libmesh-users — General information for libmesh users

Re: [Libmesh-users] Suitable version for libMesh

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

On Wed, Apr 24, 2019 at 3:48 PM Nikrouz <nik...@gm...> wrote:

> Dear All libMesh users
>
> For some examples, it is necessary to configure libMesh with slepc.
>
> Currently, I have PetSC version 3.10.0 which is not compatible with the
> new version of slepc.
>
> How can I find a slepc version suitable for my case?
>

SLEPc 3.x should work with PETSc 3.x, i.e. the minor versions must match.

-- 
John

[Libmesh-users] Fwd: Suitable version of slepc

[Nikrouz <nik...@gm...>]

Dear All libMesh users

For some examples, it is necessary to configure libMesh with slepc.

Currently, I have PetSC version 3.10.0 which is not compatible with the 
new version of slepc.

How can I find a slepc version suitable for my case?

Thanks you again!

[Libmesh-users] Suitable version for libMesh

[Nikrouz <nik...@gm...>]

Dear All libMesh users

For some examples, it is necessary to configure libMesh with slepc.

Currently, I have PetSC version 3.10.0 which is not compatible with the 
new version of slepc.

How can I find a slepc version suitable for my case?

Thanks you again!

Re: [Libmesh-users] Boost Libraries

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

On Tue, Apr 23, 2019 at 5:01 AM Nikhil Vaidya <nik...@gm...>
wrote:

> Hi all,
>
> What is the correct way to use the boost libraries in the contrib folder
> while configuring libmesh? The version of boost on my system is older than
> required and I do not have root access. I would like to use the boost
> libraries in the contrib folder instead. I tried providing the contrib
> directory path as $BOOST_ROOT but that did not work.
>

Hmm... from what I recall you should get the boost in contrib
automatically, i.e. don't set $BOOST_ROOT or pass --with-boost to
configure.

If that is not working on your system, we might have a bug in our configure.

--
John

[Libmesh-users] Boost Libraries

[Nikhil V. <nik...@gm...>]

Hi all,

What is the correct way to use the boost libraries in the contrib folder
while configuring libmesh? The version of boost on my system is older than
required and I do not have root access. I would like to use the boost
libraries in the contrib folder instead. I tried providing the contrib
directory path as $BOOST_ROOT but that did not work.

Best,
Nikhil

Re: [Libmesh-users] Problem in importing mesh file from gmesh

[Povolotskyi, M. <mpo...@pu...>]

Did you try to save the mesh in the 2.0 version format directly from gmsh? I did it and libmesh was able to read it.

Sent from my Verizon LG Smartphone

------ Original message------
From: Nikrouz
Date: Mon, Apr 15, 2019 2:37 PM
To: lib...@li...<mailto:lib...@li...>;
Cc:
Subject:[Libmesh-users] Problem in importing mesh file from gmesh


Dear All libMesh users,

Thanks for your help

I had a problem in importing *.msh file produced by gmesh which was
about gmesh version.

In order to solve it, I manually edited the msh file and change the
version from 4.1 to 2.0.

After this edit, I faced with another error which is about ntag.

I do not know how to solve this issue.

*./example-opt d 2 Corr-Mortzea-1.ms<http://Corr-Mortzea-1.ms>h **
**Warning, ntags=377738, but we currently only support reading 2 flags.**
**Element type 52414 not found!**
**Stack frames: 9**
**0: libMesh::print_trace(std::ostream&)**
**1: libMesh::MacroFunctions::report_error(char const*, int, char
const*, char const*)**
**2: libMesh::GmshIO::read_mesh(std::istream&)**
**3: libMesh::GmshIO::read(std::__cxx11::basic_string, std::allocator > const&)**
**4: libMesh::NameBasedIO::read(std::__cxx11::basic_string, std::allocator > const&)**
**5: libMesh::UnstructuredMesh::read(std::__cxx11::basic_string, std::allocator > const&, void*, bool, bool)**
**6: ./example-opt(+0x157c4) [0x55824fe737c4]**
**7: __libc_start_main**
**8: ./example-opt(+0x15b5a) [0x55824fe73b5a]**
**[0] ../LIBMESH/src/mesh/gmsh_io.C, line 371, compiled Mar 22 2019 at
21:22:33**
**--------------------------------------------------------------------------**
**MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD**
**with errorcode 1.**
**
**NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.**
**You may or may not see output from other processes, depending on**
**exactly when Open MPI kills them.*

I am highly thankful for your help and guidance,

Thank  users and developers of libMesh



_______________________________________________
Libmesh-users mailing list
Lib...@li...<mailto:
Lib...@li...>
https://lists.sourceforge.net/lists/listinfo/libmesh-users

[Libmesh-users] Problem in importing mesh file from gmesh

[Nikrouz <nik...@gm...>]

Dear All libMesh users,

Thanks for your help

I had a problem in importing *.msh file produced by gmesh which was 
about gmesh version.

In order to solve it, I manually edited the msh file and change the 
version from 4.1 to 2.0.

After this edit, I faced with another error which is about ntag.

I do not know how to solve this issue.

*./example-opt d 2 Corr-Mortzea-1.msh **
**Warning, ntags=377738, but we currently only support reading 2 flags.**
**Element type 52414 not found!**
**Stack frames: 9**
**0: libMesh::print_trace(std::ostream&)**
**1: libMesh::MacroFunctions::report_error(char const*, int, char 
const*, char const*)**
**2: libMesh::GmshIO::read_mesh(std::istream&)**
**3: libMesh::GmshIO::read(std::__cxx11::basic_string<char, 
std::char_traits<char>, std::allocator<char> > const&)**
**4: libMesh::NameBasedIO::read(std::__cxx11::basic_string<char, 
std::char_traits<char>, std::allocator<char> > const&)**
**5: libMesh::UnstructuredMesh::read(std::__cxx11::basic_string<char, 
std::char_traits<char>, std::allocator<char> > const&, void*, bool, bool)**
**6: ./example-opt(+0x157c4) [0x55824fe737c4]**
**7: __libc_start_main**
**8: ./example-opt(+0x15b5a) [0x55824fe73b5a]**
**[0] ../LIBMESH/src/mesh/gmsh_io.C, line 371, compiled Mar 22 2019 at 
21:22:33**
**--------------------------------------------------------------------------**
**MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD**
**with errorcode 1.**
**
**NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.**
**You may or may not see output from other processes, depending on**
**exactly when Open MPI kills them.*

I am highly thankful for your help and guidance,

Thank  users and developers of libMesh

Re: [Libmesh-users] Select quadrature rule order based on element type

[Yuxiang W. <yw...@vi...>]

Dear Vikram,

Thank you again for the pointer (and the patience)! I used the PerfLog
class and compared. As you mentioned, the assembly time change is quite
small (1.8772 vs 1.8845 sec).

And I appreciate your suggestion for checking directly on the type of
element as well!

Have a great week ahead,
Shawn

PS the complete timing report:

Before including the qrule creation in the loop:
 ------------------------------------------------------------------------------------------------------------
| Assemble Performance: Alive time=1.88073, Active time=1.87716
                                  |
 ------------------------------------------------------------------------------------------------------------
| Event                         nCalls     Total Time  Avg Time    Total
Time  Avg Time    % of Active Time  |
|                                          w/o Sub     w/o Sub     With
Sub    With Sub    w/o S    With S   |
|------------------------------------------------------------------------------------------------------------|
|
                                  |
| Entire assembly               1          1.8772      1.877163    1.8772
    1.877163    100.00   100.00   |
 ------------------------------------------------------------------------------------------------------------
| Totals:                       1          1.8772
                100.00            |
 ------------------------------------------------------------------------------------------------------------

After including the qrule creation in the loop:

------------------------------------------------------------------------------------------------------------
| Assemble Performance: Alive time=1.88795, Active time=1.88449
                                  |
 ------------------------------------------------------------------------------------------------------------
| Event                         nCalls     Total Time  Avg Time    Total
Time  Avg Time    % of Active Time  |
|                                          w/o Sub     w/o Sub     With
Sub    With Sub    w/o S    With S   |
|------------------------------------------------------------------------------------------------------------|
|
                                  |
| Entire assembly               1          1.8845      1.884490    1.8845
    1.884490    100.00   100.00   |
 ------------------------------------------------------------------------------------------------------------
| Totals:                       1          1.8845
                100.00            |
 ------------------------------------------------------------------------------------------------------------

On Sun, Apr 14, 2019 at 4:11 PM Vikram Garg <vik...@gm...> wrote:

> Hi Yuxiang, glad to hear you are getting the expected results. This change
> looks correct for your case and should not affect the assembly time by a
> significant amount. You could also check for the actual type of element
> (QUAD4 or TRI) instead of checking indirectly via the number of nodes.
>
> You can check the performance change by checking the performance log which
> is included at the end of the program's output. Look for something like:
>
> | System                                                                                                          |
> |   assemble()                       1          0.0014      0.001422    0.0028      0.002767    17.59    34.22    |
>
> Thanks.
> Vikram Garg
>
> vikramvgarg.github.io/
>
>
> On Sun, Apr 14, 2019 at 5:22 PM Yuxiang Wang <yw...@vi...> wrote:
>
>> Hi Vikram,
>>
>> Thank you for your response!
>>
>> I didn't think about that - I tried to add that inside the loop over
>> elements and got the correct results!
>>
>> Question - do you think that will significantly slow down the assembly,
>> because we are now creating qrule and attaching it for every element loop?
>>
>> What I did was the following:
>>
>> for (const auto & elem : mesh.active_local_element_ptr_range()) {
>>
>> const unsigned int n_nodes = elem->n_nodes();
>>
>> Order qrule_order;
>>
>> switch (n_nodes)
>> {
>> case 3:
>> qrule_order = SECOND;
>> break;
>>
>> case 4:
>> qrule_order = THIRD;
>> break;
>>
>> default:
>> qrule_order = fe_type.default_quadrature_order();
>> break;
>> }
>>
>> QGauss qrule (dim, qrule_order);
>> fe->attach_quadrature_rule (&qrule);
>>
>> Thanks!
>>
>> Best,
>> Shawn
>>
>> On Sun, Apr 14, 2019 at 2:53 PM Vikram Garg <vik...@gm...>
>> wrote:
>>
>>> Hi Yuxiang,
>>>                    It should be possible to move the construction of the
>>> finite element and the specification of the quadrature rule inside the loop
>>> over elements. Did this give any errors, or is otherwise unfeasible for
>>> performance reasons ?
>>>
>>> Thanks.
>>> Vikram Garg
>>>
>>> vikramvgarg.github.io/
>>>
>>>
>>> On Sun, Apr 14, 2019 at 4:30 PM Yuxiang Wang <yw...@vi...> wrote:
>>>
>>>> Dear all,
>>>>
>>>> Sorry for the spam.
>>>>
>>>> I have a mix of QUAD4 and TRI3 elements in my mesh, and would like to
>>>> use
>>>> different quadrature rule orders for each type. Specifically, I'd like
>>>> to
>>>> have order THIRD for QUAD4 and SECOND for TRI3. By default, the orders
>>>> are
>>>> both THIRD.
>>>>
>>>> In most examples, I noticed that the specification of qrule is only for
>>>> the
>>>> entire FEType and not dependent on the element type (e.g. QUAD4 vs
>>>> TRI3).
>>>> Could you please share with me some hints on how to make
>>>> element-dependent
>>>> qrule order selection happen?
>>>>
>>>> Best,
>>>> Shawn
>>>>
>>>>
>>>> --
>>>> Yuxiang "Shawn" Wang, PhD
>>>> yw...@vi...
>>>> +1 (434) 284-0836
>>>>
>>>> _______________________________________________
>>>> Libmesh-users mailing list
>>>> Lib...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>>
>>>
>>
>> --
>> Yuxiang "Shawn" Wang, PhD
>> yw...@vi...
>> +1 (434) 284-0836
>>
>

-- 
Yuxiang "Shawn" Wang, PhD
yw...@vi...
+1 (434) 284-0836

Re: [Libmesh-users] Select quadrature rule order based on element type

[Vikram G. <vik...@gm...>]

Hi Yuxiang, glad to hear you are getting the expected results. This change
looks correct for your case and should not affect the assembly time by a
significant amount. You could also check for the actual type of element
(QUAD4 or TRI) instead of checking indirectly via the number of nodes.

You can check the performance change by checking the performance log which
is included at the end of the program's output. Look for something like:

| System
                                           |
|   assemble()                       1          0.0014      0.001422
 0.0028      0.002767    17.59    34.22    |

Thanks.
Vikram Garg

vikramvgarg.github.io/


On Sun, Apr 14, 2019 at 5:22 PM Yuxiang Wang <yw...@vi...> wrote:

> Hi Vikram,
>
> Thank you for your response!
>
> I didn't think about that - I tried to add that inside the loop over
> elements and got the correct results!
>
> Question - do you think that will significantly slow down the assembly,
> because we are now creating qrule and attaching it for every element loop?
>
> What I did was the following:
>
> for (const auto & elem : mesh.active_local_element_ptr_range()) {
>
> const unsigned int n_nodes = elem->n_nodes();
>
> Order qrule_order;
>
> switch (n_nodes)
> {
> case 3:
> qrule_order = SECOND;
> break;
>
> case 4:
> qrule_order = THIRD;
> break;
>
> default:
> qrule_order = fe_type.default_quadrature_order();
> break;
> }
>
> QGauss qrule (dim, qrule_order);
> fe->attach_quadrature_rule (&qrule);
>
> Thanks!
>
> Best,
> Shawn
>
> On Sun, Apr 14, 2019 at 2:53 PM Vikram Garg <vik...@gm...>
> wrote:
>
>> Hi Yuxiang,
>>                    It should be possible to move the construction of the
>> finite element and the specification of the quadrature rule inside the loop
>> over elements. Did this give any errors, or is otherwise unfeasible for
>> performance reasons ?
>>
>> Thanks.
>> Vikram Garg
>>
>> vikramvgarg.github.io/
>>
>>
>> On Sun, Apr 14, 2019 at 4:30 PM Yuxiang Wang <yw...@vi...> wrote:
>>
>>> Dear all,
>>>
>>> Sorry for the spam.
>>>
>>> I have a mix of QUAD4 and TRI3 elements in my mesh, and would like to use
>>> different quadrature rule orders for each type. Specifically, I'd like to
>>> have order THIRD for QUAD4 and SECOND for TRI3. By default, the orders
>>> are
>>> both THIRD.
>>>
>>> In most examples, I noticed that the specification of qrule is only for
>>> the
>>> entire FEType and not dependent on the element type (e.g. QUAD4 vs TRI3).
>>> Could you please share with me some hints on how to make
>>> element-dependent
>>> qrule order selection happen?
>>>
>>> Best,
>>> Shawn
>>>
>>>
>>> --
>>> Yuxiang "Shawn" Wang, PhD
>>> yw...@vi...
>>> +1 (434) 284-0836
>>>
>>> _______________________________________________
>>> Libmesh-users mailing list
>>> Lib...@li...
>>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>
>>
>
> --
> Yuxiang "Shawn" Wang, PhD
> yw...@vi...
> +1 (434) 284-0836
>

Re: [Libmesh-users] Select quadrature rule order based on element type

[Yuxiang W. <yw...@vi...>]

Hi Vikram,

Thank you for your response!

I didn't think about that - I tried to add that inside the loop over
elements and got the correct results!

Question - do you think that will significantly slow down the assembly,
because we are now creating qrule and attaching it for every element loop?

What I did was the following:

for (const auto & elem : mesh.active_local_element_ptr_range()) {

const unsigned int n_nodes = elem->n_nodes();

Order qrule_order;

switch (n_nodes)
{
case 3:
qrule_order = SECOND;
break;

case 4:
qrule_order = THIRD;
break;

default:
qrule_order = fe_type.default_quadrature_order();
break;
}

QGauss qrule (dim, qrule_order);
fe->attach_quadrature_rule (&qrule);

Thanks!

Best,
Shawn

On Sun, Apr 14, 2019 at 2:53 PM Vikram Garg <vik...@gm...> wrote:

> Hi Yuxiang,
>                    It should be possible to move the construction of the
> finite element and the specification of the quadrature rule inside the loop
> over elements. Did this give any errors, or is otherwise unfeasible for
> performance reasons ?
>
> Thanks.
> Vikram Garg
>
> vikramvgarg.github.io/
>
>
> On Sun, Apr 14, 2019 at 4:30 PM Yuxiang Wang <yw...@vi...> wrote:
>
>> Dear all,
>>
>> Sorry for the spam.
>>
>> I have a mix of QUAD4 and TRI3 elements in my mesh, and would like to use
>> different quadrature rule orders for each type. Specifically, I'd like to
>> have order THIRD for QUAD4 and SECOND for TRI3. By default, the orders are
>> both THIRD.
>>
>> In most examples, I noticed that the specification of qrule is only for
>> the
>> entire FEType and not dependent on the element type (e.g. QUAD4 vs TRI3).
>> Could you please share with me some hints on how to make element-dependent
>> qrule order selection happen?
>>
>> Best,
>> Shawn
>>
>>
>> --
>> Yuxiang "Shawn" Wang, PhD
>> yw...@vi...
>> +1 (434) 284-0836
>>
>> _______________________________________________
>> Libmesh-users mailing list
>> Lib...@li...
>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>
>

-- 
Yuxiang "Shawn" Wang, PhD
yw...@vi...
+1 (434) 284-0836

Re: [Libmesh-users] Select quadrature rule order based on element type

[Vikram G. <vik...@gm...>]

Hi Yuxiang,
                   It should be possible to move the construction of the
finite element and the specification of the quadrature rule inside the loop
over elements. Did this give any errors, or is otherwise unfeasible for
performance reasons ?

Thanks.
Vikram Garg

vikramvgarg.github.io/


On Sun, Apr 14, 2019 at 4:30 PM Yuxiang Wang <yw...@vi...> wrote:

> Dear all,
>
> Sorry for the spam.
>
> I have a mix of QUAD4 and TRI3 elements in my mesh, and would like to use
> different quadrature rule orders for each type. Specifically, I'd like to
> have order THIRD for QUAD4 and SECOND for TRI3. By default, the orders are
> both THIRD.
>
> In most examples, I noticed that the specification of qrule is only for the
> entire FEType and not dependent on the element type (e.g. QUAD4 vs TRI3).
> Could you please share with me some hints on how to make element-dependent
> qrule order selection happen?
>
> Best,
> Shawn
>
>
> --
> Yuxiang "Shawn" Wang, PhD
> yw...@vi...
> +1 (434) 284-0836
>
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users
>

[Libmesh-users] Select quadrature rule order based on element type

[Yuxiang W. <yw...@vi...>]

Dear all,

Sorry for the spam.

I have a mix of QUAD4 and TRI3 elements in my mesh, and would like to use
different quadrature rule orders for each type. Specifically, I'd like to
have order THIRD for QUAD4 and SECOND for TRI3. By default, the orders are
both THIRD.

In most examples, I noticed that the specification of qrule is only for the
entire FEType and not dependent on the element type (e.g. QUAD4 vs TRI3).
Could you please share with me some hints on how to make element-dependent
qrule order selection happen?

Best,
Shawn


-- 
Yuxiang "Shawn" Wang, PhD
yw...@vi...
+1 (434) 284-0836

Re: [Libmesh-users] Error reading gmesh file

[Stogner, R. H <roy...@ic...>]

On Tue, 9 Apr 2019, Nikrouz wrote:

> I have made a very simple mesh file with gmesh software, but I can not read 
> it by example code(introduction/ex1).
>
> I faced with this error:
>
> *poiseuille4@poiseuille4-pc:~/samples_libmesh/samples_intro/ex1-0$ 
> ./example-opt d 3 untitled.msh **

In the future run in dbg mode before posting bug reports if possible;
in this case it didn't matter, but in general the output is usually
more informative.

> **Error: Unknown msh file version 4**

What version of libMesh are you using?  We only got version 4 support
added to libMesh a couple weeks ago:

https://github.com/libMesh/libmesh/pull/2082

So if you want to use it you'll need to be using the git master, I
believe.
---
Roy

[Libmesh-users] Error reading gmesh file

[Nikrouz <nik...@gm...>]

Dear All,

I am highly thankful for the help of all of member of this mailings list.

I have made a very simple mesh file with gmesh software, but I can not 
read it by example code(introduction/ex1).

I faced with this error:

*poiseuille4@poiseuille4-pc:~/samples_libmesh/samples_intro/ex1-0$ 
./example-opt d 3 untitled.msh **
**Error: Unknown msh file version 4**
**Stack frames: 9**
**0: libMesh::print_trace(std::ostream&)**
**1: libMesh::MacroFunctions::report_error(char const*, int, char 
const*, char const*)**
**2: libMesh::GmshIO::read_mesh(std::istream&)**
**3: libMesh::GmshIO::read(std::__cxx11::basic_string<char, 
std::char_traits<char>, std::allocator<char> > const&)**
**4: libMesh::NameBasedIO::read(std::__cxx11::basic_string<char, 
std::char_traits<char>, std::allocator<char> > const&)**
**5: libMesh::UnstructuredMesh::read(std::__cxx11::basic_string<char, 
std::char_traits<char>, std::allocator<char> > const&, void*, bool, bool)**
**6: ./example-opt(+0x157c4) [0x55f7b133f7c4]**
**7: __libc_start_main**
**8: ./example-opt(+0x15b5a) [0x55f7b133fb5a]**
**[0] ../LIBMESH/src/mesh/gmsh_io.C, line 216, compiled Mar 22 2019 at 
21:22:33**
**--------------------------------------------------------------------------**
**MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD**
**with errorcode 1.**
**
**NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.**
**You may or may not see output from other processes, depending on**
**exactly when Open MPI kills them.*

How can I solve this issue?

Thanks everybody,

Re: [Libmesh-users] [RB] Eigenproblem Solver in SCM

[David K. <dav...@ak...>]

I agree that LAPACK is slow since it computes all eigenvalues, but I found
that alternative eigensolvers (like SLEPc) generally failed to converge for
the SCM eigenproblems, so in my experience LAPACK is the only reliable
choice. I don't have any other suggestion that I can offer on this,
unfortunately, since I have never found a better option than LAPACK for
this. Also, I don't think there is a way to get only the min or max
eigenvalues from LAPACK, I think it automatically computes all eigenvalues
(but you could check the LAPACK documentation if you want to be sure about
that).

In practice I have rarely used the SCM since I generally don't compute
rigorous error bounds, as I explained in some earlier emails. But if you do
want rigorous error bounds then I agree that the SCM is necessary.

Best regards,
David


On Thu, Apr 4, 2019 at 8:52 PM <ss...@pu...> wrote:

> Hello, David.
>
>
>
> I have applied SCM in my 3-D elasticity problem with the fine mesh.
>
> Although the SCM process works, It took too long to compute eigenvalues
> using LAPACK.
>
>
>
> The LAPACK yielded in almost all eigenvalues, which was a time-consuming
> cause.
>
> I tried to find ways to reduce the eigenvalue computation time, but I
> could not obtain a solution.
>
> Therefore, I would like to ask you for help.
>
>
>
> My questions are:
>
> 1.       Can we use only the LAPACK in SCM? I tried to use Krylov-Schur
> solver, but there was an error that failed to convergence the eigenvalue in
> the “compute_SCM_bounding_box()” process.
>
> 2.       Is there a way to derive only the minimum or maximum eigenvalue
> in LAPACK?
>
>
>
> I am always grateful for your help.
>
>
>
> Best regards,
>
>
>
> SKang
>

[Libmesh-users] [RB] Eigenproblem Solver in SCM

[<ss...@pu...>]

[Libmesh-users] question about an output from a system with vector elements

[Povolotskyi, M. <mpo...@pu...>]

Hello,

could you, please, advise me on the following problem:

I'm solving a system with Nedelec elements.

After I get a solution, I would like to output a curl of it.

I know how to compute curl on any point, this is very convenient with 
LibMesh, but how to output it?

Thank you,

Michael.

Re: [Libmesh-users] Error in Configure script

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

On Wed, Apr 3, 2019 at 3:10 PM Povolotskyi, Mykhailo <mpo...@pu...>
wrote:

> Hello,
>
> I have got the same error in 1.4.0, but then I used --disable-metaphysicl
>

I think it wouldn't be exactly the same error, since metaphysicl became a
submodule at some point between the 1.3 and 1.4 releases and we don't
specifically use version 0.2.0 any more, but it's possible the same error
is present in metaphysicl's configure.

Just to be clear: this error *kills* configure instead of just disabling
metaphysicl, correct? If so we really need to fix that.

Can you guys please let me know what OS you are using and what boost
packages are installed?

-- 
John

Re: [Libmesh-users] Error in Configure script

[Povolotskyi, M. <mpo...@pu...>]

Hello,

I have got the same error in 1.4.0, but then I used --disable-metaphysicl

To me it looked like a missing target definition in a makefile.

Michael.

On 4/3/2019 3:14 AM, John Peterson wrote:
> On Mon, Apr 1, 2019 at 2:25 PM Nikhil Vaidya <nik...@gm...>
> wrote:
>
>> I am trying to configure libMesh 1.3. I get the following error in my
>> configure script:
>>
>> configure: WARNING: boost/system/error_code.hpp: present but cannot be
>> compiled
>> configure: WARNING: boost/system/error_code.hpp:     check for missing
>> prerequisite headers?
>> configure: WARNING: boost/system/error_code.hpp: see the Autoconf
>> documentation
>> configure: WARNING: boost/system/error_code.hpp:     section "Present
>> But Cannot Be Compiled"
>> configure: WARNING: boost/system/error_code.hpp: proceeding with the
>> compiler's result
>> configure: WARNING:     ## --------------------------------------- ##
>> configure: WARNING:     ## Report this to roy...@ic... ##
>> configure: WARNING:     ## --------------------------------------- ##
>> checking for boost/system/error_code.hpp... no
>> configure: error: cannot find boost/system/error_code.hpp
>> configure: error: ../../../../contrib/metaphysicl/0.2.0/configure
>> failed for contrib/metaphysicl/0.2.0
>>
>>
>> The config.log file is also attached. What is going wrong?
>>
> It's difficult to say, possibly something is weird with your boost
> installation?
>
> If you don't specifically need metaphysicl, a quick fix you can try is
> simply configuring with --disable-metaphysicl. Also, unless you have a
> specific reason to be using libmesh 1.3, you might want to try version 1.4
> instead.
>
> https://github.com/libMesh/libmesh/releases/tag/v1.4.0
>

Re: [Libmesh-users] Error in Configure script

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

On Mon, Apr 1, 2019 at 2:25 PM Nikhil Vaidya <nik...@gm...>
wrote:

> I am trying to configure libMesh 1.3. I get the following error in my
> configure script:
>
> configure: WARNING: boost/system/error_code.hpp: present but cannot be
> compiled
> configure: WARNING: boost/system/error_code.hpp:     check for missing
> prerequisite headers?
> configure: WARNING: boost/system/error_code.hpp: see the Autoconf
> documentation
> configure: WARNING: boost/system/error_code.hpp:     section "Present
> But Cannot Be Compiled"
> configure: WARNING: boost/system/error_code.hpp: proceeding with the
> compiler's result
> configure: WARNING:     ## --------------------------------------- ##
> configure: WARNING:     ## Report this to roy...@ic... ##
> configure: WARNING:     ## --------------------------------------- ##
> checking for boost/system/error_code.hpp... no
> configure: error: cannot find boost/system/error_code.hpp
> configure: error: ../../../../contrib/metaphysicl/0.2.0/configure
> failed for contrib/metaphysicl/0.2.0
>
>
> The config.log file is also attached. What is going wrong?
>

It's difficult to say, possibly something is weird with your boost
installation?

If you don't specifically need metaphysicl, a quick fix you can try is
simply configuring with --disable-metaphysicl. Also, unless you have a
specific reason to be using libmesh 1.3, you might want to try version 1.4
instead.

https://github.com/libMesh/libmesh/releases/tag/v1.4.0

-- 
John

Re: [Libmesh-users] hp-EIM

[David K. <dav...@ak...>]

On Tue, Apr 2, 2019 at 10:30 AM Nikhil Vaidya <nik...@gm...>
wrote:

> Hello,
>
> I was wondering if there is a way to perform hp-EIM using the reduced basis
> module.
>

It's not implemented at the moment. You could try to extend the current EIM
code in order to support it, if you like.

Best,
David

Re: [Libmesh-users] hp-EIM

[David K. <dav...@ak...>]

On Tue, Apr 2, 2019 at 10:39 AM Nikhil Vaidya <nik...@gm...>
wrote:

> Hi David,
>
> Thanks for your reply. Could you give me some tips for extending the
> current EIM code?
>

You'd have to read through the EIM code and familiarize yourself with it...
I don't see any blockers to supporting hp-EIM, but it would take some work
to make sure you're managing all the data correctly. I don't have any
specific suggestions I'm afraid, other than to make sure you understand the
current code (I can answer questions on that if needed) and then you should
be able to see how it could be extended to do what you need (via
subclassing the relevant parts, for example).

Best,
David

>

Re: [Libmesh-users] hp-EIM

[Nikhil V. <nik...@gm...>]

Hi David,

Thanks for your reply. Could you give me some tips for extending the
current EIM code?

Best regards,
Nikhil

On Tue, Apr 2, 2019 at 4:31 PM David Knezevic <dav...@ak...>
wrote:

> On Tue, Apr 2, 2019 at 10:30 AM Nikhil Vaidya <nik...@gm...>
> wrote:
>
>> Hello,
>>
>> I was wondering if there is a way to perform hp-EIM using the reduced
>> basis
>> module.
>>
>
> It's not implemented at the moment. You could try to extend the current
> EIM code in order to support it, if you like.
>
> Best,
> David
>

[Libmesh-users] hp-EIM

[Nikhil V. <nik...@gm...>]

Hello,

I was wondering if there is a way to perform hp-EIM using the reduced basis
module.

Best regards,
Nikhil Vaidya

Re: [Libmesh-users] How to define Neuman Boundary Condition in libMesh

[Vikram G. <vik...@gm...>]

Hello Nikrouz,
                      You can use the side_time_derivative method to
specify a Neumann boundary. The ElasticitySystem::side_time_derivative
from fem_system_ex3, which applies a traction force at the boundary is
an illustration of this
(https://github.com/libMesh/libmesh/blob/master/examples/fem_system/fem_system_ex3/elasticity_system.C).

Adjoints example 1 and 2 provide examples of enforcing penalty
boundary conditions (which can be seen as a type of forcing) using
side_constraint
(https://github.com/libMesh/libmesh/blob/master/examples/adjoints/adjoints_ex1/L-shaped.C).

Thanks.
Vikram Garg

vikramvgarg.github.io/

On Mon, Apr 1, 2019 at 11:37 AM Nikrouz <nik...@gm...> wrote:
>
> Dear All libMesh users
>
> I am currently working with Example Fem_system example No2 titled
> "Nonlinear Elasticity with FEMSystem
> <http://libmesh.github.io/examples/fem_system_ex2.html>".
>
> The boundary conditions used in the code are defined based on
> displacement(Drichlet Boundary condition).
>
> How can I apply force boundary condition on one of the surfaces instead
> of displacement?
>
> Which of the examples is suitable for learning how to define load(s) on
> different surfaces?
>
> Thanks for your help and following!
>
>
> _______________________________________________
> Libmesh-users mailing list
> Lib...@li...
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