Unlisted keyword Error

chivier · Post by **chivier** » 26 Apr 2020, 13:14

Hi everyone. I am new to elmer and need help.

I compiled Elmerice on my own today. But when I test it with:
```
ctest -L netcdf
```
it cannot work.

I turn on `echo` in .sif file, and the output is like this:

Code: Select all

ELMER SOLVER (v 8.4) STARTED AT: 2020/04/26 09:53:56
ParCommInit:  Initialize #PEs:            1
MAIN: 
MAIN: =============================================================
MAIN: ElmerSolver finite element software, Welcome!
MAIN: This program is free software licensed under (L)GPL
MAIN: Copyright 1st April 1995 - , CSC - IT Center for Science Ltd.
MAIN: Webpage http://www.csc.fi/elmer, Email elmeradm@csc.fi
MAIN: Version: 8.4 (Rev: unknown, Compiled: 2020-04-26)
MAIN:  Running one task without MPI parallelization.
MAIN:  Running with just one thread per task.
MAIN: =============================================================
MAIN: 
MAIN: 
MAIN: -------------------------------------
MAIN: Reading Model: case.sif
LoadInputFile: Scanning input file: case.sif







Header
Mesh DB "." "mesh2D"
End


Constants
End


Simulation
Coordinate System  = Cartesian
 Cartesian
Simulation Type = Steady State
 Steady State

Steady State Min Iterations = 1
 1
Steady State Max Iterations = 1
 1


Post File = "Reference.vtu"
 "Reference.vtu"
max output level = 4
 4
End


Body 1
Equation = 1
 1
Initial Condition = 1
 1
End


Initial Condition 1

TZs = Variable Coordinate 1, Coordinate 2
 Variable Coordinate 1, Coordinate 2
REAL MATC "zs(tx)"
End




Solver 1

Exec Solver = never
 never
Equation = "Navier-Stokes"
 "Navier-Stokes"



Stabilize = logical True
 logical True
flow model = Stokes
 Stokes


Exported Variable 1 = TZs
 TZs
Exported Variable 1 DOFS = 1
 1

Exported Variable 2 = ZsNNI
 ZsNNI
Exported Variable 2 DOFS = 1
 1

Exported Variable 3 = ZsNNIW
 ZsNNIW
Exported Variable 3 DOFS = 1
 1

Exported Variable 4 = ZsNNINS
 ZsNNINS
Exported Variable 4 DOFS = 1
 1

Exported Variable 5 = ZsLin
 ZsLin
Exported Variable 5 DOFS = 1
 1

Exported Variable 6 = ZsFlight
 ZsFlight
Exported Variable 6 DOFS = 1
 1

Exported Variable 7 = ZsCS
 ZsCS
Exported Variable 7 DOFS = 1
 1
End

Solver 2
Exec Solver = Before simulation
 Before simulation

Equation = "ScatteredInter"
 "ScatteredInter"

procedure = "Scattered2DDataInterpolator" "Scattered2DDataInterpolator"
 "Scattered2DDataInterpolator" "Scattered2DDataInterpolator"

Look for NaN = Logical True 
 Logical True 
	
	





Variable 1 = String "ZsNNI"
 String "ZsNNI"
Variable 1 data file = File "Rand200.txt"
 File "Rand200.txt"

Variable 2 = String "ZsNNIW"
 String "ZsNNIW"
Variable 2 data file = File "Rand200.txt"
 File "Rand200.txt"
Variable 2 W = Real 0.
 Real 0.







Variable 3 = String "ZsNNINS"
 String "ZsNNINS"
Variable 3 data file = File "Rand200.txt"
 File "Rand200.txt"
Variable 3 method = String "ns"
 String "ns"


Variable 4 = String "ZsLin"
 String "ZsLin"
Variable 4 data file = File "Rand200.txt"
 File "Rand200.txt"
Variable 4 method = String "li"
 String "li"


Variable 5 = String "ZsFlight"
 String "ZsFlight"
Variable 5 data file = File "FlightLines.txt"
 File "FlightLines.txt"



Variable 6 = String "ZsCS"
 String "ZsCS"
Variable 6 data file = File "Rand200.txt"
 File "Rand200.txt"
Variable 6 method = String "cs"
 String "cs"

Variable 6 nppc = integer 5
 integer 5



Variable 6 k = integer 140
 integer 140


End

Solver 3
Equation = SaveScalars
 SaveScalars
Procedure =  "SaveData" "SaveScalars"
  "SaveData" "SaveScalars"
Filename = f.dat
 f.dat
Show Norm Index = Integer 1
 Integer 1
Variable 1 = String "ZsNNI"
 String "ZsNNI"
Operator 1 = mean
 mean
End


Equation 1
Active Solvers(2) = 1  2 3
Size 2  = 1  2 3
 1  2 3
NS Convect = Logical False
 Logical False
End


Solver 3 :: Reference Norm = Real 3.99292792E+02
 Reference Norm = Real 3.99292792E+02
 Real 3.99292792E+02
Solver 3 :: Reference Norm Tolerance = Real 1E-06
 Reference Norm Tolerance = Real 1E-06
 Real 1E-06
TEST CASE 1

RUN
LoadInputFile: Loading input file: case.sif




check keywords warn
echo on







Header
Mesh DB "." "mesh2D"
End


Constants
End


Simulation
Coordinate System  = Cartesian
 Cartesian
Simulation Type = Steady State
 Steady State

Steady State Min Iterations = 1
 1
Steady State Max Iterations = 1
 1


Post File = "Reference.vtu"
 "Reference.vtu"
max output level = 4
 4
End


Body 1
Equation = 1
 1
Initial Condition = 1
 1
End


Initial Condition 1

TZs = Variable Coordinate 1, Coordinate 2
 Variable Coordinate 1, Coordinate 2
REAL MATC "zs(tx)"
Model Input:  Unlisted keyword: [tzs] in section: [initial condition 1]
End




Solver 1

Exec Solver = never
 never
Equation = "Navier-Stokes"
 "Navier-Stokes"



Stabilize = logical True
 logical True
flow model = Stokes
 Stokes


Exported Variable 1 = TZs
 TZs
Exported Variable 1 DOFS = 1
 1

Exported Variable 2 = ZsNNI
 ZsNNI
Exported Variable 2 DOFS = 1
 1

Exported Variable 3 = ZsNNIW
 ZsNNIW
Exported Variable 3 DOFS = 1
 1

Exported Variable 4 = ZsNNINS
 ZsNNINS
Exported Variable 4 DOFS = 1
 1

Exported Variable 5 = ZsLin
 ZsLin
Exported Variable 5 DOFS = 1
 1

Exported Variable 6 = ZsFlight
 ZsFlight
Exported Variable 6 DOFS = 1
 1

Exported Variable 7 = ZsCS
 ZsCS
Exported Variable 7 DOFS = 1
 1
End

Solver 2
Exec Solver = Before simulation
 Before simulation

Equation = "ScatteredInter"
 "ScatteredInter"

procedure = "Scattered2DDataInterpolator" "Scattered2DDataInterpolator"
 "Scattered2DDataInterpolator" "Scattered2DDataInterpolator"

Look for NaN = Logical True 
 Logical True 
Model Input:  Unlisted keyword: [look for nan] in section: [solver 2]
	
	





Variable 1 = String "ZsNNI"
 String "ZsNNI"
Variable 1 data file = File "Rand200.txt"
 File "Rand200.txt"
Model Input:  Unlisted keyword: [variable 1 data file] in section: [solver 2]

Variable 2 = String "ZsNNIW"
 String "ZsNNIW"
Variable 2 data file = File "Rand200.txt"
 File "Rand200.txt"
Model Input:  Unlisted keyword: [variable 2 data file] in section: [solver 2]
Variable 2 W = Real 0.
 Real 0.
Model Input:  Unlisted keyword: [variable 2 w] in section: [solver 2]







Variable 3 = String "ZsNNINS"
 String "ZsNNINS"
Variable 3 data file = File "Rand200.txt"
 File "Rand200.txt"
Model Input:  Unlisted keyword: [variable 3 data file] in section: [solver 2]
Variable 3 method = String "ns"
 String "ns"
Model Input:  Unlisted keyword: [variable 3 method] in section: [solver 2]


Variable 4 = String "ZsLin"
 String "ZsLin"
Variable 4 data file = File "Rand200.txt"
 File "Rand200.txt"
Model Input:  Unlisted keyword: [variable 4 data file] in section: [solver 2]
Variable 4 method = String "li"
 String "li"
Model Input:  Unlisted keyword: [variable 4 method] in section: [solver 2]


Variable 5 = String "ZsFlight"
 String "ZsFlight"
Variable 5 data file = File "FlightLines.txt"
 File "FlightLines.txt"
Model Input:  Unlisted keyword: [variable 5 data file] in section: [solver 2]



Variable 6 = String "ZsCS"
 String "ZsCS"
Variable 6 data file = File "Rand200.txt"
 File "Rand200.txt"
Model Input:  Unlisted keyword: [variable 6 data file] in section: [solver 2]
Variable 6 method = String "cs"
 String "cs"
Model Input:  Unlisted keyword: [variable 6 method] in section: [solver 2]

Variable 6 nppc = integer 5
 integer 5
Model Input:  Unlisted keyword: [variable 6 nppc] in section: [solver 2]



Variable 6 k = integer 140
 integer 140
Model Input:  Unlisted keyword: [variable 6 k] in section: [solver 2]


End

Solver 3
Equation = SaveScalars
 SaveScalars
Procedure =  "SaveData" "SaveScalars"
  "SaveData" "SaveScalars"
Filename = f.dat
 f.dat
Show Norm Index = Integer 1
 Integer 1
Variable 1 = String "ZsNNI"
 String "ZsNNI"
Operator 1 = mean
 mean
End


Equation 1
Active Solvers(2) = 1  2 3
Size 2  = 1  2 3
 1  2 3
NS Convect = Logical False
 Logical False
End


Solver 3 :: Reference Norm = Real 3.99292792E+02
 Reference Norm = Real 3.99292792E+02
 Real 3.99292792E+02
Solver 3 :: Reference Norm Tolerance = Real 1E-06
 Reference Norm Tolerance = Real 1E-06
 Real 1E-06
TEST CASE 1

RUN
WARNING:: LoadInputFile: There are no BCs in the system!
LoadInputFile: Number of Body Forces: 0
LoadInputFile: Number of Initial Conditions: 1
LoadInputFile: Number of Materials: 0
LoadInputFile: Number of Equations: 1
LoadInputFile: Number of Solvers: 3
LoadInputFile: Number of Bodies: 1
Loading user function library: [Scattered2DDataInterpolator]...[Scattered2DDataInterpolator_Init0]
Scattered2DDataInterpolator: cannot open shared object file: No such file or directory
Scattered2DDataInterpolator.so: cannot open shared object file: No such file or directory
./Scattered2DDataInterpolator: cannot open shared object file: No such file or directory
./Scattered2DDataInterpolator.so: cannot open shared object file: No such file or directory
/usr/local/Elmer-devel/share/elmersolver/lib/Scattered2DDataInterpolator: cannot open shared object file: No such file or directory
/usr/local/Elmer-devel/share/elmersolver/lib/Scattered2DDataInterpolator.so: cannot open shared object file: No such file or directory

I think the I installed elmerice correctly since I passed most of test cases in `ctest -L elmerice`.
I wanna to learn some method how to deal with problems like this.

kevinarden · Post by **kevinarden** » 26 Apr 2020, 13:25

Variable 6 nppc = integer 5

Unlisted keyword is not an error just a notification, if the keyword is unlisted you have to declare the type in this case you did (integer), but you still get the notification.

the last error is a missing file
/usr/local/Elmer-devel/share/elmersolver/lib/Scattered2DDataInterpolator.so: cannot open shared object file: No such file or directory

chivier · Post by **chivier** » 26 Apr 2020, 14:26

Thanks, I compiled Scattered2DDataInterpolator manually. However, there is still some confusing problems:

Code: Select all

Scattered2DDataInterpolator: cannot open shared object file: No such file or directory
Scattered2DDataInterpolator.so: cannot open shared object file: No such file or directory
./Scattered2DDataInterpolator: cannot open shared object file: No such file or directory
./Scattered2DDataInterpolator.so: cannot open shared object file: No such file or directory
libnetcdff.so.6: cannot open shared object file: No such file or directory
libnetcdff.so.6: cannot open shared object file: No such file or directory

I do not understand why it cannot find this library.
First, I have installed libnetcdff before. And I can find them in `/usr/local/lib`.

Code: Select all

$ find netcdff  
./include/CMakeFiles/netcdff.dir
./lib/libnetcdff.so
./lib/libnetcdff.la
./lib/libnetcdff.so.6.1.1
./lib/libnetcdff.so.6
./lib/libnetcdff.a

Besides, I have no idea when I used the library. I cannot find any words like 'netcdf' in the '*.sif' file.

kevinarden · Post by **kevinarden** » 26 Apr 2020, 14:56

you don't refer to netcdf in the sif but it is a library to write and read files, particularly scientific data files.

the application is not finding libraries in /usr/local

https://stackoverflow.com/questions/178 ... -not-found

chivier · Post by **chivier** » 26 Apr 2020, 15:14

Thanks a lot!

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