Calling method in the GNU Scientific Library
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Paul Reiners
on 2 Mar 2021
Commented: Matthew Faulkner
on 29 Mar 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.)
Accepted Answer
Paul Reiners
on 9 Mar 2021
1 Comment
Matthew Faulkner
on 29 Mar 2023
Hi, where did you obtain/find the directory -L/home/reine097/c-libs/lib/ ?
More Answers (1)
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