I'm trying to call R from c++ on linux via RInside, I compiled R-2.15.1 from source with gcc version 4.5.3 (Debian 4.5.3-1) , I don't have sudo rights to use apt-get install. I'm using OpenBlas and a system optimized lapack. The blas and lapack libraries work fine for many scalapack applications
I installed R with
./configure --with-blas="-I/lib/OpenBLAS-v0.2.3-0/xianyi-OpenBLAS-48f075c/install/include -L/lib/OpenBLAS-v0.2.3-0/xianyi-OpenBLAS-48f075c/install/lib -lopenblas -lgfortran" --with-lapack="/usr/lib/liblapack.so -lgfortran" --enable-BLAS-shlib=yes --enable-R-shlib --enable-R-static-lib --prefix= .
which installed and runs fine,I ran make check with no errors, also all the packages (Rcpp and RInside) installed fine..
however when i use the given RInside makefile , the basic hello world example from /standard/rinside_sample0.cpp compiles! but it does not run and i get the following error
./rinside_sample0: error while loading shared libraries: libRblas.so: cannot open shared object file: No such file or directory
the file libRblas.so exists and is in the R/lib folder,
when i try to link it manually with the g++ command the make file creates or linking as follows i get a segmentation fault
/R/lib/libRblas.so ./hello_world
Segmentation fault
EDIT: heres how the example make file tries to compile an example, (which compiles fine) but won't run with the above missing libRblas.so error
g++ -I/nfs/user03/jimmie21/libs/lib64/R/include -I/nfs/user03/jimmie21/libs/lib64/R/library/Rcpp/include -I/nfs/user03/jimmie21/libs/lib64/R/library/RInside/include -g -O2 -Wall -I/usr/local/include hello_world.cpp -L/nfs/user03/jimmie21/libs/lib64/R/lib -lR -L/nfs/user03/jimmie21/libs/lib64/R/lib -lRblas -L/nfs/user03/jimmie21/libs/lib64/R/lib -lRlapack -L/nfs/user03/jimmie21/libs/lib64/R/lib -lRblas -L/nfs/user03/jimmie21/libs/lib64/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/nfs/user03/jimmie21/libs/lib64/R/library/Rcpp/lib -L/nfs/user03/jimmie21/libs/lib64/R/library/RInside/lib -lRInside -Wl,-rpath,/nfs/user03/jimmie21/libs/lib64/R/library/RInside/lib -o hello_world
Couple of things:
Reproducible examples, please
You have a non-standard setup
With the script from 1), try it on a standard setting as that is how Rcpp / RInside get developed and tested (on Ubuntu / Debian)
The Rcpp test suite now contains almost 800 unit tests from around 350 unit test functions. These do not seg.fault, so the issue is at your end. Similarly, RInside has dozens of examples in the four examples/ subdirectories. This also works.
It may be as easy as tweaking the Makefile / Makevars files to make sure you get your libraries in all cases. But we can't tell as there is nothing reproducible here.
Edit If you want to link with libRblas.so then you have a completely non-standard setup as the R packages for Debian / Ubuntu as use the external BLAS. Again, not an RInside issue.
I fixed the problem by adding the R install path lib ../R/lib: to the beginning of LD_LIBRARY_PATH after that all the examples compiled and run fine
Related
Im currently trying to compile a cpp program with gcc that uses SDL2 library, and im using Ubuntu 20.04 LTS. Here is my folder structure
project
-out
-SDL2
-src
-main.cpp
Excluding the library i have uploaded everything to this repo https://github.com/probottpric/libtest if it gives a better understanding.
To install SDL2, I installed source code and ran ./configure and make all. I dont want to run make install which installs it on /usr/*. I want the library to be on the local folder.
To compile program im using this command
gcc -o ./out/main ./src/main.cpp -ISDL2 -lSDL2 -lSDL2main -lm -std=c++11
But It shows library not found error. What am i doing wrong ?
I am attempting to import a C++ Game Server project into Xcode.
But I am running into the following error:
'uWS/uWS.h' file not found in XCode
I have tried importing the library by dragging it into the project, and ran the following commands to compile the uWebSockets library in Terminal:
git clone https://github.com/uNetworking/uWebSockets
cd uWebSockets
make
sudo make install
cd ..
But am running into this error. I have tried to search for how to resolve this is issue for a couple of hours, but still can't figure it out.
XCode Error
Here is my project hierarchy, I have tried to import/add the library in various different ways:
Project Hierarchy
Prior to using XCode, I would compile my code through terminal by running the following command:
g++ -O3 -L/usr/lib64 -std=c++14 src/main.cpp -pthread -lz -luWS -lssl -luv -o main
Any help would be highly appreciated.
I'm working on a project on a Raspberry Pi 2 Model B. I started coding and compiling directly on the Pi and now I want to work on a Windows 7 PC. I already installed the SysGCC Cross-Compiler and managed to compile a simple Hello-World program.
Problem is, for my Project i use curl and jsoncpp. Natively on the Raspberry i have no problems compiling it, but the cross-compiler on Windows gives me following error:
c:/sysgcc/raspberry/bin/../lib/gcc/arm-linux-gnueabihf/6/../../../../arm-linux-gnueabihf/bin/ld.exe: cannot find -lcurl
c:/sysgcc/raspberry/bin/../lib/gcc/arm-linux-gnueabihf/6/../../../../arm-linux-gnueabihf/bin/ld.exe: cannot find -ljsoncpp
I don't use a makefile or so because i never really worked with that and on the raspi it just worked fine with this command:
g++ ../src/rpi/main.cpp ../src/rpi/connection.cpp ../src/rpi/jsonparser.cpp ../src/rpi/idchecker.cpp ../src/rpi/eventoperator.cpp -o ../bin/main -lcurl -ljsoncpp
On the Windows system i tried it with a command like this:
arm-linux-gnueabihf-g++.exe -std=c++11 ../src/rpi/main.cpp ../src/rpi/connection.cpp ../src/rpi/jsonparser.cpp ../src/rpi/idchecker.cpp ../src/rpi/eventoperator.cpp -o ../bin/main -L"C:/SysGCC/raspberry/arm-linux-gnueabihf/sysroot/usr/include/jsoncpp/json/" -L"C:/SysGCC/raspberry/arm-linux-gnueabihf/sysroot/usr/include/arm-linux-gnueabihf/curl/" -lcurl -ljsoncpp
So i read that i have to tell the compiler/linker where the libraries are, but i don't really understand why since it works perfectly without the -L flag on the Raspi. I think i put the libraries in the same folder as on the Raspi, so i don't understand why they are not found. I hope someone can help me ore give me some short basic explanation on how this stuff works, cause i don't find any working tutorial or other helpful questions for my problem.
On raspberry-pi the libraries are most likely to be linked from system directory like /usr/lib or /usr/local/lib. On Windows, you need to specify the correct path(s) with -L flag.
So I follow the official tutorial for the installation : https://mongodb.github.io/mongo-cxx-driver/mongocxx-v3/installation/
Neverless, I can't use the produced libraries as static.
So I managed to compile the C version of the driver as described, I've enabled the flag --enable-static=yes with the ./configure before doing make && sudo make install and I got the libmongoc-1.0.a and the libbson-1.0.a which are static. So this far, everything it's alright.
Then I have done the cxx version of the driver, except that there is no configuration file as in the C version. So I've juste done a
cmake -DCMAKE_BUILD_TYPE=Release -DBSONCXX_POLY_USE_BOOST=1 -DCMAKE_INSTALL_PREFIX=/usr/local
from the build folder, followed by a make && sudo make install
So I got the libmongocxx.a and the libbsoncxx.a, but when I try to compile with them, I can't run the binary because I got the following error :
error while loading shared libraries: libmongocxx.so._noabi: cannot open shared object file: No such file or directory
So I understand that is because there is some symbols missing and then I need to use the shared library to run the binary but I don't want this to happend, I want the symbols within the binary that I can run it without any LD_PRELOAD.
Any suggestions ?
I had the same issue in an Ubuntu 16.04 and I run a apt-get update & apt-get upgrade and the problem was solved.
It seems that there were some update to the compiler and some libraries that prevent some test from reaching the shared libraries.
I have a similar question, and solved, now I compiled and run my binary with static libs successfully.
I write my build script using newlisp, but the static link options are very helpful, I paste it here.
c++ /to/your/path/site/code/back_end/builder/object/files1.cc.o ... /to/your/path/site/code/back_end/builder/object/files10.cc.o -o bin/site -static-libgcc -static-libstdc++ -L/usr/lib -lpthread -l:libmongocxx.a -l:libbsoncxx.a -l:libmongoc-1.0.a -l:libbson-1.0.a -lrt -lssl -lcrypto -lsasl2 -l:libboost_log.a -l:libboost_log_setup.a -l:libboost_system.a -l:libboost_thread.a -l:libboost_filesystem.a -lcppcms -lbooster -lcurl -ljsoncpp
Background
Hi All,
I'm trying to use Boost::MPI, at the moment I'm just trying to run the simple first example from the tutorial. I am having trouble building/running it.
I installed boost using apt-get and installed boost_mpi & boost_serialization (1.48.0) using synaptic package manager. I installed MPICH2 using apt-get.
Even though OpenMPI was never explicitly installed it appears to be on my system, I assume this is a dependency for Boost::MPI but it appears MPICH2 and OpenMPI are treading on each other's toes.
Info
If I build using
g++ test.cpp -I/usr/include/mpich2 -L/usr/lib -lboost_mpi -lboost_serialization
then run using
mpiexec -n 2 ./a.out
It throws a bunch of errors which seem to come from OpenMPI. If I try and build by linking against the OpenMPI library using
g++ test.cpp -L/usr/lib -lboost_mpi -lboost_serialization -lmpi -I/usr/include/openmpi
I get the following errors:
/usr/bin/ld: /tmp/ccJ5ezv7.o: undefined reference to symbol 'ompi_op_set_cxx_callback'
/usr/bin/ld: note: 'ompi_op_set_cxx_callback' is defined in DSO /usr/lib/libmpi.so.0 so try adding it to the linker command line
/usr/lib/libmpi.so.0: could not read symbols: Invalid operation
If I try building using mpic++ with the following command
mpic++ test.cpp -lboost_mpi -lboost_serialization
It will not link returning a bunch of errors of the form
/usr/lib/libmpich.so: undefined reference to `MPL_trid'
so I tried linking against libmpi i.e.
mpic++ test.cpp -lboost_mpi -lboost_serialization -lmpi
This builds but on running with mpiexec yields the following errors
Fatal error in PMPI_Errhandler_set: Invalid communicator, error stack:
PMPI_Errhandler_set(118): MPI_Errhandler_set(comm=0x370500, errh=0x370be0) failed
PMPI_Errhandler_set(70).: Invalid communicator
Question
It seems to me that somehow OpenMPI and MPICH2 are getting intertwined where there really shouldn't. Does anybody know how I can build against only OpenMPI or MPICH2 then run using the correct mpiexec?
Mixing code compiled against different MPI libraries is not supported in general. If your Boost::MPI is linked against Open MPI, then you must use Open MPI for the rest of your application.
To get the mpic++ as well as the other compiler wrappers and all the header files you should install the -dev package for Open MPI. If the library has been installed as a dependency then only the run-time part will be there.