Troubleshooting

Discussion Forum

If your issue can not be solved here, please submit your question to the MOOSE Discussion forum for help!

Conda Issues

Conda issues can be the root cause for just about any issue on this page. Scroll through this section, for what may look familiar, and follow those instructions:

• 404 error, The channel is not accessible or is invalid.

  If you are receiving this, you may be victim of us changing the channel name out from underneath you (Sorry!). Remove the offending channel(s):

  
  conda config --remove channels https://mooseframework.org/conda/moose
  conda config --remove channels https://mooseframework.com/conda/moose
  conda config --remove channels https://mooseframework.inl.gov/conda/moose
  

  If you receive errors about a channel not present (CondaKeyError), please ignore. You most likely will not have all three 'old' channels. Next, add the correct channel:

  
  conda config --add channels idaholab
  

  When you're finished, a conda config --show channels should resemble the following:

  
  $ conda config --show channels
  channels:
    - idaholab
    - conda-forge
    - defaults
  

• command not found: conda

  You have yet to install conda, or your path to it is incorrect or not set. You will need to recall how you installed conda. Our instructions ask to have Miniconda3 installed to your home directory: ~/miniconda3. Which requires you to set your PATH accordingly:

  
  export PATH=~/miniconda3/bin:$PATH
  

  With PATH set, try to run again, what ever command you were initially attempting.

• conda activate moose

  If conda activate moose is failing like so:

  
  CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
  To initialize your shell, run
  
      $ conda init <SHELL_NAME>
  
  Currently supported shells are:
    - bash
    - fish
    - tcsh
    - xonsh
    - zsh
    - powershell
  
  See 'conda init --help' for more information and options.
  
  IMPORTANT: You may need to close and restart your shell after running 'conda init'.
  

  ...it's possible you have yet to perform a conda init properly. See conda init below.

  It could also mean you have an older version of Conda, or that the environment you are trying to activate is somewhere other than where conda thinks it should be, or simply missing / not yet created. Unfortunately, much of what can be diagnosed, is going to be beyond the scope of this document, and better left to the support teams at Conda. What we can attempt, is to create a new environment and go from there:

  
  conda create --name testing --quiet --yes
  

  The above should create an empty environment. Try and activate it:

  
  conda activate testing
  

  If the above is asking you to initialize conda, see conda init below.

  If the command failed, or the conda create command before it, the error will likely be involved with how Conda was first installed (perhaps with sudo rights, or as another user). You should look into removing this installation of conda, and starting over with our Getting Started instructions. Failures of this nature can also mean your conda resource file (~/.condarc) is in bad shape. We have no way of diagnosing this in a troubleshooting fashion, as this file can contain more than just moose-related configs. For reference, the bare minimum should resemble the following:

  
  channels:
    - idaholab
    - conda-forge
    - defaults
  

• conda init

  If conda init is failing, or similarly doing nothing, it is possible that Conda simply does not know what shell you are operating in, and it created a 'configuration' for the wrong shell, or not at all.

  To figure out what shell you are operating in:

  
  echo $0
  

  What ever returns here, is the type of shell you are operating in, and is also what you should be instructing Conda to 'initialize'. Example:

  
  conda init zsh
  

  Hint: For Linux, this will most likely be conda init bash. For Macintosh, this can either be bash or zsh.

• Your issue not listed

  The quick fix-attempt, is to re-install the moose-packages:

  
  conda deactivate
  conda remove moose --all --yes
  conda create moose moose-libmesh moose-tools
  

  If the above re-install method ultimately failed, it is time to submit your errors to the discussion forum.

Build Issues

Build issues are normally caused by an invalid environment, or perhaps an update to your repository occurred, and you now have a mismatch between MOOSE and your application, or a combination of the two with the moose-libmesh Conda package being out of date.

• Verify the Conda Environment is active and up to date, with the latest version of our moose packages:

  
  conda activate moose
  conda update --all
  

  if conda activate moose failed, see Conda Issues above.

  commentnote

  When ever an update is performed in Conda, it is a good idea to re-build MOOSE and your application. While specific updates to moose-libmesh and/or moose-petsc may not have occurred, there are several other libraries out of our control which may have been upgraded, requiring you to rebuild.

• Verify the MOOSE repository is up to date, with the correct vetted version of libMesh:

  warningwarning

  Be sure you have committed/saved your work. The following commands will delete untracked files!

  
  cd moose
  git checkout master
  git clean -xfd
  
  <output snipped>
  
  git fetch upstream
  git pull
  git submodule update --init
  

• Verify you either have no moose directory set, or it is set correctly.

  
  [~] > echo $MOOSE_DIR
  
  [~] >
  

  The above should return nothing, or it should point to the correct moose repository.

  commentnote

  Most users, do not use or set MOOSE_DIR. If the above command returns something, and you are not sure why, just unset it:

  
  unset MOOSE_DIR
  

• Try building a simple hello world example (there is more text than what is visible, be sure to copy it all):

  
  cd /tmp
  cat << EOF > hello.C
  #include <mpi.h>
  #include <stdio.h>
  
  int main(int argc, char** argv) {
    // Initialize the MPI environment
    MPI_Init(NULL, NULL);
  
    // Get the number of processes
    int world_size;
    MPI_Comm_size(MPI_COMM_WORLD, &world_size);
  
    // Get the rank of the process
    int world_rank;
    MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);
  
    // Get the name of the processor
    char processor_name[MPI_MAX_PROCESSOR_NAME];
    int name_len;
    MPI_Get_processor_name(processor_name, &name_len);
  
    // Print off a hello world message
    printf("Hello world from processor %s, rank %d out of %d processors\n",
           processor_name, world_rank, world_size);
  
    // Finalize the MPI environment.
    MPI_Finalize();
  }
  EOF
  
  mpicxx -fopenmp hello.C
  

  If the above build fails, and you have the correct Conda environment loaded (conda activate moose), then something is failing beyond the scope of this document, and you should now contact us via the disussion forum.

  If the build was successfull, attempt to execute the hello word example:

  
  mpiexec -n 4 /tmp/a.out
  

  You should receive a response similar to the following:

  
  Hello world from processor my_hostname, rank 0 out of 4 processors
  Hello world from processor my_hostname, rank 1 out of 4 processors
  Hello world from processor my_hostname, rank 3 out of 4 processors
  Hello world from processor my_hostname, rank 2 out of 4 processors
  

• If all of the above has succeeded, you should attempt to rebuild MOOSE or your application again. If you've made it this far, and the above is working, but MOOSE fails to build, then it is time to ask us why on the discussion forum.

Failing Tests

If many, or all tests are failing, it is a good chance the fix is simple. Follow through these steps to narrow down the possible cause.

First, run a test that should always pass:

cd moose/test
make -j 8
./run_tests -i always_ok -p 2

This test, proves the TestHarness is available. That libMesh is built, and the TestHarness has a working MOOSE framework available to it. Meaning, your test that is failing may be beyond the scope of this troubleshooting guide. However, do continue to read through the bolded situations below. If the error is not listed, please submit your failed test results to the MOOSE Discussion forum for help.

If the test did fail, chances are your test and our test is failing for the same reason:

• Environment Variables is somehow instructing the TestHarness to use improper paths. Try each of the following and re-run your test again. You may find you receive a different error each time. Simply continue troubleshooting using that new error, and work your way down. If the error is not listed here, then it is time to ask the MOOSE Discussion forum for help:

  • check if echo $METHOD returns anything. If it does, try unsetting it with unset METHOD

  • check if echo $MOOSE_DIR returns anything. If it does, try unsetting it with unset MOOSE_DIR

  • check if echo $PYTHONPATH returns anything. If it does, try unsetting it with unset PYTHONPATH

    commentnote:METHOD and MOOSE_DIR

    If these were set, it will be necessary to perform a rebuild. See Build Issues above.

• Failed to import hit:

  • Verify you have activated the conda moose environment: echo $CONDA_DEFAULT_ENV. This command should return 'moose'. If not, see Conda Issues above.

• Application not found

  • Your Application has not yet been built. You need to successfully perform a make. If make is failing, please see Build Issues above.

  • Perhaps you have specified invalid arguments to run_tests? See TestHarness More Options. Specifically for help with:

    • --opt

    • --dbg

    • --oprof

• gethostbyname failed, localhost (errno 3)

  • This is a fairly common occurrence which happens when your internal network stack / route, is not correctly configured for the local loopback device. Thankfully, there is an easy fix:

    • Obtain your hostname:

      
      hostname
      
      mycoolname
      

    • Linux & Macintosh : Add the results of hostname to your /etc/hosts file. Like so:

      
      sudo vi /etc/hosts
      
      127.0.0.1  localhost
      
      # The following lines are desirable for IPv6 capable hosts
      ::1        localhost ip6-localhost ip6-loopback
      ff02::1    ip6-allnodes
      ff02::2    ip6-allrouters
      
      127.0.0.1  mycoolname  # <--- add this line to the end of your hosts file
      

      Everyones host file is different. But the results of adding the necessary line described above will be the same.

    • Macintosh only, 2nd method:

      
      sudo scutil --set HostName mycoolname
      

      We have received reports where the second method sometimes does not work.

• TIMEOUT

  • If your tests fail due to timeout errors, it is most likely you have a good installation, but a slow machine (or slow filesystem). You can adjust the amount of time that the TestHarness allows a test to run before timing out, by adding a paramater to your test file:

    
    [Tests]
      [./timeout]
        type = RunApp
        input = my_input_file.i
        max_time = 300   <-- time in seconds before a timeout occurs. 300 is the default for all tests.
      [../]
    []
    

• CRASH

  • A crash indicates the TestHarness executed your application (correctly), but then your application exited with a non-zero return code. See Build Issues above for a possible solution.

• EXODIFF

  • An exodiff indicates the TestHarness executed your application, and your application exited correctly. However, the generated results differs from the supplied gold file. If this test passes on some machines, and fails on others, this would indicate you may have applied too tight a tolerance to the acceptable error values for that specific machine. We call this phenomena machine noise.

• CSVDIFF

  • A different file format following the same error checking paradigm as an exodiff test.