Calling method in the GNU Scientific Library

2021 3 2
2 个回答
回答已采纳
更新时间：2023 3 29
11 次查看（30 天）

0 个投票

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

Bjorn Gustavsson
Bjorn Gustavsson 2021-3-2
Why do you want to use that SVD-decomposition-function instead of the LAPACK-based one matlab uses?
Paul Reiners
Paul Reiners 2021-3-2
Does the LAPACK=based one that MATLAB uses run as fast as the GSL version? If it does, I'd be happy to continue using it.
Bjorn Gustavsson
Bjorn Gustavsson 2021-3-3
(I don't work in the field of numerical linear algebra) I've lived with the impression that LAPACK (et al.) are the state-of-the-art when it comes to linear algebra algorithms. That might be wrong. You might have some special matrices where other algorithms are faster. Perhaps you can time the SVD-algorithms on your type of matrices? Not by interfacing to matlab in the first place but to write a test-program in C...
Paul Reiners
Paul Reiners 2021-3-9
The GSL C function is aboutI’m 200x faster than the MATLAB function.
Bjorn Gustavsson
Bjorn Gustavsson 2021-3-9
That's not bad as such. But my idea was that you'd compare directly with the LAPACK routines also in C: LAPACK-routines for Singular Value Decomposition. If you're building an interface with an external library (which I've never done...) I'd expect you want the best bang for your effort...
Paul Reiners
Paul Reiners 2021-3-9
How do you install SVD_LAPACK? That seems to be what I want.

请先登录，再进行评论。

请先登录，再回答此问题。

 采纳的回答

Paul Reiners
Paul Reiners 2021-3-9

0 个投票

>> 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
Matthew Faulkner 2023-3-29
Hi, where did you obtain/find the directory -L/home/reine097/c-libs/lib/ ?

请先登录，再进行评论。

更多回答（1 个）

Jan
Jan 2021-3-2
编辑：Jan 2021-3-2

0 个投票

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 个评论
显示 -1更早的评论 隐藏 -1更早的评论

Paul Reiners
Paul Reiners 2021-3-9
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.

请先登录，再进行评论。

类别

在 帮助中心 和 File Exchange 中查找有关 Execution Speed 的更多信息

标签

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by