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Calling method in the GNU Scientific Library

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I want to call a function in the GNU Scientific Library (GSL) from MATLAB. In particular, I want to call this method:
int gsl_linalg_SV_decomp(gsl_matrix * A, gsl_matrix * V, gsl_vector * S, gsl_vector * work)
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.)
  7 Comments
Paul Reiners
Paul Reiners on 9 Mar 2021
How do you install SVD_LAPACK? That seems to be what I want.

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Accepted Answer

Paul Reiners
Paul Reiners on 9 Mar 2021
>> mex -v -L/home/reine097/c-libs/lib/ -R2017b run_svd.c calculate_svd_example.c -lgsl -lgslcblas -lm

More Answers (1)

Jan
Jan on 2 Mar 2021
Edited: Jan on 2 Mar 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.
  1 Comment
Paul Reiners
Paul Reiners on 9 Mar 2021
Hi Jan,
I added more details to my description, including attaching the source code files. If you could take another look, that would be great.

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