Building App on MOOSE

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carter...@gmail.com

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Jan 25, 2018, 11:33:39 PM1/25/18
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Hello all,
 I am having trouble building an application on MOOSE. It successfully compiled before the newest version of MOOSE was pulled. I tried the fixes mentioned in earlier posts, but to no avail unfortunately.
Here is the error I receive when I run make:

MOOSE Compiling C++ (in opt mode) /home/clr56/Documents/MechFail/src/base/SheepApp.C...
In file included from /home/clr56/projects/moose/framework/build/header_symlinks/Parser.h:16:0,
                 from /home/clr56/projects/moose/framework/build/header_symlinks/MooseApp.h:15,
                 from /home/clr56/Documents/MechFail/build/header_symlinks/SheepApp.h:4,
                 from /home/clr56/Documents/MechFail/src/base/SheepApp.C:1:
/home/clr56/projects/moose/framework/build/header_symlinks/InputParameters.h: In instantiation of ‘InputParameters validParams() [with T = ElasticEnergyMaterial2DFrac]’:
/home/clr56/projects/moose/framework/build/header_symlinks/Factory.h:180:43:   required from ‘void Factory::reg(const string&, const string&, int) [with T = ElasticEnergyMaterial2DFrac; std::__cxx11::string = std::__cxx11::basic_string<char>]’
/home/clr56/Documents/MechFail/src/base/SheepApp.C:81:1:   required from here
/home/clr56/projects/moose/framework/build/header_symlinks/InputParameters.h:1385:3: error: static assertion failed: Missing validParams declaration!
   static_assert(false && sizeof(T), "Missing validParams declaration!");
   ^
make: *** [/home/clr56/Documents/MechFail/src/base/SheepApp.x86_64-unknown-linux-gnu.opt.lo] Error 1

Andrs, David

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Jan 26, 2018, 9:19:30 AM1/26/18
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Check that you declared and defined validParams for ElasticEnergyMaterial2DFrac class.
 
make: *** [/home/clr56/Documents/MechFail/src/base/SheepApp.x86_64-unknown-linux-gnu.opt.lo] Error 1

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Carter Rhea

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Jan 26, 2018, 9:40:47 AM1/26/18
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You are absolutely correct! I am not sure why that never raised an error before!


On Friday, January 26, 2018 at 9:19:30 AM UTC-5, david.andrs wrote:
On Thu, Jan 25, 2018 at 9:33 PM, <carter...@gmail.com> wrote:
Hello all,
 I am having trouble building an application on MOOSE. It successfully compiled before the newest version of MOOSE was pulled. I tried the fixes mentioned in earlier posts, but to no avail unfortunately.
Here is the error I receive when I run make:

MOOSE Compiling C++ (in opt mode) /home/clr56/Documents/MechFail/src/base/SheepApp.C...
In file included from /home/clr56/projects/moose/framework/build/header_symlinks/Parser.h:16:0,
                 from /home/clr56/projects/moose/framework/build/header_symlinks/MooseApp.h:15,
                 from /home/clr56/Documents/MechFail/build/header_symlinks/SheepApp.h:4,
                 from /home/clr56/Documents/MechFail/src/base/SheepApp.C:1:
/home/clr56/projects/moose/framework/build/header_symlinks/InputParameters.h: In instantiation of ‘InputParameters validParams() [with T = ElasticEnergyMaterial2DFrac]’:
/home/clr56/projects/moose/framework/build/header_symlinks/Factory.h:180:43:   required from ‘void Factory::reg(const string&, const string&, int) [with T = ElasticEnergyMaterial2DFrac; std::__cxx11::string = std::__cxx11::basic_string<char>]’
/home/clr56/Documents/MechFail/src/base/SheepApp.C:81:1:   required from here
/home/clr56/projects/moose/framework/build/header_symlinks/InputParameters.h:1385:3: error: static assertion failed: Missing validParams declaration!
   static_assert(false && sizeof(T), "Missing validParams declaration!");
   ^

Check that you declared and defined validParams for ElasticEnergyMaterial2DFrac class.
 
make: *** [/home/clr56/Documents/MechFail/src/base/SheepApp.x86_64-unknown-linux-gnu.opt.lo] Error 1

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Andrs, David

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Jan 26, 2018, 10:31:54 AM1/26/18
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On Fri, Jan 26, 2018 at 7:40 AM, Carter Rhea <cr...@g.cofc.edu> wrote:
You are absolutely correct! I am not sure why that never raised an error before!

Because this was merged just yesterday...
 
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selarem

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Feb 16, 2018, 5:19:08 AM2/16/18
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Hi all,

For me my application compiles on my Labtop, but not (anymore)  on my Dell Tower. Although  I have the same OS, moose version ....

What should I change here:

#include "meComputeLinearElasticPFFractureStress.h"

template <>
InputParameters
validParams<meComputeLinearElasticPFFractureStress>()
{
  InputParameters params = validParams<ComputeStressBase>();
  params.addClassDescription("Phase-field fracture model energy contribution to fracture for elasticity and undamaged stress under compressive strain");
  params.addRequiredCoupledVar("c", "Order parameter for damage");
  params.addParam<Real>("kdamage", 1e-6, "Stiffness of damaged matrix");
  params.addParam<MaterialPropertyName>("F_name", "E_el", "Name of material property storing the elastic energy");
  return params;
}

Because it said :
/home/elarem/projects/moose/framework/build/header_symlinks/Factory.h:180:43:   required from ‘void Factory::reg(const string&, const string&, int) [with T = meComputeLinearElasticPFFractureStress; std::__cxx11::string = std::__cxx11::basic_string<char>]’
/home/elarem/projects/bifurcation/src/base/BifurcationApp.C:56:1:   required from here
/home/elarem/projects/moose/framework/build/header_symlinks/InputParameters.h:1385:3: error: static assertion failed: Missing validParams declaration!

   static_assert(false && sizeof(T), "Missing validParams declaration!");


And it used to work on both computers.

Regards,

Ian Greenquist

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Feb 16, 2018, 2:49:45 PM2/16/18
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I'm having a similar problem. I updated to MacOS High Sierra today, installed the new MOOSE package for that OS, reinstalled command-line tools, updated MOOSE, installed libmesh, then went to compile the phase field module, and got the following error:

MOOSE Compiling C++ (in opt mode) /Users/i.greenquist/projects/marmot/moose/modules/tensor_mechanics/src/kernels/InertialTorque.C...
In file included from /Users/i.greenquist/projects/marmot/moose/modules/phase_field/src/base/PhaseFieldApp.C:10:
In file included from /Users/i.greenquist/projects/marmot/moose/modules/phase_field/build/header_symlinks/PhaseFieldApp.h:13:
In file included from /Users/i.greenquist/projects/marmot/moose/framework/build/header_symlinks/MooseApp.h:15:
In file included from /Users/i.greenquist/projects/marmot/moose/framework/build/header_symlinks/Parser.h:16:
/Users/i.greenquist/projects/marmot/moose/framework/build/header_symlinks/InputParameters.h:1385:3: error: static_assert failed
      "Missing validParams declaration!"
  static_assert(false && sizeof(T), "Missing validParams declaration!");
  ^             ~~~~~~~~~~~~~~~~~~
/Users/i.greenquist/projects/marmot/moose/framework/build/header_symlinks/ActionFactory.h:80:35: note: in instantiation of function template
      specialization 'validParams<GPMKernelAction>' requested here
    build_info._params_pointer = &validParams<T>;
                                  ^
/Users/i.greenquist/projects/marmot/moose/modules/phase_field/src/base/PhaseFieldApp.C:607:3: note: in instantiation of function template
      specialization 'ActionFactory::reg<GPMKernelAction>' requested here
  registerAction(GPMKernelAction, "add_kernel");
  ^
/Users/i.greenquist/projects/marmot/moose/framework/build/header_symlinks/ActionFactory.h:26:18: note: expanded from macro 'registerAction'
  action_factory.reg<tplt>(stringifyName(tplt), action, __FILE__, __LINE__)
                 ^
1 error generated.
make: *** [/Users/i.greenquist/projects/marmot/moose/modules/phase_field/src/base/PhaseFieldApp.x86_64-apple-darwin17.2.0.opt.lo] Error 1
make: *** Waiting for unfinished jobs....

Any ideas on what is causing this to happen? The only MOOSE object I have that is not checked in is an action in the phase field module.
Thanks,

Alexander Lindsay

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Feb 16, 2018, 3:25:32 PM2/16/18
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In your GPMKernelAction.h file, do you have a declaration of the validParams<GPMKernelAction> function? You should have these lines:

template<>
InputParameters validParams<GPMKernelAction>();
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S. EL AREM

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Feb 17, 2018, 4:40:04 PM2/17/18
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I am still having trouble in compiling my App. Have this error now:

                                                              ^
/home/elarem/projects/bifurcation/src/base/BifurcationApp.C: In constructor ‘BifurcationApp::BifurcationApp(const InputParameters&)’:
/home/elarem/projects/bifurcation/src/base/BifurcationApp.C:49:10: error: ‘registerExecFlags’ is not a member of ‘Moose’
   Moose::registerExecFlags(_factory);
          ^~~~~~~~~~~~~~~~~
/home/elarem/projects/bifurcation/src/base/BifurcationApp.C:49:10: note: suggested alternative: ‘registerActions’
   Moose::registerExecFlags(_factory);
          ^~~~~~~~~~~~~~~~~
          registerActions
/home/elarem/projects/bifurcation/src/base/BifurcationApp.C: In static member function ‘static void BifurcationApp::registerExecFlags(Factory&)’:
/home/elarem/projects/bifurcation/src/base/BifurcationApp.C:132:50: error: no matching function for call to ‘ChemicalReactionsApp::registerExecFlags(Factory&)’
   ChemicalReactionsApp::registerExecFlags(factory);

in my Bifurcation.h, I have:

#ifndef BIFURCATIONAPP_H
#define BIFURCATIONAPP_H

#include "MooseApp.h"

class BifurcationApp;

template <>
InputParameters validParams<BifurcationApp>();

class BifurcationApp : public MooseApp
{
public:
....

I have the same moose version, on the same OS working fine on my labtop which is a little strange.

regards,

saber

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Ian Greenquist

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Feb 19, 2018, 9:05:16 AM2/19/18
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I didn't have that. Adding it appears to have fixed the problem.

Thank you

Alexander Lindsay

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Feb 19, 2018, 9:26:16 AM2/19/18
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What is your MOOSE revision? We added registerExecFlags to their current locations on January 25th

S. EL AREM

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Feb 19, 2018, 9:52:35 AM2/19/18
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My application compiles fine with :
 
MOOSE version:           git commit af16bf1 on 2017-10-25
PETSc Version:           3.7.5

but not with :

MOOSE Version:           git commit 0b5dcb9 on 2018-01-18
LibMesh Version:         09776becfb3255a41c8e70d4c354721f3d82c547
PETSc Version:           3.7.6

regards,

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Cody Permann

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Feb 19, 2018, 10:24:01 AM2/19/18
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The ExecFlags did change a bit between those two dates. We can either assist you with making the API change if your application is somewhere where we can access it. Alternatively, you can take a look at a similar App file and make the changes yourself. See the LevelSet module here as an example:

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Slaughter, Andrew E

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Feb 19, 2018, 3:40:19 PM2/19/18
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There is also a utility in MOOSE:

cd ~/projects/your_app_name_here
./path_to_moose/scripts/add_exec_flag_registration.py


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selarem

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Feb 20, 2018, 1:46:23 PM2/20/18
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Solved,

In fact I have a new material defined like this:

class marigo : public ComputeStressBase
{
public:
  marigo(const InputParameters & parameters);

protected:
  virtual void computeQpStress();
  virtual void updateVar();
  virtual void updateJacobian();

I have added  at the top:
 

class marigo;
template <>
InputParameters validParams<marigo>();
 
and now it compiles.

Thank you.

Cody Permann

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Feb 20, 2018, 2:25:33 PM2/20/18
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Great, Thanks for reporting back!

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selarem

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Feb 27, 2018, 11:12:12 AM2/27/18
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Now it compiles but when I want to test, I get :

*** ERROR ***
The supplied id 0 already exists in the enumeration, cannot not add 'NONE'.


application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
....


I compiled with different threads, I made "make clean" many times and recompiled ...
It is always impossible to run an example with the generated application-opt file.
I have no problem in compiling or running (the same application) when using older moose distro.

regards,

Cody Permann

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Feb 27, 2018, 2:33:53 PM2/27/18
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You can probably get out a stack trace if you run it serially. It looks like one of your objects is trying to register a duplicate enum flag. I can't really be more specific with the error message you've supplied so far. Can you get the error in serial? Did you take a look at the utility that Andrew pointed out?

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S. EL AREM

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Feb 28, 2018, 6:40:36 AM2/28/18
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Cody,
I have tried all the suggestions.
I have deleted everything, and now I have a new moose install.

I compiled and tested and got everything ok.

I created a new application using the script: it is called bifurcation

In the bifurcation folder I made:
make -j 4
and it compiles fine.
After this I copied a material file (LinearIsoElasticPFDamage.C) and put it in
bifurcation/src/materials/
and copied its header and put it in
bifurcation/include/materials
I made the necessary changes to rename it marigo instead of  LinearIsoElasticPFDamage.

When I recompile it said:

/home/elarem/projects/bifurcation/build/header_symlinks/marigo.h:13:10: fatal error: ComputeStressBase.h: No such file or directory
 #include "ComputeStressBase.h"
          ^~~~~~~~~~~~~~~~~~~~~

so I copied  ComputeStressBase.h and put it in bifurcation/include/materials

make clean
make -j 4

and I obtained

                                              ^
Linking Library /home/elarem/projects/bifurcation/test/lib/libbifurcation_test-opt.la...
Linking Library /home/elarem/projects/bifurcation/lib/libbifurcation-opt.la...
Linking Executable /home/elarem/projects/bifurcation/bifurcation-opt...
/home/elarem/projects/bifurcation/lib/libbifurcation-opt.so: undefined reference to `ComputeStressBase::ComputeStressBase(InputParameters const&)'
/home/elarem/projects/bifurcation/lib/libbifurcation-opt.so: undefined reference to `InputParameters validParams<ComputeStressBase>()'
/home/elarem/projects/bifurcation/lib/libbifurcation-opt.so: undefined reference to `ComputeStressBase::initQpStatefulProperties()'
/home/elarem/projects/bifurcation/lib/libbifurcation-opt.so: undefined reference to `ComputeStressBase::computeQpProperties()'
/home/elarem/projects/bifurcation/lib/libbifurcation-opt.so: undefined reference to `typeinfo for ComputeStressBase'
/home/elarem/projects/bifurcation/lib/libbifurcation-opt.so: undefined reference to `vtable for ComputeStressBase'
collect2: error: ld returned 1 exit status
/home/elarem/projects/moose/framework/app.mk:296: recipe for target '/home/elarem/projects/bifurcation/bifurcation-opt' failed
make: *** [/home/elarem/projects/bifurcation/bifurcation-opt] Error 1


saber


2018-02-27 20:33 GMT+01:00 Cody Permann <codyp...@gmail.com>:
You can probably get out a stack trace if you run it serially. It looks like one of your objects is trying to register a duplicate enum flag. I can't really be more specific with the error message you've supplied so far. Can you get the error in serial? Did you take a look at the utility that Andrew pointed out?

On Tue, Feb 27, 2018 at 9:12 AM selarem <saber...@gmail.com> wrote:
Now it compiles but when I want to test, I get :

*** ERROR ***
The supplied id 0 already exists in the enumeration, cannot not add 'NONE'.


application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
....


I compiled with different threads, I made "make clean" many times and recompiled ...
It is always impossible to run an example with the generated application-opt file.
I have no problem in compiling or running (the same application) when using older moose distro.

regards,

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Cody Permann

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Feb 28, 2018, 9:31:52 AM2/28/18
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These errors mean you are missing the definitions of the listed methods (e.g. you have the header, but you don't have the source). I'm not surprised since you shouldn't ever need to copy a file from any module or the framework into your application so if you find yourself doing that, you've already taken the wrong action. Instead of copying files into your new application, go into your new Makefile and enable the various modules that you would like to use. You'll see a list of "physics names" in your make file, just change the corresponding "no" to "yes" and MOOSE will automatically build and compile those modules. You'll have access to the appropriate headers and definitions so that you can extend those models for your own research. 

So, from here, I'd undo the two copies you've done, change the Makefile and recompile and let's see where we are at.

Cody
 

saber


2018-02-27 20:33 GMT+01:00 Cody Permann <codyp...@gmail.com>:
You can probably get out a stack trace if you run it serially. It looks like one of your objects is trying to register a duplicate enum flag. I can't really be more specific with the error message you've supplied so far. Can you get the error in serial? Did you take a look at the utility that Andrew pointed out?

On Tue, Feb 27, 2018 at 9:12 AM selarem <saber...@gmail.com> wrote:
Now it compiles but when I want to test, I get :

*** ERROR ***
The supplied id 0 already exists in the enumeration, cannot not add 'NONE'.


application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
....


I compiled with different threads, I made "make clean" many times and recompiled ...
It is always impossible to run an example with the generated application-opt file.
I have no problem in compiling or running (the same application) when using older moose distro.

regards,

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selarem

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Feb 28, 2018, 10:05:26 AM2/28/18
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I run the script for a new application.
Put
ALL_MODULES         := yes
in the Makefile

compile the application and got no errors.

copied the  /projects/moose/modules/combined/test/tests/phase_field_fracture_viscoplastic/crack2d.i
to test with, and got:


*** ERROR ***
A 'SplitPFFractureBulkRate' is not a registered object.

If you are trying to find this object in a dynamically linked library, make sure that
the library can be found either in your "Problem/library_path" parameter or in the
MOOSE_LIBRARY_PATH environment variable.




Cody Permann

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Feb 28, 2018, 10:52:15 AM2/28/18
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That Kernel is definitely in the phase_field module so it should be available in your new application once you've turned on the phase_field module (or ALL as you have done). 

I just created a new test application, turned on "ALL_MODULES", copied that test file (and the associated mesh to my new test application) and it worked perfectly.

Let me ask you another question, when you compile, are you seeing objects in the phase_field module (and all the others) being compiled. Right at the end of the build you'll see several libraries being linked (one for each module). You'll also see a special module loader file getting build with a huge name.

Linking Library /Users/permcj/projects/moose/modules/rdg/lib/librdg-devel.la...

Linking Library /Users/permcj/projects/moose/modules/fluid_properties/lib/libfluid_properties-devel.la...

Linking Library /Users/permcj/projects/moose/modules/misc/lib/libmisc-devel.la...

Linking Library /Users/permcj/projects/moose/modules/navier_stokes/lib/libnavier_stokes-devel.la...

Linking Library /Users/permcj/projects/moose/modules/heat_conduction/lib/libheat_conduction-devel.la...

Linking Library /Users/permcj/projects/moose/modules/level_set/lib/liblevel_set-devel.la...

Linking Library /Users/permcj/projects/moose/modules/contact/lib/libcontact-devel.la...

Linking Library /Users/permcj/projects/moose/modules/functional_expansion_tools/lib/libfunctional_expansion_tools-devel.la...

Linking Library /Users/permcj/projects/moose/modules/chemical_reactions/lib/libchemical_reactions-devel.la...

Linking Library /Users/permcj/projects/moose/modules/richards/lib/librichards-devel.la...

Linking Library /Users/permcj/projects/moose/framework/libmoose-devel.la...

Linking Library /Users/permcj/projects/moose/modules/tensor_mechanics/lib/libtensor_mechanics-devel.la...

Linking Library /Users/permcj/projects/moose/modules/solid_mechanics/lib/libsolid_mechanics-devel.la...

Linking Library /Users/permcj/projects/moose/modules/porous_flow/lib/libporous_flow-devel.la...

Linking Library /Users/permcj/projects/moose/modules/phase_field/lib/libphase_field-devel.la...

Linking Library /Users/permcj/projects/moose/modules/xfem/lib/libxfem-devel.la...

Linking Library /Users/permcj/projects/moose/modules/combined/lib/libcombined-devel.la...

Linking Library /Users/permcj/projects/moose/modules/module_loader/lib/libmodule_loader_with_cr_con_fp_fet_hc_ls_misc_ns_tm_pf_pflow_rdg_rich_sm_st_ws_xfem_comb-devel.la...

Are you seeing all of that?


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S. EL AREM

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Feb 28, 2018, 10:59:29 AM2/28/18
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Yes. I have compiled all modules.

[~/projects/moose/modules]> lsr module_loader/lib/*
-rwxr-xr-x 1 elarem elarem  66K févr. 28 12:13 module_loader/lib/libmodule_loader_with-opt.so.0.0.0
lrwxrwxrwx 1 elarem elarem   34 févr. 28 12:13 module_loader/lib/libmodule_loader_with-opt.so.0 -> libmodule_loader_with-opt.so.0.0.0
lrwxrwxrwx 1 elarem elarem   34 févr. 28 12:13 module_loader/lib/libmodule_loader_with-opt.so -> libmodule_loader_with-opt.so.0.0.0
-rwxr-xr-x 1 elarem elarem 1,3K févr. 28 12:13 module_loader/lib/libmodule_loader_with-opt.la
-rwxr-xr-x 1 elarem elarem  82K févr. 28 16:27 module_loader/lib/libmodule_loader_with_cr_con_fp_fet_hc_ls_misc_ns_tm_pf_pflow_rdg_rich_sm_st_ws_xfem-opt.so.0.0.0
lrwxrwxrwx 1 elarem elarem   97 févr. 28 16:27 module_loader/lib/libmodule_loader_with_cr_con_fp_fet_hc_ls_misc_ns_tm_pf_pflow_rdg_rich_sm_st_ws_xfem-opt.so.0 -> libmodule_loader_with_cr_con_fp_fet_hc_ls_misc_ns_tm_pf_pflow_rdg_rich_sm_st_ws_xfem-opt.so.0.0.0
lrwxrwxrwx 1 elarem elarem   97 févr. 28 16:27 module_loader/lib/libmodule_loader_with_cr_con_fp_fet_hc_ls_misc_ns_tm_pf_pflow_rdg_rich_sm_st_ws_xfem-opt.so -> libmodule_loader_with_cr_con_fp_fet_hc_ls_misc_ns_tm_pf_pflow_rdg_rich_sm_st_ws_xfem-opt.so.0.0.0
-rwxr-xr-x 1 elarem elarem 4,2K févr. 28 16:27 module_loader/lib/libmodule_loader_with_cr_con_fp_fet_hc_ls_misc_ns_tm_pf_pflow_rdg_rich_sm_st_ws_xfem-opt.la

[~/projects/moose/modules]> lsr combined/lib/

-rwxr-xr-x 1 elarem elarem  78K févr. 28 16:27 libcombined-opt.so.0.0.0
lrwxrwxrwx 1 elarem elarem   24 févr. 28 16:27 libcombined-opt.so.0 -> libcombined-opt.so.0.0.0
lrwxrwxrwx 1 elarem elarem   24 févr. 28 16:27 libcombined-opt.so -> libcombined-opt.so.0.0.0
-rwxr-xr-x 1 elarem elarem 4,9K févr. 28 16:27 libcombined-opt.la
[elarem][~/projects/moose/modules]> lsr phase_field/lib
total 12M
-rwxr-xr-x 1 elarem elarem  12M févr. 28 16:27 libphase_field-opt.so.0.0.0
lrwxrwxrwx 1 elarem elarem   27 févr. 28 16:27 libphase_field-opt.so.0 -> libphase_field-opt.so.0.0.0
lrwxrwxrwx 1 elarem elarem   27 févr. 28 16:27 libphase_field-opt.so -> libphase_field-opt.so.0.0.0
-rwxr-xr-x 1 elarem elarem 1,4K févr. 28 16:27 libphase_field-opt.la
[elarem][~/projects/moose/modules]> lsr tensor_mechanics/lib
total 11M
-rwxr-xr-x 1 elarem elarem  11M févr. 28 16:26 libtensor_mechanics-opt.so.0.0.0
lrwxrwxrwx 1 elarem elarem   32 févr. 28 16:26 libtensor_mechanics-opt.so.0 -> libtensor_mechanics-opt.so.0.0.0
lrwxrwxrwx 1 elarem elarem   32 févr. 28 16:26 libtensor_mechanics-opt.so -> libtensor_mechanics-opt.so.0.0.0
-rwxr-xr-x 1 elarem elarem 1,3K févr. 28 16:26 libtensor_mechanics-opt.la


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Cody Permann

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Feb 28, 2018, 11:11:25 AM2/28/18
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All that looks good. I can see the "_pf_" in those libraries which tells me that the phase_field library is compiled in.

I can't seem to replicate your problem. Is your application available where I can clone and try to replicate?

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selarem

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Feb 28, 2018, 11:19:44 AM2/28/18
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I just created a new application.
put yes for ALL MODULES in Makefile
tried to run crack2d.i
The application is here:

https://drive.google.com/file/d/1VyzIcFE7ujUfqhqVXrfpKjygRdj3SYe1/view?usp=sharing

Cody Permann

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Feb 28, 2018, 3:22:33 PM2/28/18
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It looks like you modified your Makefile to include the "modules.mk" BEFORE you set the variables that the module.mk needs. The result is that even though you turned all of the modules on. The make system wasn't seeing that. You really shouldn't need to modify the Makefile in your application. Once I removed that line, everything worked.

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selarem

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Mar 1, 2018, 8:28:12 AM3/1/18
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Cody,
I have removeed that line, but it is not working:
same error message.
regards,

Cody Permann

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Mar 1, 2018, 10:00:04 AM3/1/18
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I'm not sure how to replicate. I used your zip file and built everything successfully. We test every single contribution to the repo to ensure that the stork capability always works. Those results can be found under our "External Apps tests" (search for stork):


The only thing I can think of, is try it again from scratch. This time don't make any modifications except for turning on ALL_MODULES. You will be able to run the input file after compiling. This has to work, it's how everyone starts their own MOOSE-based application.


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S. EL AREM

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Mar 1, 2018, 10:14:27 AM3/1/18
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I did it. I deleted my application and created a new one using the script.
I put yes for ALL Modules, and got :




*** ERROR ***
A 'SplitPFFractureBulkRate' is not a registered object.

If you are trying to find this object in a dynamically linked library, make sure that
the library can be found either in your "Problem/library_path" parameter or in the
MOOSE_LIBRARY_PATH environment variable.

2018-03-01 15:59 GMT+01:00 Cody Permann <codyp...@gmail.com>:
I'm not sure how to replicate. I used your zip file and built everything successfully. We test every single contribution to the repo to ensure that the stork capability always works. Those results can be found under our "External Apps tests" (search for stork):


The only thing I can think of, is try it again from scratch. This time don't make any modifications except for turning on ALL_MODULES. You will be able to run the input file after compiling. This has to work, it's how everyone starts their own MOOSE-based application.


On Thu, Mar 1, 2018 at 6:28 AM selarem <saber...@gmail.com> wrote:
Cody,
I have removeed that line, but it is not working:
same error message.
regards,

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Andrs, David

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Mar 1, 2018, 10:51:15 AM3/1/18
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I did:
```
$ cd projects/
$ ./moose/scripts/stork.sh godzilla
Initialized empty Git repository in /Users/andrsd/projects/godzilla/.git/
[master (root-commit) 38e1dae] Initial files
 21 files changed, 1342 insertions(+)
 create mode 100644 .clang-format
 create mode 100644 .gitignore
 create mode 100644 LICENSE
 create mode 100644 Makefile
 create mode 100644 README.md
 create mode 100644 include/base/godzillaApp.h
 create mode 100755 run_tests
 create mode 100755 scripts/install-format-hook.sh
 create mode 100644 src/base/godzillaApp.C
 create mode 100644 src/main.C
 create mode 100644 test/include/base/godzillaTestApp.h
 create mode 100644 test/src/base/godzillaTestApp.C
 create mode 100644 test/tests/kernels/simple_diffusion/gold/simple_diffusion_out.e
 create mode 100644 test/tests/kernels/simple_diffusion/simple_diffusion.i
 create mode 100644 test/tests/kernels/simple_diffusion/tests
 create mode 100644 testroot
 create mode 100644 unit/Makefile
 create mode 100644 unit/include/place_holder
 create mode 100755 unit/run_tests
 create mode 100644 unit/src/SampleTest.C
 create mode 100644 unit/src/main.C
MOOSE app created in '/Users/andrsd/projects/godzilla'

To store your changes on github:
    1. log in to your account
    2. Create a new repository named godzilla
    3. in this terminal run the following commands:
         cd /Users/andrsd/projects/godzilla
         git remote add origin https://github.com/YourGitHubUserName/godzilla
         git commit -m "initial commit"
         git push -u origin master

To automatically enforce MOOSE C++ code style in your commits, run:

    cd /Users/andrsd/projects/godzilla
    ./scripts/install-format-hook.sh

$ cd godzilla/
$ vim Makefile
$ git diff
diff --git a/Makefile b/Makefile
index b7dd53f..7858fb6 100644
--- a/Makefile
+++ b/Makefile
@@ -24,7 +24,7 @@ include $(FRAMEWORK_DIR)/moose.mk
 # yes as needed.  Or set ALL_MODULES to yes to turn on everything (overrides
 # other set variables).
 
-ALL_MODULES         := no
+ALL_MODULES         := yes
 
 CHEMICAL_REACTIONS  := no
 CONTACT             := no
$ cp ../moose/modules/combined/test/tests/phase_field_fracture/void2d.i .
$ cp ../moose/modules/combined/test/tests/phase_field_fracture/void2d_mesh.xda .
$ make -j4
$ ./godzilla-opt -i void2d.i 
Framework Information:
MOOSE Version:           git commit 097a7342b7 on 2018-02-27
LibMesh Version:         cdeee56489cc8ddcc4415ae9dc6d074ba5b75f5c
PETSc Version:           3.8.3
Current Time:            Thu Mar  1 08:38:47 2018
Executable Timestamp:    Thu Mar  1 08:38:10 2018

Parallelism:
  Num Processors:          1
  Num Threads:             1

Mesh: 
  Parallel Type:           replicated
  Mesh Dimension:          2
  Spatial Dimension:       2
  Nodes:                   
    Total:                 433
    Local:                 433
  Elems:                   
    Total:                 367
    Local:                 367
  Num Subdomains:          1
  Num Partitions:          1

Nonlinear System:
  Num DOFs:                1732
  Num Local DOFs:          1732
  Variables:               { "disp_x" "disp_y" "c" "b" } 
  Finite Element Types:    "LAGRANGE" 
  Approximation Orders:    "FIRST" 

Auxiliary System:
  Num DOFs:                1233
  Num Local DOFs:          1233
  Variables:               { "resid_x" "resid_y" } "stress_yy" 
  Finite Element Types:    "LAGRANGE" "MONOMIAL" 
  Approximation Orders:    "FIRST" "CONSTANT" 

Execution Information:
  Executioner:             Transient
  TimeStepper:             ConstantDT
  Solver Mode:             Preconditioned JFNK




Time Step  0, time = 0
                dt = 0

Postprocessor Values:
+----------------+----------------+----------------+
| time           | resid_x        | resid_y        |
+----------------+----------------+----------------+
|   0.000000e+00 |   0.000000e+00 |   0.000000e+00 |
+----------------+----------------+----------------+


Time Step  1, time = 0.0001
                dt = 0.0001
 0 Nonlinear |R| = 6.058515e-02
      0 Linear |R| = 6.058515e-02
      1 Linear |R| = 1.084226e-04
      2 Linear |R| = 2.095974e-07
 1 Nonlinear |R| = 6.771084e-03
      0 Linear |R| = 6.771084e-03
      1 Linear |R| = 1.970788e-09
 2 Nonlinear |R| = 4.842615e-06
      0 Linear |R| = 4.842615e-06
      1 Linear |R| = 2.640946e-11
 3 Nonlinear |R| = 1.288272e-08
      0 Linear |R| = 1.288272e-08
      1 Linear |R| = 7.190962e-13
      2 Linear |R| = 5.955094e-18
 4 Nonlinear |R| = 3.338931e-11
      0 Linear |R| = 3.338931e-11
      1 Linear |R| = 1.171506e-15
      2 Linear |R| = 5.957210e-21
 5 Nonlinear |R| = 1.180355e-15
 Solve Converged!

Outlier Variable Residual Norms:
  disp_y: 9.508668e-16

Postprocessor Values:
+----------------+----------------+----------------+
| time           | resid_x        | resid_y        |
+----------------+----------------+----------------+
|   0.000000e+00 |   0.000000e+00 |   0.000000e+00 |
|   1.000000e-04 |   9.832333e-05 |   1.633493e-02 |
+----------------+----------------+----------------+


Time Step  2, time = 0.0002
                dt = 0.0001
 0 Nonlinear |R| = 6.092778e-02
      0 Linear |R| = 6.092778e-02
      1 Linear |R| = 9.182587e-08
 1 Nonlinear |R| = 6.694104e-03
      0 Linear |R| = 6.694104e-03
      1 Linear |R| = 2.081308e-09
 2 Nonlinear |R| = 4.380778e-06
      0 Linear |R| = 4.380778e-06
      1 Linear |R| = 1.056944e-11
 3 Nonlinear |R| = 1.391877e-14
 Solve Converged!

Outlier Variable Residual Norms:
  c: 1.060922e-14

Postprocessor Values:
+----------------+----------------+----------------+
| time           | resid_x        | resid_y        |
+----------------+----------------+----------------+
|   0.000000e+00 |   0.000000e+00 |   0.000000e+00 |
|   1.000000e-04 |   9.832333e-05 |   1.633493e-02 |
|   2.000000e-04 |   1.966410e-04 |   3.266920e-02 |
+----------------+----------------+----------------+
```
And all worked as supposed.

Note that:
- my MOOSE dir is in the projects directory right next to godzilla and libmesh is already built
- I used a test file using the kernel that you get an error for
- final version of the repo is on https://github.com/andrsd/godzilla so you can check what is different on your machine





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Miller, Jason M

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Mar 1, 2018, 11:15:36 AM3/1/18
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I just tested this on an Ubuntu 16 machine, and things seem to work fine.. I cloned moose, built libmesh, created an app using stork, modified the newly created Makefile to reflect: ALL_MODULES         := yes, built and tested fine...


test_app]> ./run_tests 
test:kernels/simple_diffusion.test ................................ OK
----------------------------------------------------------------------
Ran 1 tests in 0.6 seconds
1 passed, 0 skipped, 0 pending, 0 failed


I can't seem to replicate the issue. Which suggests something other than the moose git repo is causing the issue. You may have some environment variables possibly interfering with your build. Are you using a moose-environment package or some other compiler stack? I would also take a look at the LD_LIBRARY_PATH and PATH variables at this point to make sure those are what they should be.





selarem

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Mar 2, 2018, 4:22:22 AM3/2/18
to moose-users

I did everything as per your suggestions; I can not have it working.

I reinstall the environment
reinstall moose
all tests pass
recompile all modules one by one
.
.
.

I will keep working with my older version of November 2017.
thank you for your time
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