MOOSE Installation Help

[Robert Hickman]

Hi all,

I don’t have a lot of direct experience with modeling and programming in general so sorry in advance if these are basic issues. My background is more on the materials side. I’m hoping to learn as I go. I’m having problems with the MOOSE installation on my Mac with Mavericks 10.9. I followed the step 1 procedure, but ended up not having the xcode command line tools for Mavericks installed prior to installing XQuartz and the MOOSE package. I went ahead and installed the tools anyway. When I enter “module list” to verify the setup, it says “command not found”. 

I probably should have posted at that point, but It looks like I have all the required directories so I proceeded with step 2. I cloned MOOSE using Git, which seemed to go ok. I then compiled libMesh per the instructions. When I enter "make –j8” to test, there are a lot of errors. I pasted some of the last parts below for reference. When I enter "./run_tests –j8” I get "Error determining PETSC version”. 

Any help on getting MOOSE installed would be much appreciated. Hopefully, this is not beyond my capability. If nothing else, I would like to at least understand the overall process for fuels performance modeling work that we plan to fund in the near future.

Thanks

Robert Hickman

NASA MSFC

/Users/rrhickma/projects/moose/framework/include/materials/MaterialProperty.h:202:59: error: 

      use of undeclared identifier 'MPI_Abort'

  MaterialProperty(const MaterialProperty<T> & /*src*/) { mooseError("Ma...

                                                          ^

/Users/rrhickma/projects/moose/framework/include/base/MooseError.h:26:141: note: 

      expanded from macro 'mooseError'

  ...== 1) print_trace(); libmesh_here(); MPI_Abort(libMesh::GLOBAL_COMM_WORL...

                                          ^

In file included from /Users/rrhickma/projects/moose/framework/src/actions/AddConstraintAction.C:16:

In file included from /Users/rrhickma/projects/moose/framework/include/base/FEProblem.h:24:

In file included from /Users/rrhickma/projects/moose/framework/include/materials/MaterialPropertyStorage.h:19:

/Users/rrhickma/projects/moose/framework/include/materials/MaterialProperty.h:202:59: error: 

      use of undeclared identifier 'MPI_Abort'

  MaterialProperty(const MaterialProperty<T> & /*src*/) { mooseError("Ma...

                                                          ^

/Users/rrhickma/projects/moose/framework/include/base/MooseError.h:26:141: note: 

      expanded from macro 'mooseError'

  ...== 1) print_trace(); libmesh_here(); MPI_Abort(libMesh::GLOBAL_COMM_WORL...

                                          ^

fatal error: too many errors emitted, stopping now [-ferror-limit=]

In file included from /Users/rrhickma/projects/moose/framework/src/actions/AddBCAction.C:16:

In file included from /Users/rrhickma/projects/moose/framework/include/base/FEProblem.h:24:

In file included from /Users/rrhickma/projects/moose/framework/include/materials/MaterialPropertyStorage.h:19:

/Users/rrhickma/projects/moose/framework/include/materials/MaterialProperty.h:202:59: error: 

      use of undeclared identifier 'MPI_Abort'

  MaterialProperty(const MaterialProperty<T> & /*src*/) { mooseError("Ma...

                                                          ^

/Users/rrhickma/projects/moose/framework/include/base/MooseError.h:26:141: note: 

      expanded from macro 'mooseError'

  ...== 1) print_trace(); libmesh_here(); MPI_Abort(libMesh::GLOBAL_COMM_WORL...

                                          ^

fatal error: too many errors emitted, stopping now [-ferror-limit=]

fatal error: too many errors emitted, stopping now [-ferror-limit=]

fatal error: too many errors emitted, stopping now [-ferror-limit=]

fatal error: too many errors emitted, stopping now [-ferror-limit=]

20 errors generated.

make: *** [/Users/rrhickma/projects/moose/framework/src/actions/AddConstraintAction.x86_64-apple-darwin13.1.0.opt.lo] Error 1

20 errors generated.

20 errors generated.

make: *** [/Users/rrhickma/projects/moose/framework/src/actions/AddAuxVariableAction.x86_64-apple-darwin13.1.0.opt.lo] Error 1

make: *** [/Users/rrhickma/projects/moose/framework/src/actions/AddBoundsVectorsAction.x86_64-apple-darwin13.1.0.opt.lo] Error 1

20 errors generated.

make: *** [/Users/rrhickma/projects/moose/framework/src/actions/AdaptivityAction.x86_64-apple-darwin13.1.0.opt.lo] Error 1

20 errors generated.

make: *** [/Users/rrhickma/projects/moose/framework/src/actions/AddBCAction.x86_64-apple-darwin13.1.0.opt.lo] Error 1

MSSLA40018044:test rrhickma$

[Cody Permann]

The order of the installation doesn't matter.  Did you close your terminal and reopen a new one after installing all of the packages?  The module command as well as the necessary environment variables should all be loaded in the new terminal. This is why MOOSE can't find PETSc or MPI when you build.

Cody

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[Robert Hickman]

Yes. Looks like the environment variables are not loading. How can I resolve that issue?

Robert

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[Cody Permann]

Verify that the moose installer placed the correct lines in your bash profile to load the moose environment.  See the "more information" section on the getting started page.

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[Robert Hickman]

This is whats in the .bash_profile. 

#!/bin/bash

# Uncomment to enable pretty prompt:

# export MOOSE_PROMPT=true

# Uncomment to enable autojump:

# export MOOSE_JUMP=true

# Source MOOSE profile

if [ -f /opt/moose/environments/moose_profile ]; then

        . /opt/moose/environments/moose_profile

fi

Should I put the following to the end of my .bash_profile? I got these from the basic installation instructions on the Wiki.

# Compiler Variables
export CC=mpicc
export CXX=mpicxx
export F77=mpif77
export FC=mpif90

# Library location
export PACKAGES_DIR=/opt/moose

# Helper variables
export GCC_HOME=$PACKAGES_DIR/gcc_4.7.2
export MPI_HOME=$PACKAGES_DIR/openmpi/openmpi-1.6.5/gcc-opt
export HYPRE_HOME=$PACKAGES_DIR/hypre/openmpi_hypre-2.8.0b/gcc-opt
export PETSC_DIR=$PACKAGES_DIR/petsc/openmpi_petsc-3.4.3/gcc-opt

# Libraries
export DYLD_LIBRARY_PATH=$GCC_HOME/lib:$MPI_HOME/lib:$MPI_HOME/lib/openmpi:$DYLD_LIBRARY_PATH

# PATH
export PATH=$GCC_HOME/bin:$MPI_HOME/bin:$PATH

# JOB Count (the number of cores available on this machine)
export MOOSE_JOBS=4

[Robert Hickman]

From the more information section, looks like the moose installer added the lines to load the moose profile. The moose profile is in the right place and looks correct.

Robert

[Cody Permann]

Yet your environment still isn't correct?  Can your run these commands?

module avail

module list

Cody

On Sat, Jun 7, 2014 at 10:22 AM, Robert Hickman <rhick...@gmail.com> wrote:

From the more information section, looks like the moose installer added the lines to load the moose profile. The moose profile is in the right place and looks correct.

Robert

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[Robert Hickman]

No. I get "command not found".

MSSLA40018044:~ rrhickma$ module avail

-sh: module: command not found

MSSLA40018044:~ rrhickma$ module list

-sh: module: command not found

MSSLA40018044:~ rrhickma$ 

[Daniel Schwen]

---------- Forwarded message ----------
From: "Daniel Schwen" <dan...@schwen.de>
Date: Jun 7, 2014 10:37 AM
Subject: Re: MOOSE Installation Help
To: "Robert Hickman" <rhick...@gmail.com>
Cc:

Did you change your shell?
Can you run
 . /opt/moose/environments/moose_profile
In your terminal and try the thing Cody asked again?
Can you put an echo command at the end of your bash profile
echo hello world
To see if that file gets sourced when you open a terminal.

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[Robert Hickman]

I tried that command and looks like it worked. 

MSSLA40018044:~ rrhickma$ . /opt/moose/environments/moose_profile

-sh: /opt/moose/Modules/3.2.10/init/bash_completion: line 14: syntax error near unexpected token `('

-sh: /opt/moose/Modules/3.2.10/init/bash_completion: line 14: ` comm -23  <(_module_avail|sort)  <(tr : '\n' <<<${LOADEDMODULES}|sort)'

MSSLA40018044:~ rrhickma$ module list

Currently Loaded Modulefiles:

  1) moose/.gcc_4.7.2                   5) moose/.openmpi_petsc-3.4.3-clang

  2) moose/.clang                       6) moose-dev-clang

  3) moose/.cppunit-clang               7) moose-tools

  4) moose/.openmpi-1.6.5_clang

MSSLA40018044:~ rrhickma$ 

[Robert Hickman]

Do I need to execute that command each time or can I change the shell? I closed and opened a new terminal and the module command does not work again. Should I load the moose_profile and run the test?

[Cody Permann]

That's just the thing. That command is already in your bash profile yet it's not getting run.  You should never need to execute that command directly on your system.  As a workaround you will need to execute that command each time you open a new terminal until you figure out why your bash profile is not getting read.  Other than that you should be ready to proceed with building libMesh and continuing.

Cody

On Saturday, June 7, 2014, Robert Hickman <rhick...@gmail.com> wrote:

Do I need to execute that command each time or can I change the shell? I closed and opened a new terminal and the module command does not work again. Should I load the moose_profile and run the test?

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[Daniel Schwen]

What about my other questions?

On Jun 7, 2014 10:53 AM, "Robert Hickman" <rhick...@gmail.com> wrote:

Do I need to execute that command each time or can I change the shell? I closed and opened a new terminal and the module command does not work again. Should I load the moose_profile and run the test?

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[Robert Hickman]

Daniel,

I dont recall changing my shell.

As mentioned above, running the moose_profile command you supplied worked for using the module commands, but reverts back when I open a new terminal

I tried to put an echo command in my bash_profile, but not sure if I did it correctly. How do I see if the file gets sourced when I open a terminal? 

Thanks

Robert

[Daniel Schwen]

If you put in
echo "hello world"
You should see
hello world
Above your first shell prompt.

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[Robert Hickman]

I put in the echo command in .bash_profile and nothing. Its not showing up when I open a new terminal.

However, I did run the test after executing the moose_profile first and looks like it passed (see below). Does that look normal?

Ran 751 tests in 59.1 seconds

751 passed, 16 skipped, 0 pending, 0 failed

MSSLA40018044:test rrhickma$ 

[Peterson, JW]

On Sat, Jun 7, 2014 at 12:27 PM, Robert Hickman <rhick...@gmail.com> wrote:

I put in the echo command in .bash_profile and nothing. Its not showing up when I open a new terminal.

I think that narrows down the problem to something with the .bash_profile file itself.

What are the file permissions on that file?  You can see them by typing "ls -l .bash_profile".  They should be -rw-r--r--

--
John

[Robert Hickman]

I tried both commands. Here is what I get...

MSSLA40018044:~ rrhickma$ ls -l .bash_profile

-rw-r--r--@ 1 rrhickma  NDC\Domain Users  304 Jun  7 13:47 .bash_profile

MSSLA40018044:~ rrhickma$ bash

bash-3.2$ module list

bash: module: command not found

bash-3.2$ 

On Mon, Jun 9, 2014 at 9:46 AM, Daniel Schwen <dan...@schwen.de> wrote:

> I think that narrows down the problem to something with the .bash_profile
> file itself.

I don't think so. His "echo $0" returned "-sh". It should have returned "-bash".
The problem seems to be that he isn't using bash as his login shell,
so tis profile never gets sourced.

Robert. Please type in
bash
in your terminal window and retest the "module list" command.
Daniel

[Peterson, JW]

On Mon, Jun 9, 2014 at 9:16 AM, Robert Hickman <rhick...@gmail.com> wrote:

I tried both commands. Here is what I get...

MSSLA40018044:~ rrhickma$ ls -l .bash_profile

-rw-r--r--@ 1 rrhickma  NDC\Domain Users  304 Jun  7 13:47 .bash_profile

MSSLA40018044:~ rrhickma$ bash

bash-3.2$ module list

bash: module: command not found

bash-3.2$ 

Can you please run

cat -vet .bash_profile

and paste the exact output into an email?  I just want to see if there are any weird characters in that file...

--
John

[Robert Hickman]

Here it is...

MSSLA40018044:~ rrhickma$ cat -vet .bash_profile

#!/bin/bash$

$

echo ?M-^@M-^\test?M-^@M-^]$

$

# Uncomment to enable pretty prompt:$

# export MOOSE_PROMPT=true$

$

# Uncomment to enable autojump:$

# export MOOSE_JUMP=true$

$

# Source MOOSE profile$

if [ -f /opt/moose/environments/moose_profile ]; then$

        . /opt/moose/environments/moose_profile$

fi$

$

echo ?M-^@M-^\hello world?M-^@M-^]MSSLA40018044:~ rrhickma$ 

[Peterson, JW]

On Mon, Jun 9, 2014 at 9:26 AM, Robert Hickman <rhick...@gmail.com> wrote:

Here it is...

MSSLA40018044:~ rrhickma$ cat -vet .bash_profile

#!/bin/bash$

$

echo ?M-^@M-^\test?M-^@M-^]$

$

# Uncomment to enable pretty prompt:$

# export MOOSE_PROMPT=true$

$

# Uncomment to enable autojump:$

# export MOOSE_JUMP=true$

$

# Source MOOSE profile$

if [ -f /opt/moose/environments/moose_profile ]; then$

        . /opt/moose/environments/moose_profile$

fi$

$

echo ?M-^@M-^\hello world?M-^@M-^]MSSLA40018044:~ rrhickma$ 

Hmm... the quote characters look a little different than what I was expecting, but the line end characters look OK.

Let's try changing your default shell to /bin/bash... Can you type

chsh -s /bin/bash

and then type your password.  Then restart the Terminal app (by the way, you are using OSX Terminal app, right?), and verify that the "echo $0" command returns "-bash".

--
John

[Robert Hickman]

Yes I'm using OSX Terminal app. I think that worked. Check out below. The echo statement I put in the bash file showed up right away. The module list command worked as well. I opened a new terminal window and it looks like the bash file loaded. The module list command worked in the new one. Thanks for the help! 

Last login: Mon Jun  9 11:09:45 on ttys000

Warning! This is a US Government Computer. This system is for the use of authorized users only. By accessing and using this computer system you are consenting to system monitoring, including the monitoring of keystrokes. Unauthorized use of, or access to, this computer system may subject you to disciplinary action and criminal prosecution.

“test”

“hello world”

MSSLA40018044:~ rrhickma$ echo $0

-bash

MSSLA40018044:~ rrhickma$ module list

Currently Loaded Modulefiles:

  1) moose/.gcc_4.7.2                   5) moose/.openmpi_petsc-3.4.3-clang

  2) moose/.clang                       6) moose-dev-clang

  3) moose/.cppunit-clang               7) moose-tools

  4) moose/.openmpi-1.6.5_clang

MSSLA40018044:~ rrhickma$ 

[Peterson, JW]

On Mon, Jun 9, 2014 at 10:19 AM, Robert Hickman <rhick...@gmail.com> wrote:

Yes I'm using OSX Terminal app. I think that worked. Check out below. The echo statement I put in the bash file showed up right away. The module list command worked as well. I opened a new terminal window and it looks like the bash file loaded. The module list command worked in the new one. Thanks for the help! 

Last login: Mon Jun  9 11:09:45 on ttys000

Warning! This is a US Government Computer. This system is for the use of authorized users only. By accessing and using this computer system you are consenting to system monitoring, including the monitoring of keystrokes. Unauthorized use of, or access to, this computer system may subject you to disciplinary action and criminal prosecution.

“test”

“hello world”

MSSLA40018044:~ rrhickma$ echo $0

-bash

Glad it worked.

Interesting that your default shell was changed in this way, it's the first time I've seen that on OSX.  Do you recall doing it yourself, or do you by chance have MacPorts/fink/homebrew installed on this system? 

--
John

[Peterson, JW]

Actually, Jason Miller just raised an interesting point: if your Mac is connected to some kind of user credential system such as LDAP or Active Directory, that service can set your shell to /bin/sh.  So, hopefully the change you made will be permanent, but if you restart your computer and have /bin/sh as your shell again, and you might have to contact your sysadmins to resolve the issue...

--
John

[Robert Hickman]

John,

I dont recall changing the default shell, at least not on purpose. It has been a long time since I have worked with terminal and this type of programming in general, so I could have done something in the process. I'm not using Macports, fink, or homebrew. I was worried about the NASA credential system being a problem but I just restarted the computer and the bash file is still loading. Looks like I'm good to go. Thanks again for all the help from the team.

Robert