________________________________
> From: codyperm...@gmail.com
> Date: Tue, 16 Aug 2016 19:37:52 +0000
> Subject: Re: [Libmesh-users] Example files won't run a second time
> To: harroontheg...@gmail.com; marchy...@hotmail.com
> CC: libmesh-users@lists.sourceforge.net
>
> You need to spend some time updating your code. Many of these changes
> occurred more than a one to two years ago. The fixes are generally
> small. Just use the current examples to get your old example back in
> line.
> Just to get started, libMesh has a communicator class so that you can
> split communicators and not necessarily work with just the global
> communicator so you won't find processor_id() in a namespace any more
> as a result. The Mesh constructors was changed a few years ago. AutoPtr
> is deprecated in favor of UniquePtr, etc...
>
> Mike, UniquePtr is actually quite nice! You can't accidentally assign a
> UniquePtr resulting in having the resource stolen like you could freely
> do with AutoPtr. Overall these changes shouldn't be viewed on as "bad",
> these are positive changes that reflect new capabilities and feature
> evolution of the project.
Does it somehow end up allowing or encouraging better usage of
memory for these calculations, say avoiding low level cache thrashing?
>
> On Tue, Aug 16, 2016 at 12:19 PM Harry Pearce
> <harroontheg...@gmail.com<mailto:harroontheg...@gmail.com>> wrote:
>>Again, I would not worry about adding an example but rather just try
>>to build and test standalone. I just reinstalled libmesh adding petsc
>>and other things, repeated the process of running "make -n example-opt"
>>and extracting the compile and link lines and it seems to work ok,
>
> I was wondering if you tried that with my code. I tried to use the output
> and named my file by the same name but errors appeared. I also tried using
> the compile and link lines and errors seemed to appear. As a test I tried
> running the make example-opt on an example that I added a comment line to
> (so it would know there was a change in the .C file and recompile the
> example-opt program and that worked fine. When I used my .C program instead
> (which I named eigenproblems_ex2.C and put in the eigenprobmes_ex2.C
> example folder) and ran make example-opt errors appeared. These errors are:
>
>
> CXX example_opt-eigenproblems_ex2.o
> eigenproblems_ex2.C: In function ‘int main(int, char**)’:
> eigenproblems_ex2.C:44:13: error: ‘processor_id’ is not a member of
> ‘libMesh’
> if (libMesh::processor_id() == 0)
> ^
> eigenproblems_ex2.C:65:10: error: no matching function for call to
> ‘libMesh::Mesh::Mesh()’
> Mesh mesh;
> ^
> eigenproblems_ex2.C:65:10: note: candidates are:
> In file included from eigenproblems_ex2.C:3:0:
> ../../../include/libmesh/mesh.h:75:3: note: libMesh::Mesh::Mesh(const
> libMesh::UnstructuredMesh&)
> Mesh (const UnstructuredMesh & other_mesh) : DefaultMesh(other_mesh) {}
> ^
> ../../../include/libmesh/mesh.h:75:3: note: candidate expects 1 argument,
> 0 provided
> ../../../include/libmesh/mesh.h:56:3: note: libMesh::Mesh::Mesh(const
> libMesh::Parallel::Communicator&, unsigned char)
> Mesh (const Parallel::Communicator & comm_in,
> ^
> ../../../include/libmesh/mesh.h:56:3: note: candidate expects 2
> arguments, 0 provided
> ../../../include/libmesh/mesh.h:46:7: note: libMesh::Mesh::Mesh(const
> libMesh::Mesh&)
> class Mesh : public DefaultMesh
> ^
> ../../../include/libmesh/mesh.h:46:7: note: candidate expects 1 argument,
> 0 provided
> eigenproblems_ex2.C:93:32: error: invalid initialization of reference of
> type ‘const libMesh::Point&’ from expression of type ‘libMesh::Node’
> const Point& p = **node_it;
> ^
> eigenproblems_ex2.C: In function ‘void
> assemble_mass(libMesh::EquationSystems&, const string&)’:
> eigenproblems_ex2.C:178:52: error: no matching function for call to
> ‘libMesh::AutoPtr<libMesh::FEGenericBase<double>
>>::AutoPtr(libMesh::UniquePtr<libMesh::FEGenericBase<double>>)’
> AutoPtr<FEBase> fe (FEBase::build(dim, fe_type));
> ^
> eigenproblems_ex2.C:178:52: note: candidates are:
> In file included from ../../../include/libmesh/parallel.h:25:0,
> from ../../../include/libmesh/libmesh.h:28,
> from eigenproblems_ex2.C:2:
> ../../../include/libmesh/auto_ptr.h:355:3: note:
> libMesh::AutoPtr<Tp>::AutoPtr(libMesh::AutoPtrRef<Tp>) [with Tp =
> libMesh::FEGenericBase<double>]
> AutoPtr(AutoPtrRef<element_type> ref)
> ^
> ../../../include/libmesh/auto_ptr.h:355:3: note: no known conversion for
> argument 1 from ‘libMesh::UniquePtr<libMesh::FEGenericBase<double>> {aka
> std::unique_ptr<libMesh::FEGenericBase<double>,
> std::default_delete<libMesh::FEGenericBase<double>>>}’ to
> ‘libMesh::AutoPtrRef<libMesh::FEGenericBase<double>>’
> ../../../include/libmesh/auto_ptr.h:215:3: note: template<class Tp1>
> libMesh::AutoPtr<Tp>::AutoPtr(libMesh::AutoPtr<Tp1>&)
> AutoPtr(AutoPtr<Tp1> & a)
> ^
> ../../../include/libmesh/auto_ptr.h:215:3: note: template argument
> deduction/substitution failed:
> eigenproblems_ex2.C:178:52: note:
> ‘libMesh::UniquePtr<libMesh::FEGenericBase<double>> {aka
> std::unique_ptr<libMesh::FEGenericBase<double>,
> std::default_delete<libMesh::FEGenericBase<double>>>}’ is not derived
> from ‘libMesh::AutoPtr<Tp>’
> AutoPtr<FEBase> fe (FEBase::build(dim, fe_type));
> ^
> In file included from ../../../include/libmesh/parallel.h:25:0,
> from ../../../include/libmesh/libmesh.h:28,
> from eigenproblems_ex2.C:2:
> ../../../include/libmesh/auto_ptr.h:200:3: note:
> libMesh::AutoPtr<Tp>::AutoPtr(libMesh::AutoPtr<Tp>&) [with Tp =
> libMesh::FEGenericBase<double>]
> AutoPtr(AutoPtr & a)
> ^
> ../../../include/libmesh/auto_ptr.h:200:3: note: no known conversion for
> argument 1 from ‘libMesh::UniquePtr<libMesh::FEGenericBase<double>> {aka
> std::unique_ptr<libMesh::FEGenericBase<double>,
> std::default_delete<libMesh::FEGenericBase<double>>>}’ to
> ‘libMesh::AutoPtr<libMesh::FEGenericBase<double>>&’
> ../../../include/libmesh/auto_ptr.h:185:3: note:
> libMesh::AutoPtr<Tp>::AutoPtr(libMesh::AutoPtr<Tp>::element_type*) [with Tp
> = libMesh::FEGenericBase<double>; libMesh::AutoPtr<Tp>::element_type =
> libMesh::FEGenericBase<double>]
> AutoPtr(element_type * p = 0)
> ^
> ../../../include/libmesh/auto_ptr.h:185:3: note: no known conversion for
> argument 1 from ‘libMesh::UniquePtr<libMesh::FEGenericBase<double>> {aka
> std::unique_ptr<libMesh::FEGenericBase<double>,
> std::default_delete<libMesh::FEGenericBase<double>>>}’ to
> ‘libMesh::AutoPtr<libMesh::FEGenericBase<double>>::element_type* {aka
> libMesh::FEGenericBase<double>*}’
> make: *** [example_opt-eigenproblems_ex2.o] Error 1
>
>
> Also I ran make check and the examples do rerun when I do that but now when
> I do make run_examples. When I do make run_examples it looks in each
> directory but doesn't do anything other than "make all-am". Then it says
> there is nothing to do in the directory of the example and looks at the
> next example.
>
> Harry Pearce
>
> On Fri, Aug 12, 2016 at 12:48 PM, Mike Marchywka
> <marchy...@hotmail.com<mailto:marchy...@hotmail.com>>
> wrote:
>
>> Again, I would not worry about adding an example but rather just try
>> to build and test standalone. I just reinstalled libmesh adding petsc
>> and other things, repeated the process of running "make -n example-opt"
>> and extracting the compile and link lines and it seems to work ok,
>>
>> Silent failures can be hard to track down. Normally, you could just
>> start in a debugger. Or, if you think you are missing a library
>> run ldd. It turns out the output of the libtool step is a script
>> that runs .libs/lt-foo. and you can run ldd on this if you want.
>>
>> If you mean it only makes once, you need to insure the dependencies
>> are right but for testing I usually just write a script that rebuilds
>> everything although checking for "newer" would not be too hard.
>>
>> Again, the compile seems normal but maybe someone could explain the
>> odd linking lol. What is the point of this?
>>
>> When I get some simple examples to work and think
>> Iunderstand FEM, I was going to link
>> to a larger program I have which uses tcl and things like jdft.
>> I have no idea how this will go but curious what you find :)
>>
>>
>>
>>
>>
>>
>> ----------------------------------------
>>> From: harroontheg...@gmail.com<mailto:harroontheg...@gmail.com>
>>> Date: Fri, 12 Aug 2016 12:34:41 -0700
>>> To:
> libmesh-users@lists.sourceforge.net<mailto:libmesh-users@lists.sourceforge.net>
>
>>> Subject: [Libmesh-users] Example files won't run a second time
>>>
>>> Hello libmesh users!,
>>> I tried to run the example programs using make run_examples but after the
>>> makefile descends into the individual example files it keeps saying
>>> "Nothing to be done for all-am" after trying to make all-am. It doesn't
>> try
>>> to run or modify the programs. I wanted to recompile the
>> eigenproblems_ex2
>>> with my own .C file in it instead of the one that comes with the
>> examples.
>>>
>>> I did modify the Makefile.am in the example directory, but just to add an
>>> example to the SUBDIRS variable, following the directions of
>>> https://github.com/libMesh/libmesh/wiki/Adding-a-new-example
>> (instructions
>>> for adding a new example program to libMesh). I changed it back though
>> and
>>> now the only difference that I know of between it and the original
>>> Makefile.am is that I commented out the members of the SUBDIRS variable
>>> other than eigenproblems_ex2 which I modified the .C file of.
>>>
>>> My Professor never used make check when downloading libmesh-1.0.0-rc1.
>>> Instead he used make run_examples.
>>>
>>> Does anyone know why the example programs aren't running (they ran the
>>> first time) and how to fix it?
>>>
>>> Thankfully,
>>> Harry Pearce
>>> ------------------------------------------------------------
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