Known issues and fixes

The postprocessor in Peacock doesn't work

See this thread: https://groups.google.com/forum/#!topic/moose-users/VzU3yapallM

To fix, uninstall PyQt4.

OSX:

sudo conda uninstall pyqt

Linux/VM:

cd ~/../../opt/moose/miniconda
sudo ./conda uninstall pyqt

MPI error

If you see an MPI error like this one (obtained on a Mac) when running a moose or redback simulation:

Fatal error in MPI_Init_thread: Other MPI error, error stack:
MPIR_Init_thread(498)..............: 
MPID_Init(187).....................: channel initialization failed
MPIDI_CH3_Init(89).................: 
MPID_nem_init(320).................: 
MPID_nem_tcp_init(171).............: 
MPID_nem_tcp_get_business_card(418): 
MPID_nem_tcp_init(377).............: gethostbyname failed, boquier-ri (errno 1)

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 42430 RUNNING AT boquier-ri
=   EXIT CODE: 1
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================

A working solution (even though not the best or cleanest, so please help improve if you can) is to edit the file /etc/hosts (sudo vi /etc/hosts) and replace the name localhost in the line 127.0.0.1 localhost with the name of your machine, which you can find in the error message displayed above (in my case boquier-ri). In practise you should keep the line and simply comment it with a # sign, giving you the following content

(...)
#127.0.0.1       boquier-ri
127.0.0.1       localhost
(...)

Use_displaced_mesh

This bool can be true or false. It is used in materials, kernels, boundary conditions, postprocessors. It has to be turned on for running NS simulations on a displaced mesh. It has to be turned off to run simulations of mechanics (using displacement as main variables).

WHY ?

Running Redback in debug mode

Running Redback in debug mode is useful to debug some issues.

• The starting page to learn about running Moose in debug mode is http://mooseframework.org/wiki/MooseExamples/Example_21/
• You might want to go through a LLDB tutorial (e.g. https://lldb.llvm.org/tutorial.html)

In short, here are some of the main commands you might need:

• to compile Redback in debug mode: METHOD=dbg make -j8
• to run all tests from the Redback directory: ./run_tests --dbg -j8
• to run specific tests only: ./run_tests --dbg --re 3_M
• to run a given test in debug mode, from that test input file directory: lldb -- ../../redback-dbg -i bench_THM_DP.i (note that you might need to use sudo if you get an "unable to attach" error)
  • you can then set a breakpoint with: breakpoint set -n libmesh_handleFPE
  • type r to run
  • type frame variable to see all variables and their values at that point
  • type bt to see a backtrace
• to find the line number from RedbackMaterial::computeRedbackTerms() + 9435 for instance, see this webpage. Basically, type the following 2 commands:
  • image lookup -v -F "RedbackMaterial::computeRedbackTerms" to find range = [0x0000000100186370-0x00000001001891d9)
  • source list -a `0x0000000100186370 + 9435`