So I recently installed Theano on a python 2.7 environment within Anaconda 3, on windows 10. Theano passed theano.test() at least. I am using example code from deeplearning.net. I heva sucessfully run the first block on the linked page which defines a Theano function. When I go to install pylab via pip install pylab so that I can use skimage for the second block, my installer quits while doing some gcc call for the portion that looks like it says "shared geometry". One thing I noticed right away is the -DEBUG flag is misspelled -DDEBUG. Could this be the cause? Does it have something to do with msvcr90.dll and if so what is that and what do I need to do about it? Also, probably important, I'm using a slightly (6 months or so) outdated TDM-GCC which is 4.9 something. Here is the line in question, as well as a few others that might be interesting:
`copying skimage\_shared\tests\__init__.py -> build\lib.win-amd64-2.7\skimage\_shared\tests
running build_ext
Looking for python27.dll
Cannot build msvcr library: "msvcr90d.dll" not found
customize Mingw32CCompiler
customize Mingw32CCompiler using build_ext
building 'skimage._shared.geometry' extension
compiling C sources
C compiler: gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes
creating build\temp.win-amd64-2.7
creating build\temp.win-amd64-2.7\Release
creating build\temp.win-amd64-2.7\Release\skimage
creating build\temp.win-amd64-2.7\Release\skimage\_shared
compile options: '-DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x0900 -I"C:\Users\USE DIS\Anaconda3\envs\py27\lib\site-packages\numpy\core\include" -I"C:\Users\USE DIS\Anaconda3\envs\py27\include" -I"C:\Users\USE DIS\Anaconda3\envs\py27\PC" -c'
gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x0900 -I"C:\Users\USE DIS\Anaconda3\envs\py27\lib\site-packages\numpy\core\include" -I"C:\Users\USE DIS\Anaconda3\envs\py27\include" -I"C:\Users\USE DIS\Anaconda3\envs\py27\PC" -c skimage\_shared\geometry.c -o build\temp.win-amd64-2.7\Release\skimage\_shared\geometry.o
Found executable C:\Users\USE DIS\Anaconda3\envs\py27\Scripts\gcc.bat
'C:\Users\USE' is not recognized as an internal or external command,
operable program or batch file.
error: Command "gcc -g -DDEBUG -DMS_WIN64 -O0 -Wall -Wstrict-prototypes -DNPY_MINGW_USE_CUSTOM_MSVCR -D__MSVCRT_VERSION__=0x0900 -I"C:\Users\USE DIS\Anaconda3\envs\py27\lib\site-packages\numpy\core\include" -I"C:\Users\USE DIS\Anaconda3\envs\py27\include" -I"C:\Users\USE DIS\Anaconda3\envs\py27\PC" -c skimage\_shared\geometry.c -o build\temp.win-amd64-2.7\Release\skimage\_shared\geometry.o" failed with exit status 1
----------------------------------------
Related
I am trying to set up debugging with VScode for nvc++ on Ubuntu 20.04
I am using CMake to build my program that is using openmp and have cmake-tools as vscode extensions.
My c++ project is well setup with CMake, GCC, and openMP. After installing HPC SDK and setting up the nvcc and nvc++ compilers, when I switch the tools, the build is failing, complaining about openMP. By default VScode is using nvcc -fopenmp -v -fPIE -std=gnu99 -o outputfile.o. When I compile my code in the terminal window with just a simple addition of -Xcompiler flag such as nvcc -Xcompiler -fopenmp -v -fPIE -std=gnu99 -o outputfile.o it is working. But how do I set that up in vscode?
Below is the exact error I am getting:
/opt/nvidia/hpc_sdk/Linux_x86_64/22.5/compilers/bin/nvcc -fopenmp -v -fPIE -std=gnu99 -o CMakeFiles/cmTC_568be.dir/OpenMPTryFlag.c.o -c /directory/program/build/CMakeFiles/FindOpenMP/OpenMPTryFlag.c
nvcc fatal : Value ‘gnu99’ is not defined for option ‘std’
Any help is would be appreciated!
Software info:
Linux Kernel: 4.14.83-1-MANJARO
R: 3.5.1
Rcpp: 1.0.0
g++ g++ (GCC) 8.2.1 20180831
I'm trying to install the later package from CRAN, but it fails due to a compilation error and I can't figure out whether there is something wrong with my own configuration or the package. The installation stops after the call
g++ -I"/usr/include/R/" -DNDEBUG -pthread -DTHREADS_H_SUPPORT=1 -I"/home/karpfen/R-libs/Rcpp/include" -I"/usr/lib/R/library/BH/include" -D_FORTIFY_SOURCE=2 -fopenmp -fpic -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -c timestamp_win32.cpp -o timestamp_win32.o
with the error message
make: *** No rule to make target '-fopenmp', needed by 'later.so'. Stop.
Rcpp and other packages depending on it work as expected. Is there anything that I could be doing wrong here? I tried reinstalling R + packages already, but no changes here.
Edit:
The first few lines of the installation output are
* installing *source* package ‘later’ ...
** package ‘later’ successfully unpacked and MD5 sums checked
Running configure script
Using CC=gcc
Using CFLAGS=-march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt
Using CPPFLAGS=-D_FORTIFY_SOURCE=2
C11-style threads.h support detected.
Edit2:
System information (from /etc/lsb-release)
DISTRIB_ID=ManjaroLinux
DISTRIB_RELEASE=18.0.0
DISTRIB_CODENAME=Illyria
DISTRIB_DESCRIPTION="Manjaro Linux"
I am trying to use gdb to debug an hdf5 C++ application that I have written. The h5 package that I am using was installed using conda. The command that I am using is:
h5c++ hdf5.cpp
This generates an executable which I then run with gdb as follows:
gdb a.out
gdb launches alright. But when I add breakpoint using:
b 10
or any line number, it gives a message: No line 10 in file "init.c"
When I press run, it runs the whole program at once (which I don't want) and exits. The h5c++ -show command gives the following output:
x86_64-conda_cos6-linux-gnu-c++ -I/i3c/hpcl/sms821/software/tensorflow/anaconda2/include -D_FORTIFY_SOURCE=2 -O2 -g -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/i3c/hpcl/sms821/software/tensorflow/anaconda2/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -L/i3c/hpcl/sms821/software/tensorflow/anaconda2/lib /i3c/hpcl/sms821/software/tensorflow/anaconda2/lib/libhdf5_hl_cpp.a /i3c/hpcl/sms821/software/tensorflow/anaconda2/lib/libhdf5_cpp.a /i3c/hpcl/sms821/software/tensorflow/anaconda2/lib/libhdf5_hl.a /i3c/hpcl/sms821/software/tensorflow/anaconda2/lib/libhdf5.a -L/i3c/hpcl/sms821/software/tensorflow/anaconda2/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/i3c/hpcl/sms821/software/tensorflow/anaconda2/lib -L/i3c/hpcl/sms821/software/tensorflow/anaconda2/lib -g -lrt -lpthread -lz -ldl -lm -Wl,-rpath -Wl,/i3c/hpcl/sms821/software/tensorflow/anaconda2/lib
I think this has to do with the compiler the compiler that it is using. I tried replacing x86_64-conda_cos6-linux-gnu-c++ with my native g++ compiler in the h5c++ script but that gives linker error.
Please suggest how should make my h5 application work with gdb. Should I install hdf5 from source since I don't have sudo access? I am working on a Linux machine.
I simply installed hdf5 from the source files. While configuring the installation I turned the --enable-build-mode and --enable-symbol switches. Hdf5 has a dependency on szip which I also installed from source code. My exact configuration was as follows:
./configure --prefix=<hdf5 install directory> --enable-cxx --enable-build-mode=debug --enable-symbols=yes --enable-profiling=yes --with-szlib=<szip install directory>
The above solution worked and I was able to compile my h5 application using h5c++ hdf5.cpp and also use gdb to debug it.
Ubuntu 17.10
GCC Version: 5.4
Bazel Version: 0.9.0
TensorFlow: r1.5
CUDA 8.0 / cuDNN 6 / GTX 1080 Ti
How do I make Bazel use gcc for building TensorFlow from source?
While building, its running into compiler errors like:
error: 'errno' was not declared in this scope
while (nanosleep(&ts, &ts) != 0 && errno == EINTR) {}
Setting --verbose_failures flag, it shows that its not using /usr/bin/gcc-5 or /usr/bin/gcc for compiling
external/local_config_cuda/crosstool/clang/bin/crosstool_wrapper_driver_is_not_gcc -U_FORTIFY_SOURCE '-D_FORTIFY_SOURCE=1' -fstack-protector -fPIE -Wall -Wunused-but-set-parameter -Wno-free-nonheap-object -fno-omit-frame-pointer -g0 -O2 -DNDEBUG -ffunction-sections -fdata-sections -g0 -DGEMMLOWP_ALLOW_SLOW_SCALAR_FALLBACK '-march=native' '-std=c++11' -g0 -MD -MF
Searching online, I found that the path to gcc and CC, CXX variables must be set in tools/cpp/CROSSTOOL. But where exactly is tools/cpp/CROSSTOOL?? How do I force bazel to use gcc-5?
I know next to nothing about cuda and tensorflow, but tensorflow doesn't use the same C++ toolchain that bazel autoconfigures when compiling with cuda, so the CC env variable trick won't work. The file crosstool_wrapper_driver_is_not_gcc is just a shell wrapper that could in theory still call your gcc (or it will be cuda). I'd run bazel with --subcommands to see the complete invocation of the failing action, then reproduce without bazel, and then go from there.
I just installed cygwin and eclipse on my win7 x64 machine, and after importing my code from svn, I get this weird error:
**** Build of configuration Default for project platform ****
make all
g++ -O2 -g -Wall -fmessage-length=0 -c -o platform.o platform.cpp
process_begin: CreateProcess(C:\cygwin\bin\g++.exe, g++ -O2 -g -Wall -fmessage-length=0 -c -o platform.o platform.cpp, ...) failed.
make (e=5): Access is denied.
make: *** [platform.o] Error 5
I've tried running eclipse as administrator, but that doesn't make any difference. Any clue how to fix this?
My windows PATH variable is C:\WinAVR-20100110\bin;C:\WinAVR-20100110\utils\bin;c:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\;C:\Program Files\Java\jre6\bin\;C:\cygwin\bin
C:\cygwin\bin\g++.exe is a Cygwin symbolic link pointing to either g++-3.exe or g++-4.exe. Native Windows functions such as CreateProcess() don't understand Cygwin symbolic links though. Hence you need to configure Eclipse to execute g++-3.exe or g++-4.exe directly.