I'm on Windows 10 and using the latest version of MSYS2 (with gcc installed: pacman -S gcc)
I'm trying to compile mingw-w64-headers and mingw-w64-crt from mingw-w64-v7.0.0
Inside of my MSYS2 installation directory C:\msys2 I have created the folder mingw-w64 which I reference in the prefix argument below.
To compile each of these I use the same steps (replace name of library where appropriate):
mkdir mingw-w64-crt && cd mingw-w64-crt
../mingw-w64-v7.0.0/mingw-w64-crt/configure --prefix=/mingw-w64
make
make install
This works for mingw-w64-headers however for mingw-w64-crt I encounter errors at the make step. Specifically: incompatible types when assigning to type 'mbstate_t' {aka 'struct anonymous'} from type 'int'. A more detailed error image can be found here.
I would appreciate some guidance as to how to proceed.
I suggest that you just open one of MSYS2's MinGW environments (by running mingw32.exe or mingw64.exe) and then install the complete MinGW-w64 toolchain by running this:
pacman -S $MINGW_PACKAGE_PREFIX-toolchain
The toolchain includes GCC, the MinGW-w64 libraries, and the MinGW-w64 headers. If those prebuilt MinGW-w64 things are good enough for you, then you're done.
If you want to compile your own MinGW-w64, then should be able to use the environment you just installed to do it. To double-check that you are using the right toolchain, run which gcc and make sure it returns /mingw64/bin/gcc or /mingw32/bin/gcc.
Performing the following has allowed me to successfully compile:
pacman -S $MINGW_PACKAGE_PREFIX-toolchain
mkdir mingw-w64-crt && cd mingw-w64-crt
../mingw-w64-v7.0.0/mingw-w64-crt/configure --prefix=/mingw-w64 --with-sysroot=/mingw64
make -j %NUMBER_OF_PROCESSORS%
make install
Related
when I compile my script with only
#include <mpi.h>
it tells me that there is no such file or directory.
But when i include the path to mpi.h as
#include "/usr/include/mpi/mpi.h"
(the path is correct) it returns:
In file included from /usr/include/mpi/mpi.h:2087:0,
from lbm.cc:7:
/usr/include/mpi/openmpi/ompi/mpi/cxx/mpicxx.h:35:17: fatal error: mpi.h: No such file or directory
#include "mpi.h"
^
compilation terminated.
Anyone know how to fix this?
The problem is almost certainly that you're not using the MPI compiler wrappers. Whenever you're compiling an MPI program, you should use the MPI wrappers:
C - mpicc
C++ - mpiCC, mpicxx, mpic++
FORTRAN - mpifort, mpif77, mpif90
These wrappers do all of the dirty work for you of making sure that all of the appropriate compiler flags, libraries, include directories, library directories, etc. are included when you compile your program.
On my system, I was just missing the Linux package.
sudo apt install libopenmpi-dev
pip install mpi4py
(example of something that uses it that is a good instant test to see if it succeeded)
Succeded.
You can execute:
$ mpicc -showme
result :
gcc -I/Users/<USER_NAME>/openmpi-2.0.1/include -L/Users/<USER_NAME>/openmpi-2.0.1/lib -lmp
This command shows you the necessary libraries to compile mpicc
Example:
$ mpicc -g -I/Users/<USER_NAME>/openmpi-2.0.1/include -o [nameExec] [objetcs.o...] [program.c] -lm
$ mpicc -g -I/Users/<USER_NAME>/openmpi-2.0.1/include -o example file_object.o my_program.c otherlib.o -lm
this command generates executable with your program in example, you can execute :
$ ./example
On my system Ubuntu 16.04. I installed :
sudo apt install libopenmpi-dev
after I used mpiCC to compile and it works
As suggested above the inclusion of
/usr/lib/openmpi/include
in the include path takes care of this (in my case)
Debian appears to include the following:
mpiCC.openmpi
mpic++.openmpi
mpicc.openmpi
mpicxx.openmpi
mpif77.openmpi
mpif90.openmpi
I'll test symlinks of each for mpic, etc., and see if that helps the likes of HDF5-openmpi enabled find mpi.h.
Take that back Debian includes symlinks via their alternatives system and it still cannot find the proper paths between HDF5 openmpi packages and mpi.h referenced in the H5public.h header.
On Ubuntu 18.04 I had to install:
sudo apt install lam4-dev
On Fedora:
dnf install openmpi-devel
On Mac 12.2, I installed with brew install openmpi. The header file is under /opt/homebrew/Cellar/open-mpi/x.x.x/include.
once you have mpi installed:
$ sudo apt install mpich
see where the library is installed, each case is different:
$ mpicc -show
in my case: (Ubuntu 20.0)
and add...
#include </usr/lib/x86_64-linux-gnu/openmpi/include/openmpi>
:-)
I installed gcc version 5.1 locally on a cluster having OS as CentOS where I dont have root access (so i cant use any commands like 'sudo'). (The global gcc version installed is 4.4). I also modified the path variable to include the path to my local version at the beginning of the path variable. Before, when I was trying to install boost using the global version, it worked fine. But now, when I try to install boost, it shows the following error:
/users/home/head/cmp/soft/sft/gcc/bin/../libexec/gcc/x86_64-unknown-linux-gnu/5.1.0/cc1: error while loading shared libraries: libisl.so.10: cannot open shared object file: No such file or directory
Any ideas on how to fix this will be highly appreciated.
Follow the instructions at https://gcc.gnu.org/wiki/InstallingGCC
Specifically, don't install ISL manually in some non-standard path, because GCC needs to find its shared libraries at run-time.
The simplest solution is to use the download_prerequisites script to add the GMP, MPFR, MPC and ISL source code to the GCC source tree, which will cause GCC to build them for you automatically, and link to them statically.
I have the same issue. I solved it as follows:
Download the source code of isl available here
Unzip and install: ./configure && make && make install
cp /usr/local/lib/libisl* /usr/lib
Note: a symlink also works:
$ cd /usr/lib
$ ln -s /usr/local/lib/libisl.so.10 libisl.so.10
You can do the same in Debian distros:
apt-get install libisl-dev
Adjust the references of shared libs:
$ cp /usr/local/lib/libisl* /usr/lib
Note: a symlink also works:
$ cd /usr/lib
$ ln -s /usr/local/lib/libisl.so.10 libisl.so.10
I need to install a package (ROOT) from source on OSX using GCC 4.7.3 as a compiler. Default compiler on OSX is clang, so I look to configure command options to change it. I see that I can change it:
with compiler options, prefix with --with-, overrides default value
cc alternative C compiler and options to be used
cxx alternative C++ compiler and options to be used
But when I run:
./configure --with-cxx=g++ --with-cc=gcc
I see:
Checking for C compiler ... gcc
Checking for C++ compiler ... g++
Checking for linker (LD) ... clang++
So it trying to compile with gcc and link with clang, this obviously leads to failure. But I can't find an option in configure how to change linker used by make.
Is there a default options of configure to change linker? Something like --with-cxxlinker.
If not - how can I find and change the linker used by specific package?
The recommended way of building ROOT from source is to use git and obtain the most recent production version available. As of today that is version 5.34.19.
Open Terminal.app (then use each of the commands in succession):
cd ~/desktop && mkdir root
git clone http://root.cern.ch/git/root.git && cd root
./configure
make
make install
The nice thing about using git is that it contains a complete source tree for all systems (72 MB). You shouldn't need to use any special ./configure commands (unless you want to use add-on components).
You could also install the Mac Ports version by using the command:
sudo port install root
I'm running debian wheezy and wanted to upgrade from GCC 4.7.2 to GCC 4.9.0.
As per these instructions I installed libgmp-dev, libmpfr-dev and libmpc-dev (my package manager gave me versions 2:5.0.5+dfsg-2, 3.1.0-5 and 0.9-4 respectively) and ran the following to compile gcc (note that in my case it was 4.9.0 instead of 4.6.2):
tar xzf gcc-4.6.2.tar.gz
cd gcc-4.6.2
./contrib/download_prerequisites
cd ..
mkdir objdir
cd objdir
$PWD/../gcc-4.6.2/configure --prefix=$HOME/gcc-4.6.2
make
make install
I now have a objdir directory full of stuff, but where is g++, and where should I put this directory?
I'm guessing I should move it to usr/local and add something to my PATH variable, but I don't know what exactly, and how to make sure it is searched before my old gcc install.
After doing these commands (note the --prefix option of configure)
$PWD/../gcc-4.9.0/configure --prefix=$HOME/gcc-4.9.0
make install
the new gcc will be installed in $HOME/gcc-4.9.0 directory (there should be subdirectories like bin, lib, share inside it).
Full path to gcc will be $HOME/gcc-4.9.0/bin/gcc, and g++ (which is symlink to gcc) will be here: $HOME/gcc-4.9.0/bin/g++.
There can be no separate g++ in objdir because gcc compiler driver implements drivers for several languages; the mode (C or C++) is selected based on argv[0] (name of binary, which was used to run driver: gcc or g++; this mode also affects linking flags) and on source file extensions (gcc accepts both C and C++ programs as input for compilation into object files). So, g++ may be generated as symlink by make install, and the place to store generated symlink is $prefix/bin.
After building the GCC and installing it in the $HOME/gcc-4.9.0 directory, you can use it; but default system gcc will be not updated. Update of distributive gcc should be done via distributive tools (apt, dpkg-build, etc). Current prebuild version of system-wide gcc for Wheezy is 4.7.2, 4.8.2 for Jessie and Sid and 4.9-2 for "Experimental".
According to this post (https://github.com/mxcl/homebrew/pull/2953), the flag "--with-mpi" should enable boost_mpi build support for the related homebrew formula, so I am trying to install boost via homebrew like this:
brew install boost --with-mpi
However, the actual boost mpi library is not being build and can not be found.
There is currently some work being done around this, according to: https://github.com/mxcl/homebrew/pull/15689
In summary, I can currently build boost, but it seems the "--with-mpi" flag is being ignored. Could someone please check, if I should be able to build boost (with mpi support) on Mac OS X Mountain Lion (10.8)?
The (verbose) output generates these lines:
MPI auto-detection failed: unknown wrapper compiler mpic++
Please report this error to the Boost mailing list: http://www.boost.org
You will need to manually configure MPI support.
warning: skipping optional Message Passing Interface (MPI) library.
note: to enable MPI support, add "using mpi ;" to user-config.jam.
note: to suppress this message, pass "--without-mpi" to bjam.
note: otherwise, you can safely ignore this message.
Not sure how exactly I can fix this and get the mpi stuff to be build - any ideas?
Just in case this helps anyone else along the line, here's how I fixed this. The main error is MPI auto-detection failed: unknown wrapper compiler mpic++, any typing mpic++ at the command line verified that it was not working properly for me. I used brew to install open-mpi, but the same error was showing in the verbose output for installing boost. A run of brew doctor showed that openmpi was not linked properly, so I fixed those errors and reran brew -v install boost --with-mpi --without-single and it finally built and installed all of the libraries without a problem
To anyone that comes across this, the package migrated to boost-python and boost-mpi separate from boost. Use brew install boost-mpi
Just get it worked on OSX 10.11.5. I've tried brew, but with no luck.
Suppose you already have gcc installed. Here are what I've done:
1. Find and disable (but do not remove) clang
clang alway cause headaches. There would be a lot of warnings when building Boost.
which clang, which should give you /usr/bin/clang
Rename it: sudo mv clang clang_mac_remove, also for clang++: sudo mv clang++ clang++_mac_remove. You can change the names back if you need them in future.
2. Install OpenMPI
If you already installed using brew, uninstall first. Becasue it would have used clang as the compiler wrapper by default. You need to change the wrapper to gcc.
Download the package.
Specify the wrapper compiler to gcc and g++:
./configure CC=gcc CXX=g++ F77=ifort FC=ifort --prefix=/usr/local
Below may take a long time.
make all
sudo make install
Reference: https://wiki.helsinki.fi/display/HUGG/Open+MPI+install+on+Mac+OS+X
3. Install Boost MPI
Download the package.
Run ./bootstrap.sh (can open it first and specify the toolset to gcc, otherwise, the default option is darwin for mac).
Add using mpi ; in project-config.jam file. Then ./b2 —with-mpi will only build the mpi library.
Then, all built libraries can be found in the folder ~/Downloads/boost_1_61_0/stage/lib.
Copy or move them to /usr/local/lib or any other commonly used library path.
Reference: http://www.boost.org/doc/libs/1_61_0/doc/html/mpi/getting_started.html
4. Compile with Boost MPI
LIBRARY DIR = -L/usr/local/lib
INCLUDE = -I/usr/local/include/
LINKER = -lboost_mpi -lboost_serialization
e.g.
mpic++ -std=c++11 -I/usr/local/include/ -c boost_test.cpp -L/usr/local/lib -lboost_mpi -lboost_serialization
Good luck!