Re: [deal.II] dealii/spack on apple m1

[Alberto Salvadori]

Hi Praveen,

here is my experience on apple M1 and deal.ii.

1 - After opening a terminal rosetta, installing gcc, installing deal.ii
via spack and using gfortran from gcc installation, it works just fine
2 - Even in a rosetta terminal, the current dmg package does not seem to
work
3 - After opening a terminal rosetta, NOT installing gcc, installing
deal.ii via spack and using gfortran from homebrew installation, deal.ii
apparently does not work
4 - I had some issues with openmpi after installation, because of the
dynamic library that apparently conflicts with cmake. My skills are very
limited, but with some further work (that I cannot recall now)
I made it, even with Xcode projects.

Hope it helps
Alberto


*Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale
(DIMI)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3715426

e-mail:
 alberto.salvad...@unibs.it
web-page:
 http://m4lab.unibs.it/faculty.html



On Thu, Apr 15, 2021 at 7:00 AM Praveen C  wrote:

> Dear all
>
> Has anyone succeeded in installing dealii via spack on an apple m1 ?
>
> What works/does not work ?
>
> spack gives me a spec but also gives some warnings
>
> $ spack spec dealii
> Input spec
> 
> dealii
>
> Concretized
> 
> sysctl: unknown oid 'machdep.cpu.leaf7_features'
> sysctl: unknown oid 'machdep.cpu.vendor'
> sysctl: unknown oid 'machdep.cpu.model'
> sysctl: unknown oid 'machdep.cpu.leaf7_features'
> sysctl: unknown oid 'machdep.cpu.vendor'
> sysctl: unknown oid 'machdep.cpu.model'
>
> Or have you been able to compile dealii via some other method on m1 ?
>
> Thanks
> praveen
>
> --
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> 
> .
>

-- 


Informativa sulla Privacy: http://www.unibs.it/node/8155 


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[deal.II] dealii/spack on apple m1

[Praveen C]

Dear all

Has anyone succeeded in installing dealii via spack on an apple m1 ?

What works/does not work ?

spack gives me a spec but also gives some warnings

$ spack spec dealii
Input spec

dealii

Concretized

sysctl: unknown oid 'machdep.cpu.leaf7_features'
sysctl: unknown oid 'machdep.cpu.vendor'
sysctl: unknown oid 'machdep.cpu.model'
sysctl: unknown oid 'machdep.cpu.leaf7_features'
sysctl: unknown oid 'machdep.cpu.vendor'
sysctl: unknown oid 'machdep.cpu.model'

Or have you been able to compile dealii via some other method on m1 ?

Thanks
praveen

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Re: [deal.II] Solving a local DG problem on each cell

[Wolfgang Bangerth]

On 4/13/21 8:03 PM, Corbin Foucart wrote:


One thing I am still unclear on is if FEInterfaceValues is the best (or only) 
way to access the face values of a field on a neighboring cell, or if this can 
be done manually. Right now, I'm using an approach like


std::vector field_at_qpts(sd.fe_interface_values.n_quadrature_points);
sd.fe_interface_values.get_fe_face_values(1).get_function_values(field, 
field_at_qpts);


where 'sd' is a typical scratchdata object with an FEInterfaceValues instance 
as a class attribute. Is this typically how neighboring data is accessed for 
DG-like methods?


If you're only accessing data stored in FEInterfaceValues through one of the 
two FEFaceValues objects, then you might as well initialize an FEFaceValues 
object with the neighboring cell and the common face. In the same way as you 
access information from the current face using only an FEFaceValues.


Best
 W.

--

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

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Re: [deal.II] Bug in FEInterfaceValues?

[Timo Heister]

Hi Corbin,

Indeed, the following code:

sd.fe_interface_values.reinit(cell, face_index);

initializes the object as a boundary face. You need to pass the two
neighboring cells to the other reinit() function.




On Tue, Apr 13, 2021 at 11:08 PM Corbin Foucart
 wrote:
>
> I took a look at the unit tests for FEInterfaceValues in 
> tests/feinterface/fe_interface_values_0*.cc, and found that the following 
> modification to the code in the face loop, changing how reinit and the 
> boundary check is done:
>
> for ( cell loop)
>   for ( face loop)
>   ...
>
>   // detect top face
>   if (nrml[0][1] > 0 && !(cell->at_boundary(face_index)))
>   {
> std::cout << std::endl;
> sd.fe_interface_values.reinit(cell,
>   face_index,
>   numbers::invalid_unsigned_int,
>   cell->neighbor(face_index),
>   
> cell->neighbor_of_neighbor(face_index),
>   numbers::invalid_unsigned_int);
>...
>
> sd.fe_interface_values.get_fe_face_values(1).get_function_values(field, 
> uhat_qpt);
>}
>
> Works fine at getting the values from the other side of the interface. 
> Perhaps I used the reinit(...) function incorrectly.
>
> Best,
> Corbin
>
>
> On Tue, Apr 13, 2021 at 9:56 PM Corbin Foucart  
> wrote:
>>
>> Hello all,
>>
>> I have found an unexpected behavior in using the FEInterfaceValues object. 
>> Namely, it seems that a line like,
>>
>> fe_interface_values.get_fe_face_values(1).get_function_values(...);
>>
>> returns the following error
>>
>> > The violated condition was:
>> > cell_index == 0 || !at_boundary()
>> > Additional information:
>> > You are on a boundary, so you can only ask for the first FEFaceValues 
>> > object.
>>
>> ...if the cell is on a boundary, but the face is an interior face.
>>
>> I've attached code for a small test case illustrating the issue. It consists 
>> of a 2x2 2D mesh, and attempts to use FEInterfaceValues to get field values 
>> from the cell "above".
>>
>> Is this indeed a bug, or am I misunderstanding the intended usage of 
>> FEInterfaceValues? I'm using deal.II, version 9.2.0.
>>
>> Best,
>> Corbin
>>
>> --
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>
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-- 
Timo Heister
http://www.math.clemson.edu/~heister/

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Re: [deal.II] HDF5 output on multiple nodes at HPC cluster

['Christian Burkhardt' via deal.II User Group]

Yes, following the command 'df -Th', the type of file system where the 
error occurred is 'nfs'.

Thanks again.


Timo Heister schrieb am Dienstag, 13. April 2021 um 17:50:42 UTC+2:

> Great to hear. Was it a standard NFS filesystem that produced the failures?
>
> On Tue, Apr 13, 2021 at 4:03 AM 'Christian Burkhardt' via deal.II User
> Group  wrote:
> >
> > Thanks for your quick answer.
> > The problem persisted for the parallel vtu output.
> > Changing the file system where the output is written to, to a xfs solved 
> the problem. Sorry for the inconvinience, but we are quite new to cluster 
> systems.
> >
> > Thanks,
> > Christian
> >
> > Timo Heister schrieb am Montag, 12. April 2021 um 18:37:32 UTC+2:
> >>
> >> Christian,
> >>
> >> What kind of filesystem is this file written to? Does our parallel vtu
> >> output that also uses MPI IO work correctly? (step-40 with grouping
> >> set to a single file)
> >>
> >> On Mon, Apr 12, 2021 at 12:15 PM 'Christian Burkhardt' via deal.II
> >> User Group  wrote:
> >> >
> >> > Hi everyone,
> >> >
> >> > we installed dea...@9.2.0 on our HPC cluster (centos7) using spack 
> and the intel compilers 
> (dea...@9.2.0%in...@19.0.4~assimp~petsc~slepc~ginkgo~adol-c+mpi^intel-mpi^intel-mkl^boost).
> >> > When running our code, which uses hdf5 for output, on the front node 
> and when submitting it via the batch script everything works fine as long 
> as we run on a single node (up to 40 cores).
> >> > As soon as we increase the node number above 1 (eg 41 cores) the code 
> fails.
> >> > We were able to reproduce the problem with an adapted version of 
> step-40 of the dealii tutorials that outputs using hdf5 (see attached 
> step-40).
> >> > The restriction to 32 MPI Processes for the output was bypassed by 
> setting the limit to 42.
> >> > The code can overwrite existing files (created during a previous run 
> with 40 processes or less and 1 node), but crashes when new files are to be 
> created with the following error message, which is related to the hdf5 
> output:
> >> >
> >> > ...
> >> > HDF5-DIAG: Error detected in HDF5 (1.8.21) MPI-process 41:
> >> > #000: H5F.c line 520 in H5Fcreate(): unable to create file
> >> > major: File accessibilty
> >> > minor: Unable to open file
> >> > #001: H5Fint.c line 990 in H5F_open(): unable to open file: time = 
> Mon Apr 12 11:25:30 2021
> >> > , name = 'Solution_0.h5', tent_flags = 13
> >> > major: File accessibilty
> >> > minor: Unable to open file
> >> > #002: H5FD.c line 991 in H5FD_open(): open failed
> >> > major: Virtual File Layer
> >> > minor: Unable to initialize object
> >> > #003: H5FDmpio.c line 1057 in H5FD_mpio_open(): MPI_File_open failed
> >> > major: Internal error (too specific to document in detail)
> >> > minor: Some MPI function failed
> >> > #004: H5FDmpio.c line 1057 in H5FD_mpio_open(): File does not exist, 
> error stack:
> >> > ADIOI_UFS_OPEN(39): File Solution_0.h5 does not exist
> >> > major: Internal error (too specific to document in detail)
> >> > minor: MPI Error String
> >> > ...
> >> >
> >> > The file mentioned in the error message is still created, but remains 
> empty (file size 0)
> >> > (see testRunMPI.e1448739 for the full error message).
> >> > We tried different hdf5 versions (1.10.7, 1.8.21).
> >> > We also looked into https://github.com/choderalab/yank/issues/1165 
> and tried setting the environment variable "HDF5_USE_FILE_LOCKING=FALSE" 
> which didn't alter the outcome.
> >> > As our configuration includes MPI "WITH_MPI=ON" the issue 
> https://github.com/dealii/dealii/issues/605 is about something different, 
> right?
> >> >
> >> > In the tutorial description it is mentioned that a limitation of 16 
> processors was chosen because such large examples have problems being 
> visualised.
> >> > Is there a general rule of thumb that states graphical output for DOF 
> numbers over a certain threshold are unfeasible?
> >> >
> >> > Any help is much appreciated.
> >> >
> >> > Christian
> >> >
> >> > --
> >> > The deal.II project is located at http://www.dealii.org/
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> .
> >>
> >>
> >>
> >> --
> >> Timo Heister
> >> http://www.math.clemson.edu/~heister/
> >
> > --
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