcc-8'
and then compile using
gcc -fopenmp hello.c
Note: I'm leaving the original post here in case it is useful to somebody.
The standard gcc available on OS X through XCode and Clang doesn't support OpenMP. To install the Homebrew version of gcc with OpenMP support you need to install it with
brew install gcc --without-multilib
or as pointed out by #Mark Setchell
brew reinstall gcc --without-multilib
This will install it to the /usr/local/bin directory. Homebrew will install it as gcc-<version> so as not to clobber the gcc bundled with XCode.
I finally did some research and I finally came across a solution here: <omp.h> library isn't found in the GCC version (4.2.1) in Mavericks.
I got a new gcc complier from http://hpc.sourceforge.net/
Then I placed a new executable folder by
$ sudo tar -xvf gcc-4.9-bin.tar -C /
Later I switched to it by
export PATH=/usr/local/bin:$PATH that seemed to do the trick!

"make[2]: g++: Command not found" in Netbeans

I get the error message:
make[2]: g++: Command not found
which I know means it cannot find the C++ compiler. However, in Netbeans if I go to the configuration to choose my C++ compiler it shows the following being in /usr/bin:
g++4.6
g++4.7
g++4.8
but it doesn't have just g++.
Tried sudo aptitude install g++ but it didnt work.
If I do g++ --version I get:
The program 'g++' can be found in the following packages:
* g++
* pentium-builder
1) Verify you can run "g++" from the command line,
2) type whereis g++ to get the path,
3) Make sure you have the NetBeans C++ plugin installed
Go to Tools->Options->C++->Build Tools
4) Configure the path in NetBeans
Usually, /usr/bin/g++ is a symlink to some /usr/bin/g++-4.7 (or g++-4.8 etc...); just make it again (which is usually provided by the g++ virtual package on Debian or Ubuntu), e.g.
% sudo -s
# cd /usr/bin
# ln -sv g++-4.8 g++
Above % and # are shell prompts that you should not type.
Of course, don't forget the sudo apt-get install g++ etc...
BTW, you might put that link from $HOME/bin/g++ to /usr/bin/g++-4.8 and you don't need root permission for that.
(sometimes, these symlinks go indirectly thru /etc/alternatives etc...)
Your issue is a sysadmin issue; you should rather ask it (with a big lot more details) on askubuntu or superuser; it is off-topic on Stack Overflow.
BTW, NetBeans is not a compiler, but an editor (sometimes called IDE). You could use something better/simpler (e.g. emacs or vim) with e.g. make as a builder (to be run inside a terminal). Before using NetBeans ensure that g++ -v is working alone in some terminal

Linking g++ 4.8 to libstdc++

I downloaded and built gcc 4.8.1 on my desktop, running 64-bit Ubuntu 12.04. I built it out of source, like the docs recommend, and with the commands
../../gcc-4.8.1/configure --prefix=$HOME --program-suffix=-4.8
make
make -k check
make install
It seemed to pass all the tests, and I installed everything into my home directory w/ the suffix -4.8 to distinguish from the system gcc, which is version 4.6.3.
Unfortunately when I compile c++ programs using g++-4.8 it links to the system libc and libstdc++ rather than the newer ones compiled from gcc-4.8.1. I downloaded and built gcc 4.8 because I wanted to play around with the new C++11 features in the standard library, so this behaviour is definitely not what I wanted. What can I do to get gcc-4.8 to automatically link to the standard libraries that came with it rather than the system standard libraries?
When you link with your own gcc you need to add an extra run-time linker search path(s) with -Wl,-rpath,$(PREFIX)/lib64 so that at run-time it finds the shared libraries corresponding to your gcc.
I normally create a wrapper named gcc and g++ in the same directory as gcc-4.8 and g++-4.8 which I invoke instead of gcc-4.8 and g++-4.8, as prescribed in Dynamic linker is unable to find GCC libraries:
#!/bin/bash
exec ${0}SUFFIX -Wl,-rpath,PREFIX/lib64 "$#"
When installing SUFFIX and PREFIX should be replaced with what was passed to configure:
cd ${PREFIX}/bin && rm -f gcc g++ c++ gfortran
sed -e 's#PREFIX#${PREFIX}#g' -e 's#SUFFIX#${SUFFIX}#g' gcc-wrapper.sh > ${PREFIX}/bin/gcc
chmod +x ${PREFIX}/bin/gcc
cd ${PREFIX}/bin && ln gcc g++ && ln gcc c++ && ln gcc gfortran
(gcc-wrapper.sh is that bash snippet).
The above solution does not work with some versions of libtool because g++ -Wl,... -v assumes linking mode and fails with an error.
A better solution is to use specs file. Once gcc/g++ is built, invoke the following command to make gcc/g++ add -rpath to the linker command line (replace ${PREFIX}/lib64 as necessary):
g++ -dumpspecs | awk '/^\*link:/ { print; getline; print "-rpath=${PREFIX}/lib64", $0; next } { print }' > $(dirname $(g++ -print-libgcc-file-name))/specs
I just had the same problem when building gcc-4.8.2. I don't have root access on that machine and therefore need to install to my home directory. It took several attempts before I figured out the magic required to get this to work so I will reproduce it here so other people will have an easier time. These are the commands that I used to configure gcc:
prefix=/user/grc/packages
export LDFLAGS=-Wl,-rpath,$prefix/lib
export LD_RUN_PATH=$prefix/lib
export LD_LIBRARY_PATH=$prefix/lib
../../src/gmp-4.3.2/configure --prefix=$prefix
../../src/mpfr-2.4.2/configure --prefix=$prefix
../../src/mpc-0.8.1/configure --prefix=$prefix --with-mpfr=$prefix --with-gmp=$prefix
../../src/gcc-4.8.2/configure --prefix=$prefix --with-mpfr=$prefix --with-gmp=$prefix --with-mpc=$prefix --enable-languages=c,c++
That got me a working binary but any program I built with that version of g++ wouldn't run correctly unless I built it with the -Wl,-rpath,$prefix/lib64 option. It is possible to get g++ to automatically add that option by providing a specs file. If you run
strace g++ 2>&1 | grep specs
you can see which directories it checks for a specs file. In my case it was $prefix/lib/gcc/x86_64-unknown-linux-gnu/4.8.2/specs so I ran g++ -dumpspecs to create a new specs file:
cd $prefix/lib/gcc/x86_64-unknown-linux-gnu/4.8.2
$prefix/bin/g++ -dumpspecs > xx
mv xx specs
and then edited that file to provide the -rpath option. Search for the lines like this:
*link_libgcc:
%D
and edit to add the rpath option:
*link_libgcc:
%D -rpath /user/grc/packages/lib/%M
The %M expands to either ../lib or ../lib64 depending on whether you are building a 32-bit or a 64-bit executable.
Note that when I tried this same trick on an older gcc-4.7 build it didn't work because it didn't expand the %M. For older versions you can remove the %M and just hardcode lib or lib64 but that is only a viable solution if you only ever build 32-bit executables (with lib) or only ever build 64-bit executables (with lib64).
gcc -print-search-dirs will tell you where your compiler is looking for runtime libraries, etc. You can override this with the -B<prefix> option.

PARI/GP and gcc

I am trying to install PARI/GP and in the configuration step I get:
$ ./Configure
[...]
Looking for the compilers ...
...cc is /usr/bin/cc
...gcc is /usr/local/bin/gcc
GNU compiler version 4.8.0 20120705 (experimental) (GCC)
###
### C compiler does not work. PARI/GP requires an ANSI C compiler! Aborting.
###
### Compiler was: /usr/local/bin/gcc
$ gcc --version
gcc (GCC) 4.8.0 20120705 (experimental)
This is strange because the documentation says:
"Only ANSI C and C++ compilers are supported. Choosing the GNU compiler
gcc/g++ enables the inlining of kernel routines (about 20% speedup; if you
use g++, it is a good idea to include the -fpermissive flag). If you choose
not to use gcc, the C++ version of Pari will be a little faster because of
general inlining, but can be used in library mode only with C++ programs.
We strongly recommand using gcc all the way through."
I have also tried with g++ with the same result.
I am trying to compile on a linux x86_64.
Any ideas?
Thanks in advance,
M;
The config/get_cc script in PARI's top level tried to compile a test program
and failed.
Look for the line
$CC $CFLAGS $extraflag -o $exe ansi.c 2>/dev/null && $RUNTEST $exe
and remove the 2>/dev/null. Configure should now print out explicit error
messages from the compiler. They should provide a hint.
I had the same problem. Here is the solution for Linux Mint 17.1 64-bit:
sudo apt-get install gcc libc6-dev libgmp-dev
This command also installs the GMP library (recommended for PARI/GP).
Thanks to K.B. for the hint on how to see the problem.