Re: [MRST Users] installing/building VEmax

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Knut-Andreas Lie

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May 6, 2021, 4:25:16 AM5/6/21
to Markus Zechner, MRST-users: The Matlab Reservoir Simulation Toolbox User Group
Hi,

I think this error message indicates that MATLAB/MRST is not able to find a function from the MATLAB Boost Graph Library. I suggest that you try to run the downloadMBGL function supplied in the matlab_bgl module. If you have already downloaded the software and it is still not working, it may be that MATLAB has not been able to compile it and create the necessary mex interface.

 - Knut-Andreas


--
Knut-Andreas Lie, Professor, PhD
Chief Scientist, SINTEF Digital, Mathematics & Cybernetics, Oslo
Phone: +47 930 58 721 (mobile)
http://folk.ntnu.no/andreas
From: sinte...@googlegroups.com <sinte...@googlegroups.com> on behalf of Markus Zechner <zechner...@gmail.com>
Sent: Thursday, May 6, 2021 12:42 AM
To: MRST-users: The Matlab Reservoir Simulation Toolbox User Group <sinte...@googlegroups.com>
Subject: [MRST Users] installing/building VEmax
 
Hey!

I hope you are doing well!

I am trying to run a VEmax simulation on my Mac computer (big sur). I built VEmax following the instructions and it seems ok (see screenshot).

But when I run 'runSlopingAquifer.m" I am getting this error: Unrecognized function or variable 'dfs_mex'. (also screenshot)

Thanks a lot for your help!

Best,

Markus


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Markus Zechner

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May 6, 2021, 10:53:29 AM5/6/21
to Knut-Andreas Lie, MRST-users: The Matlab Reservoir Simulation Toolbox User Group
Thanks a lot your answer!

I think the issue is with the build - I had a couple of small issues but I wasn’t able to fix the last one (attached). I tried to google it but without success.

Did anybody have that error as well?

Thanks a lot for your help!

Best,

Markus

Bård Skaflestad

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May 6, 2021, 11:29:53 AM5/6/21
to Markus Zechner, Knut-Andreas Lie, MRST-users: The Matlab Reservoir Simulation Toolbox User Group

Hi,

 

I just wanted to chime in on one possible cause of this issue.  You mentioned earlier that you're on a Mac.  I assume, since that's the case for pretty much all Macs nowadays, that you're on a 64-bit version of the platform?  If so, that's the direct cause of MatlabBGL, of which 'dfs_mex' is one function, failing to load.  MRST provides download functionality for MatlabBGL, but does not build the package directly.

 

By now, the official MEX interfaces of MatlabBGL are rather old and do not have a 64-bit pre-compiled version for Macs.  Another user encountered this same issue about a month ago and their work-around was to use a non-official version of MatlabBGL from

 

https://dgleich.wordpress.com/2010/07/08/matlabbgl-osx-64-bit/

 

Do please let us know if doing the same thing gets you further in your work.

 

 

Best Regards,

 

Bård Skaflestad

SINTEF Digital, Mathematics & Cybernetics

Computational Geosciences group

Markus Zechner

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May 10, 2021, 2:23:53 PM5/10/21
to Bård Skaflestad, Knut-Andreas Lie, MRST-users: The Matlab Reservoir Simulation Toolbox User Group
Hey!

Thanks a lot for your help!

I replaced the matlab__bgl with the version for Mac and it is able to load the module now. But when I run ‘runSlopingAquifer.m’ I am getting the following error:

Invalid MEX-file '/Users/markuszechner/Documents/MATLAB/mrst-2020b/utils/3rdparty/matlab_bgl/matlab_bgl/private/dfs_mex.mexmaci64':
dlopen(/Users/markuszechner/Documents/MATLAB/mrst-2020b/utils/3rdparty/matlab_bgl/matlab_bgl/private/dfs_mex.mexmaci64, 6): Library not
loaded: @loader_path/libmex.dylib
  Referenced from: /Users/markuszechner/Documents/MATLAB/mrst-2020b/utils/3rdparty/matlab_bgl/matlab_bgl/private/dfs_mex.mexmaci64
  Reason: image not found

I am also having issues when building VEmax:

CMakeLists.txt
PastedGraphic-1.png

Olav Møyner

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May 10, 2021, 3:08:35 PM5/10/21
to Markus Zechner, Bård Skaflestad, Knut-Andreas Lie, MRST-users: The Matlab Reservoir Simulation Toolbox User Group
Hi,

These are still issues related to the external matlab_bgl mex files so I'm not sure if we have any more tips on that end.

Regarding the build script, it seems like there are issues with the OpenMP flags. It might be possible to modify the make files for that part. To be perfectly honest, the VEMex simulator is fairly old and it is not something we actively use anymore. Is there a particular reason why you want to build it? I think this script has an alternate solver that uses just Matlab and should work fine, even if it is a bit slower.

Best regards,
Olav
Sent: Monday, May 10, 2021 20:23
To: Bård Skaflestad <Bard.Sk...@sintef.no>
Cc: Knut-Andreas Lie <Knut-And...@sintef.no>; MRST-users: The Matlab Reservoir Simulation Toolbox User Group <sinte...@googlegroups.com>

Subject: Re: [MRST Users] installing/building VEmax
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Google told me to install llvm and libomp and add the following lines to CMakeLists.txt (attached)

include_directories("/usr/local/include" "/usr/local/opt/llvm/include")
link_directories("/usr/local/lib" "/usr/local/opt/llvm/lib”)

But I am getting the same error again.


Thanks a lot again!

Best,

Markus


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On May 6, 2021, at 8:29 AM, Bård Skaflestad <Bard.Sk...@sintef.no> wrote:

Hi,
 
I just wanted to chime in on one possible cause of this issue.  You mentioned earlier that you're on a Mac.  I assume, since that's the case for pretty much all Macs nowadays, that you're on a 64-bit version of the platform?  If so, that's the direct cause of MatlabBGL, of which 'dfs_mex' is one function, failing to load.  MRST provides download functionality for MatlabBGL, but does not build the package directly.
 
By now, the official MEX interfaces of MatlabBGL are rather old and do not have a 64-bit pre-compiled version for Macs.  Another user encountered this same issue about a month ago and their work-around was to use a non-official version of MatlabBGL from
 
 
Do please let us know if doing the same thing gets you further in your work.
 
 
Best Regards,
 
Bård Skaflestad
SINTEF Digital, Mathematics & Cybernetics
Computational Geosciences group
 
From: sinte...@googlegroups.com <sinte...@googlegroups.com> On Behalf Of Markus Zechner
Sent: Thursday, May 6, 2021 4:53 PM
To: Knut-Andreas Lie <Knut-And...@sintef.no>
Cc: MRST-users: The Matlab Reservoir Simulation Toolbox User Group <sinte...@googlegroups.com>
Subject: Re: [MRST Users] installing/building VEmax
 
Thanks a lot your answer!
 
I think the issue is with the build - I had a couple of small issues but I wasn’t able to fix the last one (attached). I tried to google it but without success.
 
Did anybody have that error as well?
 
Thanks a lot for your help!
 
Best,
 
Markus


On May 6, 2021, at 1:25 AM, Knut-Andreas Lie <Knut-And...@sintef.no> wrote:
 
Hi,
 
I think this error message indicates that MATLAB/MRST is not able to find a function from the MATLAB Boost Graph Library. I suggest that you try to run the downloadMBGL function supplied in the matlab_bgl module. If you have already downloaded the software and it is still not working, it may be that MATLAB has not been able to compile it and create the necessary mex interface.
 
 - Knut-Andreas
 
 
--
Knut-Andreas Lie, Professor, PhD
Chief Scientist, SINTEF Digital, Mathematics & Cybernetics, Oslo
Phone: +47 930 58 721 (mobile)
http://folk.ntnu.no/andreas
From: sinte...@googlegroups.com <sinte...@googlegroups.com> on behalf of Markus Zechner <zechner...@gmail.com>
Sent: Thursday, May 6, 2021 12:42 AM
To: MRST-users: The Matlab Reservoir Simulation Toolbox User Group <sinte...@googlegroups.com>
Subject: [MRST Users] installing/building VEmax
 
Hey!
 
I hope you are doing well!
 
I am trying to run a VEmax simulation on my Mac computer (big sur). I built VEmax following the instructions and it seems ok (see screenshot).
 
But when I run 'runSlopingAquifer.m" I am getting this error: Unrecognized function or variable 'dfs_mex'. (also screenshot)
 
Thanks a lot for your help!
 
Best,
 
Markus
 
 
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