Writing XDMF in parallel computing

General
1

Hi, I am trying to use parallel computing method and write a XDMF file as a result.

from dolfin import *
import math
from mpi4py import MPI

comm = MPI.COMM_WORLD

height = 1.
width = 1.

t        = Constant(0.0)

set_log_level(30)

parameters["form_compiler"]["cpp_optimize"] = True
parameters["form_compiler"]["representation"] = "uflacs"
parameters["form_compiler"]["cpp_optimize_flags"] = "-O3 -ffast-math -march=native"
parameters["form_compiler"]["quadrature_degree"] = 2

mesh = Mesh()
mesh = BoxMesh(comm, Point(0,0,0), Point(width,height,width), 10, 10, 10)
x = SpatialCoordinate(mesh)
ELEMENT = VectorElement("Lagrange", mesh.ufl_cell(), 1)
FS = FunctionSpace(mesh, ELEMENT)
wtest = TestFunction(FS)
w = Function(FS)
dw = TrialFunction(FS)

output_file = XDMFFile(comm, "output.xdmf")
output_file.parameters["flush_output"] = True
output_file.parameters["functions_share_mesh"] = True
u_v = project(w,FS)
u_v.rename("disp", "Displacement")
output_file.write(u_v, float(t))
output_file.close()

compiled it with: mpirun -n 4 python3 (filename).py
but an errors occur like this:

HDF5-DIAG: Error detected in HDF5 (1.10.7) MPI-process 0:
  #000: ../../../src/H5F.c line 366 in H5Fcreate(): unable to create file
    major: File accessibility
    minor: Unable to open file
  #001: ../../../src/H5Fint.c line 1713 in H5F_open(): unable to lock the file
    major: File accessibility
    minor: Unable to lock file
  #002: ../../../src/H5FD.c line 1675 in H5FD_lock(): driver lock request failed
    major: Virtual File Layer
    minor: Unable to lock file
  #003: ../../../src/H5FDsec2.c line 990 in H5FD__sec2_lock(): unable to lock file, errno = 11, error message = 'Resource temporarily unavailable'
    major: Virtual File Layer
    minor: Unable to lock file
HDF5-DIAG: Error detected in HDF5 (1.10.7) MPI-process 0:
  #000: ../../../src/H5F.c line 366 in H5Fcreate(): unable to create file
    major: File accessibility
    minor: Unable to open file
  #001: ../../../src/H5Fint.c line 1713 in H5F_open(): unable to lock the file
    major: File accessibility
    minor: Unable to lock file
  #002: ../../../src/H5FD.c line 1675 in H5FD_lock(): driver lock request failed
    major: Virtual File Layer
    minor: Unable to lock file
  #003: ../../../src/H5FDsec2.c line 990 in H5FD__sec2_lock(): unable to lock file, errno = 11, error message = 'Resource temporarily unavailable'
    major: Virtual File Layer
    minor: Unable to lock file

befor I ran the code, there is no file on the directory.
I think output.xdmf and output.h5 files were well generated because I could open the xdmf file in paraview, but I don’t know why the errors occur.
Thank you.

2

I cannot reproduce this with the ghcr.io/scientificcomputing/fenics-gmsh:2024-05-30 docker image.

I would try:

  1. Set "flush_output" to False. Does that help?

Secondly, how did you install dolfin on your system?

3

Hi dokken,

  1. It also makes errors.
HDF5-DIAG: Error detected in HDF5 (1.10.7) MPI-process 0:
  #000: ../../../src/H5F.c line 366 in H5Fcreate(): unable to create file
    major: File accessibility
HDF5-DIAG: Error detected in HDF5 (1.10.7) MPI-process     minor: Unable to open file
  #001: 0:
  #000: ../../../src/H5F.c ../../../src/H5Fint.c line 1713 in H5F_open()line 366 in H5Fcreate(): unable to create file
    m: unable to lock the file
    major: File accessibility
    miajor: File accessibility
    minor: Unable to open file
nor: Unable to lock file
  #002  #001: ../../../src/H5Fint.c line 1713: ../../../src/H5FD.c line 1675 in  in H5F_open(): unable to lock the file
    major:H5FD_lock(): driver lock request failed
    major:  File accessibility
    minor: Unable to lock file
  #Virtual File Layer
    minor: Unable to lock file
  #002: ../../../src/H5FD.c line 1675 in H5FD_lock(): 003: ../../../src/H5FDsec2.c line 990 in H5FD__sec2_lock(): unable to lock file, errno = 11, error message = 'Resource temporarily unavailable'
    majodriver lock request failed
    major: Virtual File Layer
    minor: Unable to lock file
  #003: ../../../src/H5FDsec2.c line r: Virtual File Layer
    minor: Unable to lock file
990 in H5FD__sec2_lock(): unable to lock file, errno = 11, error message = 'Resource temporarily unavailable'
    major: Virtual File Layer
    minor: Unable to lock file
  1. I use fenics (2019.2.0.13.dev0) in ubuntu system. I am not using doker now. I think I should re-install fenics.
    + I updated fenics to 2019.2.0.64.dev0 but it makes same errors.
4

To me, this seems like you are having issues with the file system you are running this code at, as you are not able to lock the file.
See for instance: OSError: Unable to open file (unable to lock file, errno = 37, error message = 'No locks available') · Issue #1101 · h5py/h5py · GitHub for possible workarounds

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