Calling method in the GNU Scientific Library

Question

Paul Reiners 2021-3-2

0
链接

此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/760826-calling-method-in-the-gnu-scientific-library

评论： Matthew Faulkner 2023-3-29

采纳的回答： Paul Reiners

callCFromMatlab.zip

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 个评论
显示 5更早的评论隐藏 5更早的评论

Jan 2021-3-9

this might be useful: https://www.mathworks.com/matlabcentral/fileexchange/16777-lapack

Paul Reiners 2021-3-9

How do you install SVD_LAPACK? That seems to be what I want.

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Answer 1

Paul Reiners 2021-3-9

0
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/760826-calling-method-in-the-gnu-scientific-library#answer_643497

>> mex -v -L/home/reine097/c-libs/lib/ -R2017b run_svd.c calculate_svd_example.c -lgsl -lgslcblas -lm

1 个评论
显示 -1更早的评论隐藏 -1更早的评论

Matthew Faulkner 2023-3-29

Hi, where did you obtain/find the directory -L/home/reine097/c-libs/lib/ ?

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Answer 2

Jan 2021-3-2

0
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/760826-calling-method-in-the-gnu-scientific-library#answer_637526

编辑：Jan 2021-3-2

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.