I'm trying to install Python 3.7 on my Linux machine, but it's telling me it's unable to run C compiled programs:
root#kvm-RPJared2:~/Python-3.7.3# sudo ./configure --enable-optimizations
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for python3.7... no
checking for python3... python3
checking for --enable-universalsdk... no
checking for --with-universal-archs... no
checking MACHDEP... checking for --without-gcc... no
checking for --with-icc... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... configure: error: in `/root/Python-3.7.3':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
root#kvm-RPJared2:~/Python-3.7.3# gcc --version
gcc (Debian 6.3.0-18+deb9u1) 6.3.0 20170516
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
As you can see, I already have GCC installed, so I'm a bit lost on how to solve this issue.
Edit: I've already tried to download directly from git using apt-get, but the program is running into trouble with invalidated GPG keys. I've also tried using make as a different su, and that runs into the same error as I've shown above. If anyone has answers to either the apt-get issue (--allow-inauthenticated hasn't worked either) or the error I've pasted above, please help me out!
Related
I have written a "hello world" C code:
#include<stdio.h>
int main()
{
printf("hello world");
return 0;
}
When running the below command:
gcc main.c -o main
I am getting below error:
main.c: In function ‘main’:
main.c:8:1: internal compiler error: Segmentation fault
}
^
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-7/README.Bugs> for instructions.
Below is the output of lsb_release -a:
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 18.04.6 LTS
Release: 18.04
Codename: bionic
gcc version:
gcc (Ubuntu/Linaro 7.5.0-3ubuntu1~18.04) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
How can I resolve this issue?
Edit
I compiled the code with g++:
g++ main.c -o main
and it worked fine with no errors.
Given your GCC version of gcc (Ubuntu/Linaro 7.5.0-3ubuntu1~18.04) 7.5.0 this is an Ubuntu problem. Ubuntu 18.04 was released 4 1/2 years ago, and the odds of this being a problem with GCC itself are rather slim. As #thebusybee noted in the comments, this is almost certainly something caused by some problem with the compiler installation.
What you need to do is find out what's wrong with your Ubuntu GCC installation. First, make sure you're not doing something that causes the problem. Environment variables such as LD_PRELOAD (or any of the LD_* envvals) can effect GCC. There's also many other envvals that can.
Since you post that you can't upgrade the OS, that implies you're working in an organization with separate system administrator(s) that control the OS installation. So if GCC's failing is not caused by something you're doing this is really the system administrators' problem to solve. If your organization gives them control of the OS installation, that includes everything that they control and you're unable to change, such as the OS-supplied GCC installation here.
What you can do to keep working:
First, make sure you're not doing something to cause the problem
Check your environment for any LD_* envvals such as LD_PRELOAD. Make sure they're not causing the problem.
Check for other envvals that could effect GCC.
Install a version of GCC somewhere you are allowed to modify,
such as your home directory
Modify your PATH and other necessary envvals to used your local GCC copy
Use your organization's process(es) to create a trouble ticket to have your system administrator(s) investigate and repair your system. If you're not allowed to modify it, it's their problem.
If you have the time, you add something like the -v verbose flag or use GCC's Developer Options such as -freport-bug to try to figure out what's wrong with your system and help your system administrator(s) in solving the real problem here.
I am pretty new to the MacOS environment and I previously had some issue compiling C scripts. I had the following issue:
fatal error: stdio.h: No such file or directory
#include <stdio.h>
^
compilation terminated.
I tried to re-install xcode-select --install but keep telling me
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
I updated everything and nothing. Apparently it is because I don't have the /usr/includes file. I found a way to compile my software by using
/Library/Developer/CommandLineTools/usr/bin/g++ XXXX.cpp
However, now I am trying to ./compile and make another software but I don't know how to use this gcc interpreter by default. When I try to ./configure I got this error
configure: error: cannot run C compiled programs. If you meant to
cross compile, use '--host'. See 'config.log' for more details
So when I do look into config.log :
configure:3224: checking for gcc
configure:3240: found /usr/local/bin/gcc
configure:3251: result: gcc
configure:3282: checking for C compiler version
configure:3291: gcc --version >&5
gcc (GCC) 4.9.2 20141029 (prerelease)
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
configure:3302: $? = 0
configure:3291: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin14.0.0/4.9.2/lto-wrapper
Target: x86_64-apple-darwin14.0.0
Configured with: ../gcc-4.9-20141029/configure --enable-languages=c++,fortran
Thread model: posix
gcc version 4.9.2 20141029 (prerelease) (GCC)
configure:3302: $? = 0
configure:3291: gcc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:3302: $? = 1
configure:3291: gcc -qversion >&5
gcc: error: unrecognized command line option '-qversion'
gcc: fatal error: no input files
compilation terminated.
configure:3302: $? = 1
configure:3322: checking whether the C compiler works
configure:3344: gcc conftest.c >&5
configure:3348: $? = 0
configure:3396: result: yes
configure:3399: checking for C compiler default output file name
configure:3401: result: a.out
configure:3407: checking for suffix of executables
configure:3414: gcc -o conftest conftest.c >&5
configure:3418: $? = 0
configure:3440: result:
configure:3462: checking whether we are cross compiling
configure:3470: gcc -o conftest conftest.c >&5
conftest.c:15:19: fatal error: stdio.h: No such file or directory
#include <stdio.h>
^
compilation terminated.
configure:3474: $? = 1
configure:3481: ./conftest
./configure: line 3483: ./conftest: No such file or directory
configure:3485: $? = 127
configure:3492: error: in `/Users/XXXX/phyml':
configure:3494: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
Do you have any ideas of how I can fix it ?
Thanks a lot !
It's really easy to miss the answer from melpomene in the small comments to this question so let me post this here for everyone to see. This error usually means you're missing compiler tools (headers actually) that have been removed from Xcode.
You can find them in /Library/Developer/CommandLineTools/Packages/ since their name might be different depending on your version of macOS in the future.
Assuming you're running macOS Mojave (10.14), you need to run:
open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
And an macOS-style package installer will start, asking you for your adminstrator password. This is an official Apple package and although it might be weird to install something out of a random directory, you can trust it. You don't have to take my word for it though. Apple buried this change in the Xcode 10 release notes and you can find their explanation here: https://developer.apple.com/documentation/xcode_release_notes/xcode_10_release_notes#3035623
I'll reproduce this here in case this link ever goes away or gets changed:
The Command Line Tools package installs the macOS system headers inside the macOS SDK. Software that compiles with the installed tools will search for headers within the macOS SDK provided by either Xcode at:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
or the Command Line Tools at:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
depending on which is selected using xcode-select.
The command line tools will search the SDK for system headers by default. However, some software may fail to build correctly against the SDK and require macOS headers to be installed in the base system under /usr/include. If you are the maintainer of such software, we encourage you to update your project to work with the SDK or file a bug report for issues that are preventing you from doing so. As a workaround, an extra package is provided which will install the headers to the base system. In a future release, this package will no longer be provided. You can find this package at:
/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
> To make sure that you're using the intended version of the command line tools, run xcode-select -s or xcode select -s /Library/Developer/CommandLineTools after installing.
Following this tutorial, I tried to compile a C program to WebAssembly by using the following command.
emcc hello.c -s WASM=1 -o hello.html
But I ecounter the "No available targets are compatible with this triple." problem.
$ emcc hello.c -s WASM=1 -o hello.html
WARNING root: LLVM version appears incorrect (seeing "(https://github.com/kripken/emscripten-fastcomp-clang/", expected "3.4")
INFO root: (Emscripten: Running sanity checks)
WARNING root: Assigning a non-existent settings attribute "WASM"
WARNING root: - did you mean one of ASM_JS?
WARNING root: - perhaps a typo in emcc's -s X=Y notation?
WARNING root: - (see src/settings.js for valid values)
/home/casper/Desktop/test/emsdk/clang/fastcomp/build_incoming_64/bin/lli: error creating EE: No available targets are compatible with this triple.
FAIL: Running the generated program failed!
How to solve it?
EMCC Version
$ emcc --version
emcc (Emscripten GCC-like replacement) 1.22.1 ()
Copyright (C) 2014 the Emscripten authors (see AUTHORS.txt)
This is free and open source software under the MIT license.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Basic Information
OS : Ubuntu 16.10
emcc Location: /usr/bin/emcc
You're running emcc version 1.22.1 which dates back from 8/7/2014, before WebAssembly was started.
emsdk in the instruction you followed must have installed a very recent emscripten version (this is what sdk-incoming-64bit from these instructions does: incoming is the latest branch), but an older emscripten is found in your system.
Run:
which emcc
echo $PATH
What do they say? I suspect you have an old emscripten lying in there. You probably also want to check and/or delete your ~/.emscripten file which may also contain obsolete information.
You can alter your path, delete the older emscripten, or invoke the SDK's emscripten using its absolute path (though this may fail later if other scripts pick up older versions along the path).
Don't forget (from the tutorial's instructions) to activate the SDK you've installed:
./emsdk activate --build=Release sdk-incoming-64bit binaryen-master-64bit
And run:
source ./emsdk_env.sh
This last command needs to be run for every shell session. If you open a new shell you need to re-source then SDK.
I'm trying to install tidalcycles (http://tidalcycles.org/getting_started.html), but i had problems running the cabal install tidal command.
Originally i had an issue due to windows10 compatibility, so I installed Cygwin and i tried to run the command from his shell. But then this occurs:
Andrea#Pc_di_Andrea ~
$ cabal install tidal
Resolving dependencies...
Configuring old-time-1.1.0.3...
Configuring network-2.6.2.1...
Failed to install old-time-1.1.0.3
Build log ( C:\Users\Andrea\AppData\Roaming\cabal\logs\old-time-1.1.0.3.log):
Configuring old-time-1.1.0.3...
configure: WARNING: unrecognized options: --with-compiler
checking for gcc... C:\PROGRA~1\HASKEL~1\802E01~1.1\mingw\bin\gcc.exe
checking whether the C compiler works... no
configure: error: in `/tmp/cabal-tmp-8957/old-time-1.1.0.3':
configure: error: C compiler cannot create executables
See `config.log' for more details
cabal: Leaving directory 'C:\cygwin\tmp\cabal-tmp-8957\old-time-1.1.0.3'
Failed to install network-2.6.2.1
Build log ( C:\Users\Andrea\AppData\Roaming\cabal\logs\network-2.6.2.1.log ):
Configuring network-2.6.2.1...
configure: WARNING: unrecognized options: --with-compiler
checking build system type... i686-pc-cygwin
checking host system type... i686-pc-cygwin
checking for gcc... C:\PROGRA~1\HASKEL~1\802E01~1.1\mingw\bin\gcc.exe
checking whether the C compiler works... no
configure: error: in `/tmp/cabal-tmp-8956/network-2.6.2.1':
configure: error: C compiler cannot create executables
See `config.log' for more details
cabal: Leaving directory 'C:\cygwin\tmp\cabal-tmp-8956\network-2.6.2.1'
cabal.exe: Error: some packages failed to install:
hosc-0.15 depends on network-2.6.2.1 which failed to install.
mersenne-random-pure64-0.2.0.5 depends on old-time-1.1.0.3 which failed to
install.
network-2.6.2.1 failed during the configure step. The exception was:
ExitFailure 77
old-time-1.1.0.3 failed during the configure step. The exception was:
ExitFailure 77
tidal-0.8 depends on old-time-1.1.0.3 which failed to install.
websockets-0.9.6.2 depends on network-2.6.2.1 which failed to install.
So, it says that the
configure: error: C compiler cannot create executables
is the problem. I'm running the 32bit version, and the c compiler should be installed, since i get this reply from the system:
Andrea#Pc_di_Andrea ~
$ echo; gcc --version; echo; g++ --version;
gcc (GCC) 5.4.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
g++ (GCC) 5.4.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
I'm a total newbie to this 'cygwin enviroment' and I apologize if my question is not appropriate, but I read some guides about this c compiler problem and i didn't understand what i'm doing wrong, at all.
Found the problem: I didn't complete Haskell installation editing the cabal config.file, with
extra-prog-path: C:\Program Files\Haskell Platform\8.0.1\msys\usr\bin
extra-lib-dirs: C:\Program Files\Haskell Platform\8.0.1\mingw\lib
extra-include-dirs: C:\Program Files\Haskell Platform\8.0.1\mingw\include+
as this source https://www.haskell.org/platform/ says.
I'm new to Homebrew (I usually use Macports, but I'm trying out Homebrew on a 2nd computer), and I wish to install the openmpi (or mpich2) package. Steps are as follows (carried out on Mac OS X Yosemite with Xcode 6 installed):
brew install gcc
brew install openmpi
However, I suspect the linking may have been done incorrectly, due to the following reasons:
The symbolic link for /usr/local/bin/gcc is missing:
$ which gcc
/usr/bin/gcc
$ gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.0.0
Thread model: posix
$ which gcc-4.9
/usr/local/bin/gcc-4.9
$ gcc-4.9 --version
gcc-4.9 (Homebrew gcc 4.9.2) 4.9.2
Copyright (C) 2014 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
mpicc may have been linked to the Apple gcc:
$ which mpicc
/usr/local/bin/mpicc
$ mpicc --version
Apple LLVM version 6.0 (clang-600.0.54) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.0.0
Thread model: posix
My questions are as follows:
How do I get the /usr/local/bin/gcc symbolic link? Or is Homebrew deliberately avoiding this for certain reasons? e.g. if Homebrew is compiling all its packages using Apple gcc, which is assumed to be in the path, would changing the path to gcc-4.9 mean that Homebrew now compiles its packages with gcc-4.9 instead?
Is the Homebrew-installed Open MPI linked to the Apple gcc (and not the Homebrew gcc)? If yes, is it possible (or advisable) to change the linking?
Alternatively, how necessary is it to fix the linkages? Could I run into certain problems if I choose not to fix it? For example, I'm considering using ln -s to forcibly create the /usr/local/bin/gcc symbolic link. But is this a good idea (*)?
(*) I understand there are likely to be issues when linking object files created by different compilers. So with (1), (2) and (3), I'm hoping to find a solution that avoids combinations whereby I'm creating object files with different compilers (some with gcc-4.9 and some with the Apple gcc).
You need to do the following:
1) Add environment variables for homebrew (you can also add these lines to your ~\.bashrc):
$ export HOMEBREW_CC=gcc-4.9
$ export HOMEBREW_CXX=g++-4.9
2) Rebuild and reinstall openmpi and its dependencies from source
$ brew reinstall openmpi --build-from-source
3) In the end you will get a message like:
==> Reinstalling open-mpi
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.
==> Downloading http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.
Already downloaded: /Library/Caches/Homebrew/open-mpi-1.8.4.tar.bz2
==> ./configure --prefix=/usr/local/Cellar/open-mpi/1.8.4 --disable-silent-rules
==> make all
==> make check
==> make install
Warning: open-mpi dependency gcc was built with a different C++ standard
library (libstdc++ from clang). This may cause problems at runtime.
🍺 /usr/local/Cellar/open-mpi/1.8.4: 785 files, 23M, built in 41.2 minutes
$ mpicc --showme
gcc-4.9 -I/usr/local/Cellar/open-mpi/1.8.4/include -L/usr/local/opt/libevent/lib -L/usr/local/Cellar/open-mpi/1.8.4/lib -lmpi
On my MacBook I had some conflicts with XCode 6.2, which were solved following this instructions
If you want to install mpich
$ unlink openmpi
$ brew unlink gcc
$ brew install homebrew/versions/gcc5
$ brew install mpich --build-from-source
$ mpicc -v
mpicc for MPICH version 3.2
Using built-in specs.
COLLECT_GCC=gcc-5
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc5/5.4.0/libexec/gcc/x86_64-apple-darwin14.5.0/5.4.0/lto-wrapper
Target: x86_64-apple-darwin14.5.0
Configured with: ../configure --build=x86_64-apple-darwin14.5.0 --prefix=/usr/local/Cellar/gcc5/5.4.0 --libdir=/usr/local/Cellar/gcc5/5.4.0/lib/gcc/5 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-5 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl014 --with-system-zlib --enable-libstdcxx-time=yes --enable-stage1-checking --enable-checking=release --enable-lto --disable-werror --with-pkgversion='Homebrew gcc5 5.4.0' --with-bugurl=https://github.com/Homebrew/homebrew-versions/issues --enable-plugin --disable-nls --enable-multilib
Thread model: posix
gcc version 5.4.0 (Homebrew gcc5 5.4.0)
It would probably be cleaner if you simply modify the configuration file for the Open MPI compiler wrapper and make it invoke gcc-4.9 instead of simply gcc. As I have no idea where exactly Homebrew puts Open MPI and therefore cannot give you the correct path directly, you should search for it:
$ find /usr/local -name mpicc-wrapper-data.txt
Once you have found mpicc-wrapper-data.txt, find the line that starts with compiler= and modify it to read:
compiler=gcc-4.9
You should also modify all other files that match the shell glob mpi*-wrapper-data.txt and modify the compiler=... line accordingly. Use g++-4.9 in mpic++, mpicxx, and mpiCC. Use gfortran-4.9 (if installed) in mpif77 and mpif90 (for Open MPI versions < 1.8) or for mpifort (for versions >= 1.8).
Mixing object code produced by different compilers on the same platform should be fine as long as all of them adhere to the same ABI, which is more or less the case with Clang and GCC. In the end, all programs are linked against the system libraries that come with OS X and those are compiled with Clang only.