Installation error

Issue #18 invalid
Murat Keceli created an issue

I got the following error during installation after pulling the latest changes:

running build_ext
SLEPC_DIR:   /home/keceli/2015/slepc
PETSC_DIR:   /home/keceli/2015/petsc
PETSC_ARCH:  arch-gccpetsc4py
version:     3.6.1 development
scalar-type: real
precision:   double
language:    CONLY
compiler:    mpicc
linker:      mpicc
Traceback (most recent call last):
  File "setup.py", line 256, in <module>
    main()
  File "setup.py", line 253, in main
    run_setup()
  File "setup.py", line 134, in run_setup
    **setup_args)
  File "/bgsys/tools/Python-2.6/lib64/python2.6/distutils/core.py", line 152, in setup
    dist.run_commands()
  File "/bgsys/tools/Python-2.6/lib64/python2.6/distutils/dist.py", line 975, in run_commands
    self.run_command(cmd)
  File "/bgsys/tools/Python-2.6/lib64/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/gpfs/vesta-home/keceli/2015/slepc4py/conf/baseconf.py", line 563, in run
    _install.run(self)
  File "/bgsys/tools/Python-2.6/lib64/python2.6/distutils/command/install.py", line 577, in run
    self.run_command('build')
  File "/bgsys/tools/Python-2.6/lib64/python2.6/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/bgsys/tools/Python-2.6/lib64/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/bgsys/tools/Python-2.6/lib64/python2.6/distutils/command/build.py", line 134, in run
    self.run_command(cmd_name)
  File "/bgsys/tools/Python-2.6/lib64/python2.6/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/bgsys/tools/Python-2.6/lib64/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/bgsys/tools/Python-2.6/lib64/python2.6/distutils/command/build_ext.py", line 340, in run
    self.build_extensions()
  File "/gpfs/vesta-home/keceli/2015/slepc4py/conf/baseconf.py", line 512, in build_extensions
    _build_ext.build_extensions(self, *args,**kargs)
  File "/bgsys/tools/Python-2.6/lib64/python2.6/distutils/command/build_ext.py", line 449, in build_extensions
    self.build_extension(ext)
  File "/gpfs/vesta-home/keceli/2015/slepc4py/conf/baseconf.py", line 504, in build_extension
    config.configure(newext, self.compiler)
  File "/gpfs/vesta-home/keceli/2015/slepc4py/conf/baseconf.py", line 114, in configure
    self.configure_extension(extension)
  File "/gpfs/vesta-home/keceli/2015/slepc4py/conf/slepcconf.py", line 70, in configure_extension
    PETSc = ImportPETSc(PETSC_ARCH)
  File "/home/keceli/.local/lib64/python2.6/site-packages/petsc4py/lib/__init__.py", line 29, in ImportPETSc
    return Import('petsc4py', 'PETSc', path, arch)
  File "/home/keceli/.local/lib64/python2.6/site-packages/petsc4py/lib/__init__.py", line 64, in Import
    module = imp.load_module(fullname, fo, fn, stuff)
ImportError: /home/keceli/.local/lib64/python2.6/site-packages/petsc4py/lib/arch-gccpetsc4py/PETSc.so: undefined symbol: DMShellSetCreateSubDM

Thanks in advance for any help.

Comments (4)

  1. Lisandro Dalcin

    I guess you are trying to build the latest in-development petsc4py without updating your copy of the in-development PETSc. So please try to cd /home/keceli/2015/petsc && git pull && make and let me know if that solved your issue.

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