libmesh-users — General information for libmesh users

Re: [Libmesh-users] errno error

[John P. <jwp...@gm...>]

On Tue, Nov 14, 2017 at 11:23 PM, Griffith, Boyce Eugene <
bo...@em...> wrote:

> We are running into a problem with errno and/or ENOMEM on an Ubuntu system
> using either Clang 3.8 or GCC 5.4, which are the compilers on whatever LTS
> version of Ubuntu is being used on this system.
>
> With clang, the error looks like:
>
> ==========
>
> make[2]: Entering directory '/srv/clang-sfw/linux/libmesh/
> 1.2.0/objs-debug'
> CXX      src/mesh/libmesh_dbg_la-exodusII_io_helper.lo
> In file included from ../LIBMESH/src/mesh/exodusII_io_helper.C:32:
> In file included from ./include/libmesh/system.h:30:
> In file included from ./include/libmesh/fem_function_base.h:29:
> In file included from ./include/libmesh/dense_vector.h:31:
> In file included from ../LIBMESH/contrib/eigen/eigen/Eigen/Dense:1:
> In file included from ../LIBMESH/contrib/eigen/eigen/Eigen/Core:256:
> ../LIBMESH/contrib/eigen/eigen/Eigen/src/Core/util/Memory.h:168:5: error:
> use of undeclared identifier
>     '__errno_location'; did you mean 'exII::__errno_location'?
>   errno = ENOMEM; // according to the standard
>   ^
> /usr/include/x86_64-linux-gnu/bits/errno.h:54:20: note: expanded from
> macro 'errno'
> #   define errno (*__errno_location ())
>                  ^
> /usr/include/x86_64-linux-gnu/bits/errno.h:50:13: note:
> 'exII::__errno_location' declared here
> extern int *__errno_location (void) __THROW __attribute__ ((__const__));
>           ^
> 1 error generated.
> Makefile:14763: recipe for target 'src/mesh/libmesh_dbg_la-exodusII_io_helper.lo'
> failed
> make[2]: *** [src/mesh/libmesh_dbg_la-exodusII_io_helper.lo] Error 1
> CXX      src/mesh/libmesh_dbg_la-nemesis_io_helper.lo
> In file included from ../LIBMESH/src/mesh/nemesis_io_helper.C:31:
> In file included from ./include/libmesh/numeric_vector.h:32:
> In file included from ./include/libmesh/dense_subvector.h:25:
> In file included from ./include/libmesh/dense_vector.h:31:
> In file included from ../LIBMESH/contrib/eigen/eigen/Eigen/Dense:1:
> In file included from ../LIBMESH/contrib/eigen/eigen/Eigen/Core:256:
> ../LIBMESH/contrib/eigen/eigen/Eigen/src/Core/util/Memory.h:168:5: error:
> use of undeclared identifier
>     '__errno_location'; did you mean 'exII::__errno_location'?
>   errno = ENOMEM; // according to the standard
>   ^
> /usr/include/x86_64-linux-gnu/bits/errno.h:54:20: note: expanded from
> macro 'errno'
> #   define errno (*__errno_location ())
>                  ^
> /usr/include/x86_64-linux-gnu/bits/errno.h:50:13: note:
> 'exII::__errno_location' declared here
> extern int *__errno_location (void) __THROW __attribute__ ((__const__));
>           ^
> 1 error generated.
> Makefile:14987: recipe for target 'src/mesh/libmesh_dbg_la-nemesis_io_helper.lo'
> failed
>
> ==========
>
> It looks like there is an attempt to work around this on some compilers
> (LIBMESH_COMPILER_HAS_BROKEN_ERRNO_T), but manually setting that flag to
> 1 did not seem to make any difference.
>
> This is with libMesh 1.2.0.
>
> Is there an easy workaround?
>

I think that --disable-eigen can also "fix" this, with the obvious caveat
that you won't be able to use eigen.

Short of that fix, using a different compiler is probably the quickest
thing to try.

My theory about this error was that it is caused when the C header file
<errno.h> is included from within a C++ namespace.

A workaround that fixed the problem on at least one system was to just
#include <errno.h> before the enclosing namespace, but that fix does not
appear to work in general...

-- 
John

Re: [Libmesh-users] Given a physical (or reference, outside of domain) point, which element does it belong to?

[Roy S. <roy...@ic...>]

On Wed, 15 Nov 2017, Zack Vitoh wrote:

> I think
> http://libmesh.github.io/doxygen/classlibMesh_1_1SubdomainPartitioner.html#details
>
> May help, but still not sure if this is the best approach

No, that's unrelated to what you want to do.

The class you should look up is
https://libmesh.github.io/doxygen/classlibMesh_1_1PointLocatorBase.html

and the method you want to look at in the library is
"sub_point_locator" in MeshBase.

The default PointLocatorTree implementation uses a binary/quad/oct
tree (in 1/2/3D) and will give you a logarithmic search time.

If you have *really* large meshes, then you might be able to come up
with a faster custom locator (e.g. if you know your quadrature points
will be in an element touching the current element, then you could use
Elem::find_point_neighbors() to get all those elements, and check just
those for an O(1) search with a lousy constant), but the point locator
will probably be the best way to get started simply.
---
Roy

> On Tue, Nov 14, 2017 at 10:17 PM, Zack Vitoh <jan...@gm...> wrote:
>
>> I could loop over (a subset of) all elements in the mesh, but is there a
>> function within a class that achieves this (possibly more efficiently?)
>>
>> Thanks!
>>
>> PS: I am trying to incorporate a "nonlocal quadrature rule" where the
>> nonlocal quadrature involves points outside of the current element.  If any
>> other advice can be provided (e.g. specific classes/functions to look at)
>> to this end, I'd appreciate it, as I am going about this in what feels to
>> be a hackish, wrong way.
>>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>
>

Re: [Libmesh-users] Given a physical (or reference, outside of domain) point, which element does it belong to?

[Zack V. <jan...@gm...>]

I think
http://libmesh.github.io/doxygen/classlibMesh_1_1SubdomainPartitioner.html#details

May help, but still not sure if this is the best approach


On Tue, Nov 14, 2017 at 10:17 PM, Zack Vitoh <jan...@gm...> wrote:

> I could loop over (a subset of) all elements in the mesh, but is there a
> function within a class that achieves this (possibly more efficiently?)
>
> Thanks!
>
> PS: I am trying to incorporate a "nonlocal quadrature rule" where the
> nonlocal quadrature involves points outside of the current element.  If any
> other advice can be provided (e.g. specific classes/functions to look at)
> to this end, I'd appreciate it, as I am going about this in what feels to
> be a hackish, wrong way.
>

[Libmesh-users] errno error

[Griffith, B. E. <bo...@em...>]

We are running into a problem with errno and/or ENOMEM on an Ubuntu system using either Clang 3.8 or GCC 5.4, which are the compilers on whatever LTS version of Ubuntu is being used on this system.

With clang, the error looks like:

==========

make[2]: Entering directory '/srv/clang-sfw/linux/libmesh/1.2.0/objs-debug'
CXX      src/mesh/libmesh_dbg_la-exodusII_io_helper.lo
In file included from ../LIBMESH/src/mesh/exodusII_io_helper.C:32:
In file included from ./include/libmesh/system.h:30:
In file included from ./include/libmesh/fem_function_base.h:29:
In file included from ./include/libmesh/dense_vector.h:31:
In file included from ../LIBMESH/contrib/eigen/eigen/Eigen/Dense:1:
In file included from ../LIBMESH/contrib/eigen/eigen/Eigen/Core:256:
../LIBMESH/contrib/eigen/eigen/Eigen/src/Core/util/Memory.h:168:5: error: use of undeclared identifier
    '__errno_location'; did you mean 'exII::__errno_location'?
  errno = ENOMEM; // according to the standard
  ^
/usr/include/x86_64-linux-gnu/bits/errno.h:54:20: note: expanded from macro 'errno'
#   define errno (*__errno_location ())
                 ^
/usr/include/x86_64-linux-gnu/bits/errno.h:50:13: note: 'exII::__errno_location' declared here
extern int *__errno_location (void) __THROW __attribute__ ((__const__));
          ^
1 error generated.
Makefile:14763: recipe for target 'src/mesh/libmesh_dbg_la-exodusII_io_helper.lo' failed
make[2]: *** [src/mesh/libmesh_dbg_la-exodusII_io_helper.lo] Error 1
CXX      src/mesh/libmesh_dbg_la-nemesis_io_helper.lo
In file included from ../LIBMESH/src/mesh/nemesis_io_helper.C:31:
In file included from ./include/libmesh/numeric_vector.h:32:
In file included from ./include/libmesh/dense_subvector.h:25:
In file included from ./include/libmesh/dense_vector.h:31:
In file included from ../LIBMESH/contrib/eigen/eigen/Eigen/Dense:1:
In file included from ../LIBMESH/contrib/eigen/eigen/Eigen/Core:256:
../LIBMESH/contrib/eigen/eigen/Eigen/src/Core/util/Memory.h:168:5: error: use of undeclared identifier
    '__errno_location'; did you mean 'exII::__errno_location'?
  errno = ENOMEM; // according to the standard
  ^
/usr/include/x86_64-linux-gnu/bits/errno.h:54:20: note: expanded from macro 'errno'
#   define errno (*__errno_location ())
                 ^
/usr/include/x86_64-linux-gnu/bits/errno.h:50:13: note: 'exII::__errno_location' declared here
extern int *__errno_location (void) __THROW __attribute__ ((__const__));
          ^
1 error generated.
Makefile:14987: recipe for target 'src/mesh/libmesh_dbg_la-nemesis_io_helper.lo' failed

==========

It looks like there is an attempt to work around this on some compilers (LIBMESH_COMPILER_HAS_BROKEN_ERRNO_T), but manually setting that flag to 1 did not seem to make any difference.

This is with libMesh 1.2.0.

Is there an easy workaround?

Thanks!

-- Boyce

[Libmesh-users] question about NumericVector

[Michael P. <mpo...@pu...>]

Dear Libmesh community,

I would like to output a nodal data stored in NumericVector, using

void libMesh::MeshOutput< MT >::write_nodal_data     ( const std::string 
&      fname,
         const NumericVector< Number > & parallel_soln,
         const std::vector< std::string > &      names
     )

I need to fill NumericVector with values.

As far as I understand, I need to provide data both for active and 
non-active nodes, because the NumericVector contains entities for all 
local nodes.

Questions:

1. Will I get correct order if I iterate from mesh.local_nodes_begin() 
to mesh.local_nodes_end() ?

2. Will the values I set for non active nodes matter for the output?

Thank you,

Michael.

[Libmesh-users] Given a physical (or reference, outside of domain) point, which element does it belong to?

[Zack V. <jan...@gm...>]

I could loop over (a subset of) all elements in the mesh, but is there a
function within a class that achieves this (possibly more efficiently?)

Thanks!

PS: I am trying to incorporate a "nonlocal quadrature rule" where the
nonlocal quadrature involves points outside of the current element.  If any
other advice can be provided (e.g. specific classes/functions to look at)
to this end, I'd appreciate it, as I am going about this in what feels to
be a hackish, wrong way.

Re: [Libmesh-users] try-catch in a PETSc solve()

[Jed B. <je...@je...>]

"Salazar De Troya, Miguel" <sal...@ll...> writes:

> I ran the code with –info and got a quite lengthy output that I am attaching. For some reason, now the error is (last line of the attached output):

I'm still not sure what triggers the error and with the non-determinism
you seem to have just observed, I would start by ruling out memory
corruption.  Can you reproduce with a smaller problem size and/or fewer
processes?  Can you run with a memory checker (valgrind is easy but
slow, alternative is to compile your whole stack with gcc
-fsanitize=address)?

If those are clean, it would be faster if you can share code to
reproduce versus trying to operate a debugging session via email.  Can
you share code to reproduce, either on this list or to
pet...@mc... (private list with PETSc developers)?

> Linear Elasticity_ solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0
> PCSETUP_FAILED due to SUBPC_ERROR
>
> Not sure why, because I am not specifying any –sub_pc in my options. Which other messages should I look into?

Re: [Libmesh-users] try-catch in a PETSc solve()

[John P. <jwp...@gm...>]

On Sat, Nov 11, 2017 at 2:14 PM, Salazar De Troya, Miguel <
sal...@ll...> wrote:

> Hello
>
>
> I have an optimization problem for which at a certain iteration, PETSc
> fails to build the preconditioner. I would like to catch that error and
> print my EquationSystem to disk so I can rerun the PETSc solve at that
> optimization iteration from the start. I cannot just rerun my optimization
> and write to disk at the iteration I know it is going to fail. The reason
> is that in parallel the optimization slightly differs every time I run it
> so the iteration it is going to fail at keeps changing. Maybe something
> along this lines:
>
>
> try{
>
>     system.solve()
>
> }
>
> catch(...){
>
>    EquationSystem & es = system.get_equation_systems();
>
>    es.write("eq_output.xdr")
>
> }
>

I'm pretty sure we don't throw an exception when a solve fails, so there's
not going to be anything for you to catch here...

For a LinearImplicitSystem, the usual approach is to inspect the value of

system.get_linear_solver()->get_converged_reason();

and then decide what to do (retry the last time step, etc.) from there.

When you say "optimization problem" are you actually using the TAO-based
OptimizationSystem class that is in libmesh?

-- 
John

Re: [Libmesh-users] libMesh Make Error

[Braden F. <bf...@um...>]

I am still having difficulties with this issue. Any suggestions are welcome.

Thanks,
Braden Frigoletto

Braden Frigoletto

On Fri, Nov 10, 2017 at 11:35 AM, John Peterson <jwp...@gm...>
wrote:

>
>
> On Fri, Nov 10, 2017 at 9:30 AM, Braden Frigoletto <bf...@um...>
> wrote:
>
>> No Im trying to build libMesh for the first time through VirtualBox.
>>
>> It's interesting you mention netcdf. When I first tried to configure
>> libMesh I received an error about netcdf and dap and there was an auto
>> suggestion that I should try running configure with netcdf-4 and dap
>> disabled. I disabled them and ran configure again and it worked fine. Could
>> this be where the problem is arising? Do I need to have netcdf-4 and dap
>> enabled?
>>
>
>
> Sorry, but you've quickly exceeded my limited knowledge of netcdf
> configure options. I don't think I've ever had to stray from the default
> netcdf configuration flags in order to get libmesh to build...
>
> --
> John
>

Re: [Libmesh-users] try-catch in a PETSc solve()

[Jed B. <je...@je...>]

"Salazar De Troya, Miguel" <sal...@ll...> writes:

> No. There does not seem to be more output. The program keeps running, but after the first time I see this error, all subsequent solves return a "nan" residual norm and the same preconditioner error pops up. Is there any way to obtain more output? This is the output in the context of the KSPSolve:
>
>
> First solve where the preconditioner fails:
>
>
> Residual norms for Elasticity_ solve.
> 0 KSP unpreconditioned resid norm 1.421591570438e+02 true resid norm 1.421591570438e+02 ||r(i)||/||b|| 1.000000000000e+00
> Linear Elasticity_ solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0
> PCSETUP_FAILED due to FACTOR_NOERROR

What code is printing this last line?  The PC isn't of type Factor so I
don't see why it would be printed.  You could try running with -info to
get more detailed information from PETSc.  Or run in a debugger.

The Libmesh/user code on the outside probably shouldn't naively continue
after the first error.  It could, for example, recompute the operators
with a smaller time step and retry the solve.

> Following solves (the optimization keeps running) all look like this:
>
> Residual norms for Elasticity_ solve.
> 0 KSP unpreconditioned resid norm 1.450166975748e+02 true resid norm           -nan ||r(i)||/||b||           -nan
> Linear Elasticity_ solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0
> PCSETUP_FAILED due to FACTOR_NOERROR
>
> Any way I can catch this PCSETUP_FAILED due to FACTOR_NOERROR?
>
>
> Miguel
>
> ________________________________
> From: Jed Brown <je...@je...>
> Sent: Sunday, November 12, 2017 12:11:29 PM
> To: Salazar De Troya, Miguel; lib...@li...
> Subject: Re: [Libmesh-users] try-catch in a PETSc solve()
>
> "Salazar De Troya, Miguel" <sal...@ll...> writes:
>
>> The error is:
>>
>>
>> Linear Elasticity_ solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0
>
> This is PETSc output due to
>
>   -Elasticity_ksp_converged_reason
>
> It doesn't set an error.
>
>>                                       PCSETUP_FAILED due to FACTOR_NOERROR
>
> Is there really no other output?  Always send all the output.
>
>> The program actually continues, Is there any way I can catch this divergence and do some operation like writing to disk?
>>
>> Thanks
>> Miguel
>>
>>
>>
>> ________________________________
>> From: Jed Brown <je...@je...>
>> Sent: Saturday, November 11, 2017 1:43:32 PM
>> To: Salazar De Troya, Miguel; lib...@li...
>> Subject: Re: [Libmesh-users] try-catch in a PETSc solve()
>>
>> What is your error message?  If the error is raised in PETSc, there is
>> usually a setting to make it return without raising an error (instead
>> setting a "diverged" reason).
>>
>> "Salazar De Troya, Miguel" <sal...@ll...> writes:
>>
>>> Hello
>>>
>>>
>>> I have an optimization problem for which at a certain iteration, PETSc fails to build the preconditioner. I would like to catch that error and print my EquationSystem to disk so I can rerun the PETSc solve at that optimization iteration from the start. I cannot just rerun my optimization and write to disk at the iteration I know it is going to fail. The reason is that in parallel the optimization slightly differs every time I run it so the iteration it is going to fail at keeps changing. Maybe something along this lines:
>>>
>>>
>>> try{
>>>
>>>     system.solve()
>>>
>>> }
>>>
>>> catch(...){
>>>
>>>    EquationSystem & es = system.get_equation_systems();
>>>
>>>    es.write("eq_output.xdr")
>>>
>>> }
>>>
>>>
>>> Thanks
>>>
>>> Miguel
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> Libmesh-users mailing list
>>> Lib...@li...
>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users

Re: [Libmesh-users] try-catch in a PETSc solve()

[Salazar De T. M. <sal...@ll...>]

No. There does not seem to be more output. The program keeps running, but after the first time I see this error, all subsequent solves return a "nan" residual norm and the same preconditioner error pops up. Is there any way to obtain more output? This is the output in the context of the KSPSolve:


First solve where the preconditioner fails:


Residual norms for Elasticity_ solve.
0 KSP unpreconditioned resid norm 1.421591570438e+02 true resid norm 1.421591570438e+02 ||r(i)||/||b|| 1.000000000000e+00
Linear Elasticity_ solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0
PCSETUP_FAILED due to FACTOR_NOERROR

Following solves (the optimization keeps running) all look like this:

Residual norms for Elasticity_ solve.
0 KSP unpreconditioned resid norm 1.450166975748e+02 true resid norm           -nan ||r(i)||/||b||           -nan
Linear Elasticity_ solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0
PCSETUP_FAILED due to FACTOR_NOERROR

Any way I can catch this PCSETUP_FAILED due to FACTOR_NOERROR?


Miguel

________________________________
From: Jed Brown <je...@je...>
Sent: Sunday, November 12, 2017 12:11:29 PM
To: Salazar De Troya, Miguel; lib...@li...
Subject: Re: [Libmesh-users] try-catch in a PETSc solve()

"Salazar De Troya, Miguel" <sal...@ll...> writes:

> The error is:
>
>
> Linear Elasticity_ solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0

This is PETSc output due to

  -Elasticity_ksp_converged_reason

It doesn't set an error.

>                                       PCSETUP_FAILED due to FACTOR_NOERROR

Is there really no other output?  Always send all the output.

> The program actually continues, Is there any way I can catch this divergence and do some operation like writing to disk?
>
> Thanks
> Miguel
>
>
>
> ________________________________
> From: Jed Brown <je...@je...>
> Sent: Saturday, November 11, 2017 1:43:32 PM
> To: Salazar De Troya, Miguel; lib...@li...
> Subject: Re: [Libmesh-users] try-catch in a PETSc solve()
>
> What is your error message?  If the error is raised in PETSc, there is
> usually a setting to make it return without raising an error (instead
> setting a "diverged" reason).
>
> "Salazar De Troya, Miguel" <sal...@ll...> writes:
>
>> Hello
>>
>>
>> I have an optimization problem for which at a certain iteration, PETSc fails to build the preconditioner. I would like to catch that error and print my EquationSystem to disk so I can rerun the PETSc solve at that optimization iteration from the start. I cannot just rerun my optimization and write to disk at the iteration I know it is going to fail. The reason is that in parallel the optimization slightly differs every time I run it so the iteration it is going to fail at keeps changing. Maybe something along this lines:
>>
>>
>> try{
>>
>>     system.solve()
>>
>> }
>>
>> catch(...){
>>
>>    EquationSystem & es = system.get_equation_systems();
>>
>>    es.write("eq_output.xdr")
>>
>> }
>>
>>
>> Thanks
>>
>> Miguel
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Libmesh-users mailing list
>> Lib...@li...
>> https://lists.sourceforge.net/lists/listinfo/libmesh-users

Re: [Libmesh-users] Defining Quadrature Rule (like QGauss) to be used with FEBase

[Zack V. <jan...@gm...>]

Thanks, that should simplify things a bit!

I am making a (double integral) quadrature rule that, for each element,
uses information (phi, J, etc) from the neighbors (within a physical
horizon) of that element.

I'm trying to figure out how to do this elegantly (and hopefully,
efficiently).

Specifically: I can't seem to find a way to explicitly compute, given a
physical point (and possibly a reference to the element that contains it)
the values of the shape functions etc
(at least, not without going through fe->reinit(...), which is complicated
enough that it makes me question if I have used it incorrectly)

Thanks again

On Wed, Nov 8, 2017 at 10:24 AM, John Peterson <jwp...@gm...> wrote:

>
>
> On Wed, Nov 8, 2017 at 6:56 AM, Roy Stogner <roy...@ic...>
> wrote:
>
>>
>> On Tue, 7 Nov 2017, Zack Vitoh wrote:
>>
>> I want to develop a nonstandard quadrature rule and use it as in
>>> introduction_ex3.  Is there a way to do this simply,
>>>
>>
>> Yes: after you add your new files (and the corresponding entry in
>> quadrature_build.C), run a few scripts (as detailed in
>> https://github.com/libMesh/libmesh/wiki/Adding-or-removing-source-files
>> on the wiki) to put them into the build systems, and run "make" again.
>>
>> without rebuilding everything?
>>>
>>
>> Probably not, I fear.  Putting new files into the build system will
>> cause configure to re-run, configure will probably generate a new
>> libmesh_config.h, pretty much every object file depends on
>> libmesh_config.h, and so the entire tree will be rebuilt.
>>
>
> True, but it's not strictly necessary to add new quadrature code to the
> library in order to test it out in an app.
>
> Just put a class derived from libMesh::QBase in your application directory
> and construct one manually i.e. don't call the static QBase::build() method
> yet.
>
> --
> John
>

Re: [Libmesh-users] Installation Error of Libmesh v1.0.0 on Linux Arch

[John P. <jwp...@gm...>]

On Fri, Nov 10, 2017 at 4:05 PM, Dafang Wang <daf...@jh...> wrote:

> Hi John,
> Please see my replies below.
>
> On 11/10/2017 11:31 AM, John Peterson wrote:
>
>> On Thu, Nov 9, 2017 at 8:32 PM, Dafang Wang <daf...@jh... <mailto:
>> daf...@jh...>> wrote:
>>
>>     Hi,
>>
>>     I got the following error when installing Libmesh v1.0.0 with
>>     PETSC v3.6.4/3.5.4 (neither Petsc worked).
>>
>> What does this mean? What were the error messages? 1.0.0 was tagged in
>> June 2016, PETSc 3.6 was tagged in summer 2015 and should definitely work
>> with that version of libmesh.
>>
>>     I am installing an older version of Libmesh because only that
>>     version is compatible with my user code.
>>
>>
>> I'm curious how extensive the incompatibilities are. It may be something
>> that can be remedied fairly easily with some mailing list support.
>>
> The last time my code was successfully built, it was with Libmesh 1.0.0
> and Petsc 3.5.4; it was built in Aug 2016.  However, I couldn't even
> reproduce the same installation on another linux desktop yesterday.
>
> My code got different errors when compiling with various recent versions
> of Libmesh (see below). It seems Libmesh removed some data structures such
> as "mesh_data.h", so I am not sure how much work it will take to adapt my
> user code to the latest version of Libmesh.
>

Yes, MeshData was deprecated for several years and finally removed in
1.2.0. Were you actually using it in your application? The standard advice
is to store data fields on an ExplicitSystem object, as this approach works
in parallel and on adaptively-refined grids.




>
> _*When compiling my code with Libmesh 1.2.0 and the latest Petsc (both
> were successfully built), I got the following error:*_
> /home/dwang/research/libmesh_mech/latest/CardiacSystemMaker.hpp:7:10:
> fatal error: petsc.h: No such file or directory
>  #include <petsc.h>
>           ^~~~~~~~~
> compilation terminated.
>


There is most likely something wrong with your application Makefile. You
should be using the "libmesh-config --cxxflags" script to pass the list of
the include paths to the compiler while compiling your app...



> make[2]: *** [CMakeFiles/cardiacMech.dir/build.make:92:
> CMakeFiles/cardiacMech.dir/CardiacSystemMaker.cpp.o] Error 1
> [ 33%] Building CXX object CMakeFiles/cardiacMech.dir/CarpMeshIO.cpp.o
> /home/dwang/research/libmesh_mech/latest/CarpMeshIO.cpp:24:10: fatal
> error: libmesh/mesh_data.h: No such file or directory
>  #include <libmesh/mesh_data.h>
>           ^~~~~~~~~~~~~~~~~~~~~
> compilation terminated.
>

Right, the MeshData object was removed.




> ------------------------------------------------------------------------
> *_When compiling my code with Libmesh 1.1.0 and Petsc 3.7.7, I got the
> folliwng error:_*
>
> /home/dwang/research/libmesh_mech/LibmeshMechanic_2017_0701/parallel.cpp:8:15:
> error: template-id ‘send<unsigned int>’ for ‘void
> libMesh::Parallel::Communicator::send(unsigned int, unsigned int&, const
> libMesh::Parallel::MessageTag&) const’ does not match any template
> declaration
>  template void libMesh::Parallel::Communicator::send<unsigned
> int>(unsigned int, unsigned int&, libMesh::Parallel::MessageTag const&)
> const;
>                ^~~~~~~
> In file included from /home/dwang/program/libmesh-1.
> 1.0/RelWithDebInfo/include/libmesh/parallel.h:1302:0,
>                  from /home/dwang/research/libmesh_m
> ech/LibmeshMechanic_2017_0701/utility.hpp:14,
>                  from /home/dwang/research/libmesh_m
> ech/LibmeshMechanic_2017_0701/parallel.cpp:4:
> /home/dwang/program/libmesh-1.1.0/RelWithDebInfo/include/lib
> mesh/parallel_communicator_specializations:114:10: note: candidates are:
> template<class T> void libMesh::Parallel::Communicator::send(unsigned
> int, const std::vector<T>&, const libMesh::Parallel::DataType&,
> libMesh::Parallel::Request&, const libMesh::Parallel::MessageTag&) const
>      void send (const unsigned int dest_processor_id,
>           ^~~~
> /home/dwang/program/libmesh-1.1.0/RelWithDebInfo/include/lib
> mesh/parallel_communicator_specializations:108:10: note:
> template<class T> void libMesh::Parallel::Communicator::send(unsigned
> int, const std::vector<T>&, const libMesh::Parallel::DataType&, const
> libMesh::Parallel::MessageTag&) const
>      void send (const unsigned int dest_processor_id,
>           ^~~~
> /home/dwang/program/libmesh-1.1.0/RelWithDebInfo/include/lib
> mesh/parallel_communicator_specializations:102:10: note:
> template<class T> void libMesh::Parallel::Communicator::send(unsigned
> int, const std::vector<T>&, libMesh::Parallel::Request&, const
> libMesh::Parallel::MessageTag&) const
>      void send (const unsigned int dest_processor_id,



This has nothing to do with PETSc and I don't think it's a version
incompatibility thing either. You might need to post the actual line of
code that triggers this error message for us to diagnose it further. It's
possible that we are missing a particular specialization for
Communicator::Send, but then I am confused how this line of code would have
ever worked...

-- 
John

Re: [Libmesh-users] try-catch in a PETSc solve()

[Jed B. <je...@je...>]

"Salazar De Troya, Miguel" <sal...@ll...> writes:

> The error is:
>
>
> Linear Elasticity_ solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0

This is PETSc output due to

  -Elasticity_ksp_converged_reason

It doesn't set an error.

>                                       PCSETUP_FAILED due to FACTOR_NOERROR

Is there really no other output?  Always send all the output.

> The program actually continues, Is there any way I can catch this divergence and do some operation like writing to disk?
>
> Thanks
> Miguel
>
>
>
> ________________________________
> From: Jed Brown <je...@je...>
> Sent: Saturday, November 11, 2017 1:43:32 PM
> To: Salazar De Troya, Miguel; lib...@li...
> Subject: Re: [Libmesh-users] try-catch in a PETSc solve()
>
> What is your error message?  If the error is raised in PETSc, there is
> usually a setting to make it return without raising an error (instead
> setting a "diverged" reason).
>
> "Salazar De Troya, Miguel" <sal...@ll...> writes:
>
>> Hello
>>
>>
>> I have an optimization problem for which at a certain iteration, PETSc fails to build the preconditioner. I would like to catch that error and print my EquationSystem to disk so I can rerun the PETSc solve at that optimization iteration from the start. I cannot just rerun my optimization and write to disk at the iteration I know it is going to fail. The reason is that in parallel the optimization slightly differs every time I run it so the iteration it is going to fail at keeps changing. Maybe something along this lines:
>>
>>
>> try{
>>
>>     system.solve()
>>
>> }
>>
>> catch(...){
>>
>>    EquationSystem & es = system.get_equation_systems();
>>
>>    es.write("eq_output.xdr")
>>
>> }
>>
>>
>> Thanks
>>
>> Miguel
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> Libmesh-users mailing list
>> Lib...@li...
>> https://lists.sourceforge.net/lists/listinfo/libmesh-users

Re: [Libmesh-users] try-catch in a PETSc solve()

[Salazar De T. M. <sal...@ll...>]

The petsc options for the system are as follows:


-Elasticity_ksp_monitor_true_residual
-Elasticity_ksp_converged_reason
-Elasticity_ksp_type cg
-Elasticity_log_view
-Elasticity_mg_levels_esteig_ksp_type cg
-Elasticity_mg_levels_ksp_chebyshev_esteig_steps 50
-Elasticity_mg_levels_ksp_type chebyshev
-Elasticity_mg_levels_pc_type sor
-Elasticity_pc_type gamg
-Elasticity_pc_gamg_verbose 7
-Elasticity_pc_gamg_type agg
-Elasticity_pc_gamg_agg_nsmooths 1
-Elasticity_pc_gamg_threshold 0.001
-Elasticity_snes_linesearch_type basic
-Elasticity_snes_atol 1e-6
-Elasticity_ksp_atol 1e-7
-Elasticity_ksp_rtol 1e-9
-Elasticity_ksp_norm_type unpreconditioned


I pass the rigid body modes to the solver.

________________________________
From: Jed Brown <je...@je...>
Sent: Saturday, November 11, 2017 1:43:32 PM
To: Salazar De Troya, Miguel; lib...@li...
Subject: Re: [Libmesh-users] try-catch in a PETSc solve()

What is your error message?  If the error is raised in PETSc, there is
usually a setting to make it return without raising an error (instead
setting a "diverged" reason).

"Salazar De Troya, Miguel" <sal...@ll...> writes:

> Hello
>
>
> I have an optimization problem for which at a certain iteration, PETSc fails to build the preconditioner. I would like to catch that error and print my EquationSystem to disk so I can rerun the PETSc solve at that optimization iteration from the start. I cannot just rerun my optimization and write to disk at the iteration I know it is going to fail. The reason is that in parallel the optimization slightly differs every time I run it so the iteration it is going to fail at keeps changing. Maybe something along this lines:
>
>
> try{
>
>     system.solve()
>
> }
>
> catch(...){
>
>    EquationSystem & es = system.get_equation_systems();
>
>    es.write("eq_output.xdr")
>
> }
>
>
> Thanks
>
> Miguel
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users

Re: [Libmesh-users] try-catch in a PETSc solve()

[Salazar De T. M. <sal...@ll...>]

The error is:


Linear Elasticity_ solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0
                                      PCSETUP_FAILED due to FACTOR_NOERROR

The program actually continues, Is there any way I can catch this divergence and do some operation like writing to disk?

Thanks
Miguel



________________________________
From: Jed Brown <je...@je...>
Sent: Saturday, November 11, 2017 1:43:32 PM
To: Salazar De Troya, Miguel; lib...@li...
Subject: Re: [Libmesh-users] try-catch in a PETSc solve()

What is your error message?  If the error is raised in PETSc, there is
usually a setting to make it return without raising an error (instead
setting a "diverged" reason).

"Salazar De Troya, Miguel" <sal...@ll...> writes:

> Hello
>
>
> I have an optimization problem for which at a certain iteration, PETSc fails to build the preconditioner. I would like to catch that error and print my EquationSystem to disk so I can rerun the PETSc solve at that optimization iteration from the start. I cannot just rerun my optimization and write to disk at the iteration I know it is going to fail. The reason is that in parallel the optimization slightly differs every time I run it so the iteration it is going to fail at keeps changing. Maybe something along this lines:
>
>
> try{
>
>     system.solve()
>
> }
>
> catch(...){
>
>    EquationSystem & es = system.get_equation_systems();
>
>    es.write("eq_output.xdr")
>
> }
>
>
> Thanks
>
> Miguel
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users

Re: [Libmesh-users] try-catch in a PETSc solve()

[Jed B. <je...@je...>]

What is your error message?  If the error is raised in PETSc, there is
usually a setting to make it return without raising an error (instead
setting a "diverged" reason).

"Salazar De Troya, Miguel" <sal...@ll...> writes:

> Hello
>
>
> I have an optimization problem for which at a certain iteration, PETSc fails to build the preconditioner. I would like to catch that error and print my EquationSystem to disk so I can rerun the PETSc solve at that optimization iteration from the start. I cannot just rerun my optimization and write to disk at the iteration I know it is going to fail. The reason is that in parallel the optimization slightly differs every time I run it so the iteration it is going to fail at keeps changing. Maybe something along this lines:
>
>
> try{
>
>     system.solve()
>
> }
>
> catch(...){
>
>    EquationSystem & es = system.get_equation_systems();
>
>    es.write("eq_output.xdr")
>
> }
>
>
> Thanks
>
> Miguel
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users

[Libmesh-users] try-catch in a PETSc solve()

[Salazar De T. M. <sal...@ll...>]

Hello


I have an optimization problem for which at a certain iteration, PETSc fails to build the preconditioner. I would like to catch that error and print my EquationSystem to disk so I can rerun the PETSc solve at that optimization iteration from the start. I cannot just rerun my optimization and write to disk at the iteration I know it is going to fail. The reason is that in parallel the optimization slightly differs every time I run it so the iteration it is going to fail at keeps changing. Maybe something along this lines:


try{

    system.solve()

}

catch(...){

   EquationSystem & es = system.get_equation_systems();

   es.write("eq_output.xdr")

}


Thanks

Miguel

Re: [Libmesh-users] Installation Error of Libmesh v1.0.0 on Linux Arch

[Dafang W. <daf...@jh...>]

Hi John,
Please see my replies below.

On 11/10/2017 11:31 AM, John Peterson wrote:
> On Thu, Nov 9, 2017 at 8:32 PM, Dafang Wang <daf...@jh... 
> <mailto:daf...@jh...>> wrote:
>
>     Hi,
>
>     I got the following error when installing Libmesh v1.0.0 with
>     PETSC v3.6.4/3.5.4 (neither Petsc worked). 
>
>
> What does this mean? What were the error messages? 1.0.0 was tagged in 
> June 2016, PETSc 3.6 was tagged in summer 2015 and should definitely 
> work with that version of libmesh.
>
>     I am installing an older version of Libmesh because only that
>     version is compatible with my user code.
>
>
> I'm curious how extensive the incompatibilities are. It may be 
> something that can be remedied fairly easily with some mailing list 
> support.
The last time my code was successfully built, it was with Libmesh 1.0.0 
and Petsc 3.5.4; it was built in Aug 2016.  However, I couldn't even 
reproduce the same installation on another linux desktop yesterday.

My code got different errors when compiling with various recent versions 
of Libmesh (see below). It seems Libmesh removed some data structures 
such as "mesh_data.h", so I am not sure how much work it will take to 
adapt my user code to the latest version of Libmesh.

_*When compiling my code with Libmesh 1.2.0 and the latest Petsc (both 
were successfully built), I got the following error:*_
/home/dwang/research/libmesh_mech/latest/CardiacSystemMaker.hpp:7:10: 
fatal error: petsc.h: No such file or directory
  #include <petsc.h>
           ^~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/cardiacMech.dir/build.make:92: 
CMakeFiles/cardiacMech.dir/CardiacSystemMaker.cpp.o] Error 1
[ 33%] Building CXX object CMakeFiles/cardiacMech.dir/CarpMeshIO.cpp.o
/home/dwang/research/libmesh_mech/latest/CarpMeshIO.cpp:24:10: fatal 
error: libmesh/mesh_data.h: No such file or directory
  #include <libmesh/mesh_data.h>
           ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
------------------------------------------------------------------------
*_When compiling my code with Libmesh 1.1.0 and Petsc 3.7.7, I got the 
folliwng error:_*

/home/dwang/research/libmesh_mech/LibmeshMechanic_2017_0701/parallel.cpp:8:15: 
error: template-id ‘send<unsigned int>’ for ‘void 
libMesh::Parallel::Communicator::send(unsigned int, unsigned int&, const 
libMesh::Parallel::MessageTag&) const’ does not match any template 
declaration
  template void libMesh::Parallel::Communicator::send<unsigned 
int>(unsigned int, unsigned int&, libMesh::Parallel::MessageTag const&) 
const;
                ^~~~~~~
In file included from 
/home/dwang/program/libmesh-1.1.0/RelWithDebInfo/include/libmesh/parallel.h:1302:0,
                  from 
/home/dwang/research/libmesh_mech/LibmeshMechanic_2017_0701/utility.hpp:14,
                  from 
/home/dwang/research/libmesh_mech/LibmeshMechanic_2017_0701/parallel.cpp:4:
/home/dwang/program/libmesh-1.1.0/RelWithDebInfo/include/libmesh/parallel_communicator_specializations:114:10: 
note: candidates are: template<class T> void 
libMesh::Parallel::Communicator::send(unsigned int, const 
std::vector<T>&, const libMesh::Parallel::DataType&, 
libMesh::Parallel::Request&, const libMesh::Parallel::MessageTag&) const
      void send (const unsigned int dest_processor_id,
           ^~~~
/home/dwang/program/libmesh-1.1.0/RelWithDebInfo/include/libmesh/parallel_communicator_specializations:108:10: 
note:                 template<class T> void 
libMesh::Parallel::Communicator::send(unsigned int, const 
std::vector<T>&, const libMesh::Parallel::DataType&, const 
libMesh::Parallel::MessageTag&) const
      void send (const unsigned int dest_processor_id,
           ^~~~
/home/dwang/program/libmesh-1.1.0/RelWithDebInfo/include/libmesh/parallel_communicator_specializations:102:10: 
note:                 template<class T> void 
libMesh::Parallel::Communicator::send(unsigned int, const 
std::vector<T>&, libMesh::Parallel::Request&, const 
libMesh::Parallel::MessageTag&) const
      void send (const unsigned int dest_processor_id,

>  Any advice would be appreciated. I only found 3 threads on Google 
> regarding this error.
>
>
>     nc4internal.c:393:1: error: conflicting types for
>     ‘nc4_rec_find_nc_type’
>      nc4_rec_find_nc_type(NC_GRP_INFO_T *start_grp, nc_type
>     target_nc_typeid)
>      ^~~~~~~~~~~~~~~~~~~~
>     In file included from nc4internal.c:16:0:
>     ../include/nc4internal.h:319:17: note: previous declaration of
>     ‘nc4_rec_find_nc_type’ was here
>      NC_TYPE_INFO_T *nc4_rec_find_nc_type(NC_GRP_INFO_T *start_grp,
>     hid_t target_nc_typeid);
>                      ^~~~~~~~~~~~~~~~~~~~
>     make[3]: *** [Makefile:493: libnetcdf4_la-nc4internal.lo] Error 1
>     make[3]: *** Waiting for unfinished jobs....
>     make[3]: Leaving directory
>     '/home/dwang/program/libmesh-1.0.0/contrib/netcdf/v4/libsrc4'
>     make[2]: *** [Makefile:610: install-recursive] Error 1
>     make[2]: Leaving directory
>     '/home/dwang/program/libmesh-1.0.0/contrib/netcdf/v4'
>     make[1]: *** [Makefile:978: install-recursive] Error 1
>     make[1]: Leaving directory '/home/dwang/program/libmesh-1.0.0/contrib'
>     make: *** [Makefile:28784: install-recursive] Error 1
>
>
> I believe this bug was fixed by Martin Luethi in libmesh 
> commit 896268d7, however the first version of libmesh that contains 
> that fix is 1.1.0. You could try cherry-picking that commit and seeing 
> if it fixes the problem, but your best long term bet is to just update 
> your user code if possible.
John, you are correct. The above error didn't arise when I was building 
with Libmesh 1.1.0.  However, I got another error (see my replies above).

In summary, my last working code was using Libmesh 1.0.0 and Petsc 
3.5.4, and it was built over 1 year ago. My goal now is to make my code 
work again with minimum effort. Which version of Libmesh/Petsc would you 
suggest me try?    Thanks very much for your advice!

Best,
Dafang

Re: [Libmesh-users] libMesh Make Error

[John P. <jwp...@gm...>]

On Fri, Nov 10, 2017 at 9:30 AM, Braden Frigoletto <bf...@um...> wrote:

> No Im trying to build libMesh for the first time through VirtualBox.
>
> It's interesting you mention netcdf. When I first tried to configure
> libMesh I received an error about netcdf and dap and there was an auto
> suggestion that I should try running configure with netcdf-4 and dap
> disabled. I disabled them and ran configure again and it worked fine. Could
> this be where the problem is arising? Do I need to have netcdf-4 and dap
> enabled?
>


Sorry, but you've quickly exceeded my limited knowledge of netcdf configure
options. I don't think I've ever had to stray from the default netcdf
configuration flags in order to get libmesh to build...

-- 
John

[Libmesh-users] Fwd: libMesh Make Error

[John P. <jwp...@gm...>]

---------- Forwarded message ----------
From: John Peterson <jwp...@gm...>
Date: Fri, Nov 10, 2017 at 9:19 AM
Subject: Re: [Libmesh-users] libMesh Make Error
To: Braden Frigoletto <bf...@um...>




On Fri, Nov 10, 2017 at 8:47 AM, Braden Frigoletto <bf...@um...> wrote:

> Hello,
>
> I'm trying to install libMesh on my Linux system and I'm getting an error
> when running make. It seemed to configure without any issues so I'm not
> sure why this is happening. I've attached my config.log just in case anyone
> would care to look at it. When I run make I receive the following error:
>
>   CXX      src/apps/solution_components_dbg-solution_components.o
>   CXX      src/apps/splitter_dbg-splitter.o
>   CXXLD    libmesh_dbg.la
>   CXXLD    libmesh_opt.la
>   CXXLD    fparser_parse-opt
>   CXXLD    getpot_parse-opt
>   CXXLD    amr-opt
> ./.libs/libmesh_opt.so: undefined reference to `nc_def_var_deflate'
> collect2: error: ld returned 1 exit status
> Makefile:11037: recipe for target 'getpot_parse-opt' failed
> make[1]: *** [getpot_parse-opt] Error 1
> make[1]: *** Waiting for unfinished jobs....
> ./.libs/libmesh_opt.so: undefined reference to `nc_def_var_deflate'
> collect2: error: ld returned 1 exit status
> Makefile:10959: recipe for target 'amr-opt' failed
> make[1]: *** [amr-opt] Error 1
> ./.libs/libmesh_opt.so: undefined reference to `nc_def_var_deflate'
> collect2: error: ld returned 1 exit status
> Makefile:11019: recipe for target 'fparser_parse-opt' failed
> make[1]: *** [fparser_parse-opt] Error 1
> make[1]: Leaving directory '/home/braden/Codes/libmesh'
> Makefile:29211: recipe for target 'all-recursive' failed
> make: *** [all-recursive] Error 1
>
> Any ideas on how to fix this?
>

Did you by any chance have an old libmesh build sitting around for a while
and recently do an update?

We upgraded the version of netcdf that gets distributed with libmesh and I
think I have seen errors similar to this caused by building in an existing
build directory. If that's the case, removing your build directory
completely and rebuilding should get rid of the issue.

-- 
John



-- 
John

Re: [Libmesh-users] Installation Error of Libmesh v1.0.0 on Linux Arch

[John P. <jwp...@gm...>]

On Thu, Nov 9, 2017 at 8:32 PM, Dafang Wang <daf...@jh...> wrote:

> Hi,
>
> I got the following error when installing Libmesh v1.0.0 with PETSC
> v3.6.4/3.5.4 (neither Petsc worked).


What does this mean? What were the error messages? 1.0.0 was tagged in June
2016, PETSc 3.6 was tagged in summer 2015 and should definitely work with
that version of libmesh.




> I am installing an older version of Libmesh because only that version is
> compatible with my user code.
>

I'm curious how extensive the incompatibilities are. It may be something
that can be remedied fairly easily with some mailing list support.



>
> Any advice would be appreciated. I only found 3 threads on Google
> regarding this error.
>
> nc4internal.c:393:1: error: conflicting types for ‘nc4_rec_find_nc_type’
>  nc4_rec_find_nc_type(NC_GRP_INFO_T *start_grp, nc_type target_nc_typeid)
>  ^~~~~~~~~~~~~~~~~~~~
> In file included from nc4internal.c:16:0:
> ../include/nc4internal.h:319:17: note: previous declaration of
> ‘nc4_rec_find_nc_type’ was here
>  NC_TYPE_INFO_T *nc4_rec_find_nc_type(NC_GRP_INFO_T *start_grp, hid_t
> target_nc_typeid);
>                  ^~~~~~~~~~~~~~~~~~~~
> make[3]: *** [Makefile:493: libnetcdf4_la-nc4internal.lo] Error 1
> make[3]: *** Waiting for unfinished jobs....
> make[3]: Leaving directory '/home/dwang/program/libmesh-1
> .0.0/contrib/netcdf/v4/libsrc4'
> make[2]: *** [Makefile:610: install-recursive] Error 1
> make[2]: Leaving directory '/home/dwang/program/libmesh-1
> .0.0/contrib/netcdf/v4'
> make[1]: *** [Makefile:978: install-recursive] Error 1
> make[1]: Leaving directory '/home/dwang/program/libmesh-1.0.0/contrib'
> make: *** [Makefile:28784: install-recursive] Error 1
>

I believe this bug was fixed by Martin Luethi in libmesh commit 896268d7,
however the first version of libmesh that contains that fix is 1.1.0. You
could try cherry-picking that commit and seeing if it fixes the problem,
but your best long term bet is to just update your user code if possible.

-- 
John

[Libmesh-users] libMesh Make Error

[Braden F. <bf...@um...>]

Hello,

I'm trying to install libMesh on my Linux system and I'm getting an error
when running make. It seemed to configure without any issues so I'm not
sure why this is happening. I've attached my config.log just in case anyone
would care to look at it. When I run make I receive the following error:

  CXX      src/apps/solution_components_dbg-solution_components.o
  CXX      src/apps/splitter_dbg-splitter.o
  CXXLD    libmesh_dbg.la
  CXXLD    libmesh_opt.la
  CXXLD    fparser_parse-opt
  CXXLD    getpot_parse-opt
  CXXLD    amr-opt
./.libs/libmesh_opt.so: undefined reference to `nc_def_var_deflate'
collect2: error: ld returned 1 exit status
Makefile:11037: recipe for target 'getpot_parse-opt' failed
make[1]: *** [getpot_parse-opt] Error 1
make[1]: *** Waiting for unfinished jobs....
./.libs/libmesh_opt.so: undefined reference to `nc_def_var_deflate'
collect2: error: ld returned 1 exit status
Makefile:10959: recipe for target 'amr-opt' failed
make[1]: *** [amr-opt] Error 1
./.libs/libmesh_opt.so: undefined reference to `nc_def_var_deflate'
collect2: error: ld returned 1 exit status
Makefile:11019: recipe for target 'fparser_parse-opt' failed
make[1]: *** [fparser_parse-opt] Error 1
make[1]: Leaving directory '/home/braden/Codes/libmesh'
Makefile:29211: recipe for target 'all-recursive' failed
make: *** [all-recursive] Error 1

Any ideas on how to fix this?

Thanks,
Braden Frigoletto

[Libmesh-users] Installation Error of Libmesh v1.0.0 on Linux Arch

[Dafang W. <daf...@jh...>]

Hi,

I got the following error when installing Libmesh v1.0.0 with PETSC 
v3.6.4/3.5.4 (neither Petsc worked). I am installing an older version of 
Libmesh because only that version is compatible with my user code.

I put the error message and config.log below. My question is that I am 
not sure whether this error was due to the version conflict between 
Libmesh and Petsc, because this error didn't occur when I was installing 
the latest version of libmesh/petsc. (Unfortunately the latest version 
is incompatible with my user code.)

Any advice would be appreciated. I only found 3 threads on Google 
regarding this error.

Cheers,
Dafang

nc4internal.c:393:1: error: conflicting types for ‘nc4_rec_find_nc_type’
  nc4_rec_find_nc_type(NC_GRP_INFO_T *start_grp, nc_type target_nc_typeid)
  ^~~~~~~~~~~~~~~~~~~~
In file included from nc4internal.c:16:0:
../include/nc4internal.h:319:17: note: previous declaration of 
‘nc4_rec_find_nc_type’ was here
  NC_TYPE_INFO_T *nc4_rec_find_nc_type(NC_GRP_INFO_T *start_grp, hid_t 
target_nc_typeid);
                  ^~~~~~~~~~~~~~~~~~~~
make[3]: *** [Makefile:493: libnetcdf4_la-nc4internal.lo] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory 
'/home/dwang/program/libmesh-1.0.0/contrib/netcdf/v4/libsrc4'
make[2]: *** [Makefile:610: install-recursive] Error 1
make[2]: Leaving directory 
'/home/dwang/program/libmesh-1.0.0/contrib/netcdf/v4'
make[1]: *** [Makefile:978: install-recursive] Error 1
make[1]: Leaving directory '/home/dwang/program/libmesh-1.0.0/contrib'
make: *** [Makefile:28784: install-recursive] Error 1

------------------------------------------------------------------------
Config.log:
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by libmesh configure 1.0.0, which was
generated by GNU Autoconf 2.69.  Invocation command line was

   $ ./configure --with-parmetis=PETSc --with-metis=PETSc 
--prefix=/home/dwang/program/libmesh-1.0.0/RelWithDebInfo 
--with-method=devel --enable-default-comm-world --enable-unique-ptr

## --------- ##
## Platform. ##
## --------- ##

hostname = wonderful
uname -m = x86_64
uname -r = 4.13.7-1-ARCH
uname -s = Linux
uname -v = #1 SMP PREEMPT Sat Oct 14 20:13:26 CEST 2017

/usr/bin/uname -p = unknown
/bin/uname -X     = unknown

/bin/arch              = unknown
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /usr/bin/site_perl
PATH: /usr/bin/vendor_perl
PATH: /usr/bin/core_perl
PATH: /home/dwang/local/bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:3638: result: ---------------------------------------------
configure:3640: result: ----------- Configuring libMesh -------------
configure:3642: result: ---------------------------------------------
configure:3684: checking build system type
configure:3698: result: x86_64-unknown-linux-gnu
configure:3718: checking host system type
configure:3731: result: x86_64-unknown-linux-gnu
configure:3751: checking target system type
configure:3764: result: x86_64-unknown-linux-gnu
configure:3839: checking for a BSD-compatible install
configure:3907: result: /usr/bin/install -c
configure:3918: checking whether build environment is sane
configure:3973: result: yes
configure:4124: checking for a thread-safe mkdir -p
configure:4163: result: /usr/bin/mkdir -p
configure:4170: checking for gawk
configure:4186: found /usr/bin/gawk
configure:4197: result: gawk
configure:4208: checking whether make sets $(MAKE)
configure:4230: result: yes
configure:4259: checking whether make supports nested variables
configure:4276: result: yes
configure:4365: checking whether UID '1002' is supported by ustar format
configure:4368: result: yes
configure:4375: checking whether GID '1002' is supported by ustar format
configure:4378: result: yes
configure:4386: checking how to create a ustar tar archive
configure:4397: tar --version
tar (GNU tar) 1.29
Copyright (C) 2015 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later 
<http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
configure:4400: $? = 0
configure:4440: tardir=conftest.dir && eval tar --format=ustar -chf - 
"$tardir" >conftest.tar
configure:4443: $? = 0
configure:4447: tar -xf - <conftest.tar
configure:4450: $? = 0
configure:4452: cat conftest.dir/file
GrepMe
configure:4455: $? = 0
configure:4468: result: gnutar
configure:4531: checking whether make supports nested variables
configure:4548: result: yes
configure:4587: checking whether to enable maintainer-specific portions 
of Makefiles
configure:4596: result: no
configure:4616: checking for src/base/libmesh.C
configure:4629: result: yes
configure:4668: checking for perl
configure:4686: found /usr/bin/perl
configure:4698: result: /usr/bin/perl
configure:4723: checking for style of include used by make
configure:4751: result: GNU
configure:4871: checking for mpicxx
configure:4887: found /usr/bin/mpicxx
configure:4898: result: mpicxx
configure:4925: checking for C++ compiler version
configure:4934: mpicxx --version >&5
g++ (GCC) 7.2.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:4945: $? = 0
configure:4934: mpicxx -v >&5
Using built-in specs.
COLLECT_GCC=/usr/bin/g++
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /build/gcc/src/gcc/configure --prefix=/usr 
--libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man 
--infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ 
--enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared 
--enable-threads=posix --enable-libmpx --with-system-zlib --with-isl 
--enable-__cxa_atexit --disable-libunwind-exceptions 
--enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp 
--enable-gnu-unique-object --enable-linker-build-id --enable-lto 
--enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu 
--enable-gnu-indirect-function --disable-multilib --disable-werror 
--enable-checking=release --enable-default-pie --enable-default-ssp
Thread model: posix
gcc version 7.2.0 (GCC)
configure:4945: $? = 0
configure:4934: mpicxx -V >&5
g++: error: unrecognized command line option '-V'
g++: fatal error: no input files
compilation terminated.
configure:4945: $? = 1
configure:4934: mpicxx -qversion >&5
g++: error: unrecognized command line option '-qversion'; did you mean 
'--version'?
g++: fatal error: no input files
compilation terminated.
configure:4945: $? = 1
configure:4965: checking whether the C++ compiler works
configure:4987: mpicxx -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp  >&5
configure:4991: $? = 0
configure:5039: result: yes
configure:5042: checking for C++ compiler default output file name
configure:5044: result: a.out
configure:5050: checking for suffix of executables
configure:5057: mpicxx -o conftest -Og -g  -march=native -msse -msse2 
-msse3 -mfpmath=sse   conftest.cpp  >&5
configure:5061: $? = 0
configure:5083: result:
configure:5105: checking whether we are cross compiling
configure:5113: mpicxx -o conftest -Og -g  -march=native -msse -msse2 
-msse3 -mfpmath=sse   conftest.cpp  >&5
configure:5117: $? = 0
configure:5124: ./conftest
configure:5128: $? = 0
configure:5143: result: no
configure:5148: checking for suffix of object files
configure:5170: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.cpp >&5
configure:5174: $? = 0
configure:5195: result: o
configure:5199: checking whether we are using the GNU C++ compiler
configure:5218: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.cpp >&5
configure:5218: $? = 0
configure:5227: result: yes
configure:5236: checking whether mpicxx accepts -g
configure:5256: mpicxx -c -g  conftest.cpp >&5
configure:5256: $? = 0
configure:5297: result: yes
configure:5322: checking dependency style of mpicxx
configure:5433: result: gcc3
configure:5598: result: <<< C++ compiler is unknown but accepted gcc 
version >>>
configure:5951: checking for mpicc
configure:5967: found /usr/bin/mpicc
configure:5978: result: mpicc
configure:6009: checking for C compiler version
configure:6018: mpicc --version >&5
gcc (GCC) 7.2.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:6029: $? = 0
configure:6018: mpicc -v >&5
Using built-in specs.
COLLECT_GCC=/usr/bin/gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /build/gcc/src/gcc/configure --prefix=/usr 
--libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man 
--infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ 
--enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared 
--enable-threads=posix --enable-libmpx --with-system-zlib --with-isl 
--enable-__cxa_atexit --disable-libunwind-exceptions 
--enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp 
--enable-gnu-unique-object --enable-linker-build-id --enable-lto 
--enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu 
--enable-gnu-indirect-function --disable-multilib --disable-werror 
--enable-checking=release --enable-default-pie --enable-default-ssp
Thread model: posix
gcc version 7.2.0 (GCC)
configure:6029: $? = 0
configure:6018: mpicc -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:6029: $? = 1
configure:6018: mpicc -qversion >&5
gcc: error: unrecognized command line option '-qversion'; did you mean 
'--version'?
gcc: fatal error: no input files
compilation terminated.
configure:6029: $? = 1
configure:6033: checking whether we are using the GNU C compiler
configure:6052: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:6052: $? = 0
configure:6061: result: yes
configure:6070: checking whether mpicc accepts -g
configure:6090: mpicc -c -g  conftest.c >&5
configure:6090: $? = 0
configure:6131: result: yes
configure:6148: checking for mpicc option to accept ISO C89
configure:6211: mpicc  -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:6211: $? = 0
configure:6224: result: none needed
configure:6249: checking whether mpicc understands -c and -o together
configure:6271: mpicc -c conftest.c -o conftest2.o
configure:6274: $? = 0
configure:6271: mpicc -c conftest.c -o conftest2.o
configure:6274: $? = 0
configure:6286: result: yes
configure:6305: checking dependency style of mpicc
configure:6416: result: gcc3
configure:6528: checking for mpif90
configure:6544: found /usr/bin/mpif90
configure:6555: result: mpif90
configure:6581: checking for Fortran compiler version
configure:6590: mpif90 --version >&5
GNU Fortran (GCC) 7.2.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:6601: $? = 0
configure:6590: mpif90 -v >&5
Using built-in specs.
COLLECT_GCC=/usr/bin/gfortran
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /build/gcc/src/gcc/configure --prefix=/usr 
--libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man 
--infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ 
--enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared 
--enable-threads=posix --enable-libmpx --with-system-zlib --with-isl 
--enable-__cxa_atexit --disable-libunwind-exceptions 
--enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp 
--enable-gnu-unique-object --enable-linker-build-id --enable-lto 
--enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu 
--enable-gnu-indirect-function --disable-multilib --disable-werror 
--enable-checking=release --enable-default-pie --enable-default-ssp
Thread model: posix
gcc version 7.2.0 (GCC)
configure:6601: $? = 0
configure:6590: mpif90 -V >&5
gfortran: error: unrecognized command line option '-V'
gfortran: fatal error: no input files
compilation terminated.
configure:6601: $? = 1
configure:6590: mpif90 -qversion >&5
gfortran: error: unrecognized command line option '-qversion'; did you 
mean '--version'?
gfortran: fatal error: no input files
compilation terminated.
configure:6601: $? = 1
configure:6610: checking whether we are using the GNU Fortran compiler
configure:6623: mpif90 -c   conftest.F >&5
configure:6623: $? = 0
configure:6632: result: yes
configure:6638: checking whether mpif90 accepts -g
configure:6649: mpif90 -c -g  conftest.f >&5
configure:6649: $? = 0
configure:6657: result: yes
configure:6766: checking for mpif77
configure:6782: found /usr/bin/mpif77
configure:6793: result: mpif77
configure:6819: checking for Fortran 77 compiler version
configure:6828: mpif77 --version >&5
GNU Fortran (GCC) 7.2.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:6839: $? = 0
configure:6828: mpif77 -v >&5
Using built-in specs.
COLLECT_GCC=/usr/bin/gfortran
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /build/gcc/src/gcc/configure --prefix=/usr 
--libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man 
--infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ 
--enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared 
--enable-threads=posix --enable-libmpx --with-system-zlib --with-isl 
--enable-__cxa_atexit --disable-libunwind-exceptions 
--enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp 
--enable-gnu-unique-object --enable-linker-build-id --enable-lto 
--enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu 
--enable-gnu-indirect-function --disable-multilib --disable-werror 
--enable-checking=release --enable-default-pie --enable-default-ssp
Thread model: posix
gcc version 7.2.0 (GCC)
configure:6839: $? = 0
configure:6828: mpif77 -V >&5
gfortran: error: unrecognized command line option '-V'
gfortran: fatal error: no input files
compilation terminated.
configure:6839: $? = 1
configure:6828: mpif77 -qversion >&5
gfortran: error: unrecognized command line option '-qversion'; did you 
mean '--version'?
gfortran: fatal error: no input files
compilation terminated.
configure:6839: $? = 1
configure:6848: checking whether we are using the GNU Fortran 77 compiler
configure:6861: mpif77 -c  conftest.F >&5
configure:6861: $? = 0
configure:6870: result: yes
configure:6876: checking whether mpif77 accepts -g
configure:6887: mpif77 -c -g conftest.f >&5
configure:6887: $? = 0
configure:6895: result: yes
configure:6973: checking whether mpicxx supports C++11 features by default
configure:7009: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.cpp >&5
configure:7009: $? = 0
configure:7016: result: yes
configure:8138: result: <<< Configuring libMesh with methods "devel" >>>
configure:8278: checking for C++11 std::move support
configure:8316: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:8316: $? = 0
configure:8319: result: yes
configure:8362: checking for C++11 range-based for loop support
configure:8400: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:8400: $? = 0
configure:8403: result: yes
configure:8446: checking for C++11 decltype support
configure:8476: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:8476: $? = 0
configure:8479: result: yes
configure:8522: checking for C++11 rvalue references support
configure:8554: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:8554: $? = 0
configure:8557: result: yes
configure:8600: checking for C++11 auto keyword support
configure:8630: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:8630: $? = 0
configure:8633: result: yes
configure:8676: checking for C++11 lambda support
configure:8713: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:8713: $? = 0
configure:8716: result: yes
configure:8759: checking for C++11 constexpr support
configure:8790: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:8790: $? = 0
configure:8793: result: yes
configure:8836: checking for C++11 alias declarations support
configure:8874: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:8874: $? = 0
configure:8877: result: yes
configure:8962: checking for C++11 std::shared_ptr support with devel flags
configure:8983: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  -O2 -felide-constructors -g -pedantic -W -Wall -Wextra 
-Wno-long-long -Wunused -Wpointer-arith -Wformat -Wparentheses 
-Wuninitialized -funroll-loops -fstrict-aliasing        conftest.cpp >&5
configure:8983: $? = 0
configure:8987: result: yes
configure:9043: checking for C++11 std::unique_ptr support
configure:9082: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:9082: $? = 0
configure:9085: result: yes
configure:9128: checking for C++11 std::regex support
configure:9166: mpicxx -o conftest -Og -g  -march=native -msse -msse2 
-msse3 -mfpmath=sse    conftest.cpp  >&5
configure:9166: $? = 0
configure:9166: ./conftest
configure:9166: $? = 0
configure:9169: result: yes
configure:9215: checking for C++11 override keyword support
configure:9249: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:9249: $? = 0
configure:9252: result: yes
configure:9295: checking for C++11 initializer list support
configure:9326: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:9326: $? = 0
configure:9329: result: yes
configure:9372: checking for C++11 variadic template support
configure:9412: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:9412: $? = 0
configure:9415: result: yes
configure:9458: checking for C++11 <thread> support
configure:9504: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:9504: $? = 0
configure:9507: result: yes
configure:9561: checking for C++11 <type_traits> support
configure:9698: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:9698: $? = 0
configure:9701: result: yes
configure:9764: checking for C++11 std::asinh support in <cmath>
configure:9781: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:9781: $? = 0
configure:9784: result: yes
configure:9807: checking for C++11 std::acosh support in <cmath>
configure:9824: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:9824: $? = 0
configure:9827: result: yes
configure:9850: checking for C++11 std::atanh support in <cmath>
configure:9867: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:9867: $? = 0
configure:9870: result: yes
configure:9894: checking for C++11 std::asinh(complex) support in <complex>
configure:9912: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:9912: $? = 0
configure:9915: result: yes
configure:9938: checking for C++11 std::acosh(complex) support in <complex>
configure:9956: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:9956: $? = 0
configure:9959: result: yes
configure:9982: checking for C++11 std::atanh(complex) support in <complex>
configure:10000: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:10000: $? = 0
configure:10003: result: yes
configure:10088: checking for C++11 deleted functions support
configure:10120: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:10120: $? = 0
configure:10123: result: yes
configure:10167: checking for C++11 'final' keyword support
configure:10205: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:10205: $? = 0
configure:10240: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
conftest.cpp:40:14: error: 'void A::bar()' marked 'final', but is not 
virtual
          void bar() final;
               ^~~
configure:10240: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libmesh"
| #define PACKAGE_TARNAME "libmesh"
| #define PACKAGE_VERSION "1.0.0"
| #define PACKAGE_STRING "libmesh 1.0.0"
| #define PACKAGE_BUGREPORT "lib...@li..."
| #define PACKAGE_URL "http://libmesh.github.io"
| #define CONFIGURE_INFO "./configure  '--with-parmetis=PETSc' 
'--with-metis=PETSc' 
'--prefix=/home/dwang/program/libmesh-1.0.0/RelWithDebInfo' 
'--with-method=devel' '--enable-default-comm-world' 
'--enable-unique-ptr' 'CXXFLAGS=-Og -g  -march=native -msse -msse2 
-msse3 -mfpmath=sse' 'CFLAGS=-Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse' 'METHODS=devel' 
'PETSC_DIR=/home/dwang/program/petsc-3.5.4' 'PETSC_ARCH=RelWithDebInfo'"
| #define PACKAGE "libmesh"
| #define VERSION "1.0.0"
| #define HAVE_CXX11 1
| #define HAVE_CXX11_MOVE 1
| #define HAVE_CXX11_RANGEFOR 1
| #define HAVE_CXX11_DECLTYPE 1
| #define HAVE_CXX11_RVALUE_REFERENCES 1
| #define HAVE_CXX11_AUTO 1
| #define HAVE_CXX11_LAMBDA 1
| #define HAVE_CXX11_CONSTEXPR 1
| #define HAVE_CXX11_ALIAS_DECLARATIONS 1
| #define HAVE_CXX11_SHARED_PTR 1
| #define HAVE_CXX11_UNIQUE_PTR 1
| #define HAVE_CXX11_REGEX 1
| #define HAVE_CXX11_OVERRIDE 1
| #define HAVE_CXX11_INITIALIZER_LIST 1
| #define HAVE_CXX11_VARIADIC_TEMPLATES 1
| #define HAVE_CXX11_THREAD 1
| #define HAVE_CXX11_TYPE_TRAITS 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT_COMPLEX 1
| #define HAVE_CXX11_DELETED_FUNCTIONS 1
| /* end confdefs.h.  */
|
|       struct A
|       {
|         // Error: non-virtual function cannot be final
|         void bar() final;
|       };
|
| int
| main ()
| {
|
|
|   ;
|   return 0;
| }
configure:10281: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
conftest.cpp:44:14: error: virtual function 'virtual void B::foo()'
          void foo();
               ^~~
conftest.cpp:39:22: error: overriding final function 'virtual void A::foo()'
          virtual void foo() final;
                       ^~~
configure:10281: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libmesh"
| #define PACKAGE_TARNAME "libmesh"
| #define PACKAGE_VERSION "1.0.0"
| #define PACKAGE_STRING "libmesh 1.0.0"
| #define PACKAGE_BUGREPORT "lib...@li..."
| #define PACKAGE_URL "http://libmesh.github.io"
| #define CONFIGURE_INFO "./configure  '--with-parmetis=PETSc' 
'--with-metis=PETSc' 
'--prefix=/home/dwang/program/libmesh-1.0.0/RelWithDebInfo' 
'--with-method=devel' '--enable-default-comm-world' 
'--enable-unique-ptr' 'CXXFLAGS=-Og -g  -march=native -msse -msse2 
-msse3 -mfpmath=sse' 'CFLAGS=-Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse' 'METHODS=devel' 
'PETSC_DIR=/home/dwang/program/petsc-3.5.4' 'PETSC_ARCH=RelWithDebInfo'"
| #define PACKAGE "libmesh"
| #define VERSION "1.0.0"
| #define HAVE_CXX11 1
| #define HAVE_CXX11_MOVE 1
| #define HAVE_CXX11_RANGEFOR 1
| #define HAVE_CXX11_DECLTYPE 1
| #define HAVE_CXX11_RVALUE_REFERENCES 1
| #define HAVE_CXX11_AUTO 1
| #define HAVE_CXX11_LAMBDA 1
| #define HAVE_CXX11_CONSTEXPR 1
| #define HAVE_CXX11_ALIAS_DECLARATIONS 1
| #define HAVE_CXX11_SHARED_PTR 1
| #define HAVE_CXX11_UNIQUE_PTR 1
| #define HAVE_CXX11_REGEX 1
| #define HAVE_CXX11_OVERRIDE 1
| #define HAVE_CXX11_INITIALIZER_LIST 1
| #define HAVE_CXX11_VARIADIC_TEMPLATES 1
| #define HAVE_CXX11_THREAD 1
| #define HAVE_CXX11_TYPE_TRAITS 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT_COMPLEX 1
| #define HAVE_CXX11_DELETED_FUNCTIONS 1
| /* end confdefs.h.  */
|
|       struct A
|       {
|         virtual void foo() final;
|       };
|       struct B : A
|       {
|         // Error: foo cannot be overridden as it's final in A
|         void foo();
|       };
|
| int
| main ()
| {
|
|
|   ;
|   return 0;
| }
configure:10326: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
conftest.cpp:47:14: error: cannot derive from 'final' base 'B' in 
derived type 'C'
        struct C : B
               ^
configure:10326: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libmesh"
| #define PACKAGE_TARNAME "libmesh"
| #define PACKAGE_VERSION "1.0.0"
| #define PACKAGE_STRING "libmesh 1.0.0"
| #define PACKAGE_BUGREPORT "lib...@li..."
| #define PACKAGE_URL "http://libmesh.github.io"
| #define CONFIGURE_INFO "./configure  '--with-parmetis=PETSc' 
'--with-metis=PETSc' 
'--prefix=/home/dwang/program/libmesh-1.0.0/RelWithDebInfo' 
'--with-method=devel' '--enable-default-comm-world' 
'--enable-unique-ptr' 'CXXFLAGS=-Og -g  -march=native -msse -msse2 
-msse3 -mfpmath=sse' 'CFLAGS=-Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse' 'METHODS=devel' 
'PETSC_DIR=/home/dwang/program/petsc-3.5.4' 'PETSC_ARCH=RelWithDebInfo'"
| #define PACKAGE "libmesh"
| #define VERSION "1.0.0"
| #define HAVE_CXX11 1
| #define HAVE_CXX11_MOVE 1
| #define HAVE_CXX11_RANGEFOR 1
| #define HAVE_CXX11_DECLTYPE 1
| #define HAVE_CXX11_RVALUE_REFERENCES 1
| #define HAVE_CXX11_AUTO 1
| #define HAVE_CXX11_LAMBDA 1
| #define HAVE_CXX11_CONSTEXPR 1
| #define HAVE_CXX11_ALIAS_DECLARATIONS 1
| #define HAVE_CXX11_SHARED_PTR 1
| #define HAVE_CXX11_UNIQUE_PTR 1
| #define HAVE_CXX11_REGEX 1
| #define HAVE_CXX11_OVERRIDE 1
| #define HAVE_CXX11_INITIALIZER_LIST 1
| #define HAVE_CXX11_VARIADIC_TEMPLATES 1
| #define HAVE_CXX11_THREAD 1
| #define HAVE_CXX11_TYPE_TRAITS 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT_COMPLEX 1
| #define HAVE_CXX11_DELETED_FUNCTIONS 1
| /* end confdefs.h.  */
|
|       struct A
|       {
|       };
|
|       // struct B is final
|       struct B final : A
|       {
|       };
|
|       // Error: B is final
|       struct C : B
|       {
|       };
|
| int
| main ()
| {
|
|
|   ;
|   return 0;
| }
configure:10345: result: yes
configure:10382: checking for C++11 nullptr support
configure:10416: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:10416: $? = 0
configure:10419: result: yes
configure:10543: checking for C++11 std::to_string() support
configure:10582: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse   conftest.cpp >&5
configure:10582: $? = 0
configure:10585: result: yes
configure:10676: checking how to print strings
configure:10703: result: printf
configure:10724: checking for a sed that does not truncate output
configure:10788: result: /usr/bin/sed
configure:10806: checking for grep that handles long lines and -e
configure:10864: result: /usr/bin/grep
configure:10869: checking for egrep
configure:10931: result: /usr/bin/grep -E
configure:10936: checking for fgrep
configure:10998: result: /usr/bin/grep -F
configure:11033: checking for ld used by mpicc
configure:11100: result: /usr/bin/ld
configure:11107: checking if the linker (/usr/bin/ld) is GNU ld
configure:11122: result: yes
configure:11134: checking for BSD- or MS-compatible name lister (nm)
configure:11188: result: /usr/bin/nm -B
configure:11318: checking the name lister (/usr/bin/nm -B) interface
configure:11325: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.cpp >&5
configure:11328: /usr/bin/nm -B "conftest.o"
configure:11331: output
0000000000000000 B some_variable
configure:11338: result: BSD nm
configure:11341: checking whether ln -s works
configure:11345: result: yes
configure:11353: checking the maximum length of command line arguments
configure:11484: result: 1572864
configure:11532: checking how to convert x86_64-unknown-linux-gnu file 
names to x86_64-unknown-linux-gnu format
configure:11572: result: func_convert_file_noop
configure:11579: checking how to convert x86_64-unknown-linux-gnu file 
names to toolchain format
configure:11599: result: func_convert_file_noop
configure:11606: checking for /usr/bin/ld option to reload object files
configure:11613: result: -r
configure:11687: checking for objdump
configure:11703: found /usr/bin/objdump
configure:11714: result: objdump
configure:11746: checking how to recognize dependent libraries
configure:11946: result: pass_all
configure:12031: checking for dlltool
configure:12061: result: no
configure:12091: checking how to associate runtime and link libraries
configure:12118: result: printf %s\n
configure:12178: checking for ar
configure:12194: found /usr/bin/ar
configure:12205: result: ar
configure:12242: checking for archiver @FILE support
configure:12259: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.cpp >&5
configure:12259: $? = 0
configure:12262: ar cru libconftest.a @conftest.lst >&5
ar: `u' modifier ignored since `D' is the default (see `U')
configure:12265: $? = 0
configure:12270: ar cru libconftest.a @conftest.lst >&5
ar: `u' modifier ignored since `D' is the default (see `U')
ar: conftest.o: No such file or directory
configure:12273: $? = 1
configure:12285: result: @
configure:12343: checking for strip
configure:12359: found /usr/bin/strip
configure:12370: result: strip
configure:12442: checking for ranlib
configure:12458: found /usr/bin/ranlib
configure:12469: result: ranlib
configure:12571: checking command to parse /usr/bin/nm -B output from 
mpicc object
configure:12724: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.cpp >&5
configure:12727: $? = 0
configure:12731: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ 
]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 
\2/p' | sed '/ __gnu_lto/d' \> conftest.nm
configure:12734: $? = 0
configure:12800: mpicxx -o conftest -Og -g  -march=native -msse -msse2 
-msse3 -mfpmath=sse   conftest.cpp conftstm.o >&5
configure:12803: $? = 0
configure:12841: result: ok
configure:12888: checking for sysroot
configure:12918: result: no
configure:12925: checking for a working dd
configure:12963: result: /usr/bin/dd
configure:12967: checking how to truncate binary pipes
configure:12982: result: /usr/bin/dd bs=4096 count=1
configure:13118: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.cpp >&5
configure:13121: $? = 0
configure:13311: checking for mt
configure:13341: result: no
configure:13361: checking if : is a manifest tool
configure:13367: : '-?'
configure:13375: result: no
configure:14052: checking how to run the C preprocessor
configure:14083: mpicc -E  conftest.c
configure:14083: $? = 0
configure:14097: mpicc -E  conftest.c
conftest.c:39:10: fatal error: ac_nonexistent.h: No such file or directory
  #include <ac_nonexistent.h>
           ^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:14097: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libmesh"
| #define PACKAGE_TARNAME "libmesh"
| #define PACKAGE_VERSION "1.0.0"
| #define PACKAGE_STRING "libmesh 1.0.0"
| #define PACKAGE_BUGREPORT "lib...@li..."
| #define PACKAGE_URL "http://libmesh.github.io"
| #define CONFIGURE_INFO "./configure  '--with-parmetis=PETSc' 
'--with-metis=PETSc' 
'--prefix=/home/dwang/program/libmesh-1.0.0/RelWithDebInfo' 
'--with-method=devel' '--enable-default-comm-world' 
'--enable-unique-ptr' 'CXXFLAGS=-Og -g  -march=native -msse -msse2 
-msse3 -mfpmath=sse' 'CFLAGS=-Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse' 'METHODS=devel' 
'PETSC_DIR=/home/dwang/program/petsc-3.5.4' 'PETSC_ARCH=RelWithDebInfo'"
| #define PACKAGE "libmesh"
| #define VERSION "1.0.0"
| #define HAVE_CXX11 1
| #define HAVE_CXX11_MOVE 1
| #define HAVE_CXX11_RANGEFOR 1
| #define HAVE_CXX11_DECLTYPE 1
| #define HAVE_CXX11_RVALUE_REFERENCES 1
| #define HAVE_CXX11_AUTO 1
| #define HAVE_CXX11_LAMBDA 1
| #define HAVE_CXX11_CONSTEXPR 1
| #define HAVE_CXX11_ALIAS_DECLARATIONS 1
| #define HAVE_CXX11_SHARED_PTR 1
| #define HAVE_CXX11_UNIQUE_PTR 1
| #define HAVE_CXX11_REGEX 1
| #define HAVE_CXX11_OVERRIDE 1
| #define HAVE_CXX11_INITIALIZER_LIST 1
| #define HAVE_CXX11_VARIADIC_TEMPLATES 1
| #define HAVE_CXX11_THREAD 1
| #define HAVE_CXX11_TYPE_TRAITS 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT_COMPLEX 1
| #define HAVE_CXX11_DELETED_FUNCTIONS 1
| #define HAVE_CXX11_FINAL 1
| #define HAVE_CXX11_NULLPTR 1
| #define HAVE_CXX11_TO_STRING 1
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:14122: result: mpicc -E
configure:14142: mpicc -E  conftest.c
configure:14142: $? = 0
configure:14156: mpicc -E  conftest.c
conftest.c:39:10: fatal error: ac_nonexistent.h: No such file or directory
  #include <ac_nonexistent.h>
           ^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:14156: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libmesh"
| #define PACKAGE_TARNAME "libmesh"
| #define PACKAGE_VERSION "1.0.0"
| #define PACKAGE_STRING "libmesh 1.0.0"
| #define PACKAGE_BUGREPORT "lib...@li..."
| #define PACKAGE_URL "http://libmesh.github.io"
| #define CONFIGURE_INFO "./configure  '--with-parmetis=PETSc' 
'--with-metis=PETSc' 
'--prefix=/home/dwang/program/libmesh-1.0.0/RelWithDebInfo' 
'--with-method=devel' '--enable-default-comm-world' 
'--enable-unique-ptr' 'CXXFLAGS=-Og -g  -march=native -msse -msse2 
-msse3 -mfpmath=sse' 'CFLAGS=-Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse' 'METHODS=devel' 
'PETSC_DIR=/home/dwang/program/petsc-3.5.4' 'PETSC_ARCH=RelWithDebInfo'"
| #define PACKAGE "libmesh"
| #define VERSION "1.0.0"
| #define HAVE_CXX11 1
| #define HAVE_CXX11_MOVE 1
| #define HAVE_CXX11_RANGEFOR 1
| #define HAVE_CXX11_DECLTYPE 1
| #define HAVE_CXX11_RVALUE_REFERENCES 1
| #define HAVE_CXX11_AUTO 1
| #define HAVE_CXX11_LAMBDA 1
| #define HAVE_CXX11_CONSTEXPR 1
| #define HAVE_CXX11_ALIAS_DECLARATIONS 1
| #define HAVE_CXX11_SHARED_PTR 1
| #define HAVE_CXX11_UNIQUE_PTR 1
| #define HAVE_CXX11_REGEX 1
| #define HAVE_CXX11_OVERRIDE 1
| #define HAVE_CXX11_INITIALIZER_LIST 1
| #define HAVE_CXX11_VARIADIC_TEMPLATES 1
| #define HAVE_CXX11_THREAD 1
| #define HAVE_CXX11_TYPE_TRAITS 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT_COMPLEX 1
| #define HAVE_CXX11_DELETED_FUNCTIONS 1
| #define HAVE_CXX11_FINAL 1
| #define HAVE_CXX11_NULLPTR 1
| #define HAVE_CXX11_TO_STRING 1
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:14185: checking for ANSI C header files
configure:14205: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:14205: $? = 0
configure:14278: mpicc -o conftest -Og -g  -march=native -msse -msse2 
-msse3 -mfpmath=sse   conftest.c  >&5
configure:14278: $? = 0
configure:14278: ./conftest
configure:14278: $? = 0
configure:14289: result: yes
configure:14302: checking for sys/types.h
configure:14302: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:14302: $? = 0
configure:14302: result: yes
configure:14302: checking for sys/stat.h
configure:14302: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:14302: $? = 0
configure:14302: result: yes
configure:14302: checking for stdlib.h
configure:14302: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:14302: $? = 0
configure:14302: result: yes
configure:14302: checking for string.h
configure:14302: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:14302: $? = 0
configure:14302: result: yes
configure:14302: checking for memory.h
configure:14302: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:14302: $? = 0
configure:14302: result: yes
configure:14302: checking for strings.h
configure:14302: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:14302: $? = 0
configure:14302: result: yes
configure:14302: checking for inttypes.h
configure:14302: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:14302: $? = 0
configure:14302: result: yes
configure:14302: checking for stdint.h
configure:14302: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:14302: $? = 0
configure:14302: result: yes
configure:14302: checking for unistd.h
configure:14302: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:14302: $? = 0
configure:14302: result: yes
configure:14316: checking for dlfcn.h
configure:14316: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:14316: $? = 0
configure:14316: result: yes
configure:14582: checking for objdir
configure:14597: result: .libs
configure:14861: checking if mpicc supports -fno-rtti -fno-exceptions
configure:14879: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  -fno-rtti -fno-exceptions conftest.c >&5
cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ 
but not for C
configure:14883: $? = 0
configure:14896: result: no
configure:15254: checking for mpicc option to produce PIC
configure:15261: result: -fPIC -DPIC
configure:15269: checking if mpicc PIC flag -fPIC -DPIC works
configure:15287: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  -fPIC -DPIC -DPIC conftest.c >&5
configure:15291: $? = 0
configure:15304: result: yes
configure:15333: checking if mpicc static flag -static works
configure:15361: result: no
configure:15376: checking if mpicc supports -c -o file.o
configure:15397: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  -o out/conftest2.o conftest.c >&5
configure:15401: $? = 0
configure:15423: result: yes
configure:15431: checking if mpicc supports -c -o file.o
configure:15478: result: yes
configure:15511: checking whether the mpicc linker (/usr/bin/ld -m 
elf_x86_64) supports shared libraries
configure:16770: result: yes
configure:16807: checking whether -lc should be explicitly linked in
configure:16815: mpicc -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.c >&5
configure:16818: $? = 0
configure:16833: mpicc -shared  -fPIC -DPIC conftest.o  -v -Wl,-soname 
-Wl,conftest -o conftest 2\>\&1 \| /usr/bin/grep -lc  \>/dev/null 2\>\&1
configure:16836: $? = 0
configure:16850: result: no
configure:17010: checking dynamic linker characteristics
configure:17591: mpicc -o conftest -Og -g  -march=native -msse -msse2 
-msse3 -mfpmath=sse   -Wl,-rpath -Wl,/foo conftest.c >&5
configure:17591: $? = 0
configure:17828: result: GNU/Linux ld.so
configure:17950: checking how to hardcode library paths into programs
configure:17975: result: immediate
configure:18523: checking whether stripping libraries is possible
configure:18528: result: yes
configure:18563: checking if libtool supports shared libraries
configure:18565: result: yes
configure:18568: checking whether to build shared libraries
configure:18593: result: yes
configure:18596: checking whether to build static libraries
configure:18600: result: no
configure:18623: checking how to run the C++ preprocessor
configure:18650: mpicxx -E  conftest.cpp
configure:18650: $? = 0
configure:18664: mpicxx -E  conftest.cpp
conftest.cpp:51:10: fatal error: ac_nonexistent.h: No such file or directory
  #include <ac_nonexistent.h>
           ^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:18664: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libmesh"
| #define PACKAGE_TARNAME "libmesh"
| #define PACKAGE_VERSION "1.0.0"
| #define PACKAGE_STRING "libmesh 1.0.0"
| #define PACKAGE_BUGREPORT "lib...@li..."
| #define PACKAGE_URL "http://libmesh.github.io"
| #define CONFIGURE_INFO "./configure  '--with-parmetis=PETSc' 
'--with-metis=PETSc' 
'--prefix=/home/dwang/program/libmesh-1.0.0/RelWithDebInfo' 
'--with-method=devel' '--enable-default-comm-world' 
'--enable-unique-ptr' 'CXXFLAGS=-Og -g  -march=native -msse -msse2 
-msse3 -mfpmath=sse' 'CFLAGS=-Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse' 'METHODS=devel' 
'PETSC_DIR=/home/dwang/program/petsc-3.5.4' 'PETSC_ARCH=RelWithDebInfo'"
| #define PACKAGE "libmesh"
| #define VERSION "1.0.0"
| #define HAVE_CXX11 1
| #define HAVE_CXX11_MOVE 1
| #define HAVE_CXX11_RANGEFOR 1
| #define HAVE_CXX11_DECLTYPE 1
| #define HAVE_CXX11_RVALUE_REFERENCES 1
| #define HAVE_CXX11_AUTO 1
| #define HAVE_CXX11_LAMBDA 1
| #define HAVE_CXX11_CONSTEXPR 1
| #define HAVE_CXX11_ALIAS_DECLARATIONS 1
| #define HAVE_CXX11_SHARED_PTR 1
| #define HAVE_CXX11_UNIQUE_PTR 1
| #define HAVE_CXX11_REGEX 1
| #define HAVE_CXX11_OVERRIDE 1
| #define HAVE_CXX11_INITIALIZER_LIST 1
| #define HAVE_CXX11_VARIADIC_TEMPLATES 1
| #define HAVE_CXX11_THREAD 1
| #define HAVE_CXX11_TYPE_TRAITS 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT_COMPLEX 1
| #define HAVE_CXX11_DELETED_FUNCTIONS 1
| #define HAVE_CXX11_FINAL 1
| #define HAVE_CXX11_NULLPTR 1
| #define HAVE_CXX11_TO_STRING 1
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:18689: result: mpicxx -E
configure:18709: mpicxx -E  conftest.cpp
configure:18709: $? = 0
configure:18723: mpicxx -E  conftest.cpp
conftest.cpp:51:10: fatal error: ac_nonexistent.h: No such file or directory
  #include <ac_nonexistent.h>
           ^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:18723: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libmesh"
| #define PACKAGE_TARNAME "libmesh"
| #define PACKAGE_VERSION "1.0.0"
| #define PACKAGE_STRING "libmesh 1.0.0"
| #define PACKAGE_BUGREPORT "lib...@li..."
| #define PACKAGE_URL "http://libmesh.github.io"
| #define CONFIGURE_INFO "./configure  '--with-parmetis=PETSc' 
'--with-metis=PETSc' 
'--prefix=/home/dwang/program/libmesh-1.0.0/RelWithDebInfo' 
'--with-method=devel' '--enable-default-comm-world' 
'--enable-unique-ptr' 'CXXFLAGS=-Og -g  -march=native -msse -msse2 
-msse3 -mfpmath=sse' 'CFLAGS=-Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse' 'METHODS=devel' 
'PETSC_DIR=/home/dwang/program/petsc-3.5.4' 'PETSC_ARCH=RelWithDebInfo'"
| #define PACKAGE "libmesh"
| #define VERSION "1.0.0"
| #define HAVE_CXX11 1
| #define HAVE_CXX11_MOVE 1
| #define HAVE_CXX11_RANGEFOR 1
| #define HAVE_CXX11_DECLTYPE 1
| #define HAVE_CXX11_RVALUE_REFERENCES 1
| #define HAVE_CXX11_AUTO 1
| #define HAVE_CXX11_LAMBDA 1
| #define HAVE_CXX11_CONSTEXPR 1
| #define HAVE_CXX11_ALIAS_DECLARATIONS 1
| #define HAVE_CXX11_SHARED_PTR 1
| #define HAVE_CXX11_UNIQUE_PTR 1
| #define HAVE_CXX11_REGEX 1
| #define HAVE_CXX11_OVERRIDE 1
| #define HAVE_CXX11_INITIALIZER_LIST 1
| #define HAVE_CXX11_VARIADIC_TEMPLATES 1
| #define HAVE_CXX11_THREAD 1
| #define HAVE_CXX11_TYPE_TRAITS 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_SINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_COSINE_COMPLEX 1
| #define HAVE_CXX11_INVERSE_HYPERBOLIC_TANGENT_COMPLEX 1
| #define HAVE_CXX11_DELETED_FUNCTIONS 1
| #define HAVE_CXX11_FINAL 1
| #define HAVE_CXX11_NULLPTR 1
| #define HAVE_CXX11_TO_STRING 1
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h.  */
| #include <ac_nonexistent.h>
configure:18885: checking for ld used by mpicxx
configure:18952: result: /usr/bin/ld -m elf_x86_64
configure:18959: checking if the linker (/usr/bin/ld -m elf_x86_64) is 
GNU ld
configure:18974: result: yes
configure:19029: checking whether the mpicxx linker (/usr/bin/ld -m 
elf_x86_64) supports shared libraries
configure:20102: result: yes
configure:20138: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.cpp >&5
configure:20141: $? = 0
configure:20622: checking for mpicxx option to produce PIC
configure:20629: result: -fPIC -DPIC
configure:20637: checking if mpicxx PIC flag -fPIC -DPIC works
configure:20655: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  -fPIC -DPIC -DPIC conftest.cpp >&5
configure:20659: $? = 0
configure:20672: result: yes
configure:20695: checking if mpicxx static flag -static works
configure:20723: result: no
configure:20735: checking if mpicxx supports -c -o file.o
configure:20756: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  -o out/conftest2.o conftest.cpp >&5
configure:20760: $? = 0
configure:20782: result: yes
configure:20787: checking if mpicxx supports -c -o file.o
configure:20834: result: yes
configure:20864: checking whether the mpicxx linker (/usr/bin/ld -m 
elf_x86_64) supports shared libraries
configure:20904: result: yes
configure:21045: checking dynamic linker characteristics
configure:21790: result: GNU/Linux ld.so
configure:21855: checking how to hardcode library paths into programs
configure:21880: result: immediate
configure:22021: checking if libtool supports shared libraries
configure:22023: result: yes
configure:22026: checking whether to build shared libraries
configure:22050: result: yes
configure:22053: checking whether to build static libraries
configure:22057: result: no
configure:22409: checking for mpif77 option to produce PIC
configure:22416: result: -fPIC
configure:22424: checking if mpif77 PIC flag -fPIC works
configure:22442: mpif77 -c -g -O2 -fPIC conftest.f >&5
configure:22446: $? = 0
configure:22459: result: yes
configure:22482: checking if mpif77 static flag -static works
configure:22510: result: no
configure:22522: checking if mpif77 supports -c -o file.o
configure:22543: mpif77 -c -g -O2 -o out/conftest2.o conftest.f >&5
configure:22547: $? = 0
configure:22569: result: yes
configure:22574: checking if mpif77 supports -c -o file.o
configure:22621: result: yes
configure:22651: checking whether the mpif77 linker (/usr/bin/ld -m 
elf_x86_64) supports shared libraries
configure:23860: result: yes
configure:24001: checking dynamic linker characteristics
configure:24740: result: GNU/Linux ld.so
configure:24805: checking how to hardcode library paths into programs
configure:24830: result: immediate
configure:24967: checking if libtool supports shared libraries
configure:24969: result: yes
configure:24972: checking whether to build shared libraries
configure:24996: result: yes
configure:24999: checking whether to build static libraries
configure:25003: result: no
configure:25037: mpif90 -c -g -O2  conftest.f >&5
configure:25040: $? = 0
configure:25500: checking for mpif90 option to produce PIC
configure:25507: result: -fPIC
configure:25515: checking if mpif90 PIC flag -fPIC works
configure:25533: mpif90 -c -g -O2 -fPIC  conftest.f >&5
configure:25537: $? = 0
configure:25550: result: yes
configure:25573: checking if mpif90 static flag -static works
configure:25601: result: no
configure:25613: checking if mpif90 supports -c -o file.o
configure:25634: mpif90 -c -g -O2 -o out/conftest2.o  conftest.f >&5
configure:25638: $? = 0
configure:25660: result: yes
configure:25665: checking if mpif90 supports -c -o file.o
configure:25712: result: yes
configure:25742: checking whether the mpif90 linker (/usr/bin/ld -m 
elf_x86_64) supports shared libraries
configure:26951: result: yes
configure:27092: checking dynamic linker characteristics
configure:27831: result: GNU/Linux ld.so
configure:27896: checking how to hardcode library paths into programs
configure:27921: result: immediate
configure:28006: checking Major version
configure:28008: result: 1
configure:28010: checking Minor version
configure:28012: result: 0
configure:28014: checking Point version
configure:28016: result: 0
configure:28061: checking whether ln -s works
configure:28065: result: yes
configure:28090: checking for a sed that does not truncate output
configure:28154: result: /usr/bin/sed
configure:28174: checking for pkg-config
configure:28192: found /usr/bin/pkg-config
configure:28205: result: /usr/bin/pkg-config
configure:28219: checking whether the compiler implements namespaces
configure:28242: mpicxx -c -Og -g  -march=native -msse -msse2 -msse3 
-mfpmath=sse  conftest.cpp >&5
configure:28242: $? = 0
configure:28256: result: yes
configure:28265: result: ---------------------------------------------
configure:28267: result: ------- Configuring compiler features -------
configure:28269: result: ---------------------------------------------
configure:28356: result: <<< Default floating point is double precision 
(double) >>>
configure:28394: checking for C/C++ restrict keyword
configure:28419: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:28419: $? = 0
configure:28427: result: __restrict
configure:28464: result: <<< Configuring library with getpwuid >>>
configure:28486: result: <<< Configuring library with exception throwing 
support >>>
configure:28510: result: <<< Configuring library with compile timestamps >>>
configure:28524: checking size of short int
configure:28529: mpicxx -o conftest  -O2 -felide-constructors -g 
-pedantic -W -Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith 
-Wformat -Wparentheses -Wuninitialized -funroll-loops 
-fstrict-aliasing      conftest.cpp  >&5
configure:28529: $? = 0
configure:28529: ./conftest
configure:28529: $? = 0
configure:28543: result: 2
configure:28557: checking size of int
configure:28562: mpicxx -o conftest  -O2 -felide-constructors -g 
-pedantic -W -Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith 
-Wformat -Wparentheses -Wuninitialized -funroll-loops 
-fstrict-aliasing      conftest.cpp  >&5
configure:28562: $? = 0
configure:28562: ./conftest
configure:28562: $? = 0
configure:28576: result: 4
configure:28590: checking size of unsigned int
configure:28595: mpicxx -o conftest  -O2 -felide-constructors -g 
-pedantic -W -Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith 
-Wformat -Wparentheses -Wuninitialized -funroll-loops 
-fstrict-aliasing      conftest.cpp  >&5
configure:28595: $? = 0
configure:28595: ./conftest
configure:28595: $? = 0
configure:28609: result: 4
configure:28623: checking size of long int
configure:28628: mpicxx -o conftest  -O2 -felide-constructors -g 
-pedantic -W -Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith 
-Wformat -Wparentheses -Wuninitialized -funroll-loops 
-fstrict-aliasing      conftest.cpp  >&5
configure:28628: $? = 0
configure:28628: ./conftest
configure:28628: $? = 0
configure:28642: result: 8
configure:28656: checking size of float
configure:28661: mpicxx -o conftest  -O2 -felide-constructors -g 
-pedantic -W -Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith 
-Wformat -Wparentheses -Wuninitialized -funroll-loops 
-fstrict-aliasing      conftest.cpp  >&5
configure:28661: $? = 0
configure:28661: ./conftest
configure:28661: $? = 0
configure:28675: result: 4
configure:28689: checking size of double
configure:28694: mpicxx -o conftest  -O2 -felide-constructors -g 
-pedantic -W -Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith 
-Wformat -Wparentheses -Wuninitialized -funroll-loops 
-fstrict-aliasing      conftest.cpp  >&5
configure:28694: $? = 0
configure:28694: ./conftest
configure:28694: $? = 0
configure:28708: result: 8
configure:28722: checking size of void *
configure:28727: mpicxx -o conftest  -O2 -felide-constructors -g 
-pedantic -W -Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith 
-Wformat -Wparentheses -Wuninitialized -funroll-loops 
-fstrict-aliasing      conftest.cpp  >&5
configure:28727: $? = 0
configure:28727: ./conftest
configure:28727: $? = 0
configure:28741: result: 8
configure:28760: checking size of function_pointer
configure:28765: mpicxx -o conftest  -O2 -felide-constructors -g 
-pedantic -W -Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith 
-Wformat -Wparentheses -Wuninitialized -funroll-loops 
-fstrict-aliasing      conftest.cpp  >&5
configure:28765: $? = 0
configure:28765: ./conftest
configure:28765: $? = 0
configure:28780: result: 8
configure:28795: checking whether the compiler supports Run-Time Type 
Identification
configure:28830: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:28830: $? = 0
configure:28844: result: yes
configure:28860: checking getopt.h usability
configure:28860: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:28860: $? = 0
configure:28860: result: yes
configure:28860: checking getopt.h presence
configure:28860: mpicxx -E  conftest.cpp
configure:28860: $? = 0
configure:28860: result: yes
configure:28860: checking for getopt.h
configure:28860: result: yes
configure:28872: checking csignal usability
configure:28872: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:28872: $? = 0
configure:28872: result: yes
configure:28872: checking csignal presence
configure:28872: mpicxx -E  conftest.cpp
configure:28872: $? = 0
configure:28872: result: yes
configure:28872: checking for csignal
configure:28872: result: yes
configure:28884: checking sys/resource.h usability
configure:28884: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:28884: $? = 0
configure:28884: result: yes
configure:28884: checking sys/resource.h presence
configure:28884: mpicxx -E  conftest.cpp
configure:28884: $? = 0
configure:28884: result: yes
configure:28884: checking for sys/resource.h
configure:28884: result: yes
configure:28894: checking whether the compiler has locale
configure:28926: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:28926: $? = 0
configure:28940: result: yes
configure:28948: checking whether the compiler has stringstream
configure:28981: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:28981: $? = 0
configure:28995: result: yes
configure:29069: checking fenv.h usability
configure:29069: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:29069: $? = 0
configure:29069: result: yes
configure:29069: checking fenv.h presence
configure:29069: mpicxx -E  conftest.cpp
configure:29069: $? = 0
configure:29069: result: yes
configure:29069: checking for fenv.h
configure:29069: result: yes
configure:29081: checking xmmintrin.h usability
configure:29081: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:29081: $? = 0
configure:29081: result: yes
configure:29081: checking xmmintrin.h presence
configure:29081: mpicxx -E  conftest.cpp
configure:29081: $? = 0
configure:29081: result: yes
configure:29081: checking for xmmintrin.h
configure:29081: result: yes
configure:29110: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:29110: $? = 0
configure:29134: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:29134: $? = 0
configure:29160: checking whether the compiler supports 
std::unordered_multimap
configure:29188: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:29188: $? = 0
configure:29202: result: yes
configure:29490: checking whether the compiler supports std::unordered_map
configure:29516: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:29516: $? = 0
configure:29530: result: yes
configure:29814: checking whether the compiler supports 
std::unordered_multiset
configure:29842: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:29842: $? = 0
configure:29856: result: yes
configure:30144: checking whether the compiler supports std::unordered_set
configure:30171: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-long-long -Wunused -Wpointer-arith -Wformat 
-Wparentheses -Wuninitialized -funroll-loops -fstrict-aliasing 
conftest.cpp >&5
configure:30171: $? = 0
configure:30185: result: yes
configure:30725: checking whether the compiler supports std::hash
configure:30751: mpicxx -c  -O2 -felide-constructors -g -pedantic -W 
-Wall -Wextra -Wno-l...
 
[truncated message content]

Re: [Libmesh-users] Defining Quadrature Rule (like QGauss) to be used with FEBase

[John P. <jwp...@gm...>]

On Wed, Nov 8, 2017 at 6:56 AM, Roy Stogner <roy...@ic...>
wrote:

>
> On Tue, 7 Nov 2017, Zack Vitoh wrote:
>
> I want to develop a nonstandard quadrature rule and use it as in
>> introduction_ex3.  Is there a way to do this simply,
>>
>
> Yes: after you add your new files (and the corresponding entry in
> quadrature_build.C), run a few scripts (as detailed in
> https://github.com/libMesh/libmesh/wiki/Adding-or-removing-source-files
> on the wiki) to put them into the build systems, and run "make" again.
>
> without rebuilding everything?
>>
>
> Probably not, I fear.  Putting new files into the build system will
> cause configure to re-run, configure will probably generate a new
> libmesh_config.h, pretty much every object file depends on
> libmesh_config.h, and so the entire tree will be rebuilt.
>

True, but it's not strictly necessary to add new quadrature code to the
library in order to test it out in an app.

Just put a class derived from libMesh::QBase in your application directory
and construct one manually i.e. don't call the static QBase::build() method
yet.

-- 
John