cffi.verificationerror:compileError:command'x86_64-conda-linux-gnu-cc'failed with exit code1 while using singularity

General
1

I met this problem when using dolfinx to solve the example navier-stokes cylinder code in singularity image.Here are the full info：

Info    : Meshing 1D...
Info    : [  0%] Meshing curve 1 (Line)
Info    : [ 20%] Meshing curve 2 (Line)
Info    : [ 40%] Meshing curve 3 (Line)
Info    : [ 60%] Meshing curve 4 (Line)
Info    : [ 80%] Meshing curve 5 (Ellipse)
Info    : Done meshing 1D (Wall 0.0153243s, CPU 0.015318s)
Info    : Meshing 2D...
Info    : Meshing surface 1 (Plane, Frontal-Delaunay for Quads)
Info    : Simple recombination completed (Wall 0.00701936s, CPU 0.001787s): 103 quads, 16 triangles, 0 invalid quads, 0 quads with Q < 0.1, avg Q = 0.82361, min Q = 0.425555
Info    : Simple recombination completed (Wall 0.00738811s, CPU 0.007389s): 460 quads, 0 triangles, 0 invalid quads, 0 quads with Q < 0.1, avg Q = 0.865979, min Q = 0.499255
Info    : Done meshing 2D (Wall 0.0314113s, CPU 0.017752s)
Info    : Refining mesh...
Info    : Meshing order 2 (curvilinear on)...
Info    : [  0%] Meshing curve 1 order 2
Info    : [ 20%] Meshing curve 2 order 2
Info    : [ 40%] Meshing curve 3 order 2
Info    : [ 50%] Meshing curve 4 order 2
Info    : [ 70%] Meshing curve 5 order 2
Info    : [ 90%] Meshing surface 1 order 2
Info    : Done meshing order 2 (Wall 0.00410315s, CPU 0.004102s)
Info    : Done refining mesh (Wall 0.00449388s, CPU 0.004493s)
Info    : 1952 nodes 2069 elements
Info    : Meshing order 2 (curvilinear on)...
Info    : [  0%] Meshing curve 1 order 2
Info    : [ 20%] Meshing curve 2 order 2
Info    : [ 40%] Meshing curve 3 order 2
Info    : [ 50%] Meshing curve 4 order 2
Info    : [ 70%] Meshing curve 5 order 2
Info    : [ 90%] Meshing surface 1 order 2
Info    : Done meshing order 2 (Wall 0.0181345s, CPU 0.018131s)
Info    : Optimizing mesh (Netgen)...
Info    : Done optimizing mesh (Wall 1.43936e-06s, CPU 4e-06s)
In file included from libffcx_elements_176c32e09ce7bc0aaf86ff2f49da2c5de8ae012e.c:50:
/usr/include/python3.10/pyconfig.h:3:12: fatal error: x86_64-linux-gnu/python3.10/pyconfig.h: No such file or directory
    3 | #  include <x86_64-linux-gnu/python3.10/pyconfig.h>
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
Traceback (most recent call last):
  File "/usr/lib/python3.10/distutils/unixccompiler.py", line 117, in _compile
    self.spawn(compiler_so + cc_args + [src, '-o', obj] +
  File "/usr/lib/python3.10/distutils/ccompiler.py", line 910, in spawn
    spawn(cmd, dry_run=self.dry_run)
  File "/usr/lib/python3.10/distutils/spawn.py", line 91, in spawn
    raise DistutilsExecError(
distutils.errors.DistutilsExecError: command '/home/wulong/anaconda3/envs/drl/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.10/dist-packages/cffi/ffiplatform.py", line 51, in _build
    dist.run_command('build_ext')
  File "/usr/lib/python3.10/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/lib/python3.10/distutils/command/build_ext.py", line 340, in run
    self.build_extensions()
  File "/usr/lib/python3.10/distutils/command/build_ext.py", line 449, in build_extensions
    self._build_extensions_serial()
  File "/usr/lib/python3.10/distutils/command/build_ext.py", line 474, in _build_extensions_serial
    self.build_extension(ext)
  File "/usr/lib/python3.10/distutils/command/build_ext.py", line 529, in build_extension
    objects = self.compiler.compile(sources,
  File "/usr/lib/python3.10/distutils/ccompiler.py", line 574, in compile
    self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
  File "/usr/lib/python3.10/distutils/unixccompiler.py", line 120, in _compile
    raise CompileError(msg)
distutils.errors.CompileError: command '/home/wulong/anaconda3/envs/drl/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1

What should I do to cope with it.

2

You would need to be more specific.
What have you based your singularity image on?
It seems like it is based of conda, considering

thus you would need to provide your conda-recipe.

3

I pull this singularity image from docker.

singularity pull dolfinx/dolfinx

And conda is not installed in this image.

4

Then your error message does not make sense (as it clearly points to your conda-env)
Please also note that you should pull dolfinx/dolfinx with a tag at the end, as latest is not longer updated. Use either dolfinx/dolfinx:v0.6.0-r1 or dolfinx/dolfinx:stable

5

Should I install conda in image?

Then your error message does not make sense (as it clearly points to your conda-env)

6

No, I wouldn’t do that. Please state all the steps you are doing, from pull the image to running the code.

7

Thanks for your reply ，everything went as expected after pulling dolfinx/dolfinx:stable