[deal.II] deal.II Newsletter #18

[Rene Gassmoeller]

Hello everyone!

This is deal.II newsletter #18.
It automatically reports recently merged features and discussions about the 
deal.II finite element library.


## Below you find a list of recently proposed or merged features:

#5777: Fix typo in changelog entry (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/5777

#5776: step-42: Move a statement to where it belongs. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/5776

#5775: Require metis for a test to run (proposed by Rombur; merged) 
https://github.com/dealii/dealii/pull/5775

#5774: fix make_unique (proposed by davydden; merged) 
https://github.com/dealii/dealii/pull/5774

#5772: Use std::abs instead of abs. (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/5772

#5769: Provide general template interface for Utilities::MPI::sum/min/max 
(proposed by masterleinad) https://github.com/dealii/dealii/pull/5769

#5768: Update class doc of p::s::Triangulation. (proposed by bangerth; merged) 
https://github.com/dealii/dealii/pull/5768

#5767: Address what 'sequential' means in the context of communicators. 
(proposed by bangerth; merged) https://github.com/dealii/dealii/pull/5767

#5766: Address what 'sequential' means in the context of DoFHandlers. (proposed 
by bangerth; merged) https://github.com/dealii/dealii/pull/5766

#5765: Update a comment for PETScWrappers::PreconditionBlockJacobi. (proposed 
by bangerth; merged) https://github.com/dealii/dealii/pull/5765

#5761: Improve 2d transfinite guess (proposed by drwells; merged) 
https://github.com/dealii/dealii/pull/5761

#5760: Add tests for complex-valued add_and_dot() (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/5760

#5759: Fix DoFTools::locally_owned_dofs_per_subdomain() for empty processors. 
(proposed by bangerth; merged) https://github.com/dealii/dealii/pull/5759

#5758: Typo in the documentation of DataPostprocessorTensor (proposed by 
dangars; merged) https://github.com/dealii/dealii/pull/5758

#5757: Add static_asserts for complex-valued cases. (proposed by bangerth; 
merged) https://github.com/dealii/dealii/pull/5757

#5756: Provide HDF5 quicktest (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/5756

#5755:  Print out more info when TFI encounters errors. (proposed by drwells; 
merged) https://github.com/dealii/dealii/pull/5755

#5754: Make it clear that our CUDA wrappers only support float and double 
(proposed by Rombur; merged) https://github.com/dealii/dealii/pull/5754

#5750: Fix CUDAVector::add_and_dot() for complex-valued vectors. (proposed by 
bangerth; merged) https://github.com/dealii/dealii/pull/5750

#5749: Update documentation of *::Vector::add_and_dot for complex vectors. 
(proposed by bangerth; merged) https://github.com/dealii/dealii/pull/5749

#5748: Inline GeometryInfo members (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/5748

#5745: Initialize constexpr arrays in GeometryInfo (proposed by masterleinad; 
merged) https://github.com/dealii/dealii/pull/5745

#5744: Fix issues reported by Coverity (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/5744

#5743: Clarify documentation of (hp::)?DoFHandler::distribute_dofs(). (proposed 
by bangerth; merged) https://github.com/dealii/dealii/pull/5743

#5742: Rearrange a pointer check to satisfy coverity. (proposed by drwells; 
merged) https://github.com/dealii/dealii/pull/5742

#5740: Make parameters and variables for the internal::AlignedVector classes 
const (proposed by masterleinad; merged) 
https://github.com/dealii/dealii/pull/5740

#5737: Fix warnings: do not use Assert in CUDA kernel (proposed by Rombur; 
merged) https://github.com/dealii/dealii/pull/5737

#5736: Change .cuh extension to h (proposed by Rombur; merged) 
https://github.com/dealii/dealii/pull/5736

#5735: Add cuSPARSE support in the build system (proposed by Rombur; merged) 
https://github.com/dealii/dealii/pull/5735

#5734: Extend scalapack more (proposed by BenBrands; merged) 
https://github.com/dealii/dealii/pull/5734

#5728: Be explicit about virtual functions called in con-/destructors (proposed 
by masterleinad; merged) https://github.com/dealii/dealii/pull/5728


## And this is a list of recently opened or closed discussions:

#5773: one of the zoltan tests fails randomly (opened) 
https://github.com/dealii/dealii/issues/5773

#5771: it would be good to have macOS tester on Travis (opened) 
https://github.com/dealii/dealii/issues/5771

#5770: build broken on macOS (opened) 
https://github.com/dealii/dealii/issues/5770

#5764: Update introduction to parallel::shared::Triangulation (opened and 
closed) https://github.com/dealii/dealii/issues/5764

#5763: Update DoFRenumbering::subdomain_wise() (opened) 
https://github.com/dealii/dealii/issues/5763

#5762: Tweak documentation for 
hp::DoFHander::n_locally_owned_dofs_per_processor() (opened and closed) 

Re: [deal.II] Re: Parallel DoFRenumbering does not work on mac

[Jie Cheng]

I've reinstalled MPICH, and did a clean build of p4est, petsc and dealii, 
this problem still exists. At the linking stage of building dealii, I got 
warnings:

[526/579] Linking CXX shared library lib/libdeal_II.9.0.0-pre.dylib
   
ld: warning: could not create compact unwind for _dgehrd_: stack subq 
instruction is too different from dwarf stack size  
ld: warning: could not create compact unwind for _dhseqr_: stack subq 
instruction is too different from dwarf stack size  
ld: warning: could not create compact unwind for _sgehrd_: stack subq 
instruction is too different from dwarf stack size  
ld: warning: could not create compact unwind for _shseqr_: stack subq 
instruction is too different from dwarf stack size  
ld: warning: could not create compact unwind for _dormlq_: stack subq 
instruction is too different from dwarf stack size  
ld: warning: could not create compact unwind for _dormql_: stack subq 
instruction is too different from dwarf stack size  
ld: warning: could not create compact unwind for _dormqr_: stack subq 
instruction is too different from dwarf stack size  
ld: warning: could not create compact unwind for _sormlq_: stack subq 
instruction is too different from dwarf stack size  
ld: warning: could not create compact unwind for _sormql_: stack subq 
instruction is too different from dwarf stack size  
ld: warning: could not create compact unwind for _sormqr_: stack subq 
instruction is too different from dwarf stack size

I am not sure if this is related. Anyone has a clue?

Thanks
Jie

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Re: [deal.II] Deal.ii installation problem:- Step 40 runtime error

[Wolfgang Bangerth]

On 01/22/2018 08:48 AM, RAJAT ARORA wrote:


Running with PETSc on 2 MPI rank(s)...
Cycle 0:
Number of active cells:   1024
Number of degrees of freedom: 4225
Solved in 10 iterations.


+-+++
| Total wallclock time elapsed since start| 0.222s ||
| |||
| Section | no. calls |  wall time | % of total |
+-+---+++
| assembly| 1 | 0.026s |12% |
| output  | 1 |0.0448s |20% |
| setup   | 1 |0.0599s |27% |
| solve   | 1 |0.0176s |   7.9% |
+-+---+++


Cycle 1:
Number of active cells:   1960
Number of degrees of freedom: 8421
r001.pvt.bridges.psc.edu.27927Assertion failure at 
/nfs/site/home/phcvs2/gitrepo/ifs-all/Ofed_Delta/rpmbuild/BUILD/libpsm2-10.3.3/ptl_am/ptl.c:152: 
nbytes == req->recv_msglen
r001.pvt.bridges.psc.edu.27927step-40: Reading from remote process' memory 
failed. Disabling CMA support

[r001:27927] *** Process received signal ***


These error messages suggest that the first cycle actually worked. So your MPI 
installation is not completely broken apparently.


Is the error message reproducible? Is it always in the same place and with the 
same message? When you run two processes, are they on separate machines or on 
the same one?


Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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[deal.II] Re: Error with Transfinite Interpolation

[David Wells]

We merged the fix this morning into the development branch, including a 
test based on your code.

A suggestion: on some versions of GCC, calling 'abs' results in calling the 
C function 'int abs(int)': to be safe, use std::abs.

Let me know if things work :)

Thanks,
David Wells

On Thursday, January 18, 2018 at 8:54:09 PM UTC-5, Juan Carlos Araujo 
Cabarcas wrote:
>
> Thanks a lot for looking at this issue so quickly!
>
> No problem, you can use it. That was the idea of sharing the minimal 
> example! I am always happy to contribute with the library.
>
> So, does this mean that the way I colorize is correct? if there is a 
> better/simpler way plz let me know.
> Is the solution merged with the latest master branch? I would like to have 
> a working library for this particular example.
>
> El jueves, 18 de enero de 2018, 18:39:51 (UTC-5), David Wells escribió:
>>
>> I figured it out: we have an optimization that assumes in one particular 
>> place that, if we have eight points, they must be the vertices of a cube. 
>> However, in 2D, we use eight points to place new points on quadrilaterals: 
>> assuming these are the vertices of a cube is wrong. The original assumption 
>> created a bad initial value for a quasi-newton solver, which then failed to 
>> converge.
>>
>> I got rid of the cube assumption. see 
>> https://github.com/dealii/dealii/pull/5761 for more information.
>>
>> Do you mind if I use a modified version of your code for a new test in 
>> deal.II?
>>
>> Thanks,
>> David Wells
>>
>> On Wednesday, January 17, 2018 at 3:05:48 PM UTC-5, Juan Carlos Araujo 
>> Cabarcas wrote:
>>>
>>> Dear all,
>>>
>>> Since the inclusion of Transfinite interpolation, I have been successful 
>>> on working with this powerful technique in my research. I had coded a mesh 
>>> implementing concentric circles, where the inner most is shifted a small 
>>> distance s. All concentric circles are labeled 100+i, where i is in a loop 
>>> on all circles.
>>>
>>> The mesh was working after 4/Apr/17 when I added the following entry in 
>>> the forum:
>>> https://groups.google.com/forum/#!topic/dealii/hCZqv9g6mKk
>>>
>>> I installed the development version of dealii on the 17/nov/17. The 
>>> details of the installation are also in the forum:
>>> https://groups.google.com/forum/#!topic/dealii/ee2w2X987ig
>>>
>>> and recently I went back and tried to run thhis code, obtaining the 
>>> error at the end of the email.
>>>
>>> I prepared a minimal example that includes the definition of my grid. It 
>>> includes how I colorize each face as explained before, and the rest are 
>>> colorized "1" as the documentation suggests.
>>>
>>> The symptoms are the following:
>>> - If I use refinement=0, everything works and the mesh looks quite nice 
>>> in zeros.vtk and surface with lines mode in Paraview.
>>> - For any higher refinement, it gives the error below.
>>>
>>> Maybe there has been a major change in TransfiniteInterpolation since 
>>> Apr/2017, or maybe the way I colorize is not good anymore for some weird 
>>> reason. Any ideas or comments would be greatly appreciated.
>>>
>>> Juan Carlos Araújo,
>>> Umeå Universitet.
>>>
>>>
>>>
>>> terminate called after throwing an instance of 'dealii::Mapping<2, 
>>> 2>::ExcTransformationFailed'
>>>   what():  
>>> 
>>> An error occurred in line <1554> of file 
>>>  in function
>>> typename dealii::Triangulation::cell_iterator 
>>> dealii::TransfiniteInterpolationManifold>> spacedim>::compute_chart_points(const dealii::ArrayView>> dealii::Point >&, dealii::ArrayView) const 
>>> [with int dim = 2; int spacedim = 2; typename dealii::Triangulation>> spacedim>::cell_iterator = dealii::TriaIterator 
>>> >]
>>> The violated condition was: 
>>> false
>>> Additional information: 
>>> 
>>> 
>>>
>>> Aborted (core dumped)
>>>
>>>
>>>

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Re: AW: AW: [deal.II] step-42 clarification

[Wolfgang Bangerth]

I can do that for you. Do I understand correctly that the only change
that needs to happen is to move
   active_set_old = active_set;
to *after* the if-statement?


Exactly.


Great, thanks for confirming, Joerg!

The patch is now here:
  https://www.dealii.org/8.5.1/doxygen/deal.II/Tutorial.html

Best
 W.

--

Wolfgang Bangerth  email: bange...@colostate.edu
   www: http://www.math.colostate.edu/~bangerth/

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[deal.II] Deal.ii installation problem:- Step 40 runtime error

[RAJAT ARORA]

Hello all,

I recently installed deal.ii using candi but after everything successfully 
finishes, I am not able to run step-40 on more than 1 processor. For, 1 
processor it runs fine.


To install everything, I used candi and and loaded following modules.

  1) psc_path/1.1  2) slurm/17.02.5 3) cmake/3.7.2   4) mpi/
gcc_openmpi


I have tried several combinations of the modules in the past week but it is 
not working.
Can someone please help me finding out what is the problem with the 
installation?

I will be able to provide any relevant log file or command output if 
needed. 
Any help will be appreciated.

Here is the error message when I do

mpirun -np 2 ./step-40


Running with PETSc on 2 MPI rank(s)...
Cycle 0:
   Number of active cells:   1024
   Number of degrees of freedom: 4225
   Solved in 10 iterations.


+-+++
| Total wallclock time elapsed since start| 0.222s ||
| |||
| Section | no. calls |  wall time | % of total |
+-+---+++
| assembly| 1 | 0.026s |12% |
| output  | 1 |0.0448s |20% |
| setup   | 1 |0.0599s |27% |
| solve   | 1 |0.0176s |   7.9% |
+-+---+++


Cycle 1:
   Number of active cells:   1960
   Number of degrees of freedom: 8421
r001.pvt.bridges.psc.edu.27927Assertion failure at 
/nfs/site/home/phcvs2/gitrepo/ifs-all/Ofed_Delta/rpmbuild/BUILD/libpsm2-10.3.3/ptl_am/ptl.c:152:
 
nbytes == req->recv_msglen
r001.pvt.bridges.psc.edu.27927step-40: Reading from remote process' memory 
failed. Disabling CMA support
[r001:27927] *** Process received signal ***
[r001:27927] Signal: Aborted (6)
[r001:27927] Signal code:  (-6)
[r001:27927] [ 0] /lib64/libpthread.so.0(+0xf370)[0x2b8ccfc72370]
[r001:27927] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2b8cd04bf1d7]
[r001:27927] [ 2] /lib64/libc.so.6(abort+0x148)[0x2b8cd04c08c8]
[r001:27927] [ 3] /lib64/libpsm2.so.2(+0x14df8)[0x2b8cda72cdf8]
[r001:27927] [ 4] /lib64/libpsm2.so.2(+0xeb59)[0x2b8cda726b59]
[r001:27927] [ 5] /lib64/libpsm2.so.2(+0x8fcf)[0x2b8cda720fcf]
[r001:27927] [ 6] /lib64/libpsm2.so.2(+0x7b1a)[0x2b8cda71fb1a]
[r001:27927] [ 7] /lib64/libpsm2.so.2(+0x21012)[0x2b8cda739012]
[r001:27927] [ 8] /lib64/libpsm2.so.2(psm2_mq_ipeek2+0xa8)[0x2b8cda734198]
[r001:27927] [ 9] 
/usr/mpi/gcc/openmpi-1.10.4-hfi/lib64/openmpi/mca_mtl_psm2.so(ompi_mtl_psm2_progress+0x6b)[0x2b8cdc461d7b]
[r001:27927] [10] 
/usr/mpi/gcc/openmpi-1.10.4-hfi/lib64/libopen-pal.so.13(opal_progress+0x2a)[0x2b8cd2e381ea]
[r001:27927] [11] 
/usr/mpi/gcc/openmpi-1.10.4-hfi/lib64/libmpi.so.12(ompi_request_default_wait_all+0x225)[0x2b8ccf46f5f5]
[r001:27927] [12] 
/usr/mpi/gcc/openmpi-1.10.4-hfi/lib64/libmpi.so.12(PMPI_Waitall+0x9f)[0x2b8ccf49fdff]
[r001:27927] [13] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(hypre_MPI_Waitall+0x9)[0x2b8cc6c1c485]
[r001:27927] [14] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(hypre_ParCSRCommHandleDestroy+0x3f)[0x2b8cc6ba7664]
[r001:27927] [15] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(hypre_ParCSRMatrixExtractBExt+0x48)[0x2b8cc6bab3a7]
[r001:27927] [16] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(hypre_BoomerAMGBuildInterp+0x39b)[0x2b8cc6b649b5]
[r001:27927] [17] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(hypre_BoomerAMGSetup+0x4056)[0x2b8cc6b507f6]
[r001:27927] [18] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(HYPRE_BoomerAMGSetup+0x9)[0x2b8cc6b470d6]
[r001:27927] [19] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(+0x7ea066)[0x2b8cc67e8066]
[r001:27927] [20] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/petsc-3.7.6/lib/libpetsc.so.3.7(PCSetUp+0x551)[0x2b8cc67efcbb]
[r001:27927] [21] 
/pylon5/ss4s82p/rarora/Code-Libraries/dealii85me-gnu4.9/deal.II-v8.5.1/lib/libdeal_II.g.so.8.5.1(_ZN6dealii13PETScWrappers21PreconditionBoomerAMG10initializeERKNS0_10MatrixBaseERKNS1_14AdditionalDataE+0x63)[0x2b8cc1bcf94d]
[r001:27927] [22] 
./step-40(_ZN6Step4014LaplaceProblemILi2EE5solveEv+0x106)[0x42ca38]
[r001:27927] [23] 
./step-40(_ZN6Step4014LaplaceProblemILi2EE3runEv+0x245)[0x42ead1]
[r001:27927] [24] ./step-40(main+0x3c)[0x41d07d]
[r001:27927] [25] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b8cd04abb35]
[r001:27927] [26] ./step-40[0x41cf29]
[r001:27927] *** End of error message ***

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