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dgleich / matlab-bgl

A graph library for Matlab based on the boost graph library
http://dgleich.github.com/matlab-bgl
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MEX file errors - matlab_bgl_sp_mex.c (macOS Monterey 12.5.1) #27

Open dankozar opened 1 year ago

dankozar commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

Can you try and use a precompiled library? e.g. https://github.com/dgleich/matlab-bgl/issues/25 (see that for a link...)

David

On Wed, Oct 19, 2022 at 4:07 PM dankozar @.***> wrote:

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

— Reply to this email directly, view it on GitHub https://github.com/dgleich/matlab-bgl/issues/27, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAIJSZSYJOSWKTN4KVOOLDWEBIGXANCNFSM6AAAAAARJO5CH4 . You are receiving this because you are subscribed to this thread.Message ID: @.***>

dankozar commented 1 year ago

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 commented 1 year ago

mexa64

frankgarcea commented 1 year ago

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 commented 1 year ago

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

frankgarcea commented 1 year ago

Hi @dgleich,

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

FG