I recently upgraded to Big Sur and am having trouble running a code on mpi. I am running a test code with the following command:
mpif90 -o test.f90 ./test
I receive the following error:
-bash: mpif90: command not found
I have updated homebrew and macports yet am unable to solve the problem. I suspect it has something to do with an incorrect path name somewhere. Any ideas? Thank you.
#Oo.oO Thank you. When configuring the build of gcc (per the link in your comment) by the command:
../configure --prefix=$HOME/opt/usr/local/gcc/gcc-9.2.0 \
--enable-checking=release \
--enable-languages=c,c++,fortran \
--disable-multilib \
--with-sysroot=$HOME/opt/usr/local/gcc_system_root \
--program-suffix=-9.2.0
the following error occurs:
configure: error: in `$HOME/opt/src/gcc/gcc-9.2.0/build':
configure: error: C compiler cannot create executables
I have updated Xcode (Version 12.3). Any thoughts? Thank you.
The problem was there were other /bin/ directories that had older versions of gcc and openmpi. When updating, the new files from /lib/ directories needed to be trasnfered to the /Cellar/ directories. The problem is fixed when first uninstalling all old macports and compilers with incorrect files and/or paths as sudo port -fp uninstall installed, and brew uninstall openmpi, and brew uninstall gcc. Then reinstall new homebrew compilers brew install gcc, brew install openmpi. This gives the correct paths with configured files when submitting a make file, or in this case, using the mpif90 command.
Related
I'm trying to compile a package called Kraken on my M1 Mac running Big Sur.
MacOS fails to compile: clang gets upset. I installed gcc from Homebrew (twice) and $ brew doctor says I'm ready to go.
My path is now:
/usr/local/opt/llvm/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/opt/homebrew/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin:/opt/homebrew/bin.
The gcc-11 etc files exist at /opt/homebrew/bin
But /usr/local/bin does not exist!
MacOS does not update the command alias for gcc:
$ rm gcc
then
$ ln -s /opt/homebrew/bin/gcc-11 gcc
return no error
but then
$ which gcc
returns
/usr/bin/gcc
I'm lost and gather this compiler-pointing has been a mess; is there any new insight here? I've seen a bunch of entries but nothing I've tried has worked.
Hoping this is a stupid newbie (me) problem, I thank you for any help you can give.
Michael
Homebrew avoids linking binaries with the same name as system binaries like gcc(appleclang). ln -s /opt/homebrew/bin/gcc-11 /opt/homebrew/bin/gcc or tell your configurator to explicitly use gcc-11 via CC= etc. and the same for g++-11 if C++ is used.
If it's a ./configure script, you can try calling CC=/opt/homebrew/bin/gcc-11 CXX=/opt/homebrew/bin/g++-11 ./configure
if cmake then use cmake .. -DCMAKE_C_COMPILER=/opt/homebrew/bin/gcc-11 -DCMAKE_CXX_COMPILER=/opt/homebrew/gcc++-11
Also, try seeing where the homebrew gcc link points ls -l /opt/homebrew/bin/gcc
Since upgrading to Yosemite I cannot compile with gfortran. Initially I was getting "segmentation fault 11", then I:
Updated to gcc v.5.0 from http://hpc.sourceforge.net/
Re-installed Xcode command line utilities v.6.1.1
After doing the above, I am able to compile very simple fortran programs but the more complex code that I run gives me the following error:
gfortran: error: libgfortran.spec: No such file or directory
But in fact, the libgfortran.spec file is located in /usr/local/lib
ls /usr/local/lib | grep gfortran
libgfortran.3.dylib
libgfortran.a
libgfortran.dylib
libgfortran.la
libgfortran.spec
All of the gcc binaries are located in /usr/local/bin
which gfortran
/usr/local/bin/gfortran
And my path seems to be OK
echo $PATH
/usr/local/lib:/usr/local/bin:/usr/local:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/lib:/usr/texbin:/Users/MattCooper/bin:/Applications/MRT/bin
I also tried re-installing gcc with homebrew:
brew install gcc
Error: gcc-4.9.2 already installed
To install this version, first 'brew unlink gcc'
However, I get v. 5.0 when I ask 'gcc --version':
gcc --version
gcc (GCC) 5.0.0 20141005 (experimental)
When I try to unlink or upgrade gcc with homebrew I get a permission denied error:
brew unlink gcc
Unlinking /usr/local/Cellar/gcc/4.9.2... Error: Permission denied - /usr/local/bin/c++-4.9
similarly
brew upgrade gcc
Permission denied - /usr/local/bin/c++-4.9
Finally
which gcc
/usr/local/bin/gcc
Please help. Many thanks ahead of time. Please let me know what I've forgotten to include.
I ended up solving the problem via homebrew. I can't pinpoint the exact source of the problem but it was related to the fact that I installed gcc v4.9 from http://hpc.sourceforge.net/, then somewhere along the way I re-installed and/or updated gcc with homebrew. Then, after upgrading to Yosemite, I installed gcc v5 from http://hpc.sourceforge.net/. Somewhere within that process, the binaries within /usr/local/bin and usr/local/lib were not linked properly.
The main clue was the Permission Denied error when trying to run 'brew upgrade gcc'. I found a solution here: Brew doctor says: "Warning: /usr/local/include isn't writable."
To fix, I used:
brew doctor
which returned a bunch of directories that were not writeable, for example usr/local/lib, thus brew was unable to ugrade gcc to the v5.0 and link everything.
I went through and issued:
sudo chown -R $USER /usr/local
and did this for all of the other non-writeable directories returned by 'brew doctor'. Then, I was able to use brew to ugrade gcc:
brew upgrade gcc
During the ugrade, homebrew returned an error that stated it could not finish the upgrade because there was already an existing gfortran file located in:
/usr/local/bin/gfortran
To fix, homebrew suggested I run:
brew -link gcc
at which point everything worked. Interesting (to me, because I don't fully understand all of this) when I ask brew to clean things up, I get:
brew cleanup
Warning: Skipping (old) /usr/local/Cellar/gcc/4.9.2 due to it being linked
There's some similar information located here: How to link to a new gcc version with brew?
Similar to that user, when I look in my cellar, I find two versions of gcc, but I'm not sure if I need both
ls /usr/local/Cellar/gcc
4.9.2 4.9.2_1
I had a similar issue with similar solution. It could not find this file:
gfortran: error: libgfortran.spec: No such file or directory
So my problem was that I had installed gcc through hpc.sourceforge.net and through homebrew. I had to uninstall the homebrew version
brew uninstall gcc
Then I had to reinstall the gcc from hpc.sourceforge.net
sudo tar -xvf gcc-4.9-bin.tar.gz -C /
This worked for me when I wanted to revert to gcc 4.9 from hpc.sourceforge.net, using Yosemite.
I'm on a mac and I used homebrew to install gmp.
Kyumins-iMac:gcjlib math4tots$ g++ main.cpp -lgmp -lgmpxx
In file included from main.cpp:2:
./gcjlib.hpp:4:10: fatal error: 'gmpxx.h' file not found
#include <gmpxx.h>
^
1 error generated.
So then I explicitly told g++ to use /usr/local/include
Kyumins-iMac:gcjlib math4tots$ g++ main.cpp -lgmp -lgmpxx -I/usr/local/include
ld: library not found for -lgmp
clang: error: linker command failed with exit code 1 (use -v to see invocation)
So then I explicitly told g++ to use /usr/local/lib
Kyumins-iMac:gcjlib math4tots$ g++ main.cpp -lgmp -lgmpxx -I/usr/local/include -L/usr/local/lib
Kyumins-iMac:gcjlib math4tots$ ./a.out
sum is -4444
absolute value is 4444
So the only issue seems to be that g++ fails to acknowledge /usr/local.
But it is tedious to type all this out all the time, especially when I'm just writing small single file programs.
Is there a way for me to get g++ to acknowledge the stuff in /usr/local by default? Is there a standard way homebrew users do this?
I'm on OS X 10.9.3 with Xcode 5.1.1 in case it is relevant.
I also use Homebrew and had a similar problem on Mac OSX Maverick 10.9.5 and Xcode 6.0.1, but it was solved by running:
xcode-select --install
Note that it doesn't work without the double hyphens given by the previous answer. This installs the command-line tools that also create /usr/lib/ and /usr/include/. I don't know why Homebrew doesn't automatically check this upon installation, since it does check for Xcode...
If you want to check exactly what folders your compiler is looking through for header files you can write:
cpp -v
A workaround would be to:
export C_INCLUDE_PATH=/usr/local/include
export CPLUS_INCLUDE_PATH=/usr/local/include
At least this tricked the pre-processor to behave here :)
Try running xcode-select --install
At least on Mavericks, I've found that if I install the Xcode application without installing the command-line tools, then the tools are sort of available, but normal unix-ey builds don't work correctly. One symptom is that /usr/local/include is not on the include search path. The command-line tools seem to resolve this issue.
I have Yosemite 10.10.5 and running xcode-select --install didn't fix the problem for me. The command returned with xcode-select: error: command line tools are already installed, use "Software Update" to install updates.
When I ran xcode-select -p, it showed /Applications/Xcode.app/Contents/Developer. I ended up deleting Xcode from the Applications directory, which resulted in xcode-select -p returning /Library/Developer/CommandLineTools. This fixed compiler error for me.
That was helpful for me:
Use the latest version. 1.0.2o_1 just a current build.
brew install openssl
ln -s /usr/local/Cellar/openssl/1.0.2o_1/include/openssl /usr/local/include/openssl
ln -s /usr/local/Cellar/openssl/1.0.2o_1/lib /usr/local/lib/openssl
There are a few questions around this topic with answers that suggest putting a symlink in /usr/local/include. However I'm running macOS Monterey 12.3 (on an M1 MacBook) and that directory doesn't exist.
I had installed the Xcode command line tools by downloading the package from Apple, so xcode-select --install just tells me it's already installed and doesn't create any directories.
I ran cpp -v to see which directories are searched for #include <...>:
/Library/Developer/CommandLineTools/usr/lib/clang/13.1.6/include
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
/Library/Developer/CommandLineTools/usr/include
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks (framework directory)
I picked /Library/Developer/CommandLineTools/usr/include for the symlink. In that directory, I ran the following command (note the new location for Homebrew installations, under /opt/homebrew - some old answers are also out of date on this point):
sudo ln -s /opt/homebrew/opt/openssl#3/include/openssl .
clang was then able to find the OpenSSL files.
apk add --no-cache build-base
it works fine ！！！！
go build -tags musl -o main main.go
When running configure it fails with
checking for leptonica... yes
checking for pixCreate in -llept... no
configure: error: leptonica library missing
But I have leptonica 1.69 built (downloaded source and ran ./configure && make install)
Edit
I think configure: error: leptonica library missing is a bit misleading, please note that it first says checking for leptonica... yes, and then fails on checking for pixCreate in -llept... no. So maybe the problem is not that the library is missing, but something else.
I finally managed to make it compile, after reading this and this thread. The proper steps for were:
./autogen.sh
export LIBLEPT_HEADERSDIR=/local/include
./configure --with-extra-libraries=/local/lib
make install
for leptonica 1.69, lib renamed to .libs, so, parameters are
export LIBLEPT_HEADERSDIR=<your_path>/leptonica-1.69/src
./autogen.sh
./configure --prefix= --with-extra-libraries=<your_path>/leptonica-1.69/src/.libs
and so on
Maybe this could solve the issue:
export LIBLEPT_HEADERSDIR=/usr-or-other/local/include
I am working on redhat linux 7.2 . None of the solution worked for me I was getting following errors in config.log. Package lept was not found in the pkg-config search path.
Perhaps you should add the directory containing `lept.pc'
to the PKG_CONFIG_PATH environment variable PKG_CONFIG_PATH
configure script uses pkg-config utility to check for packages . It was not able to find lept package ( although i had installed leptonica seperately ) By setting PKG_CONFIG_PATH pointing to the directory where lept.pc is present , i was able to resolve the issue . export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig
The FAQ addresses this issue and worked for me with tesseract 3.02.02 on Mac OSX 10.6.8.
Apart from the Leptonica library, png, jpeg, tiff libraries had to passed to the configure script with CXX and CPP flags.
To run configure as non-root -
1. LIBLEPT_HEADERSDIR=; export LIBLEPT_HEADERSDIR;
2. CXXFLAGS="-ltiff -lpng -ljpeg" CPPFLAGS="-ltiff -lpng -ljpeg" ./configure --prefix= --with-extra-libraries=
In my case, this issue was caused by a missing compiler. Searching config.log revealed the following:
./configure:17287: g++ -o conftest -I/Usr/local/include/leptonica -L/usr/local/lib conftest.cpp -llept >&5
./configure: line 2040: g++ command not found
Running apt-get install g++ solved the problem. There is an issue in the tesseract issue tracker about this.
In my case (for Ubuntu/Debian) I downloaded the latest leptonica version and the error was not fixed.
To fix it I removed the package "leptonica-dev" with sudo apt-get remove libleptonica-dev and then tesseract found the leptonica version installed from the source code.
Hope it helps!
The answer is going to be slightly different for everyone, depending on the state of your system.
At a high level, the pkg-config software needs to know that leptonica is installed. It searches paths for a .pc file that has the definition for the leptonica package. That file will be in different locations for different people.
You can find it using the Linux locate utility at the command line. locate lept.pc. (If you've done some recent installing/uninstalling, you may need to refresh the locate utilities database with the command updatedb.)
Whichever directory locate finds the file in, export PKG_CONFIG_PATH as that directory (export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig for example).
Then you can continue your configure/build.
i had a similar problem with trying to compile from source, but did not experience it with
apt-get to install tesseract
sudo apt-get install tesseract-ocr
export LIBLEPT_HEADERSDIR=$dir/letonica168/include
./autogen.sh
./configure --prefix=$anotherdir --with-extra-libraries=/$dir/letonica168/lib
make
make install
I am attempting to build GCC-4.7.0 on a MacBook Pro running OS X 10.7.4. However, I am continuing to experience the same error:
configure: error: Building GCC requires GMP 4.2+, MPFR 2.3.1+ and MPC 0.8.0+.
This error occurred after running the following line:
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/
To get rid of this error I have tried the following actions:
Using homebrew I downloaded gmp-5.0.4, mpc-0.21, and mpfr-3.1.0. At this point I attempting to point to where gmp, mpc, and mpfr are located with the following command:
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/ --with-gmp=/usr/local/Cellar/ --with-mpfr=/usr/local/Cellar/ --with-mpc=/usr/local/Cellar/
However, this caused the same error. So, I tried pointing gcc to various locations around the Cellar directory:
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/ --with-gmp=/usr/local/Cellar/gmp/ --with-mpfr=/usr/local/Cellar/mpfr --with-mpc=/usr/local/Cellar/mpc/
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/ --with-gmp=/usr/local/Cellar/gmp/5.0.4/ --with-mpfr=/usr/local/Cellar/mpfr/3.1.0/ --with-mpc=/usr/local/Cellar/mpc/0.21/
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/ --with-gmp=/usr/local/Cellar/gmp/5.0.4/include/ --with-mpfr=/usr/local/Cellar/mpfr/3.1.0/include/ --with-mpc=/usr/local/Cellar/mpc/0.21/share/
In the end these all produced the same error. I then downloaded the versions of gmp, mpc, and mpfr linked from the gcc error message (found here: ftp://gcc.gnu.org/pub/gcc/infrastructure/). After building these from the source and running all the same configurations I am left with the same problem. The configurations I have tried with this installation are:
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/ --with-gmp=/usr/local/ --with-mpfr=/usr/local/ --with-mpc=/usr/local/
./configure --prefix=/Users/jreese/Documents/school/edinburgh/project/local/ --with-gmp=/usr/local/include/ --with-mpfr=/usr/local/include/ --with-mpc=/usr/local/include/
Then I read somewhere that there could be a problem if I didn't explicitly set the configuration to run in 64-bit mode. So, I tried all of these configurations again with the added setting of 'CC=gcc -m64'. But this didn't change anything. If anyone has any ideas I would be greatly appreciative.
If you don't know how to build and properly direct GCC's configure to the libraries you can put them in the source tree of GCC itself:
/some/dir/source/gcc/[libstdc++|libgomp|gcc|libiberty|....]
/some/dir/source/gcc/gmp/[configure|...]
/some/dir/source/gcc/mpfr/[configure|...]
/some/dir/source/gcc/mpc/[configure|...]
So without the version number appended. Then just run GCC configure without any arguments related to GMP/MPC/MPFR.
I've faced the same issue and it was easily solved by installing the corresponding development packages: gmp-devel, mpfr-devel and libmpc-devel
Yigal
EasyBuild (a tool to make building software easier) can be of help here. It comes with a small easyconfig file that specifies which GCC version to build, and which features to enable (see for example https://github.com/hpcugent/easybuild/blob/master/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb).
Once you've downloaded EasyBuild and configured it, you can just run
$EBHOME/easybuild.sh myGCC.eb
with EBHOME set to the location where you unpacked EasyBuild, and myGCC.eb a copy of the example GCC easyconfig, which you modified to your needs.
This command will download the GCC source tarball for you and build/install it, after doing the same to any dependencies, for example GMP, MPFR and MPC, saving you a lot of headaches.
For more information on EasyBuild, see https://github.com/hpcugent/easybuild/wiki .