getDP solver not working

Federica De

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Jul 21, 2021, 8:40:23 AM7/21/21

to roast-users

Der Andy,

I am using ROAST (Thank you for your work!) to simulate electrical fields of tRNS stimulation over P3 and P4 (I am using the nyhead).

However I get this error (printed below) which I don't know how to solve.

Could you give me some tips?

Best,

Clelia

Error:

Error using solveByGetDP (line 209)

getDP solver cannot work properly on your system. Please check any error message you got.

Error in roast (line 845)

solveByGetDP(subj,injectCurrent,conductivities,indElecSolve,uniqueTag,'');

Error in ROAST_Federica (line 1)

roast('nyhead', {'P3',2,'P4',-2'},..

The code I am using for the simulation:

roast('nyhead', {'P3',2,'P4',-2'},...

'capType', {'1020'},...

'electype', {'pad', 'pad'},...edit

'elecsize',{[70 50 3],[70 50 3]},...

'elecOri',{'si','si'}, ...

'zeroPadding', 30,...

'simulationTag', 'parietal_setting')

Yu (Andy) Huang

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Jul 21, 2021, 10:43:05 PM7/21/21

to Federica De, roast-users

Hi,

Please post your OS and Matlab version so that I can further help you. Also post any other error message you got from the Matlab command window.

Thanks!

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Federica Contò

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Jul 22, 2021, 5:24:41 AM7/22/21

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Hi Andy,

Many thanks for your quick reply, first of all.

I am using two machines:

1 --> mac: macOS Big Sur, matlab: 2019a

2 --> mac: macOS Sierra, matlab: 2015b.

Many thanks for your help!

Clelia Federica

Federica De

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Jul 22, 2021, 9:01:41 AM7/22/21

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Hi Andy,

I forgot in the response above to post the whole error message I get.

On the macOS Sierra I get this message (posted below, I report the step at which it gets stuck).

Many thanks!

Federica Clelia

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

STEP 5 (out of 6): SOLVING THE MODEL...

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

setting up boundary conditions...

Info : Running 'lib/getdp-3.2.0/bin/getdpMac example/nyhead_parietal_setting.pro -solve EleSta_v -msh example/nyhead_parietal_setting_ready.msh -pos Map' [GetDP 3.2.0, 1 node, max. 1 thread]

Info : Started (Thu Jul 22 12:35:19 2021, Wall = 0.207394s, CPU = 0.104169s, Mem = 4.98438Mb)

Info : Initializing Gmsh

[1m [31mError : Unknown number option 'Mesh.ChacoHypercubeDim' [0m

[1m [31mError : Unknown number option 'Mesh.ChacoMeshDim1' [0m

Info : Loading problem definition 'example/nyhead_parietal_setting.pro'

Info : Selected Resolution 'EleSta_v'

Info : Loading Geometric data 'example/nyhead_parietal_setting_ready.msh'

Info : System 'Sys_Ele' : Real

[34mP r e - P r o c e s s i n g . . . [0m

Info : Treatment Formulation 'Electrostatics_v'

0% : Pre-processing

10% : Pre-processing

20% : Pre-processing

30% : Pre-processing

40% : Pre-processing

50% : Pre-processing

60% : Pre-processing

70% : Pre-processing

80% : Pre-processing

90% : Pre-processing

Info : System 1/1: 2339107 Dofs

Info : (Wall = 51.7185s, CPU = 46.6292s, Mem = 1540.71Mb)

[34mE n d P r e - P r o c e s s i n g [0m

[34mP r o c e s s i n g . . . [0m

Info : Generate[Sys_Ele]

0% : Processing (Generate)

10% : Processing (Generate)

20% : Processing (Generate)

30% : Processing (Generate)

40% : Processing (Generate)

50% : Processing (Generate)

60% : Processing (Generate)

70% : Processing (Generate)

80% : Processing (Generate)

90% : Processing (Generate)

Info : Solve[Sys_Ele]

Info : N: 2339107 - preonly lu mumps

lib/getdp-3.2.0/bin/getdpMac "example/nyhead_parietal_setting.pro" -solve EleSta_v -msh "example/nyhead_parietal_setting_ready.msh" -pos Map: Killed

Error using solveByGetDP (line 209)

getDP solver cannot work properly on your system. Please check any error message you got.

Error in roast (line 845)

solveByGetDP(subj,injectCurrent,conductivities,indElecSolve,uniqueTag,'');

An error was encountered while saving the command history

Yu (Andy) Huang

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Jul 22, 2021, 11:07:05 PM7/22/21

to Federica De, roast-users

Unfortunately getDP was not tested extensively for ROAST on the Mac OS. Anyway it seemed that getDP worked on your Mac but crashed in the middle. I suspect that it's due to out of memory as NY head needs >50GB memory to solve. Please check the memory on your machine. If you do not have much memory, I recommend to use the lighter MNI152 head coming along with ROAST.

Hope this helps.

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