On Thu, Mar 27, 2014 at 10:25 AM, Seufzer, William J. (LARC-D307) <[email protected]> wrote: > Dan, > > We're not there yet. I got back to this issue late yesterday and the fix > doesn't work on my cluster. > > I added the code that was recommended at: The workaround: > https://gist.github.com/wd15/9693712 but it appears now that we hang on the > line: > > mesh = fp.Gmsh3D(mshFile)
Did you try just running that file independently from anything else? > As with reading the .geo file the cores are busy but after an hour the code > does not go past the mesh = .... command. I'm not sure what's going on, but can all the processes read the mshFile? Check that. It's odd that this works for me across nodes and not for you. Also when I run your original problem: import fipy as fp geoFile = 'tmsh3d.geo' mesh = fp.Gmsh3D(geoFile) mx,my,mz = mesh.getCellCenters() I get "IOError: [Errno 2] No such file or directory: '/tmp/tmpt49sGo.msh'". Did you actually get that error? > Question: If procID==0 runs gmsh to make the .msh file, why not just run > gmsh by hand (or script) and have the mesh file ready to go? Absolutely, just automating it away. > Is there a way to change FiPy so that the users disk space is used instead > of /tmp ? Then if one core creates the file all the cores, on various nodes, > will see it. Not FiPy, but just tell Python. I didn't think of that first time, but it is the simplest solution. http://docs.python.org/2/library/tempfile.html#tempfile.tempdir Just set 'tempfile.temdir" to a shared directory at the top of the script. I believe that will work for all uses of tempfile within the current Python session. This works for me across two nodes import tempfile tempfile.tempdir = './' import fipy as fp geoFile = 'tmsh3d.geo' mesh = fp.Gmsh3D(geoFile) mx,my,mz = mesh.getCellCenters() print mx Going forward, it would be nice to automate this. Probably always reset "tempdir" in parallel just to be safe. -- Daniel Wheeler _______________________________________________ fipy mailing list [email protected] http://www.ctcms.nist.gov/fipy [ NIST internal ONLY: https://email.nist.gov/mailman/listinfo/fipy ]
