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.
Related
I want to compile this C++ project to WASM using Emscripten. For this, I am following the documentation on building projects.
The project only has a Makefile, no Configure or CMake. It should be portable from what I can tell, and the project compiles fine using regular make, as described in the Readme.
Because there is no configure file, I skipped the emconfigure step. The documentation says that I have to edit the Makefile manually in that case, but I can't get it right.
Running emmake make works, and produces .o files in the bin directory, and an executable. This produces the same result as running make normally, from what I can tell. Both executables can be executed as normal (./zilch).
Running emcc bin\main.o is where I get issues though:
wasm-ld: error: unknown file type: bin/main.o
emcc: error: '/home/johannes/emsdk/upstream/bin/wasm-ld -o main.wasm bin/main.o -L/home/johannes/emsdk/upstream/emscripten/cache/sysroot/lib/wasm32-emscripten -lGL -lal -lhtml5 -lstubs-debug -lnoexit -lc-debug -ldlmalloc -lcompiler_rt -lc++-noexcept -lc++abi-noexcept -lsockets -mllvm -combiner-global-alias-analysis=false -mllvm -enable-emscripten-sjlj -mllvm -disable-lsr --import-undefined --strip-debug --export-if-defined=main --export-if-defined=__start_em_asm --export-if-defined=__stop_em_asm --export-if-defined=__main_argc_argv --export-if-defined=fflush --export=emscripten_stack_get_end --export=emscripten_stack_get_free --export=emscripten_stack_get_base --export=emscripten_stack_init --export=stackSave --export=stackRestore --export=stackAlloc --export=__wasm_call_ctors --export=__errno_location --export-table -z stack-size=5242880 --initial-memory=16777216 --no-entry --max-memory=16777216 --global-base=1024' failed (returned 1)
Running file bin/main.o shows: bin/main.o: ELF 64-bit LSB relocatable, x86-64, version 1 (SYSV), with debug_info, not stripped. Running emmake clearly still compiled it to x86, not wasm.
In the flags.mk file that is imported into the Makefile, the CC variable is set to g++. Changing it to em++ gives this error:
em++: error: Passing any of -msse, -msse2, -msse3, -mssse3, -msse4.1, -msse4.2, -msse4, -mavx, -mfpu=neon flags also requires passing -msimd128 (or -mrelaxed-simd)!
But adding this to CFLAGS in flags.mk only throws another cryptic error message:
em++: error: '/home/johannes/emsdk/upstream/bin/clang++ -target wasm32-unknown-emscripten -fignore-exceptions -fvisibility=default -mllvm -combiner-global-alias-analysis=false -mllvm -enable-emscripten-sjlj -mllvm -disable-lsr -DEMSCRIPTEN -D__EMSCRIPTEN_major__=3 -D__EMSCRIPTEN_minor__=1 -D__EMSCRIPTEN_tiny__=18 -Werror=implicit-function-declaration -I/home/johannes/emsdk/upstream/emscripten/cache/sysroot/include/SDL --sysroot=/home/johannes/emsdk/upstream/emscripten/cache/sysroot -D__SSE__=1 -D__SSE2__=1 -D__SSE3__=1 -D__SSSE3__=1 -D__SSE4_1__=1 -D__SSE4_2__=1 -Xclang -iwithsysroot/include/compat -O3 -g3 -Wall -fmessage-length=0 -fopenmp -maes -mtune=native -mrelaxed-simd -std=c++11 -Isrc -I/mnt/c/Users/johan/source/repos/Zilch/Zilch/framework/gadgetlib/gadgetlib/../. -I/mnt/c/Users/johan/source/repos/Zilch/Zilch/libstark/src -I/mnt/c/Users/johan/source/repos/Zilch/Zilch/algebra/algebralib/headers -I/mnt/c/Users/johan/source/repos/Zilch/Zilch/algebra/FFT/src -I/mnt/c/Users/johan/source/repos/Zilch/Zilch/framework/zilch/src -c /mnt/c/Users/johan/source/repos/Zilch/Zilch/framework/zilch/main.cpp -o /mnt/c/Users/johan/source/repos/Zilch/Zilch/bin/main.o' failed (returned 1)
I also tried to replace every $(MAKE) with $(EMMAKE) in the Makefile without success.
I am aware that I probably have to convert the project to CMake, or include a Configure file, as the documentation says. But I can't figure out for the life of me how that should look. If it isn't obvious, I am not experienced with any of these tools, so please be kind if I'm missing something super obvious.
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 have installed CPLEX 12.6.3 (CPLEX_Studio_Community1263) and I want to integrate CPLEX in my Eclipse C++ project (on Linux). But I don't know which steps I have to follow to include CPLEX in my project.
Even by following exactly the steps shown at this link, it still not working for me (I can't import cpelx.jar in my project). The path of my cplex.jar is
/opt/ibm/ILOG/CPLEX_Studio_Community1263/cplex/lib/cpelx.jar
When I right-click on my project and go to
Properties --> Settings --> GCC C++ Linker --> Libraries
to add the cplex.jar in my project, it is impossible to add the .jar because I can't select it (it is deselected and impossible to select it).
Can some one explain me how I can include CPLEX in my project?
The link you reference is for setting up a Java program. This will not help you.
Instead, you should try running one of the C++ examples shipped with CPLEX. Try the following (assuming your path is correct from above):
$ cd /opt/ibm/ILOG/CPLEX_Studio_Community1263/cplex/examples/x86-64_linux/static_pic
$ make ilolpex1 2>&1 | tee output.txt
This will save the output in output.txt so that you can look at it later. It should give you an idea of what the required command line arguments are.
For example, on my system (x86-64_linux), I see this in the output:
$ make ilolpex1
g++ -O0 -c -m64 -O -fPIC -fno-strict-aliasing -fexceptions -DNDEBUG -DIL_STD -I../../../include -I../../../../concert/include ../../../examples/src/cpp/ilolpex1.cpp -o ilolpex1.o
g++ -O0 -m64 -O -fPIC -fno-strict-aliasing -fexceptions -DNDEBUG -DIL_STD -I../../../include -I../../../../concert/include -L../../../lib/x86-64_linux/static_pic -L../../../../concert/lib/x86-64_linux/static_pic -o ilolpex1 ilolpex1.o -lconcert -lilocplex -lcplex -lm -lpthread
This tells you everything you need to know to compile and link your program. You'll just need to figure out where to enter this information in Eclipse.
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
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