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sandywang / GRETNA

A Graph-theoretical Network Analysis Toolkit in MATLAB
GNU General Public License v3.0
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Error happening at "Network Metric Analysis" #5

Open carolchang opened 4 years ago

carolchang commented 4 years ago

Hello, All,

I am running my system at catalina, with spm12 and matlab 2019b. And at "Network Metric Analysis", it would encounter "dynamic library link" issue that "betweenness_centrality_mex.mexmaci64, 6): Library not loaded: @loader_path/libmex.dylib". The complete error message is as below.

Please help. Do I need to change the DLL setting in gretna? Thanks.

========================================

< M A T L A B (R) > Copyright 1984-2019 The MathWorks, Inc. R2019b Update 4 (9.7.0.1296695) 64-bit (maci64) January 20, 2020

To get started, type doc. For product information, visit www.mathworks.com.

Warning: psom:default: The following field(s) were ignored in the structure job : OutputMatFile

In psom_set_defaults (line 101) In psom_run_job (line 111)

Log of the (matlab) job : BetweennessCentrality00063 Started on 30-Jun-2020 19:16:49 User: changjudy host : boss3.local system : unix

The job starts now !

Something went bad ... the job has FAILED ! The last error message occured was : Invalid MEX-file '/Users/xxx/Documents/GRETNA_20171121/matlab_bgl/private/betweenness_centrality_mex.mexmaci64': dlopen(/Users/xxx/Documents/GRETNA_20171121/matlab_bgl/private/betweenness_centrality_mex.mexmaci64, 6): Library not loaded: @loader_path/libmex.dylib Referenced from: /Users/xxx/Documents/GRETNA_20171121/matlab_bgl/private/betweenness_centrality_mex.mexmaci64 Reason: image not found File /Users/xxx/Documents/GRETNA_20171121/matlab_bgl/betweenness_centrality.m at line 94 File /Users/xxx/Documents/GRETNA_20171121/NetFunctions/gretna_node_betweenness.m at line 30 File /Users/xxx/Documents/GRETNA_20171121/RunFun/gretna_RUN_BetweennessCentrality.m at line 39 File /Users/xxx/Documents/GRETNA_20171121/RunFun/gretna_RUN_BetweennessCentrality.m at line 21 File /Users/xxx/Documents/GRETNA_20171121/RunFun/gretna_RUN_BetweennessCentrality.m at line 21 File /Users/xxx/Documents/GRETNA_20171121/PSOM/psom_run_job.m at line 214 File /Users/xxx/Documents/GRETNA_20171121/PSOM/psom_run_job.m at line 128

Checking outputs

The output file or directory /Volumes/xxx/Greta_CO/NetworkAnalysis/zSub_063/BC.mat has not been generated!

30-Jun-2020 19:16:50 : The job has FAILED Total time used to process the job : 1.49 sec.

ans =

logical

1

\nzSub_064\n

mmandelli commented 3 years ago

Hello, were you able to fix this problem? I am having the same issue!

ysy970 commented 3 years ago

Hello, All,

I am running my system at catalina, with spm12 and matlab 2019b. And at "Network Metric Analysis", it would encounter "dynamic library link" issue that "betweenness_centrality_mex.mexmaci64, 6): Library not loaded: @loader_path/libmex.dylib". The complete error message is as below.

Please help. Do I need to change the DLL setting in gretna? Thanks.

========================================

< M A T L A B (R) > Copyright 1984-2019 The MathWorks, Inc. R2019b Update 4 (9.7.0.1296695) 64-bit (maci64) January 20, 2020

To get started, type doc. For product information, visit www.mathworks.com.

Warning: psom:default: The following field(s) were ignored in the structure job : OutputMatFile

In psom_set_defaults (line 101) In psom_run_job (line 111)

Log of the (matlab) job : BetweennessCentrality00063 Started on 30-Jun-2020 19:16:49 User: changjudy host : boss3.local system : unix

The job starts now !

Something went bad ... the job has FAILED ! The last error message occured was : Invalid MEX-file '/Users/xxx/Documents/GRETNA_20171121/matlab_bgl/private/betweenness_centrality_mex.mexmaci64': dlopen(/Users/xxx/Documents/GRETNA_20171121/matlab_bgl/private/betweenness_centrality_mex.mexmaci64, 6): Library not loaded: @loader_path/libmex.dylib Referenced from: /Users/xxx/Documents/GRETNA_20171121/matlab_bgl/private/betweenness_centrality_mex.mexmaci64 Reason: image not found File /Users/xxx/Documents/GRETNA_20171121/matlab_bgl/betweenness_centrality.m at line 94 File /Users/xxx/Documents/GRETNA_20171121/NetFunctions/gretna_node_betweenness.m at line 30 File /Users/xxx/Documents/GRETNA_20171121/RunFun/gretna_RUN_BetweennessCentrality.m at line 39 File /Users/xxx/Documents/GRETNA_20171121/RunFun/gretna_RUN_BetweennessCentrality.m at line 21 File /Users/xxx/Documents/GRETNA_20171121/RunFun/gretna_RUN_BetweennessCentrality.m at line 21 File /Users/xxx/Documents/GRETNA_20171121/PSOM/psom_run_job.m at line 214 File /Users/xxx/Documents/GRETNA_20171121/PSOM/psom_run_job.m at line 128

Checking outputs

The output file or directory /Volumes/xxx/Greta_CO/NetworkAnalysis/zSub_063/BC.mat has not been generated!

30-Jun-2020 19:16:50 : The job has FAILED Total time used to process the job : 1.49 sec.

ans =

logical

1

\nzSub_064\n

I met the same problem. Have you solved it?

j-tseng commented 1 month ago

Hey @ysy970 - I had the same issue with GRETNA (2.0.0 release downloaded from NITRC website, MATLAB R2021a). Our GRETNA error indicated that it was something to do with matlabbgl *.mex files, which are included in the GRETNA distro. I'm guessing that this older matlabbgl distribution is no longer compatible with newer MATLAB installations.

I was able to fix this by:

The matlabbgl folks remain quite active over on their github issues page, so I found this solution here. Other people with similar issues were able to fix it with this sort of approach (removing matlabbgl that comes with GRETNA, then downloading through Add-Ons or other sources).