[petsc-users] Fwd: Moose install troubleshooting help

Thu Jan 2 20:04:29 CST 2020

On Thu, Jan 2, 2020 at 6:31 PM Fande Kong <fdkong.jd at gmail.com> wrote:

>
> Satish,
>
> Do you have any suggestions for this?
>
> Chris,
>
> It may be helpful if you could share the petsc configuration log file with
> us?
>
>
>
> Fande,
>
> ---------- Forwarded message ---------
> From: Chris Thompson <thompsoc91 at gmail.com>
> Date: Tue, Dec 31, 2019 at 9:53 AM
> Subject: Moose install troubleshooting help
> To: moose-users <moose-users at googlegroups.com>
>
>
> Dear All,
> I could use some help or a pointer in the right direction.
>
> I have been following the directions at
> https://mooseframework.inl.gov/getting_started/installation/hpc_install_moose.html
> All was going well until "make PETSC_DIR=$STACK_SRC/petsc-3.11.4
> PETSC_ARCH=linux-opt install".  I tried running "make --debug=v
> PETSC_DIR=$STACK_SRC/petsc-3.11.4 PETSC_ARCH=linux-opt install", but that
> didn't produce any more helpful information.
>
> This on a CentOS system running 7.6
>
> Here is the error / output I am getting.
>
> rogue /usr/local/neapps/moose/stack_temp/petsc-3.11.4 926$ make --debug=v
> PETSC_DIR=/usr/local/neapps/moose/stack_temp/petsc-3.11.4
> PETSC_ARCH=linux-opt install
> GNU Make 3.82
> Built for x86_64-redhat-linux-gnu
> Copyright (C) 2010  Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later <
> http://gnu.org/licenses/gpl.html>
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law.
> Reading makefiles...
> Reading makefile `makefile'...
> Reading makefile `linux-opt/lib/petsc/conf/petscvariables' (search path)
> (no ~ expansion)...
> Reading makefile
> `/usr/local/neapps/moose/stack_temp/petsc-3.11.4/lib/petsc/conf/variables'
> (search path) (no ~ expansion)...
> Reading makefile
> `/usr/local/neapps/moose/stack_temp/petsc-3.11.4/linux-opt/lib/petsc/conf/petscvariables'
> (search path) (no ~ expansion)...
> Reading makefile
> `/usr/local/neapps/moose/stack_temp/petsc-3.11.4/lib/petsc/conf/rules'
> (search path) (no ~ expansion)...
> Reading makefile
> `/usr/local/neapps/moose/stack_temp/petsc-3.11.4/linux-opt/lib/petsc/conf/petscrules'
> (search path) (no ~ expansion)...
> Reading makefile
> `/usr/local/neapps/moose/stack_temp/petsc-3.11.4/lib/petsc/conf/test.common'
> (search path) (no ~ expansion)...
> Updating goal targets....
> Considering target file `install'.
> File `install' does not exist.
>  Finished prerequisites of target file `install'.
> Must remake target `install'.
> Invoking recipe from makefile:250 to update target `install'.
> *** Using PETSC_DIR=/usr/local/neapps/moose/stack_temp/petsc-3.11.4
> PETSC_ARCH=linux-opt ***
> *** Installing PETSc at prefix location:
> /usr/local/neapps/moose/petsc-3.11.4  ***
> Traceback (most recent call last):
>   File "./config/install.py", line 434, in <module>
>     Installer(sys.argv[1:]).run()
>   File "./config/install.py", line 428, in run
>     self.runcopy()
>   File "./config/install.py", line 407, in runcopy
>     self.installIncludes()
>   File "./config/install.py", line 305, in installIncludes
>     self.copies.extend(self.copytree(self.rootIncludeDir,
> self.destIncludeDir,exclude = exclude))
>   File "./config/install.py", line 246, in copytree
>     raise shutil.Error(errors)
> shutil.Error:
> ['/usr/local/neapps/moose/stack_temp/petsc-3.11.4/include/petsc',
> '/usr/local/neapps/moose/petsc-3.11.4/include/petsc',
>  '[\'/usr/local/neapps/moose/stack_temp/petsc-3.11.4/include/petsc/private\',
> \'/usr/local/neapps/moose/petsc-3.11.4/include/petsc/private\',
>
>  \'[\\\'/usr/local/neapps/moose/stack_temp/petsc-3.11.4/include/petsc/private/kernels\\\',
>
>  \\\'/usr/local/neapps/moose/petsc-3.11.4/include/petsc/private/kernels\\\',
>
>  \\\'[\\\\\\\'/usr/local/neapps/moose/stack_temp/petsc-3.11.4/include/petsc/private/kernels\\\\\\\',
>
>  \\\\\\\'/usr/local/neapps/moose/petsc-3.11.4/include/petsc/private/kernels\\\\\\\',
>  "[Errno 1] Operation not permitted:
> \\\\\\\'/usr/local/neapps/moose/petsc-3.11.4/include/petsc/private/kernels\\\\\\\'"]\\\',
>  \\\'/usr/local/neapps/moose/stack_temp/petsc-3.11.4/include/petsc/private\\\',
> \\\'/usr/local/neapps/moose/petsc-3.11.4/include/petsc/private\\\',
>  "[Errno 1] Operation not permitted:
> \\\'/usr/local/neapps/moose/petsc-3.11.4/include/petsc/private\\\'"]\',
>  \'/usr/local/neapps/moose/stack_temp/petsc-3.11.4/include/petsc/finclude\',
> \'/usr/local/neapps/moose/petsc-3.11.4/include/petsc/finclude\',
>  \'[\\\'/usr/local/neapps/moose/stack_temp/petsc-3.11.4/include/petsc/finclude\\\',
> \\\'/usr/local/neapps/moose/petsc-3.11.4/include/petsc/finclude\\\',
>  "[Errno 1] Operation not permitted:
> \\\'/usr/local/neapps/moose/petsc-3.11.4/include/petsc/finclude\\\'"]\',
> \'/usr/local/neapps/moose/stack_temp/petsc-3.11.4/include/petsc\',
>  \'/usr/local/neapps/moose/petsc-3.11.4/include/petsc\', "[Errno 1]
> Operation not permitted:
> \'/usr/local/neapps/moose/petsc-3.11.4/include/petsc\'"]',
>  '/usr/local/neapps/moose/stack_temp/petsc-3.11.4/include',
> '/usr/local/neapps/moose/petsc-3.11.4/include', "[Errno 1] Operation not
> permitted: '/usr/local/neapps/moose/petsc-3.11.4/include'"]
> make: *** [install] Error 1
>
> I'm not sure how to proceed with this error.
>

It looks like you do not have permissions in the install directory. You may
want to run the install command using 'sudo'.

  Thanks,

     Matt

> Thank you,
> Chris
>
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-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

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