I have a similar issue to this question PyTables does not seem to acknowledge hdf5 though it is evidently installed. Here is a slightly abbreviated error message from pip.
(And I'm going to ramble a bit more just because I get the annoying "this is mostly code" warning.)
pip install --upgrade h5py
Requirement already up-to-date: h5py in /Library/Python/2.7/site-packages
Cleaning up...
$ pip install --upgrade tables
Downloading/unpacking tables
Downloading tables-3.1.1.tar.gz (6.7MB): 6.7MB downloaded
ld: library not found for -lhdf5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
* Using Python 2.7.5 (default, Mar 9 2014, 22:15:05)
* Found numpy 1.9.0 package installed.
* Found numexpr 2.4 package installed.
* Found Cython 0.21 package installed.
ld: library not found for -lhdf5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
.. ERROR:: Could not find a local HDF5 installation.
You may need to explicitly state where your local HDF5 headers and
library can be found by setting the ``HDF5_DIR`` environment
variable or by using the ``--hdf5`` command-line option.
Complete output from command python setup.py egg_info:
/var/folders/0w/y_9w4kq53pqfgrc72bb7cml40000gn/T/H5closekvR8zE.c:1:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
ld: library not found for -lhdf5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
* Using Python 2.7.5 (default, Mar 9 2014, 22:15:05)
* Found numpy 1.9.0 package installed.
* Found numexpr 2.4 package installed.
* Found Cython 0.21 package installed.
ld: library not found for -lhdf5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
.. ERROR:: Could not find a local HDF5 installation.
You may need to explicitly state where your local HDF5 headers and
library can be found by setting the ``HDF5_DIR`` environment
variable or by using the ``--hdf5`` command-line option.
Related
I have a Haskell stack project where I have been using the llvm-hs library for building a compiler which emits LLVM IR. I had been working with LLVM version 8.0.0 so far. Recently due to a Python upgrade in my system the LLVM version got bumped to 8.0.1.
When I attempt to do stack build I get the following error -
ld: warning: directory not found for option '-L/usr/local/Cellar/llvm-8/8.0.0/lib/llvm-8/lib'
ld: library not found for -lLLVM-8
clang: error: linker command failed with exit code 1 (use -v to see invocation)
`gcc' failed in phase `Linker'. (Exit code: 1)
It seems from the above that ld is looking for -L/usr/local/Cellar/llvm-8/8.0.0/lib/llvm-8/lib whereas on my system I currently have the version for 8.0.1. How do I point ld to the correct path?
I am running MacOS Mojave. stack version 2.3.1. Thanks
I was capable of solving this by adding the following to my .bash_profile
export LIBRARY_PATH="$LIBRARY_PATH:/usr/local/Cellar/llvm-8/8.0.1/lib/llvm-8/lib"
Hope this helps if someone ran into the same problem.
I have followed the instruction in:
https://gist.github.com/notilas/a30e29ce514970e821a34153c1e78b3f
But cannot complete it.
OSX: Sierra
Tensorflow version 1.1.0 (Google says v1.2 does not support OSX CUDA)
CUDA Tool kit : 8.0
CUDNN : 6.0
Xcode : 7.2.1
Anaconda : 4.2 (Python version 3.5)
Error Log:
ERROR: /Users/so041e/ml/tensorflow/tensorflow/python/BUILD:2534:1:
Linking of rule '//tensorflow/python:_pywrap_tensorflow_internal.so'
failed: link_dynamic_library.sh failed: error executing command
external/bazel_tools/tools/cpp/link_dynamic_library.sh no ignored
ignored ignored
external/local_config_cuda/crosstool/clang/bin/crosstool_wrapper_driver_is_not_gcc
-shared -o ... (remaining 455 argument(s) skipped): com.google.devtools.build.lib.shell.BadExitStatusException: Process
exited with status 1.
clang: warning: argument unused during compilation: '-pthread'
ld: file not found: #rpath/CUDA.framework/Versions/A/CUDA for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
Target //tensorflow/tools/pip_package:build_pip_package failed to build
Use --verbose_failures to see the command lines of failed build steps.
[.bash_profile]
export PATH="/Users/so041e/anaconda/bin:$PATH"
export CUDA_HOME=/usr/local/cuda
export HOME=/Users/so041e
export PATH="$CUDA_HOME/bin:$PATH"
export DYLD_LIBRARY_PATH="/usr/local/cuda/lib:/Developer/NVIDIA/CUDA8.0/lib":$DYLD_LIBRARY_PATH
export LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH
export PATH=$DYLD_LIBRARY_PATH:$PATH
export PATH="//anaconda/bin:$PATH"
Moved CUDNN lib and include to /user/local/cuda
sudo mv -v cuda/lib/libcudnn* /usr/local/cuda/lib
sudo mv -v cuda/include/cudnn.h /usr/local/cuda/include
Didn't use "vent" Just used single python 3.5 at this moment.
Tried both, but no difference.
bazel build --config=cuda --config=opt --action_env PATH --action_env LD_LIBRARY_PATH --action_env DYLD_LIBRARY_PATH //tensorflow/tools/pip_package:build_pip_package
bazel build --config=cuda //tensorflow/tools/pip_package:build_pip_package
This might be a bit late, but I had this exact same problem and I managed to fix it.
First, #rpath/CUDA.framework/Versions/A/CUDA is a dynamic library install name for libcuda.dylib, which is found in /usr/local/cuda/lib. So do
otool -l /usr/local/cuda/lib/libcuda.dylib
Check where you see #rpath/CUDA.framework/Versions/A/CUDA; on my system it was in the command LC_REEXPORT_DYLIB. From here, it seems dyld doesn't resolve the #rpath for the LC_REEXPORT_DYLIB command, only LC_LOAD*_DYLIB commands. Meaning, it looks for the literal path "#rpath/CUDA.framework/Versions/A/CUDA". So you're going to have to change that by doing
sudo install_name_tool -change #rpath/CUDA.framework/Versions/A/CUDA \
/Library/Frameworks/CUDA.framework/Versions/A/CUDA \
/usr/local/cuda/lib/libcuda.dylib
This should resolve your problem.
Now why your system (and mine) has this install name for libcuda.dylib? I have absolutely no clue.
I am trying to install ogre v1.9 using homebrew. brew install ogre --HEAD
At some point I get the following errors:
duplicate symbol __ZN4Ogre18ControllerFunctionIfE16getAdjustedInputEf in:
CMakeFiles/OgreMain.dir/src/OgreAlignedAllocator.cpp.o
CMakeFiles/OgreMain.dir/src/OgreAnimation.cpp.o
duplicate symbol __ZN4Ogre18ControllerFunctionIdE16getAdjustedInputEd in:
CMakeFiles/OgreMain.dir/src/OgreAlignedAllocator.cpp.o
CMakeFiles/OgreMain.dir/src/OgreAnimation.cpp.o
...
ld: 564 duplicate symbols for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [lib/macosx/Ogre.framework/Versions/1.9.0/Ogre] Error 1
make[1]: *** [OgreMain/CMakeFiles/OgreMain.dir/all] Error 2
make: *** [all] Error 2
==> Formula
Tap: osrf/homebrew-simulation
Path: /usr/local/Library/Taps/osrf/homebrew-simulation/ogre.rb
==> Configuration
HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/homebrew
HEAD: 01dd3e19f8e600c3f44a3b140103f330aa32447c
Last commit: 3 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
CPU: 8-core 64-bit haswell
OS X: 10.10.2-x86_64
Xcode: N/A
CLT: 6.2.0.0.1.1424975374
Clang: 6.0 build 600
X11: 2.7.7 => /opt/X11
System Ruby: 2.0.0-p481
Perl: /usr/bin/perl
Python: /usr/bin/python
Ruby: /usr/bin/ruby
Java: N/A
==> ENV
HOMEBREW_CC: clang
HOMEBREW_CXX: clang++
MAKEFLAGS: -j8
CMAKE_PREFIX_PATH: /usr/local
CMAKE_INCLUDE_PATH: /usr/include/libxml2:/opt/X11/include:/opt/X11/include/freetype2:/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /opt/X11/lib:/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
PKG_CONFIG_PATH:/usr/local/opt/libpng/lib/pkgconfig:/usr/local/opt/freetype/lib/pkgconfig:/usr/local/opt/libzzip/lib/pkgconfig
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Library/ENV/pkgconfig/10.10:/opt/X11/lib/pk gconfig:/opt/X11/share/pkgconfig
ACLOCAL_PATH: /usr/local/share/aclocal:/opt/X11/share/aclocal
PATH:/usr/local/Library/ENV/4.3:/usr/local/opt/cmake/bin:/usr/local/opt/doxygen/bin:/usr/local/opt/libpng/bin:/usr/local/opt/freetype/bin:/usr/local/opt/libzzip/bin:/opt/X11/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin
Error: ogre HEAD did not build
The errors are so many and all in OgreAlignedAllocator.cpp.o. I think there is something defined twice. I tried to uninstall all OGRE dependencies and reinstall them again, but I still get the same error.
Any suggestion how can I solve or debug this kind of error?
Ok! It was a mess in the last commit, I checked out a previous revision and it works.
I'm using Homebrew rbenv. brew doctor comes out fine. rbenv install 2.0.0-p451 gives the following error message:
user$ rbenv install 2.0.0-p451
Downloading ruby-2.0.0-p451.tar.gz...
-> http://dqw8nmjcqpjn7.cloudfront.net/9227787a9636551f1749ee8394b5ffe5
Installing ruby-2.0.0-p451...
BUILD FAILED
Inspect or clean up the working tree at /var/folders/4h/ty8nj6c144b5cmhcrt0hd3cw0000gn/T/ruby-build.20140501101240.6245
Results logged to /var/folders/4h/ty8nj6c144b5cmhcrt0hd3cw0000gn/T/ruby-build.20140501101240.6245.log
Last 10 log lines:
ld: warning: directory not found for option '-L/usr/local/var/rbenv/versions/2.0.0-p451/lib'
installing default openssl libraries
1 warning generated.
linking shared-object date_core.bundle
ld: warning: directory not found for option '-L/usr/local/var/rbenv/versions/2.0.0-p451/lib'
linking shared-object openssl.bundle
ld: warning: directory not found for option '-L/usr/local/var/rbenv/versions/2.0.0-p451/lib'
linking shared-object ripper.bundle
ld: warning: directory not found for option '-L/usr/local/var/rbenv/versions/2.0.0-p451/lib'
make: *** [build-ext] Error 2
I tried googling it but not luck. Any tips?
p.s. I tried other ruby versions but same issue (although the last 10 lines of the log are slightly different).
Edit: installing version 1.9.3-p545 works fine.
brew cleanup and remove this /var/folders/4h/ty8nj6c144b5cmhcrt0hd3cw0000gn/T/ruby-build.20140501101240.6245 file.
I remember i removed all /var/folders/4h folder (wasn't exactly such name, but then i removed all folders in /var/folders/ and there wasn't no problem).
Since several versions of GCC and Ubuntu I am experiencing annoying issues with paths and naming of several header and object files that are necessary for the installation of GCC.
Description: After installing ubuntu (e.g. in my case 12.04) and installing all prerequisites of the gcc, I run the following commands:
sudo mkdir /usr/local/stow/gcc-4.8.0
./configure --prefix /usr/local/stow/gcc-4.8.0
make
sudo make install
For the sake of completeness, the rest of the installation procedure:
cd /usr/local/stow
sudo stow -t /usr/local/ gcc-4.8.0
gcc -v
However, this simple and proper way of installing gcc has some issues during the 'make' step with the following error messages:
1.) The problem with 'stubs.h'
/usr/include/gnu/stubs.h:7:27: fatal error: gnu/stubs-32.h: No such file or directory
which can be fixed with the following commands added to ~/.bashrc:
if [ -z "$CPATH"]; then
export CPATH="/usr/include/i386-linux-gnu"
else
export CPATH=$CPATH:"/usr/include/i386-linux-gnu"
fi
2.) The problem with 'crti.o', 'crtn.o', and 'crt1.o'
/usr/bin/ld: cannot find crti.o: No such file or directory
/usr/bin/ld: cannot find crtn.o: No such file or directory
/usr/bin/ld: cannot find crt1.o: No such file or directory
which can be fixed with the very ugly solution:
sudo ln -s /usr/lib/i386-linux-gnu/crti.o /usr/lib/i386-linux-gnu/crtn.o /usr/lib/i386-linux-gnu/crt1.o /usr/lib
since - and I don't know why - the following commands do not solve the problem during linking steps of 'sudo make install'
if [ -z "$LIBRARY_PATH"]; then
export LIBRARY_PATH="/usr/lib/${multiarch}"
else
export LIBRARY_PATH=$LIBRARY_PATH:"/usr/lib/${multiarch}"
fi
if [ -z "$LD_LIBRARY_PATH"]; then
export LD_LIBRARY_PATH="/usr/lib/${multiarch}"
else
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:"/usr/lib/${multiarch}"
fi
(With these solutions I could compile GCC-4.7.2 on Ubuntu 12.04. - I have still issues compiling GCC-4.8.0 on Ubuntu 12.04, but that's different topic.)
My questions are: Does anybody know the reason/background that we have these issues? Does anybody know a proper solution? (With "proper solution" I mean a solution that does not require setting environment variables or symbolic linking libraries to different directories. To me these kind of changes are ugly, since they require changes to the system that one may not be able to trace back or redo.)
In the root folder of your GCC source execute ./contrib/download_prerequisites script.
These are the issues i encountered while compiling GCC 4.8.0 on Ubuntu 12.04 with solutions.
This might help you.
Compilation guide for compiling GCC 4.8 on ubuntu 12.04
ERROR 1
configure: error: Building GCC requires GMP 4.2+, MPFR 2.4.0+ and MPC 0.8.0+.
Try the --with-gmp, --with-mpfr and/or --with-mpc options to specify
their locations. Source code for these libraries can be found at
their respective hosting sites as well as at
ftp://gcc.gnu.org/pub/gcc/infrastructure/. See also
http://gcc.gnu.org/install/prerequisites.html for additional info. If
you obtained GMP, MPFR and/or MPC from a vendor distribution package,
make sure that you have installed both the libraries and the header
files. They may be located in separate packages.
SOLUTION
Download and install gmp version >=4.3.2 package because mpc needs higher version
download the source code from gmplib.org
compile the source code and install
while compiling gmp see ERROR 2 for help
Installed gmp version 5.1.1
Download and install mpfr package
Installed mpfr version 3.1.2
Download and install mpc package
Installed mpc version 1.0
Download the packages from
http://ftp.gnu.org
ERROR 2
Error while compiling gmp library
checking for suitable m4... configure: error: No usable m4 in $PATH or /usr/5bin
SOLUTION
sudo apt-get install m4
http://ubuntuforums.org/showthread.php?t=850491
ERROR 3
Cannot find g++ compiler
I got this error because I installed the OS recently and had not installed the compilers.
SOLUTION
sudo apt-get install build-essential
This installs all the standard build essential software
ERROR 4
checking for i686-pc-linux-gnu-gcc... /home/suhastheju/projects/gcc/gcc-4.8.0/host-i686-pc-linux-gnu/gcc/xgcc -B/home/suhastheju/projects/gcc/gcc-4.8.0/host-i686-pc-linux-gnu/gcc/ -B/usr/local/i686-pc-linux-gnu/bin/ -B/usr/local/i686-pc-linux-gnu/lib/ -isystem /usr/local/i686-pc-linux-gnu/include -isystem /usr/local/i686-pc-linux-gnu/sys-include
checking for suffix of object files... configure: error: in `/home/suhastheju/projects/gcc/gcc-4.8.0/i686-pc-linux-gnu/libgcc':
configure: error: cannot compute suffix of object files: cannot compile
See `config.log' for more details.
make[2]: *** [configure-stage1-target-libgcc] Error 1
make[2]: Leaving directory `/home/suhastheju/projects/gcc/gcc-4.8.0'
make[1]: *** [stage1-bubble] Error 2
make[1]: Leaving directory `/home/suhastheju/projects/gcc/gcc-4.8.0'
make: *** [all] Error 2
SOLUTION
Though gcc documentation specify , that , we can provide the path of gmp
and mpfr installtion through –with-gmp and –with-mpfr flag ,
but unfortunately , i tried to give the path but it didnt work.
I am not in position to say final word about , this , whether it is a bug
in build script or something else , but bellow is the solution of the problem.
while building , add gmp and mpfr installation path in LD_LIBRARY_PATH environment
variable. Do as follows
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
If you have the libraries in different path, add the path where libraries are present
ERROR 5
libbackend.a(tree-vect-data-refs.o):tree-vect-data-refs.c:(.text+0x87da): more undefined references to `vector_type_mode(tree_node const*)' follow
collect2: error: ld returned 1 exit status
make[3]: *** [cc1] Error 1
make[3]: Leaving directory `/home/suhastheju/projects/gcc/gcc-4.8.0/host-i686-pc-linux-gnu/gcc'
make[2]: *** [all-stage2-gcc] Error 2
make[2]: Leaving directory `/home/suhastheju/projects/gcc/gcc-4.8.0'
make[1]: *** [stage2-bubble] Error 2
make[1]: Leaving directory `/home/suhastheju/projects/gcc/gcc-4.8.0'
make: *** [all] Error 2
SOLUTION
recompiled the source code from begining, It worked magically
make clean all
ERROR 6
/home/suhastheju/projects/gcc/gcc-4.8.0/host-i686-pc-linux-gnu/gcc/../.././gcc/gcov.c:416: undefined reference to `gcc_init_libintl()'
collect2: ld returned 1 exit status
make[3]: *** [gcov] Error 1
make[3]: Leaving directory `/home/suhastheju/projects/gcc/gcc-4.8.0/host-i686-pc-linux-gnu/gcc'
SOLUTION
Added -I/usr/include