Dumbcheckpointing
Dear all, I saved a function h using DumbCheckpoint through: res = 0.1 Nx = int(Lx/res) + 1 Ny = int(Ly/res) + 1 hor_mesh = RectangleMesh(Nx,Ny,Lx,Ly,quadrilateral=True) V = FunctionSpace(hor_mesh, "CG", 1) h_n0 = Function(V) ... [assign value to h_n0] ... h_data = DumbCheckpoint("h", mode=FILE_CREATE) h_data.store(h_n0) When trying to load it in another code, with: res = 0.1 Nx = int(Lx/res) + 1 Ny = int(Ly/res) + 1 hor_mesh = RectangleMesh(Nx,Ny,Lx,Ly,quadrilateral=True) V = FunctionSpace(hor_mesh, "CG", 1) h_n1 = Function(V) dumb_file = DumbCheckpoint("h", mode=FILE_READ) dumb_file.load(h_n1) I get the following error: File "TOC.py", line 130, in <module> dumb_file.load(h_n1) File "/Users/mmfg/firedrake/src/firedrake/firedrake/checkpointing.py", line 237, in load v.load(self.vwr) File "PETSc/Vec.pyx", line 447, in petsc4py.PETSc.Vec.load (src/petsc4py.PETSc.c:95805) petsc4py.PETSc.Error: error code 76 [0] VecLoad() line 925 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/interface/vector.c [0] VecLoad_Default() line 397 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/utils/vecio.c [0] VecLoad_HDF5() line 257 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/utils/vecio.c [0] Error in external library [0] Error in HDF5 call H5Dopen2() Status -1 Exception RuntimeError: RuntimeError("Can't decrement id ref count (Can't close file, there are objects still open)",) in 'h5py._objects.ObjectID.__dealloc__' ignored Do you know what this error mean ? Thank you, Floriane
Update: after some tests, I found that the error only occur when I define another mesh in the same code. Do you know what's going wrong ? For instance: res = 0.1 Nx = int(Lx/res) + 1 Ny = int(Ly/res) + 1 hor_mesh = RectangleMesh(Nx,Ny,Lx,Ly,quadrilateral=True) V = FunctionSpace(hor_mesh, "CG", 1) h_n1 = Function(V) i=0 while i<100: dumb_file = DumbCheckpoint("h_"+str(i), mode=FILE_READ) dumb_file.load(h_n1) i+=1 works, but Nx_aux = int(Lx/0.2) + 1 Ny_aux = int(Ly/0.1) + 1 aux_mesh = RectangleMesh(Nx_aux,Ny_aux,Lx,Ly,quadrilateral=True) res = 0.1 Nx = int(Lx/res) + 1 Ny = int(Ly/res) + 1 hor_mesh = RectangleMesh(Nx,Ny,Lx,Ly,quadrilateral=True) V = FunctionSpace(hor_mesh, "CG", 1) h_n1 = Function(V) i=0 while i<100: dumb_file = DumbCheckpoint("h_"+str(i), mode=FILE_READ) dumb_file.load(h_n1) i+=1 does not work: Traceback (most recent call last): File "main.py", line 115, in <module> dumb_file.load(h_n1) File "/Users/mmfg/firedrake/src/firedrake/firedrake/checkpointing.py", line 237, in load v.load(self.vwr) File "PETSc/Vec.pyx", line 447, in petsc4py.PETSc.Vec.load (src/petsc4py.PETSc.c:95805) petsc4py.PETSc.Error: error code 76 [0] VecLoad() line 925 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/interface/vector.c [0] VecLoad_Default() line 397 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/utils/vecio.c [0] VecLoad_HDF5() line 257 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/utils/vecio.c [0] Error in external library [0] Error in HDF5 call H5Dopen2() Status -1 Exception RuntimeError: RuntimeError("Can't decrement id ref count (Can't close file, there are objects still open)",) in 'h5py._objects.ObjectID.__dealloc__' ignored ________________________________ De : firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> de la part de Floriane Gidel [RPG] <mmfg@leeds.ac.uk> Envoyé : vendredi 10 novembre 2017 19:04:12 À : firedrake Objet : [firedrake] Dumbcheckpointing Dear all, I saved a function h using DumbCheckpoint through: res = 0.1 Nx = int(Lx/res) + 1 Ny = int(Ly/res) + 1 hor_mesh = RectangleMesh(Nx,Ny,Lx,Ly,quadrilateral=True) V = FunctionSpace(hor_mesh, "CG", 1) h_n0 = Function(V) ... [assign value to h_n0] ... h_data = DumbCheckpoint("h", mode=FILE_CREATE) h_data.store(h_n0) When trying to load it in another code, with: res = 0.1 Nx = int(Lx/res) + 1 Ny = int(Ly/res) + 1 hor_mesh = RectangleMesh(Nx,Ny,Lx,Ly,quadrilateral=True) V = FunctionSpace(hor_mesh, "CG", 1) h_n1 = Function(V) dumb_file = DumbCheckpoint("h", mode=FILE_READ) dumb_file.load(h_n1) I get the following error: File "TOC.py", line 130, in <module> dumb_file.load(h_n1) File "/Users/mmfg/firedrake/src/firedrake/firedrake/checkpointing.py", line 237, in load v.load(self.vwr) File "PETSc/Vec.pyx", line 447, in petsc4py.PETSc.Vec.load (src/petsc4py.PETSc.c:95805) petsc4py.PETSc.Error: error code 76 [0] VecLoad() line 925 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/interface/vector.c [0] VecLoad_Default() line 397 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/utils/vecio.c [0] VecLoad_HDF5() line 257 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/utils/vecio.c [0] Error in external library [0] Error in HDF5 call H5Dopen2() Status -1 Exception RuntimeError: RuntimeError("Can't decrement id ref count (Can't close file, there are objects still open)",) in 'h5py._objects.ObjectID.__dealloc__' ignored Do you know what this error mean ? Thank you, Floriane
Problem solved by adding the functions' name: h_n0 = Function(V, name="h") Why is it not working without the name? Thanks, Floriane ________________________________ De : firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> de la part de Floriane Gidel [RPG] <mmfg@leeds.ac.uk> Envoyé : samedi 11 novembre 2017 10:34:55 À : firedrake Objet : Re: [firedrake] Dumbcheckpointing Update: after some tests, I found that the error only occur when I define another mesh in the same code. Do you know what's going wrong ? For instance: res = 0.1 Nx = int(Lx/res) + 1 Ny = int(Ly/res) + 1 hor_mesh = RectangleMesh(Nx,Ny,Lx,Ly,quadrilateral=True) V = FunctionSpace(hor_mesh, "CG", 1) h_n1 = Function(V) i=0 while i<100: dumb_file = DumbCheckpoint("h_"+str(i), mode=FILE_READ) dumb_file.load(h_n1) i+=1 works, but Nx_aux = int(Lx/0.2) + 1 Ny_aux = int(Ly/0.1) + 1 aux_mesh = RectangleMesh(Nx_aux,Ny_aux,Lx,Ly,quadrilateral=True) res = 0.1 Nx = int(Lx/res) + 1 Ny = int(Ly/res) + 1 hor_mesh = RectangleMesh(Nx,Ny,Lx,Ly,quadrilateral=True) V = FunctionSpace(hor_mesh, "CG", 1) h_n1 = Function(V) i=0 while i<100: dumb_file = DumbCheckpoint("h_"+str(i), mode=FILE_READ) dumb_file.load(h_n1) i+=1 does not work: Traceback (most recent call last): File "main.py", line 115, in <module> dumb_file.load(h_n1) File "/Users/mmfg/firedrake/src/firedrake/firedrake/checkpointing.py", line 237, in load v.load(self.vwr) File "PETSc/Vec.pyx", line 447, in petsc4py.PETSc.Vec.load (src/petsc4py.PETSc.c:95805) petsc4py.PETSc.Error: error code 76 [0] VecLoad() line 925 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/interface/vector.c [0] VecLoad_Default() line 397 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/utils/vecio.c [0] VecLoad_HDF5() line 257 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/utils/vecio.c [0] Error in external library [0] Error in HDF5 call H5Dopen2() Status -1 Exception RuntimeError: RuntimeError("Can't decrement id ref count (Can't close file, there are objects still open)",) in 'h5py._objects.ObjectID.__dealloc__' ignored ________________________________ De : firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> de la part de Floriane Gidel [RPG] <mmfg@leeds.ac.uk> Envoyé : vendredi 10 novembre 2017 19:04:12 À : firedrake Objet : [firedrake] Dumbcheckpointing Dear all, I saved a function h using DumbCheckpoint through: res = 0.1 Nx = int(Lx/res) + 1 Ny = int(Ly/res) + 1 hor_mesh = RectangleMesh(Nx,Ny,Lx,Ly,quadrilateral=True) V = FunctionSpace(hor_mesh, "CG", 1) h_n0 = Function(V) ... [assign value to h_n0] ... h_data = DumbCheckpoint("h", mode=FILE_CREATE) h_data.store(h_n0) When trying to load it in another code, with: res = 0.1 Nx = int(Lx/res) + 1 Ny = int(Ly/res) + 1 hor_mesh = RectangleMesh(Nx,Ny,Lx,Ly,quadrilateral=True) V = FunctionSpace(hor_mesh, "CG", 1) h_n1 = Function(V) dumb_file = DumbCheckpoint("h", mode=FILE_READ) dumb_file.load(h_n1) I get the following error: File "TOC.py", line 130, in <module> dumb_file.load(h_n1) File "/Users/mmfg/firedrake/src/firedrake/firedrake/checkpointing.py", line 237, in load v.load(self.vwr) File "PETSc/Vec.pyx", line 447, in petsc4py.PETSc.Vec.load (src/petsc4py.PETSc.c:95805) petsc4py.PETSc.Error: error code 76 [0] VecLoad() line 925 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/interface/vector.c [0] VecLoad_Default() line 397 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/utils/vecio.c [0] VecLoad_HDF5() line 257 in /private/var/folders/7h/wbj8xp7n3g5cfbr32ctcmwzcy3jf53/T/pip-yGXqPh-build/src/vec/vec/utils/vecio.c [0] Error in external library [0] Error in HDF5 call H5Dopen2() Status -1 Exception RuntimeError: RuntimeError("Can't decrement id ref count (Can't close file, there are objects still open)",) in 'h5py._objects.ObjectID.__dealloc__' ignored Do you know what this error mean ? Thank you, Floriane
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Floriane Gidel [RPG]