Calling method in the GNU Scientific Library
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Paul Reiners
el 2 de Mzo. de 2021
Comentada: Matthew Faulkner
el 29 de Mzo. de 2023
I want to call a function in the GNU Scientific Library (GSL) from MATLAB. In particular, I want to call this method:
I have the following folder structure
.
├── Makefile
├── call_gsl_svd.m
├── include
│ ├── calculate_svd_example.h
│ └── run_svd.h
├── project
└── src
├── calculate_svd_example.c
├── project.c
└── run_svd.c
I can call make and the project builds without error. I can then call ./project and a call is made to the gsl_linalg_SV_decomp function and runs fine. calculate_svd_example.c has one simple method, calculate_svd_example, that takes no input and returns no output.
I want to call this simple method from MATLAB (as a first step, anyway). My call_gsl_svd.m reads:
function [] = call_gsl_svd()
%UNTITLED Summary of this function goes here
% Detailed explanation goes here
%#codegen
% for code generation, preinitialize the output variable
% data type, size, and complexity
% generate an include in the C code
coder.cinclude('./include/calculate_svd_example.h');
% evaluate the C function
coder.ceval('./src/calculate_svd_example');
end
I then run this command:
>> codegen call_gsl_svd calculate_svd_example.c
I get this error:
[1/10] /bin/gcc -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE -O2 -fwrapv -DNDEBUG -std=c99 -I "." -I "/panfs/roc/groups/4/miran045/reine097/projects/connectotyping/src" -I "./interface" -I "/panfs/roc/msisoft/matlab/R2019a/extern/include" -I "." -c /panfs/roc/msisoft/matlab/R2019a/extern/version/c_mexapi_version.c -o build/glnxa64/c_mexapi_version.o
[2/10] /bin/gcc -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE -O2 -fwrapv -DNDEBUG -std=c99 -I "." -I "/panfs/roc/groups/4/miran045/reine097/projects/connectotyping/src" -I "./interface" -I "/panfs/roc/msisoft/matlab/R2019a/extern/include" -I "." -c call_gsl_svd.c -o build/glnxa64/call_gsl_svd.o
[3/10] /bin/gcc -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE -O2 -fwrapv -DNDEBUG -std=c99 -I "." -I "/panfs/roc/groups/4/miran045/reine097/projects/connectotyping/src" -I "./interface" -I "/panfs/roc/msisoft/matlab/R2019a/extern/include" -I "." -c call_gsl_svd_initialize.c -o build/glnxa64/call_gsl_svd_initialize.o
[4/10] /bin/gcc -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE -O2 -fwrapv -DNDEBUG -std=c99 -I "." -I "/panfs/roc/groups/4/miran045/reine097/projects/connectotyping/src" -I "./interface" -I "/panfs/roc/msisoft/matlab/R2019a/extern/include" -I "." -c interface/_coder_call_gsl_svd_api.c -o build/glnxa64/_coder_call_gsl_svd_api.o
[5/10] /bin/gcc -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE -O2 -fwrapv -DNDEBUG -std=c99 -I "." -I "/panfs/roc/groups/4/miran045/reine097/projects/connectotyping/src" -I "./interface" -I "/panfs/roc/msisoft/matlab/R2019a/extern/include" -I "." -c call_gsl_svd_data.c -o build/glnxa64/call_gsl_svd_data.o
[6/10] /bin/gcc -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE -O2 -fwrapv -DNDEBUG -std=c99 -I "." -I "/panfs/roc/groups/4/miran045/reine097/projects/connectotyping/src" -I "./interface" -I "/panfs/roc/msisoft/matlab/R2019a/extern/include" -I "." -c call_gsl_svd_terminate.c -o build/glnxa64/call_gsl_svd_terminate.o
[7/10] /bin/gcc -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE -O2 -fwrapv -DNDEBUG -std=c99 -I "." -I "/panfs/roc/groups/4/miran045/reine097/projects/connectotyping/src" -I "./interface" -I "/panfs/roc/msisoft/matlab/R2019a/extern/include" -I "." -c interface/_coder_call_gsl_svd_mex.c -o build/glnxa64/_coder_call_gsl_svd_mex.o
[8/10] /bin/gcc -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE -O2 -fwrapv -DNDEBUG -std=c99 -I "." -I "/panfs/roc/groups/4/miran045/reine097/projects/connectotyping/src" -I "./interface" -I "/panfs/roc/msisoft/matlab/R2019a/extern/include" -I "." -c /panfs/roc/groups/4/miran045/reine097/projects/connectotyping/src/calculate_svd_example.c -o build/glnxa64/calculate_svd_example.o
[9/10] /bin/gcc -fexceptions -fPIC -fno-omit-frame-pointer -pthread -D_GNU_SOURCE -DMATLAB_MEX_FILE -O2 -fwrapv -DNDEBUG -std=c99 -I "." -I "/panfs/roc/groups/4/miran045/reine097/projects/connectotyping/src" -I "./interface" -I "/panfs/roc/msisoft/matlab/R2019a/extern/include" -I "." -c interface/_coder_call_gsl_svd_info.c -o build/glnxa64/_coder_call_gsl_svd_info.o
[10/10] /bin/gcc build/glnxa64/call_gsl_svd_data.o build/glnxa64/call_gsl_svd_initialize.o build/glnxa64/call_gsl_svd_terminate.o build/glnxa64/call_gsl_svd.o build/glnxa64/_coder_call_gsl_svd_info.o build/glnxa64/_coder_call_gsl_svd_api.o build/glnxa64/_coder_call_gsl_svd_mex.o build/glnxa64/calculate_svd_example.o build/glnxa64/c_mexapi_version.o -pthread -Wl,--no-undefined -Wl,-rpath-link,/panfs/roc/msisoft/matlab/R2019a/bin/glnxa64 -shared -L"/panfs/roc/msisoft/matlab/R2019a/bin/glnxa64" -lmx -lmex -lmat -lm -lstdc++ -o call_gsl_svd_mex.mexa64 -lemlrt -lcovrt -lut -lmwmathutil -Wl,--version-script,call_gsl_svd_mex.map
FAILED: call_gsl_svd_mex.mexa64
/bin/gcc build/glnxa64/call_gsl_svd_data.o build/glnxa64/call_gsl_svd_initialize.o build/glnxa64/call_gsl_svd_terminate.o build/glnxa64/call_gsl_svd.o build/glnxa64/_coder_call_gsl_svd_info.o build/glnxa64/_coder_call_gsl_svd_api.o build/glnxa64/_coder_call_gsl_svd_mex.o build/glnxa64/calculate_svd_example.o build/glnxa64/c_mexapi_version.o -pthread -Wl,--no-undefined -Wl,-rpath-link,/panfs/roc/msisoft/matlab/R2019a/bin/glnxa64 -shared -L"/panfs/roc/msisoft/matlab/R2019a/bin/glnxa64" -lmx -lmex -lmat -lm -lstdc++ -o call_gsl_svd_mex.mexa64 -lemlrt -lcovrt -lut -lmwmathutil -Wl,--version-script,call_gsl_svd_mex.map
build/glnxa64/calculate_svd_example.o: In function `calculate_svd_example':
calculate_svd_example.c:(.text+0x73): undefined reference to `gsl_matrix_view_array'
calculate_svd_example.c:(.text+0x82): undefined reference to `gsl_matrix_alloc'
calculate_svd_example.c:(.text+0x94): undefined reference to `gsl_matrix_alloc'
calculate_svd_example.c:(.text+0xa1): undefined reference to `gsl_vector_alloc'
calculate_svd_example.c:(.text+0xae): undefined reference to `gsl_vector_alloc'
calculate_svd_example.c:(.text+0xbc): undefined reference to `gsl_matrix_transpose_memcpy'
calculate_svd_example.c:(.text+0xcd): undefined reference to `gsl_linalg_SV_decomp'
calculate_svd_example.c:(.text+0xe1): undefined reference to `pretty_print'
calculate_svd_example.c:(.text+0xf5): undefined reference to `pretty_print_vector'
calculate_svd_example.c:(.text+0x109): undefined reference to `pretty_print'
calculate_svd_example.c:(.text+0x111): undefined reference to `gsl_matrix_free'
calculate_svd_example.c:(.text+0x119): undefined reference to `gsl_matrix_free'
calculate_svd_example.c:(.text+0x121): undefined reference to `gsl_vector_free'
calculate_svd_example.c:(.text+0x129): undefined reference to `gsl_vector_free'
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.
------------------------------------------------------------------------
??? Build error: C compiler produced errors. See the Build Log for further details.
More information
Code generation failed: View Error Report
Error using codegen
How do I do this call this simple C method? Do the .c, .h. and .m files all have to be in the same directory? How do I link with the GSL libraries?
(I have attached the source files as a ZIP file.)
Respuesta aceptada
Paul Reiners
el 9 de Mzo. de 2021
1 comentario
Matthew Faulkner
el 29 de Mzo. de 2023
Hi, where did you obtain/find the directory -L/home/reine097/c-libs/lib/ ?
Más respuestas (1)
Jan
el 2 de Mzo. de 2021
Editada: Jan
el 2 de Mzo. de 2021
You can create a C++-Mex function and call the library throught it. Unfortunately all inputs must be transposed, because Matlab uses the columnwise storing in opposite to GSL. But the rest of the conversion from Matlab arrays to GSL matrices is easy.
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