Moose install troubleshooting help
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Chris Thompson
Dec 31, 2019, 11:53:14 AM12/31/19
to moose-users
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.
Thank you,
Chris
Fande Kong
Jan 2, 2020, 6:30:11 PM1/2/20
to PETSc users list, thomp...@gmail.com, moose...@googlegroups.com, Satish Balay
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,
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Chris Thompson
Jan 2, 2020, 6:52:26 PM1/2/20
to moose-users
Absolutely, and thank you for looking. The log file should be attached to this post.
Cheers,
Chris
Fande,
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Jason Miller
Jan 6, 2020, 9:14:29 AM1/6/20
to moose...@googlegroups.com
I am seeing an interesting path within the configure.log. You are following the HPC instructions, but it would appear, the installation is going to install PETSc into /usr/local/neapps/moose/, is this correct? This location will need to be available to every node on your cluster. I am not saying that it is not, but normally, /usr/ is a private location, not shared amongst each node. If it shared, please ignore this email :)
On the other hand, the place where all the building is taking place, does indeed look like a location available to all nodes:
/nfs/depot/nerc_a1/neapps/rhel5/moose
Not an answer to your issue, but just something that ultimately may derail your HPC install if we do not address it.
Cheers!
Jason
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Chris Thompson
Jan 6, 2020, 12:42:33 PM1/6/20
to moose-users
Jason,
Thanks for taking a look at my post/e-mail.
To answer your question, yes /usr/local/neapps = /nfs/depot/nerc_a1/neapps. The alias is set during login for all systems, including the HPC systems.
Cheers,
Chris
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