getDP solver cannot work properly on your system

Ziqian Huang

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Apr 27, 2023, 10:21:28 PM4/27/23

to roast-users

Dear all,

I'm getting this error when I was trying to run roast. I checked the group conversion that some users also encountered this error befor with MacOS.

I'm using MATLAB GUI through a VNC session to run the roast, the following is part of the output and the error message. Could you please help me to check the issue here?

Thank you so much!!

Best,

Ziqian Huang

PhD student@University of Florida

saving mesh...
======================================================
STEP 5 (out of 6): SOLVING THE MODEL...
======================================================
setting up boundary conditions...
Info : Running 'lib/getdp-3.2.0/bin/getdp /red/ruogu.fang/ziqian.huang/ACT_IV/FS6.0_sub-110081_ses-01_T1w/T1_tDCSLAB.pro -solve EleSta_v -msh /red/ruogu.fang/ziqian.huang/ACT_IV/FS6.0_sub-110081_ses-01_T1w/T1_tDCSLAB_ready.msh -pos Map' [GetDP 3.2.0, 1 node, max. 1 thread]
Info : Started (Thu Apr 27 15:45:38 2023, Wall = 0.000113964s, CPU = 0.002761s, Mem = 4.07422Mb)
Info : Initializing Gmsh
Info : Loading problem definition '/red/ruogu.fang/ziqian.huang/ACT_IV/FS6.0_sub-110081_ses-01_T1w/T1_tDCSLAB.pro'
Info : Selected Resolution 'EleSta_v'
Info : Loading Geometric data '/red/ruogu.fang/ziqian.huang/ACT_IV/FS6.0_sub-110081_ses-01_T1w/T1_tDCSLAB_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: 721954 Dofs
Info : (Wall = 8.18843s, CPU = 7.94135s, Mem = 572.902Mb)
[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: 721954 - preonly lu mumps
Info : SaveSolution[Sys_Ele]
Info : (Wall = 547.171s, CPU = 987.004s, Mem = 16485.3Mb)
[34mE n d P r o c e s s i n g [0m
[34mP o s t - P r o c e s s i n g . . . [0m
Info : NameOfSystem not set in PostProcessing: selected 'Sys_Ele'
Info : Selected PostProcessing 'EleSta_v'
Info : Selected Mesh '/red/ruogu.fang/ziqian.huang/ACT_IV/FS6.0_sub-110081_ses-01_T1w/T1_tDCSLAB_ready.msh'
Info : PostOperation 1/2
> '/red/ruogu.fang/ziqian.huang/ACT_IV/FS6.0_sub-110081_ses-01_T1w/T1_tDCSLAB_v.pos'
0% : Post-processing (Compute)
10% : Post-processing (Compute)
20% : Post-processing (Compute)
30% : Post-processing (Compute)
40% : Post-processing (Compute)
50% : Post-processing (Compute)
60% : Post-processing (Compute)
70% : Post-processing (Compute)
80% : Post-processing (Compute)
90% : Post-processing (Compute)

Info : PostOperation 2/2
> '/red/ruogu.fang/ziqian.huang/ACT_IV/FS6.0_sub-110081_ses-01_T1w/T1_tDCSLAB_e.pos'
0% : Post-processing (Generate)
10% : Post-processing (Generate)
20% : Post-processing (Generate)
30% : Post-processing (Generate)
40% : Post-processing (Generate)
50% : Post-processing (Generate)
60% : Post-processing (Generate)
70% : Post-processing (Generate)
80% : Post-processing (Generate)
90% : Post-processing (Generate)
lib/getdp-3.2.0/bin/getdp "/FS6.0_sub-110081_ses-01_T1w/T1_tDCSLAB.pro" -solve EleSta_v -msh "/FS6.0_sub-110081_ses-01_T1w/T1_tDCSLAB_ready.msh" -pos Map: Killed

error message:

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 rerun_roast6 (line 16)
roast(i, T1, recipe, ...

Grace Guo

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Apr 27, 2023, 11:28:45 PM4/27/23

to roast-users

Hi Ziqian,

I also encountered the "getDP cannot work on your system" problem before, and mine was fixed by upgrading getDP to the 3.5 version (replace the getDP folder in the 'lib' directory with the new version downloaded from getDP website). This may be worth trying as a quick fix and hope it works for you.

Best,

Grace

Ziqian Huang

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Apr 28, 2023, 10:54:08 AM4/28/23

to roast-users

Hey Grace,

Thank you so much for your reply! I will try to update the getDP and try it again.

Thank you!

Best,

Ziqian

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