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MEX file errors - matlab_bgl_sp_mex.c (macOS Monterey 12.5.1) #27

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dankozar opened this issue Oct 19, 2022 · 7 comments
Open

MEX file errors - matlab_bgl_sp_mex.c (macOS Monterey 12.5.1) #27

dankozar opened this issue Oct 19, 2022 · 7 comments

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@dankozar
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Hi,

Thanks for setting all of this up. I am seeking to use the BGL library for calculating directional connectivity index (DCI) on a binary matrix. I have successfully downloaded and unzipped the package folder, but I get an error message when I seek to compile the matlab_bgl_sp_mex.c file. I seek to compile the mex script with:

mex matlab_bgl_sp_mex.c -lmwlapack -lmwblas

And I get the error string below. It is a lot of text, but I figure maybe necessary to establish what is wrong. Apologies for any newbie misunderstanding.

Building with 'Xcode with Clang'.
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:246:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,initialize_vertex,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:247:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,discover_vertex,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:248:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,examine_vertex,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:249:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,finish_vertex,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:251:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,examine_edge,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:252:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,edge_relaxed,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:253:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,edge_not_relaxed,d_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:255:36: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            dijkstra_sp_visitor(n, ja, ia, a,
                                   ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:190:34: note: passing argument to parameter 'ja' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                 ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:255:40: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            dijkstra_sp_visitor(n, ja, ia, a,
                                       ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:190:49: note: passing argument to parameter 'ia' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                                ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:257:20: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex ' (aka 'int ') [-Wincompatible-pointer-types]
                d, (mwIndex)pred, dinf, d_vis);
                   ^~~~~~~~~~~~~~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:192:27: note: passing argument to parameter 'pred' here
    double d, mbglIndex *pred, double dinf,
                          ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:261:28: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            dijkstra_sp(n, ja, ia, a,
                           ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:185:34: note: passing argument to parameter 'ja' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                 ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:261:32: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            dijkstra_sp(n, ja, ia, a,
                               ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:185:49: note: passing argument to parameter 'ia' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                                ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:263:20: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex ' (aka 'int ') [-Wincompatible-pointer-types]
                d, (mwIndex)pred, dinf);
                   ^~~~~~~~~~~~~~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:187:27: note: passing argument to parameter 'pred' here
    double d, mbglIndex *pred, double dinf);
                          ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:275:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,initialize_vertex,bf_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:277:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,examine_edge,bf_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:278:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,edge_relaxed,bf_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:279:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,edge_not_relaxed,bf_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:280:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,edge_minimized,bf_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:281:13: warning: case value not in enumerated type 'mxClassID' [-Wswitch]
            CHECK_AND_SET_VISITOR_FUNCTION(vis,edge_not_minimized,bf_vis);
            ^
/Volumes/easystore/Thesis_CH1/Matrices/visitor_macros.h:32:41: note: expanded from macro 'CHECK_AND_SET_VISITOR_FUNCTION'
            case mxFUNCTION_CLASS: case 23:
                                        ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:283:40: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            bellman_ford_sp_visitor(n, ja, ia, a,
                                       ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:201:34: note: passing argument to parameter 'ja' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                 ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:283:44: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            bellman_ford_sp_visitor(n, ja, ia, a,
                                           ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:201:49: note: passing argument to parameter 'ia' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                                ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:285:16: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex ' (aka 'int ') [-Wincompatible-pointer-types]
            d, (mwIndex)pred, dinf, bf_vis);
               ^~~~~~~~~~~~~~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:203:27: note: passing argument to parameter 'pred' here
    double d, mbglIndex *pred, double dinf,
                          ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:289:32: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            bellman_ford_sp(n, ja, ia, a,
                               ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:196:34: note: passing argument to parameter 'ja' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                 ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:289:36: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
            bellman_ford_sp(n, ja, ia, a,
                                   ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:196:49: note: passing argument to parameter 'ia' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                                ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:291:16: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex ' (aka 'int ') [-Wincompatible-pointer-types]
            d, (mwIndex)pred, dinf);
               ^~~~~~~~~~~~~~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:198:27: note: passing argument to parameter 'pred' here
    double d, mbglIndex *pred, double dinf);
                          ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:298:19: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
        dag_sp(n, ja, ia, a,
                  ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:207:34: note: passing argument to parameter 'ja' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                 ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:298:23: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex *' (aka 'int *') [-Wincompatible-pointer-types]
        dag_sp(n, ja, ia, a,
                      ^~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:207:49: note: passing argument to parameter 'ia' here
    mbglIndex nverts, mbglIndex *ja, mbglIndex *ia, double weight, / connectivity params */
                                                ^
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl_sp_mex.c:300:16: warning: incompatible pointer types passing 'mwIndex *' (aka 'unsigned long *') to parameter of type 'mbglIndex ' (aka 'int ') [-Wincompatible-pointer-types]
            d, (mwIndex)pred, dinf);
               ^~~~~~~~~~~~~~
/Volumes/easystore/Thesis_CH1/Matrices/matlab_bgl.h:209:27: note: passing argument to parameter 'pred' here
    double d, mbglIndex *pred, double dinf);
                          ^
28 warnings generated.

Error using mex
Undefined symbols for architecture x86_64:
  "_bellman_ford_sp", referenced from:
      _mexFunction in matlab_bgl_sp_mex.o
  "_bellman_ford_sp_visitor", referenced from:
      _mexFunction in matlab_bgl_sp_mex.o
  "_dag_sp", referenced from:
      _mexFunction in matlab_bgl_sp_mex.o
  "_dijkstra_sp", referenced from:
      _mexFunction in matlab_bgl_sp_mex.o
  "_dijkstra_sp_visitor", referenced from:
      _mexFunction in matlab_bgl_sp_mex.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

Thanks!
-Daniel Kozar
PhD Student
UC Davis
@dgleich
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dgleich commented Oct 19, 2022

Can you try one of the precompiled ones? e.g.

www.cs.purdue.edu/homes/dgleich/scratch/matlab-bgl-full-dir-20191008.tar.gz

@dgleich
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dgleich commented Oct 19, 2022 via email

@dankozar
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Great thank you! That worked.

One more question - to use this mex file in a HPC cluster (Linux), what file extension should I use? Now that my code runs on my personal computer, I just am seeking to run it over this cluster. Any help would be great!

Thanks

@dgleich
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dgleich commented Oct 20, 2022

mexa64

@frankgarcea
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Hi @dgleich

I'm running into a similar issue and I have tried all of the suggestions you've provided in this thread and others here. In short: when I try to run the betweenness centrality analysis, I get the following error:

Invalid MEX-file '/Users/MyComputerDocuments/MATLAB/toolboxes/matlab_bgl/private/betweenness_centrality_mex.mexmaci64':
dlopen(/Users/MyComputer/Documents/MATLAB/toolboxes/matlab_bgl/private/betweenness_centrality_mex.mexmaci64, 0x0006): Library
not loaded: '@loader_path/libmex.dylib'
Referenced from: '/Users/MyComputer/Documents/MATLAB/toolboxes/matlab_bgl/private/betweenness_centrality_mex.mexmaci64'
Reason: tried: '/Users/MyComputer/Documents/MATLAB/toolboxes/matlab_bgl/private/libmex.dylib' (no such file),
'/usr/local/lib/libmex.dylib' (no such file), '/usr/lib/libmex.dylib' (no such file)

It would appear that others have had similar issues on their mac
https://www.mathworks.com/matlabcentral/answers/763346-mexfile-error-libmex-dylib-not-loaded
https://www.mathworks.com/matlabcentral/answers/463577-mexmaci64-and-dylib-issue

And I can confirm that I don't have 'libmex.dylib' in the /usr/lib folder. It's in the /Applications/Matlab/bin/maci64 folder.

Have you encountered such an issue before? Any pointers would be appreciated.

Thanks in advance,
FG

@dgleich
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dgleich commented Jan 5, 2023

I'm not going to have a chance to take a close look for a few weeks. Sorry about that.

@frankgarcea
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Hi @dgleich,

No worries. I'll continue working on it.
If I find a solution I'll let you know.

FG

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@dgleich @frankgarcea @dankozar