Error happening at "Network Metric Analysis"

[carolchang]

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]

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

[ysy970]

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]

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:

• Removing the matlabbgl folder from inside the GRETNA folder
• Install matlabbgl through MATLAB: Home panel > Add-Ons > "matlabbgl".

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).

[Cookdao]

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.嘿 - 我对 GRETNA 也有同样的问题（从 NITRC 网站下载的 2.0.0 版本，MATLAB R2021a）。我们的 GRETNA 错误表明它与matlabbgl *.mex 文件有关，这些文件包含在 GRETNA 发行版中。我猜测这个较旧的matlabbgl发行版不再与较新的 MATLAB 安装兼容。

I was able to fix this by:我能够通过以下方式解决这个问题：

• Removing the matlabbgl folder from inside the GRETNA folder从GRETNA文件夹中删除matlabbgl文件夹
• Install matlabbgl through MATLAB: Home panel > Add-Ons > "matlabbgl".通过 MATLAB 安装matlabbgl ：主页面板 > 附加组件 > “matlabbgl”。

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).matlabbgl 人员在他们的 github 问题页面上仍然非常活跃，所以我在这里找到了这个解决方案。其他有类似问题的人能够用这种方法修复它（删除 GRETNA 附带的 matlabbgl，然后通过附加组件或其他来源下载）。

After I followed your guide, it showed it as follows.
Something went bad ... the job has FAILED !
The last error message occured was :
Undefined function 'matlab_bgl_all_sp_mex' for input arguments of type 'double'.
File /Users/h4yd/Library/Application Support/MathWorks/MATLAB
Add-Ons/Collections/MatlabBGL/matlab_bgl/all_shortest_paths.m at line 97
File /Users/h4yd/Documents/MATLAB/GRETNA/NetFunctions/gretna_distance.m at line 25
File /Users/h4yd/Documents/MATLAB/GRETNA/NetFunctions/gretna_node_shortestpathlength.m at line 27
File /Users/h4yd/Documents/MATLAB/GRETNA/RunFun/gretna_RUN_SmallWorld.m at line 34
File /Users/h4yd/Documents/MATLAB/GRETNA/RunFun/gretna_RUN_SmallWorld.m at line 34
File /Users/h4yd/Documents/MATLAB/GRETNA/PSOM/psom_run_job.m at line 214
File /Users/h4yd/Documents/MATLAB/GRETNA/PSOM/psom_run_job.m at line 128