i've tried compiling the cuda sdk kit on my computer, but it failed, saying that it required glibc 2.7.
/usr/local/cuda/lib64/libcudart.so: undefined reference to
`__isoc99_sscanf#GLIBC_2.7'
so i went ahead, and installed glibc-2.7; but in /mydir/glibc-2.7. the installation ended without any errors.
however, i want to be able to link the cuda sdk kit with my glibc. i've tried
export PATH=/mydir/glibc-2.7/bin:$PATH
export LD_LIBRARY_PATH=/mydir/glibc-2.7/lib
but all i get is segmentation fault =)
i'd appreciate any help !
thanks
See here for more instructions regarding compiling with a non-primary or custom libc.
In summary in addition to your PATH and LD_LIBRARY_PATH you need to set custom CFLAGS and LDFLAGS with -nostdinc , and -I includedirectories and -b gccsetup .
Related
I have some fortran programs that would not compile in old versions of gfortran. I have to run multiple instances of this program and am using another system (a cluster system) which has centos5_x64 with gcc-4.1 !!
Therefore I had to build new version of gcc; I built both gcc-4.8.3 and gcc-4.9.2 in my home folder. These programs use hdf5 and so the latter also has to be compiled using the same compiler. I tested the fortran programs after removing the hdf5 dependency on both gfortran-4.8.3 and 4.8.9 and they get built and execute properly. I also tested simple C/C++ programs (with basic i/o and arithmetic) with the new gcc/g++(s); they work fine. Before compiling hdf5 libraries I set these environment variables:
PATH=<GCCPATH>:$PATH
LD_LIBRARY_PATH=<GCCLIB>
LD_RUN_PATH=<GCCLIB>
export PATH
export LD_LIBRARY_PATH
export LD_RUN_PATH
HDF5 specific instructions
4.3.7. Specifying other libraries and headers
Configure searches the standard places (those places known by the
systems compiler) for include files and header files. However,
additional directories can be specified by using the CPPFLAGS
and/or LDFLAGS variables:
$ CPPFLAGS=-I/home/robb/include \
LDFLAGS=-L/home/robb/lib \
LDFLAGS=-L<GCCLIB>
CPPFLAGS=-I<GCCINCLUDE>
then configured as:
./configure --prefix=$HOME/HDF5 --enable-fortran
During make I get this error:
/usr/lib/../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: error: ld returned 1 exit status
This happens with both versions of gcc but not with the versions installed in the standard location (This happened in another system too which had gcc 4.4 installed). With general searching I got to know that this error is associated with the absence of a main() and in such cases -c flag has to be passed. However all examples of this error were from people's personal scripts and were not for libraries. Please let me know if I am missing something.
Upgrading the system OS is not a choice as of now.
As indicated in the comment by doqtor, I modified the Makefile post configure. It seems that CPPFLAGS and LDFLAGS were not set.
After setting the right CPPFLAGS and LDFLAGS in the Makefile, the compilation happened successfully.
I have downloaded Bellhop, which is an underwater acoustic simulator written in Fortran. It can be found here with the Makefile.
Question 1: I would like to know if it is possible to compile Fortran code, including everything needed, so a user without gfortran installed, can run it.
I have read here the following:
static linking
This section does not apply to Windows users, except for Cygwin users with gcc4-4.3.2-2 or later.
gfortran is composed of two main parts: the compiler, which creates the executable program from your code, and the library, which is used when you run your program afterwards. That explains why, if gfortran is installed in a non-standard directory, it may compile your code fine but the executable may fail with an error message like library not found. One way to avoid this (more ideas can be found on the binaries page) is to use the so-called "static linking", available with option -static gfortran then put the library code inside the program created, thus enabling it to run without the library present (like, on a computer where gfortran is not installed). Complete example is:
gfortran -static myfile.f -o program.exe
Reading this, I suppose that it is possible to do what I'm asking but I'm not very familiarized with fortran and makefiles. I don't understand this:
put the library code inside the program created
Question 2: How can I put the library code inside the program? Where can I find the library? What does "inside the program" means?
I'm running OSX 10.9.4 and gfortran
I solved my problem about compiling Fortran code with gfortran using static libraries.
As #M.S.B. said, using static-libgfortran worked for me under MacOS.
If somebody is having issues with linking the libquadmath.0.dylb library, remove libquadmath.0.dylib and libquadmath.dylib from /usr/local/gfortran/lib/
This doest the trick. Further information can be found here
I think the meaning of the bold part is actually
gfortran then puts the library code inside the
program created
That means using -static should be enough, there is no additional step. Just be advised you will need a static version of all the libraries that you link with.
I know this is very old tracker, but maybe somebody will be still interested in the solution that works.
Let's say we have code:
! fort_sample.f90
program main
write (*,*) 'Hello'
stop
end
First, compile the stuff:
gfortran -c -o fort_sample.o fort_sample.f90
Then, link stuff
ld -o ./fort_sample -no_compact_unwind \
-arch x86_64 -macosx_version_min 10.12.0 \
-lSystem \
/usr/local/gfortran/lib/libgfortran.a \
/usr/local/gfortran/lib/libquadmath.a \
/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0/libgcc.a \
fort_sample.o
You can execute it
./fort_sample
Hello
You can notice that quadmath is no longer there
> otool -L fort_sample
fort_sample:
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.51.1)
I guess this is what you were looking for in a first place. No removing dylibs, no symbolic links, etc.
The current version of the option is -static-libgfortran. This means that the Fortran specific libraries of gfortran will be included into the executable. These are libraries are automatically found for a good installation of gfortran. This should produce an executable that should run on other computers with the same OS, even if that computer doesn't have gfortran installed. This option likely doesn't statically link all libraries, so there is some risk that some other shared library used on your computer won't be available on the other computer.
My distro (CentOS 6.3) comes with gcc 4.4.6. Since I wanted to try out the Fortran2003 features I decided to compile gcc 4.7.
I followed the steps I found online: compiled separately first gmp, mpc, mpfr, ppl and cloog and the compiled gcc.
I run the configured script as:
configure --prefix=... --with-gmp=... --with-mpfr=... --with-mpc=... --program-suffix=-4.7 --enable-cloog-backend=isl --with-ppl=... --with-cloog=... --disable-multilib
This worked all right and I was able to compile with make & make install.
Now, when trying my new compiler with a simple test program (a hello world kind of thing) I get the error:
gfortran-4.7 -o test test.F90
/home/amcastro/gcc-4.7/output/libexec/gcc/x86_64-unknown-linux-gnu/4.7.0/f951: error while loading shared libraries: libcloog-isl.so.1: cannot open shared object file: No such file or directory
So I decide to set LD_LIBRARY_PATH=/home/amcastro/gcc-4.7/output/lib
and then I can compile.
When running I get the error:
./test
./test: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
So I set LD_LIBRARY_PATH=/home/amcastro/gcc-4.7/output/lib:/home/amcastro/gcc-4.7/output/lib64
and now the program runs normally.
The question is: Why is that my distro version of gcc (4.4.6) does not need me to set LD_LIBRARY_PATH? how does the distro gcc know where to look for these dynamically liked libraries? should I somehow make them to link statically?
I read also that setting LD_LIBRARY_FLAG is not a good idea. Is there another solution?
Thank you in advance
A.
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!
I've just compiled GCC 4.7 to work with stdatomic.h, but I can't seem to -I it. stdatomic.h seems to live in /usr/include/c++/4.4.3, but then the linker tells me it needs a bunch of other files in dirs nearby. If I -I all of them, I still get the error undefined reference to atomic_flag_clear_explicit. Any ideas how I'm supposed to link this right?
First, if you are compiling with GCC 4.7 you should not be including or linking anything from a directory from GCC 4.4.
Second, -I only affects the search path for header files. "undefined reference" is a linker error and usually means it hasn't found the right library. You change the library search path with -L. The linker didn't say it didn't find a library with the right name, it says it didn't find a symbol, so clearly the library it did find didn't have that symbol. I'd suggest you have a versioning problem, perhaps caused by a installation problem.
The <stdatomic.h> header in GCC 4.4 and 4.5 was from an early draft of C++0x atomics, but is not part of the final standard, so it was removed from libstdc++.
The C++ compiler supports C++11 atomics via the C++11 <atomic> header, so you should use that header in C++ code.
When the C compiler supports C11 atomics, the <stdatomic.h> header will be provided again.
Using this command solved the problem for me:
$ scl enable devtoolset-7 bash
I got the same error as you when entering sudo make altinstall for installing Python 3.8.5 on CentOS 7.