I am using Ubuntu 14.04. And I am trying to use mex command from MATLAB, which links caffe library and protobuf. However, the problem happens when I run this script:
mex imageset_to_leveldb.cpp -lcaffe -lglog -lgflags -lprotobuf -lleveldb -llmdb ...
-L/home/wei/Caffe/build/lib ...
-I/home/wei/Caffe/build/src/caffe/proto
mex serialized_pairs_to_leveldb.cpp -lcaffe -lglog -lgflags -lprotobuf -lleveldb -llmdb ...
-L/home/wei/Caffe/build/lib ...
-I/home/wei/Caffe/build/src/caffe/proto
It returns the error:
Building with 'g++'.
Warning: You are using gcc version '4.8.4'. The version of gcc is not supported. The
version currently supported with MEX is '4.7.x'. For a list of currently supported
compilers see: http://www.mathworks.com/support/compilers/current_release.
> In compile (line 2)
Error using mex
/tmp/mex_3078197848859966_35312/imageset_to_leveldb.o: In function `process(unsigned
char*, int, int, int, char const*)':
imageset_to_leveldb.cpp:(.text+0x5dd): undefined reference to
`google::protobuf::internal::fixed_address_empty_string'
collect2: error: ld returned 1 exit status
It seems cannot find protobuf lib file. So I check the protobuf version and path as:
>>> import google.protobuf
>>> print google.protobuf.__version__
3.1.0.post1
>>> google.protobuf
<module 'google.protobuf' from '/usr/local/lib/python2.7/dist-packages/google/protobuf/__init__.pyc'>
I use Anaconda. However, the version check above is from outside of Anaconda Python. In conda environment, I do not have protobuf.
I compiled caffe inside of conda environment, which passes all the test with no error.
I google it, which suggests to conda install protobuf. It does not seem working for me.
Any idea on this?
Related
Ive installed matlab,gcc and CUDA toolkit on ubuntu .to use mexcuda .
but when i compile i get the following errors and i cant find any references on them anywhere .
Error using mex
/tmp/mex_42185702054896_15548/testmem04.o: In function `mexFunction':
tmpxft_00003e3a_00000000-5_testmem04.compute_70.cudafe1.cpp:(.text+0x152): undefined reference
to `__cudaPushCallConfiguration'
/tmp/mex_42185702054896_15548/testmem04.o: In function `__device_stub__Z9MulKernelPhPi(unsigned
char*, int*)':
tmpxft_00003e3a_00000000-5_testmem04.compute_70.cudafe1.cpp:(.text+0x35e): undefined reference
to `__cudaPopCallConfiguration'
collect2: error: ld returned 1 exit status
please note that when i first installed matlab, cuda 10 (my current version) was not supported by it , ive encountered the same thing when i installed matlab on windows , and fixed it by commenting a line in file "nvcc_g++.xml" and it works . when i did this in ubuntu matlab,matlab now detects the nvcc compiler but i get the previous error .
i realize "undefined reference errors " are linker errors , what should i do here ? i tried linking to cuda library but it didnt work .
For mexcuda, it is crucial that you match the CUDA toolkit to the version shipping with your installation of MATLAB (and Parallel Computing Toolbox). This is because Parallel Computing Toolbox ships a selection of libraries from the CUDA toolkit, and expects to be able to link against them. If you use the wrong version of the CUDA toolkit, all sorts of things can go wrong.
To check the appropriate version of the CUDA toolkit, look at the CUDA ToolkitVersion Version showing in the output from gpuDevice.
(Note that it is only the toolkit version that needs to match with MATLAB & PCT - it's almost always fine to get the latest driver).
For more details, see my answer https://uk.mathworks.com/matlabcentral/answers/432360-after-uninstalling-cuda-toolkit-still-matlab-responds-for-gpudevice over there on MATLAB Answers.
I am trying to compile swift-lldb on Ubuntu 14.04 (following instructions from https://github.com/apple/swift-lldb). I have the following dependencies installed:
Clang-3.5
Cmake version 3.5.2
Python version 2.7.6
On running the build script step which is lldb/scripts/build-swift-cmake.py --test, I am seeing the following error:
CMake Warning at cmake/modules/HandleLLVMOptions.cmake:185 (message):
-fPIC is not supported.
Call Stack (most recent call first):
cmake/modules/HandleLLVMOptions.cmake:216 (add_flag_or_print_warning)
CMakeLists.txt:616 (include)
CMake Error at cmake/modules/HandleLLVMOptions.cmake:429 (message):
LLVM requires C++11 support but the '-std=c++11' flag isn't supported.
Call Stack (most recent call first):
CMakeLists.txt:616 (include)
I have defined environment variables CC and CXX to point to the clang C and C++ compilers.
root:/myswift# echo $CC
/usr/bin/clang
root:/myswift# echo $CXX
/usr/bin/clang++
I also found in the clang documentation that c++11 is supported by clang-3.5. Not sure what I am missing here. Can someone please help?
clang-4.0 mentioned as part of the installation should support the -std=c++11 flag (just tested clang-4.0.1). However, upgrading to clang-6.0 seems to solve this build process error.
Running cmake directly in the automatically created build directory (by the swift build scripts) could be used to investigate the build failure in more detail. To specify compilers here, rather than setting CC and CXX environment variables (which works well for GNU configure scripts), compilers can be set for cmake via
cmake -DCMAKE_C_COMPILER=/usr/bin/clang -DCMAKE_CXX_COMPILER=/usr/bin/clang++ path_to_src_or_build_directory
An existing CMakeCache.txt might have to be removed, so that the above parameters are honored.
A problem with clang++ installations that I have observed is that clang++ cannot find C++ headers (i.e. if C++ headers are in non-standard locations other than /usr/include, unlikely in the case of Ubuntu though). In case /usr/bin/clang++ cannot compile a simple program like
#include <iostream>
using namespace std;
int main() {
cout << "hello" << endl;
return 0;
}
not being able to find the iostream include file, it might help to set --gcc-toolchain=/pathtoaworkinggcc, where pathtoaworkinggcc should include include, lib, bin, etc. of a working C++ compiler (possibly g++ in the case of a Ubuntu installation).
I am using Mac OSX (yosemite V 10.10.1) and running MATLAB 2014a on it.
I wanted to use SPAM library (sparse modeling software by J. Mairal) on MATLAB and for that I have to install XCode6.1 (that has gcc). First I type in command window mex -setup and result is shown below:
mex -setup
MEX configured to use 'Xcode with Clang' for C language compilation.
Warning: The MATLAB C and Fortran API has changed to support MATLAB
variables with more than 2^32-1 elements. In the near future
you will be required to update your code to utilize the
new API. You can find more information about this at:
http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html.
To choose a different language, select one from the following:
mex -setup C++
mex -setup FORTRAN
So after that I run the compile.m file in SPAM library and suddenly I saw an error that was:
add_flag =
-mmacosx-version-min=10.6
Warning: Directory already exists.
> In compile at 144
compilation of: -I./linalg/ -I./decomp/ -I./prox/ -I./dictLearn/ dictLearn/mex/mexArchetypalAnalysis.cpp
Building with 'Xcode Clang++'.
clang: warning: argument unused during compilation: '-fopenmp'
Error using mex
ld: warning: directory not found for option '-L/usr/lib/gcc/x86_64-linux-gnu/4.8/'
ld: library not found for -lgomp
clang: error: linker command failed with exit code 1 (use -v to see invocation)
Error in compile (line 439)
mex(args{:});
I don't understand what to do. please help me!
It appears that the actual error is occurring at the point of linking with precompiled libraries. The 2 issues are as follows:
The compile code apparently included in the compile.m file looks like it is intended to compile with gcc (it is trying to include files installed by GCC, possibly even linux-specific ones, are you sure that it's an OSX-compatible toolbox?), and yet the error strongly suggests that you are in fact using clang to compile it - you will either need to change the compiler (easy) or rewrite compile.m (not so easy).
One of the libraries that the code needs to have installed in order to be properly linked hasn't been found. On OSX I think this file should be called libgomp.dylib (any mac afficionados want to confirm this?). If you have it on your computer, then it's not in a directory that clang is looking in. You can confirm the library is installed by running find / | grep libgomp.dylib from the terminal - if it is there, you can add it into the compiler argument in compile.m using the -I /DIRECTORY_HOLDING_LIBRARY syntax.
It is entirely possible that fixing 1. will also remediate 2. - I have never tried using SPAM
I have tried to install the libsvm package with
mex -setup
(since "make" resulted in an error). This was followed by one choice for a compiler, so I chose "1".
Afterwards I typed in "make" got the following error though:
xcrun: error: SDK "macosx10.7" cannot be located
clang: warning: no such sysroot directory: '-mmacosx-version-min=10.7'
libsvmread.c:1:10: fatal error: 'stdio.h' file not found
#include <stdio.h>
^
1 error generated.
mex: compile of ' "libsvmread.c"' failed.
If make.m fails, please check README about detailed instructions.
What can I do?
I think the following answer from the matlab support might be helpful (http://www.mathworks.com/matlabcentral/answers/103904-can-i-use-xcode-5-as-my-c-or-c-compiler-in-matlab-8-1-r2013a-or-matlab-8-2-r2013b):
The Mac OS X 10.7 SDK, available in Xcode 4.1 through 4.6, is used by
MEX and related capabilities. This SDK is no longer available in Xcode
5, resulting in errors similar to the following when compiling:
xcodebuild: error: SDK "macosx10.7" cannot be located.
xcrun: error: unable to find utility "clang", not a developer tool or
in PATH
The simplest solution is to avoid updating Xcode to version 5 if you
are using R2013a or R2013b. If you need Xcode 5, or you have already
irreversibly upgraded to it, you can update MEX to use the 10.8 SDK:
In the MATLAB Command Window, execute the following commands:
cd(matlabroot)
cd bin
edit mexopts.sh
Save a backup copy of this file somewhere in case you make a mistake and you need to revert your changes.
Scroll down to the Mac (“maci64”) section of this file, beginning around line 120.
Replace all instances of 10.7 with 10.8; there are four of these in all (a fifth may be found in comments only)
Save the file, then execute the following command in the MATLAB Command Window:
mex -setup
Please note that this workaround links MEX files with a different SDK
than with which MATLAB was tested. Although there are no known
compatibility issues, support may be limited.
I am using eclipse to execute a cuda program. I have downloaded a CUDA PLUGIN for
eclipse. When I execute sample cuda program given by plugin its fine but when I try
to execute any other program I am getting error undefined reference to main...
make
Building target: Add_cuda
Invoking: NVCC Linker
nvcc -L/export/trainee3/dinesh/cuda5.0/lib64 -o "Add_cuda" ./mycuda.o -lcudart
/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: ld returned 1 exit status
I found in stackoverflow that some times we get this problem because of system startup file
I used flag -nostartfiles but it is not working in my case..
I have included lib64 and include path in c++ build.
So any suggestion to over come this problem....
We've been over this already.
Use nsight eclipse edition instead.
If you have cuda 5.0 or 5.5 installed, just type nsight in a terminal session.
If you really want to use that Eclipse CUDA plugin (which is no longer supported, I don't believe), then start with the C++ sample project, which you agree now and back then would work. Then modify the source code in that project. Don't create your own project.
Install CUDA 5. It comes with Nsight Eclipse version. Very Elegant to use. NV Visual profiler is integrated with Nsight. Syntax highlighting and debug mode are very easy to use.