Index: /issm/trunk-jpl/src/m/coordsystems/epsg2proj.py =================================================================== --- /issm/trunk-jpl/src/m/coordsystems/epsg2proj.py (revision 27118) +++ /issm/trunk-jpl/src/m/coordsystems/epsg2proj.py (revision 27119) @@ -2,6 +2,6 @@ -def epsg2proj(epsg): #{{{ - """EPSG2PROJ - uses gdalsrsinfo to provide PROJ.4 compatible string +def epsg2proj(epsg): #{{{ + """EPSG2PROJ - uses gdalsrsinfo to provide PROJ.4 compatible string from EPSG code @@ -21,5 +21,5 @@ #First, get GDAL version subproc_args = "gdalsrsinfo --version | awk '{print $2}' | cut -d '.' -f1" - subproc = subprocess.Popen(subproc_args, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + subproc = subprocess.Popen(subproc_args, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True) outs, errs = subproc.communicate() if errs != '': @@ -29,5 +29,5 @@ subproc_args = "gdalsrsinfo epsg:{} | command grep PROJ.4 | tr -d '\n' | sed 's/PROJ.4 : //'".format(epsg) - subproc = subprocess.Popen(subproc_args, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + subproc = subprocess.Popen(subproc_args, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True) outs, errs = subproc.communicate() if errs != '': @@ -35,5 +35,5 @@ if version_major == 1: - r = r[1:-1] + outs = outs[1:-1] return outs Index: /issm/trunk-jpl/src/m/coordsystems/gdaltransform.py =================================================================== --- /issm/trunk-jpl/src/m/coordsystems/gdaltransform.py (revision 27118) +++ /issm/trunk-jpl/src/m/coordsystems/gdaltransform.py (revision 27119) @@ -46,5 +46,5 @@ subproc_args = shlex.split("gdaltransform -s_srs '{}' -t_srs '{}'".format(proj_in, proj_out)) - subproc = subprocess.Popen(subproc_args, bufsize=-1, stdin=file_in, stdout=file_out, stderr=subprocess.PIPE, close_fds=True) + subproc = subprocess.Popen(subproc_args, bufsize=-1, stdin=file_in, stdout=file_out, stderr=subprocess.PIPE, close_fds=True, universal_newlines=True) outs, errs = subproc.communicate() if errs != '': Index: /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.py =================================================================== --- /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.py (revision 27118) +++ /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.py (revision 27119) @@ -1,6 +1,4 @@ import subprocess - import numpy as np - from MatlabFuncs import * from mesh3dsurface import * @@ -26,8 +24,7 @@ # Get Gmsh version subproc_args = 'gmsh -info 2>&1 | command grep \'Version\' | sed -e \'s/Version[[:blank:]]*:[[:blank:]]//\' | cut -d \'.\' -f1' - subproc = subprocess.Popen(subproc_args, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + subproc = subprocess.Popen(subproc_args, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True) outs, errs = subproc.communicate() - - if ((not isinstance(errs,bytes)) & (errs != '')) or (isinstance(errs,bytes) & (errs.decode() != '')): + if ((not isinstance(errs, bytes)) & (errs != '')) or (isinstance(errs, bytes) & (errs.decode() != '')): raise Exception('gmshplanet: call to gmsh failed: {}'.format(errs)) gmshmajorversion = int(outs) @@ -51,9 +48,9 @@ # # NOTE: - # - The default format in Gmsh 3 is "msh2". Rather than conditionally - # modifying our parsing scheme for Gmsh 4, for now, we simply set the + # - The default format in Gmsh 3 is "msh2". Rather than conditionally + # modifying our parsing scheme for Gmsh 4, for now, we simply set the # 'Mesh.MshFileVersion' option. - # - Decreasing the value of the 'Mesh.RandomFactor' option leads to an - # equal number of nodes and elements being produced under macOS and Linux + # - Decreasing the value of the 'Mesh.RandomFactor' option leads to an + # equal number of nodes and elements being produced under macOS and Linux # at certain resolutions using certain meshing algorithms. # @@ -126,12 +123,18 @@ for i in range(meshini.numberofelements): fid.write('ST(%g,%g,%g,%g,%g,%g,%g,%g,%g){%g,%g,%g};\n' - % (meshini.x[meshini.elements[i, 0]-1], meshini.y[meshini.elements[i, 0]-1], meshini.z[meshini.elements[i, 0]-1], - meshini.x[meshini.elements[i, 1]-1], meshini.y[meshini.elements[i, 1]-1], meshini.z[meshini.elements[i, 1]-1], - meshini.x[meshini.elements[i, 2]-1], meshini.y[meshini.elements[i, 2]-1], meshini.z[meshini.elements[i, 2]-1], - metric[meshini.elements[i, 0]-1], metric[meshini.elements[i, 1]-1], metric[meshini.elements[i, 2]-1])) + % (meshini.x[meshini.elements[i, 0] - 1], meshini.y[meshini.elements[i, 0] - 1], meshini.z[meshini.elements[i, 0] - 1], + meshini.x[meshini.elements[i, 1] - 1], meshini.y[meshini.elements[i, 1] - 1], meshini.z[meshini.elements[i, 1] - 1], + meshini.x[meshini.elements[i, 2] - 1], meshini.y[meshini.elements[i, 2] - 1], meshini.z[meshini.elements[i, 2] - 1], + metric[meshini.elements[i, 0] - 1], metric[meshini.elements[i, 1] - 1], metric[meshini.elements[i, 2] - 1])) fid.write('};\n') fid.close() #}}} + # Call gmsh + # + # NOTE: The default format in Gmsh 3 is "msh2". Rather than conditionally + # modifying our parsing scheme for Gmsh 4, for now, we simply set the + # "-format" option. + # if options.exist('refine'): subprocess.call('gmsh -2 sphere.geo -bgm sphere.pos', shell=True) @@ -187,5 +190,5 @@ #}}} - # A little technicality here. The mesh is not exactly on the sphere. We + # A little technicality here. The mesh is not exactly on the sphere. We # create lat,long coordiantes, and reproject onto an exact sphere. mesh.r = np.sqrt(mesh.x ** 2 + mesh.y ** 2 + mesh.z ** 2) Index: /issm/trunk-jpl/src/m/solve/waitonlock.py =================================================================== --- /issm/trunk-jpl/src/m/solve/waitonlock.py (revision 27118) +++ /issm/trunk-jpl/src/m/solve/waitonlock.py (revision 27119) @@ -11,6 +11,6 @@ """WAITONLOCK - wait for a file - This routine will return when a file named 'lockfilename' is written to - disk. Also check for outlog file because it might be written several + This routine will return when a file named 'lockfilename' is written to + disk. Also check for outlog file because it might be written several seconds after the lock file. @@ -21,5 +21,5 @@ TODO: - - Uncomment import of localpfe and check on cluster type once localpfe.py + - Uncomment import of localpfe and check on cluster type once localpfe.py has been translated from localpfe.m. """ @@ -79,12 +79,13 @@ sys.stdout.write('\rchecking for job completion (time: {} min {} sec) '.format(floor(elapsedtime / 60), floor(rem(elapsedtime, 60)))) # TODO: After Python 2 is deprecated, we can change this call to print([...], end='') elapsedtime = elapsedtime / 60 # Converts time from sec to min - subproc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) - outs, errs = subproc.communicate() # NOTE: Need to consume output before checking return code + subproc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True) + outs, errs = subproc.communicate() # NOTE: Need to consume output before checking return code # TODO: Debug the following check under Linux (exits after first iteration with errs = "b") # UPDATE: Works in testing under Debian Linux system. Leaving comment for now so that it is easier to backtrace this issue if someone else encounters it. + # FIXED: comunicates returns stuff in bytes in Python 3 unless you set "universal_newlines=True" # - #if errs != '': - # raise Exception('waitonlock: check for existence of files failed: {}'.format(errs)) + if errs != '': + raise Exception('waitonlock: check for existence of files failed: {}'.format(errs)) ispresent = not subproc.returncode if ispresent: