I changed my mesh to have two 'Physical Lines' using GMSH instead of one and changed the boundary conditions in the sif file accordingly (see below).

! lateral side of the glacier

Boundary Condition 1

Target Boundaries = 1

Velocity 1 = real 0.0

Velocity 2 = real 0.0

End

! the other sides

Boundary Condition 2

Target Boundaries = 2

Velocity 1 = real 0.0

Velocity 2 = real 0.0

End

! Bedrock

Boundary Condition 3

Bottom Surface = Equals BedDEM

!--------------------------------------------

! --------- No sliding

Velocity 1 = Real 0.0

Velocity 2 = Real 0.0

Velocity 3 = Real 0.0

!----------- OR -----------------------------

! --------- Sliding

! Normal-Tangential Velocity = Logical True

! Velocity 1 = Real 0.0e0

! Slip Coefficient 2 = Real 0.1

! Slip Coefficient 3 = Real 0.1

!--------------------------------------------

End

! Upper Surface

Boundary Condition 4

Top Surface = Equals ZsDEM

End

I had no issues running ElmerGrid and I can ran the diagnostic sif file without any issues. However, when I try to run the diagnostic sif file, I get the error below.

LoadInputFile: Number of BCs: 4

LoadInputFile: Number of Body Forces: 2

LoadInputFile: Number of Initial Conditions: 3

WARNING:: LoadInputFile: Entry missing for: Initial Condition 1

LoadInputFile: Number of Materials: 1

LoadInputFile: Number of Equations: 2

LoadInputFile: Number of Solvers: 6

LoadInputFile: Number of Bodies: 2

MAIN:

MAIN: -------------------------------------

MAIN: Time: 1/50: 2.738E-02

MAIN: -------------------------------------

MAIN:

ERROR:: StructuredMeshMapper: Top surface variable perm is zero!

STOP 1

I have tried generating my mesh differently (using splines and line), but that doesn't seem to be the problem. I can't find any other documentation on what this means. Any ideas?