Creating stl files

There are more than one ways, my prefered workflow is to draw the geometry in any CAD programm, export it as step file and meshing it with netgen.
(this is how to have more control over the triangle-size, I usually use max-elementsize=min-elementsize+1 to have equilateral tris, bc. most cad programms produces triangles with a high aspect ratio which is bad for parallelisation and leads to curvature errors in wall-contact-modell)
Another way is to use paraview sources (plane, circle, cylinder ..) and to export them as vtk file (bc. the save as stl file export function in PV is totaly crap) and than use gmesh

gmsh -2 -o outfile.stl infile.vtk

to remesh it as nice stl.

Many 3D cad programs don't have the ability to save surface modells as STL (I know Autodesk Inventor can only save volumes as stl meshes). The "normal" (means not academic) Version of solidworks can save surface modells als STL. The problem is, that the resulting mesh is in bad quality for LIGGGHTS(R) (high aspect ratio, bad curvature -> bad to parallize). The best workflow is to save as STEP file (almost every 3d cad programm I know can export surfaces as step file) and than mesh it with netgen (with OCC enabled) and save as stl.

This seems to be related to graphic card driver / system libs / 32bit vs 64bit libraries .. google "X Error of failed request: BadValue (integer parameter out of range for operation)" to find some hints ..
I would compile netgen from source (which is pain with occ enabled, but possible (I did it under fedora))
Do you have a radeon or a NVIDIA GPU ? Is it netgen 4 or 5 ? (I'm asking bc. the path says 5.3.1 but the first stdout is 4.9.13 ? Maybe you mixed two versions ? (one by apt-get and one by download) and started the systemwide netgen from /usr/bin/ instead the executable from download directory ? Is it netgen x64 or i386 ?