Re: [deal.II] Re: Re_Error during installation of dealii.8.4.1

[Wolfgang Bangerth]

On 02/02/2017 03:41 PM, Sathish Kumar wrote:

//
/icpc: command line warning #10006: ignoring unknown option '-fuse-ld=gold'/
/lac/CMakeFiles/obj_lac.debug.dir/sparse_matrix_inst2.cc.o: file not
recognized: File format not recognized/


This typically happens if you compile in the same directory in which a 
previous compile job aborted because of a compiler error, because you 
were out of memory, or some other reason. In that case, the previous 
compiler run left an unfinished object file that the subsequent compiler 
run recognizes as "up to date" (because it's newer than its source 
files) but can't read successfully.


The solution is to do 'make clean' or just to blow away the build 
directory and start again.


Best
 W.

--

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

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Re: [deal.II] Re: Re_Error during installation of dealii.8.4.1

[Sathish Kumar]

Bruno,

On using icc 2015 I am getting this error message :

*Scanning dependencies of target deal_II.g*
*[100%] Building CXX object source/CMakeFiles/deal_II.g.dir/dummy.cc.o*
*Linking CXX shared library ../lib/libdeal_II.g.so*
*icpc: command line warning #10006: ignoring unknown option '-fuse-ld=gold'*
*lac/CMakeFiles/obj_lac.debug.dir/sparse_matrix_inst2.cc.o: file not 
recognized: File format not recognized*
*make[2]: *** [lib/libdeal_II.g.so.8.4.1] Error 1*
*make[1]: *** [source/CMakeFiles/deal_II.g.dir/all] Error 2*
*make: *** [all] Error 2*

Is there something else that needs to changed as well ?

Kind regards
Sathish


On Thursday, 2 February 2017 20:27:40 UTC+1, Bruno Turcksin wrote:
>
> Sathish, 
>
> icc 2015 should work. We don't test deal with icc 2015 anymore but we 
> used to. I also think that deal 8.4 was tested with icc 2015. 
>
> Best, 
>
> Bruno 
>
> 2017-02-02 14:18 GMT-05:00 Sathish Kumar : 
>
> > Hi Bruno, 
> > 
> > Thanks for the quick reply. 
> > 
> > Currently I am using icc/2013.5.192. Also the available ones in the 
> cluster 
> > are : 
> > 
> > icc/11.1.080, icc/2013.5.192, icc/2013_sp1.1.106 and icc/2015.0.090. 
> > 
> > Is any of the above supported? 
> > 
> > Regards 
> > Sathish 
> > 
> > 
> > 
> > On Thursday, 2 February 2017 20:00:18 UTC+1, Bruno Turcksin wrote: 
> >> 
> >> Sathish, 
> >> 
> >> which version of the intel compiler are you using? Older versions are 
> not 
> >> tested. 
> >> 
> >> Best, 
> >> 
> >> Bruno 
> >> 
> >> On Thursday, February 2, 2017 at 1:55:07 PM UTC-5, Sathish Kumar wrote: 
> >>> 
> >>> Hi , 
> >>> 
> >>> I am trying to install dealii in a Linux environment and when I run 
> the 
> >>> command make install after the CMake step, once the make process has 
> reached 
> >>> 100 % I get the following error message: 
> >>> 
> >>> Scanning dependencies of target obj_meshworker.debug 
> >>> [100%] Building CXX object 
> >>> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker.cc.o 
> >>> [100%] Building CXX object 
> >>> 
> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker_info.cc.o 
> >>> [100%] Building CXX object 
> >>> 
> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker_vector_selector.cc.o
>  
>
> >>> [100%] Built target obj_meshworker.debug 
> >>> Scanning dependencies of target deal_II.g 
> >>> [100%] Building CXX object source/CMakeFiles/deal_II.g.dir/dummy.cc.o 
> >>> Linking CXX shared library ../lib/libdeal_II.g.so 
> >>> icpc: command line warning #10006: ignoring unknown option 
> >>> '-fuse-ld=gold' 
> >>> ": internal error: backend signals 
> >>> 
> >>> icpc: error #10014: problem during multi-file optimization compilation 
> >>> (code 4) 
> >>> make[2]: *** [lib/libdeal_II.g.so.8.4.2] Error 4 
> >>> make[1]: *** [source/CMakeFiles/deal_II.g.dir/all] Error 2 
> >>> make: *** [all] Error 2 
> >>> 
> >>> I have tried with dealii.8.4.2 as well and still the same problem 
> >>> persists. Since I am trying to install them into my university's 
> cluster 
> >>> account, I guess there might be some issues with the CMake version 
> i.e. 
> >>> CMake/2.8.12.1-intel-2014a or CMake/2.8.12.1-GCC-4.8.2 versions, that 
> are 
> >>> available by default. 
> >>> 
> >>> Any suggestions to fix this issue would be really appreciated. 
> >>> 
> >>> Thank you and Regards 
> >>> Sathish 
> >>> 
> > -- 
> > The deal.II project is located at http://www.dealii.org/ 
> > For mailing list/forum options, see 
> > https://groups.google.com/d/forum/dealii?hl=en 
> > --- 
> > You received this message because you are subscribed to a topic in the 
> > Google Groups "deal.II User Group" group. 
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> > https://groups.google.com/d/topic/dealii/SE6UClZRpbI/unsubscribe. 
> > To unsubscribe from this group and all its topics, send an email to 
> > dealii+un...@googlegroups.com . 
> > For more options, visit https://groups.google.com/d/optout. 
>

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Re: [deal.II] Re: Re_Error during installation of dealii.8.4.1

[Sathish Kumar]

Bruno,

Okay. I shall try with icc 2015 then and get back to you if there are some 
issues.

Thanks again.
Sathish

On Thursday, 2 February 2017 20:27:40 UTC+1, Bruno Turcksin wrote:
>
> Sathish, 
>
> icc 2015 should work. We don't test deal with icc 2015 anymore but we 
> used to. I also think that deal 8.4 was tested with icc 2015. 
>
> Best, 
>
> Bruno 
>
> 2017-02-02 14:18 GMT-05:00 Sathish Kumar : 
>
> > Hi Bruno, 
> > 
> > Thanks for the quick reply. 
> > 
> > Currently I am using icc/2013.5.192. Also the available ones in the 
> cluster 
> > are : 
> > 
> > icc/11.1.080, icc/2013.5.192, icc/2013_sp1.1.106 and icc/2015.0.090. 
> > 
> > Is any of the above supported? 
> > 
> > Regards 
> > Sathish 
> > 
> > 
> > 
> > On Thursday, 2 February 2017 20:00:18 UTC+1, Bruno Turcksin wrote: 
> >> 
> >> Sathish, 
> >> 
> >> which version of the intel compiler are you using? Older versions are 
> not 
> >> tested. 
> >> 
> >> Best, 
> >> 
> >> Bruno 
> >> 
> >> On Thursday, February 2, 2017 at 1:55:07 PM UTC-5, Sathish Kumar wrote: 
> >>> 
> >>> Hi , 
> >>> 
> >>> I am trying to install dealii in a Linux environment and when I run 
> the 
> >>> command make install after the CMake step, once the make process has 
> reached 
> >>> 100 % I get the following error message: 
> >>> 
> >>> Scanning dependencies of target obj_meshworker.debug 
> >>> [100%] Building CXX object 
> >>> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker.cc.o 
> >>> [100%] Building CXX object 
> >>> 
> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker_info.cc.o 
> >>> [100%] Building CXX object 
> >>> 
> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker_vector_selector.cc.o
>  
>
> >>> [100%] Built target obj_meshworker.debug 
> >>> Scanning dependencies of target deal_II.g 
> >>> [100%] Building CXX object source/CMakeFiles/deal_II.g.dir/dummy.cc.o 
> >>> Linking CXX shared library ../lib/libdeal_II.g.so 
> >>> icpc: command line warning #10006: ignoring unknown option 
> >>> '-fuse-ld=gold' 
> >>> ": internal error: backend signals 
> >>> 
> >>> icpc: error #10014: problem during multi-file optimization compilation 
> >>> (code 4) 
> >>> make[2]: *** [lib/libdeal_II.g.so.8.4.2] Error 4 
> >>> make[1]: *** [source/CMakeFiles/deal_II.g.dir/all] Error 2 
> >>> make: *** [all] Error 2 
> >>> 
> >>> I have tried with dealii.8.4.2 as well and still the same problem 
> >>> persists. Since I am trying to install them into my university's 
> cluster 
> >>> account, I guess there might be some issues with the CMake version 
> i.e. 
> >>> CMake/2.8.12.1-intel-2014a or CMake/2.8.12.1-GCC-4.8.2 versions, that 
> are 
> >>> available by default. 
> >>> 
> >>> Any suggestions to fix this issue would be really appreciated. 
> >>> 
> >>> Thank you and Regards 
> >>> Sathish 
> >>> 
> > -- 
> > The deal.II project is located at http://www.dealii.org/ 
> > For mailing list/forum options, see 
> > https://groups.google.com/d/forum/dealii?hl=en 
> > --- 
> > You received this message because you are subscribed to a topic in the 
> > Google Groups "deal.II User Group" group. 
> > To unsubscribe from this topic, visit 
> > https://groups.google.com/d/topic/dealii/SE6UClZRpbI/unsubscribe. 
> > To unsubscribe from this group and all its topics, send an email to 
> > dealii+un...@googlegroups.com . 
> > For more options, visit https://groups.google.com/d/optout. 
>

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Re: [deal.II] Re: Re_Error during installation of dealii.8.4.1

[Bruno Turcksin]

Sathish,

icc 2015 should work. We don't test deal with icc 2015 anymore but we
used to. I also think that deal 8.4 was tested with icc 2015.

Best,

Bruno

2017-02-02 14:18 GMT-05:00 Sathish Kumar :
> Hi Bruno,
>
> Thanks for the quick reply.
>
> Currently I am using icc/2013.5.192. Also the available ones in the cluster
> are :
>
> icc/11.1.080, icc/2013.5.192, icc/2013_sp1.1.106 and icc/2015.0.090.
>
> Is any of the above supported?
>
> Regards
> Sathish
>
>
>
> On Thursday, 2 February 2017 20:00:18 UTC+1, Bruno Turcksin wrote:
>>
>> Sathish,
>>
>> which version of the intel compiler are you using? Older versions are not
>> tested.
>>
>> Best,
>>
>> Bruno
>>
>> On Thursday, February 2, 2017 at 1:55:07 PM UTC-5, Sathish Kumar wrote:
>>>
>>> Hi ,
>>>
>>> I am trying to install dealii in a Linux environment and when I run the
>>> command make install after the CMake step, once the make process has reached
>>> 100 % I get the following error message:
>>>
>>> Scanning dependencies of target obj_meshworker.debug
>>> [100%] Building CXX object
>>> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker.cc.o
>>> [100%] Building CXX object
>>> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker_info.cc.o
>>> [100%] Building CXX object
>>> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker_vector_selector.cc.o
>>> [100%] Built target obj_meshworker.debug
>>> Scanning dependencies of target deal_II.g
>>> [100%] Building CXX object source/CMakeFiles/deal_II.g.dir/dummy.cc.o
>>> Linking CXX shared library ../lib/libdeal_II.g.so
>>> icpc: command line warning #10006: ignoring unknown option
>>> '-fuse-ld=gold'
>>> ": internal error: backend signals
>>>
>>> icpc: error #10014: problem during multi-file optimization compilation
>>> (code 4)
>>> make[2]: *** [lib/libdeal_II.g.so.8.4.2] Error 4
>>> make[1]: *** [source/CMakeFiles/deal_II.g.dir/all] Error 2
>>> make: *** [all] Error 2
>>>
>>> I have tried with dealii.8.4.2 as well and still the same problem
>>> persists. Since I am trying to install them into my university's cluster
>>> account, I guess there might be some issues with the CMake version i.e.
>>> CMake/2.8.12.1-intel-2014a or CMake/2.8.12.1-GCC-4.8.2 versions, that are
>>> available by default.
>>>
>>> Any suggestions to fix this issue would be really appreciated.
>>>
>>> Thank you and Regards
>>> Sathish
>>>
> --
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[deal.II] Re: Re_Error during installation of dealii.8.4.1

[Sathish Kumar]

Hi Bruno,

Thanks for the quick reply.

Currently I am using *icc/2013.5.192. *Also the available ones in the 
cluster are :

*icc/11.1.080, icc/2013.5.192, icc/2013_sp1.1.106 *and* icc/2015.0.090*.

Is any of the above supported?

Regards
Sathish



On Thursday, 2 February 2017 20:00:18 UTC+1, Bruno Turcksin wrote:
>
> Sathish,
>
> which version of the intel compiler are you using? Older versions are not 
> tested.
>
> Best,
>
> Bruno
>
> On Thursday, February 2, 2017 at 1:55:07 PM UTC-5, Sathish Kumar wrote:
>>
>> Hi ,
>>
>> I am trying to install dealii in a Linux environment and when I run the 
>> command make install after the CMake step, once the make process has 
>> reached 100 % I get the following error message:
>>
>> *Scanning dependencies of target obj_meshworker.debug*
>> *[100%] Building CXX object 
>> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker.cc.o*
>> *[100%] Building CXX object 
>> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker_info.cc.o*
>> *[100%] Building CXX object 
>> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker_vector_selector.cc.o*
>> *[100%] Built target obj_meshworker.debug*
>> *Scanning dependencies of target deal_II.g*
>> *[100%] Building CXX object source/CMakeFiles/deal_II.g.dir/dummy.cc.o*
>> *Linking CXX shared library ../lib/libdeal_II.g.so 
>> *
>> *icpc: command line warning #10006: ignoring unknown option 
>> '-fuse-ld=gold'*
>> *": internal error: backend signals*
>>
>> *icpc: error #10014: problem during multi-file optimization compilation 
>> (code 4)*
>> *make[2]: *** [lib/libdeal_II.g.so.8.4.2] Error 4*
>> *make[1]: *** [source/CMakeFiles/deal_II.g.dir/all] Error 2*
>> *make: *** [all] Error 2*
>>
>> I have tried with dealii.8.4.2 as well and still the same problem 
>> persists. Since I am trying to install them into my university's cluster 
>> account, I guess there might be some issues with the CMake version 
>> i.e. CMake/2.8.12.1-intel-2014a or CMake/2.8.12.1-GCC-4.8.2 versions, that 
>> are available by default. 
>>
>> Any suggestions to fix this issue would be really appreciated.
>>
>> Thank you and Regards
>> Sathish
>>
>>

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[deal.II] Re: Re_Error during installation of dealii.8.4.1

[Bruno Turcksin]

Sathish,

which version of the intel compiler are you using? Older versions are not 
tested.

Best,

Bruno

On Thursday, February 2, 2017 at 1:55:07 PM UTC-5, Sathish Kumar wrote:
>
> Hi ,
>
> I am trying to install dealii in a Linux environment and when I run the 
> command make install after the CMake step, once the make process has 
> reached 100 % I get the following error message:
>
> *Scanning dependencies of target obj_meshworker.debug*
> *[100%] Building CXX object 
> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker.cc.o*
> *[100%] Building CXX object 
> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker_info.cc.o*
> *[100%] Building CXX object 
> source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker_vector_selector.cc.o*
> *[100%] Built target obj_meshworker.debug*
> *Scanning dependencies of target deal_II.g*
> *[100%] Building CXX object source/CMakeFiles/deal_II.g.dir/dummy.cc.o*
> *Linking CXX shared library ../lib/libdeal_II.g.so 
> *
> *icpc: command line warning #10006: ignoring unknown option 
> '-fuse-ld=gold'*
> *": internal error: backend signals*
>
> *icpc: error #10014: problem during multi-file optimization compilation 
> (code 4)*
> *make[2]: *** [lib/libdeal_II.g.so.8.4.2] Error 4*
> *make[1]: *** [source/CMakeFiles/deal_II.g.dir/all] Error 2*
> *make: *** [all] Error 2*
>
> I have tried with dealii.8.4.2 as well and still the same problem 
> persists. Since I am trying to install them into my university's cluster 
> account, I guess there might be some issues with the CMake version 
> i.e. CMake/2.8.12.1-intel-2014a or CMake/2.8.12.1-GCC-4.8.2 versions, that 
> are available by default. 
>
> Any suggestions to fix this issue would be really appreciated.
>
> Thank you and Regards
> Sathish
>
>

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[deal.II] Re_Error during installation of dealii.8.4.1

[Sathish Kumar]

Hi ,

I am trying to install dealii in a Linux environment and when I run the 
command make install after the CMake step, once the make process has 
reached 100 % I get the following error message:

*Scanning dependencies of target obj_meshworker.debug*
*[100%] Building CXX object 
source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker.cc.o*
*[100%] Building CXX object 
source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker_info.cc.o*
*[100%] Building CXX object 
source/meshworker/CMakeFiles/obj_meshworker.debug.dir/mesh_worker_vector_selector.cc.o*
*[100%] Built target obj_meshworker.debug*
*Scanning dependencies of target deal_II.g*
*[100%] Building CXX object source/CMakeFiles/deal_II.g.dir/dummy.cc.o*
*Linking CXX shared library ../lib/libdeal_II.g.so*
*icpc: command line warning #10006: ignoring unknown option '-fuse-ld=gold'*
*": internal error: backend signals*

*icpc: error #10014: problem during multi-file optimization compilation 
(code 4)*
*make[2]: *** [lib/libdeal_II.g.so.8.4.2] Error 4*
*make[1]: *** [source/CMakeFiles/deal_II.g.dir/all] Error 2*
*make: *** [all] Error 2*

I have tried with dealii.8.4.2 as well and still the same problem persists. 
Since I am trying to install them into my university's cluster account, I 
guess there might be some issues with the CMake version 
i.e. CMake/2.8.12.1-intel-2014a or CMake/2.8.12.1-GCC-4.8.2 versions, that 
are available by default. 

Any suggestions to fix this issue would be really appreciated.

Thank you and Regards
Sathish

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Re: [deal.II] internal compiler error: Bus error

[Yi-Chung Chen]

Hi Lev, 

I was wondering if you ran out of disk. In my experience, it looks like 
your previous compilation is only partially successful.

Best
YC Chen
On Thursday, February 2, 2017 at 4:31:12 PM UTC, Lev Karatun wrote:
>
> Hi Matthias,
>
> It doesn't seem to be reproducible. In fact, when I ran the compilation 
> today again, it completed without errors. I'll check if there is an option 
> to use gcc 4.9.4. But will I have to recompile Trilinos and BLAS in this 
> case? I'd rather avoid doing it
>
> Best regards,
> Lev Karatun.
>
> 2017-02-01 23:03 GMT-05:00 Matthias Maier :
>
>> A bus error with gcc-4.8.1 on x86_64 is rare...
>>
>> Is it reproducible? I.e. if you run the compilation with
>>
>>   $ make VERBOSE=1 -j1
>>
>> you will see the full command invocation that lead to the internal
>> compiler error. Does it always stop at the same .cc file ?
>>
>> Further, can you ask the administrators to update the compiler?
>> gcc-4.9.4 is a well tested and solid choice. (the newer gcc-5* and
>> gcc-6* variants might lead to an ABI nightmare if you do not recompile
>> every C++ library).
>>
>> Best,
>> Matthias
>>
>>
>>
>> On Wed, Feb  1, 2017, at 20:05 CST, Lev Karatun > > wrote:
>>
>> > Hi Wolfgang,
>> >
>> > I was first compiling with -j8 then tried again with -j1 but got the 
>> same
>> > error.
>> >
>> > Best regards,
>> > Lev Karatun.
>> >
>> > 2017-02-01 20:41 GMT-05:00 Wolfgang Bangerth > >:
>> >
>> >> On 02/01/2017 06:23 PM, Lev Karatun wrote:
>> >>
>> >>>
>> >>> I'm trying to install the latest version of dealII on a cluster now, 
>> got
>> >>> another error unfortunately.
>> >>> The output is below, and I attached the logs too. I would appreciate 
>> any
>> >>> help with this.
>> >>>
>> >>
>> >> Are you compiling with -j4 or similar? Does the same happen if you 
>> compile
>> >> with -j1? The kind of internal compiler error you have here seems to 
>> happen
>> >> most often if you run out of memory.
>> >>
>> >> Best
>> >>  W.
>> >>
>> >> --
>> >> 
>> 
>> >> Wolfgang Bangerth  email: 
>> bang...@colostate.edu 
>> >>www: 
>> http://www.math.colostate.edu/~bangerth/
>> >>
>> >> --
>> >> The deal.II project is located at http://www.dealii.org/
>> >> For mailing list/forum options, see https://groups.google.com/d/fo
>> >> rum/dealii?hl=en
>> >> --- You received this message because you are subscribed to a topic in 
>> the
>> >> Google Groups "deal.II User Group" group.
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>> >> pic/dealii/aZvol6kHWJI/unsubscribe.
>> >> To unsubscribe from this group and all its topics, send an email to
>> >> dealii+un...@googlegroups.com .
>> >> For more options, visit https://groups.google.com/d/optout.
>> >>
>>
>> --
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Re: [deal.II] Fully distributed triangulation (level 0)

[Yi-Chung Chen]

Hi Timo, 

Thank you for your information.

On Wednesday, February 1, 2017 at 6:38:23 PM UTC, Timo Heister wrote:
>
> > I believe that it would not be impossible to develop this, but it will 
> probably not be a small exercise. You would have to develop a fair share of 
> code, and gain an understanding of parts of the library you don't usually 
> get to see if you use deal.II. 
> > 
> > If you're willing to do this, we can guide you along the process, but 
> it's going to be a bit of work for sure. 
>
> One of my students is working on the initial step to get towards being 
> able to handle very large distributed triangulations. The main 
> limitation will be (for now), that the partitioning is static and 
> needs to happen in an offline process (so you can't really do adaptive 
> refinement or change the number of processors effectively). This might 
> be enough for your problem, though. 
>
> I can go into more detail if you want. 
>
Yes, please let me know the detail or the code. I just need a fully 
distributed triangulation which stores it local owned data in use. I dont 
even need p4est. A MPI protocol handles data communication should work. 
There is no need of adaptivity since cells in my case are atomic cells. I 
can also work on the code since I believe it may help the development of 
fully distributed triangulation. Actually, my friend and I are working on 
async distribution. All these should be included at the current stage.

Best 
YC Chen



> -- 
> Timo Heister 
> http://www.math.clemson.edu/~heister/ 
>

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Re: [deal.II] Fully distributed triangulation (level 0)

[Yi-Chung Chen]

Hi Wolfgang, 


On Tuesday, January 31, 2017 at 10:57:35 PM UTC, Wolfgang Bangerth wrote:
>
>
> Yi-Chung, 
>
> > Thank you for your prompt reply. I was wondeirng if I can integrate 
> > other partition tools, such as metis or parmetis to handle the fully 
> > distributed triangulation. I can develop that part by myself (or with 
> > some help from the community). Do you have any suggestions? 
>
> I believe that it would not be impossible to develop this, but it will 
> probably not be a small exercise. You would have to develop a fair share 
> of code, and gain an understanding of parts of the library you don't 
> usually get to see if you use deal.II. 
>
> If you're willing to do this, we can guide you along the process, but 
> it's going to be a bit of work for sure. 
>
> I'm willing to work on this part. Please let me know how should I start 
it. I believe this code will help the community. 
 

> > My following 
> > project also relies on this since I will try to manage number of cells 
> > in each processor. With p4est, it is hard to manage number of cells 
> > based on a in-house algorithm. 
>
> That is actually not quite true. p4est (and the deal.II classes that use 
> it) allow you to describe a "weight" for each cell, and p4est will 
> partition in a way that the sum of weights is roughly equal among all 
> processors. 
>

I knew that p4est can do partition by weight. However, my current needs to 
control and distributed the cells in need. It would be better to control 
the partition by myself rather than p4est.
 

> > My application is about IC designs that 
> > may have million to billion cells. A fully distributed triangulation 
> > helps to reduce memory usage. The current shared_memory system can 
> > handle 20M (single core) in system of 32GB main memory. 
>
> That's already quite impressive :-) What kind of meshes do you have that 
> require so many cells? Are they geometrically incredibly complicated to 
> require that many cells already at the coarse level? 
>
Actually, this is the interesting part. We try to simulate thermal profile 
of integrated circuit. For a CPU, it has billion transistors inside and 
each of then has its own power trace as RHS. That is why we have to give it 
a large coarse mesh at beginning. I did some model reductions for 
transistors, but I still want my tool can simulate 100M cells to ensure 
accuracy.
 

>
> > Any design of 1M cells on the distributed triangulation have problem of 
> > computation time because of the reorder step. This is why I bypassed it 
> > and provided a sorted mesh to grid_in (read_msh). For a problem of 5M 
> > cells, I can save 200sec at the step of create_triangulation. 
>
> Yes, I'm willing to believe this. The algorithm wasn't intended for 
> meshes of this size, though we did test it with ~300k cells in 2d and we 
> know that it scales like O(N). So 200 seconds seems like a long time. Is 
> this in debug mode? 
>
Unfortunately not in debug mode.I guess the reorder is more like O(N^2 or 
N^4) if I may recall.
It searches the cells will minimum numbers of neighbors and then search 
again recursively for its neighbors. With increasing number of dofs, time 
increases exponentially.
For a 2-D problem it might be fast. For a 3-D, problem with >1M dofs takes 
a while to reorder.
In my setup program, a steady state 3-D thermal simulation (distributed 
trial) for a problem of 5M dofs in two cores requires 200 sec reorder, 80 
sec setup_system, 80 sec solver time (petsc-MPI). 100sec output, and 80 sec 
create_tria, and 45 sec assembly. Each core requires 9GB memory. This is 
why I want to reduce memory usage.

my solution is to create mesh by myself since I generate it from a real IC. 
here is an example, if anyone want to generate the mesh. For a 3X3 2-D 
mesh, normally I will create mesh start from x then y. However, p4est 
requires a mesh with minimum (or balanced communication), it would be 
better to group neighbors together. So cell_id becomes the following:
7 8 9 7 8 9
4 5 6  =>> 3 4 6
1 2 3 1 2 5
In this way, it is easy to map it to distributed them by linearly 
distributing. 


Best
YC Chen

Best 
>   Wolfgang 
>
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>

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Re: [deal.II] internal compiler error: Bus error

[Matthias Maier]

On Thu, Feb  2, 2017, at 10:30 CST, Lev Karatun  wrote:

> It doesn't seem to be reproducible. In fact, when I ran the compilation
> today again, it completed without errors.

In that case a hardware issue might very likely be the problem.


> I'll check if there is an option to use gcc 4.9.4. But will I have to
> recompile Trilinos and BLAS in this case? I'd rather avoid doing it

I suggested this as a possible workaround if the bus error you saw is
reproducible. Given the fact that you could compile the library on
second try, there is not much you gain by upgrading to 4.9.4.

Best,
Matthias

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Re: [deal.II] internal compiler error: Bus error

[Lev Karatun]

Hi Matthias,

It doesn't seem to be reproducible. In fact, when I ran the compilation
today again, it completed without errors. I'll check if there is an option
to use gcc 4.9.4. But will I have to recompile Trilinos and BLAS in this
case? I'd rather avoid doing it

Best regards,
Lev Karatun.

2017-02-01 23:03 GMT-05:00 Matthias Maier :

> A bus error with gcc-4.8.1 on x86_64 is rare...
>
> Is it reproducible? I.e. if you run the compilation with
>
>   $ make VERBOSE=1 -j1
>
> you will see the full command invocation that lead to the internal
> compiler error. Does it always stop at the same .cc file ?
>
> Further, can you ask the administrators to update the compiler?
> gcc-4.9.4 is a well tested and solid choice. (the newer gcc-5* and
> gcc-6* variants might lead to an ABI nightmare if you do not recompile
> every C++ library).
>
> Best,
> Matthias
>
>
>
> On Wed, Feb  1, 2017, at 20:05 CST, Lev Karatun 
> wrote:
>
> > Hi Wolfgang,
> >
> > I was first compiling with -j8 then tried again with -j1 but got the same
> > error.
> >
> > Best regards,
> > Lev Karatun.
> >
> > 2017-02-01 20:41 GMT-05:00 Wolfgang Bangerth :
> >
> >> On 02/01/2017 06:23 PM, Lev Karatun wrote:
> >>
> >>>
> >>> I'm trying to install the latest version of dealII on a cluster now,
> got
> >>> another error unfortunately.
> >>> The output is below, and I attached the logs too. I would appreciate
> any
> >>> help with this.
> >>>
> >>
> >> Are you compiling with -j4 or similar? Does the same happen if you
> compile
> >> with -j1? The kind of internal compiler error you have here seems to
> happen
> >> most often if you run out of memory.
> >>
> >> Best
> >>  W.
> >>
> >> --
> >> 
> 
> >> Wolfgang Bangerth  email:
> bange...@colostate.edu
> >>www: http://www.math.colostate.edu/
> ~bangerth/
> >>
> >> --
> >> The deal.II project is located at http://www.dealii.org/
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> >> rum/dealii?hl=en
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[deal.II] Re: Synchronization issue for parallel computation of material forces

['Seyed Ali Mohseni' via deal.II User Group]

And this is the procedure how I output them:

DataOut data_out;
data_out.attach_dof_handler(dof_handler);

std::vector configurational_forces_magnitude(dim, 
"config_forces");

std::vector 
configurational_forces_interpretation(dim, 
DataComponentInterpretation::component_is_part_of_vector);

data_out.add_data_vector(configurational_forces, 
configurational_forces_magnitude, DataOut::type_dof_data, 
configurational_forces_interpretation);

Very weird. I can compute everything correctly for one core, but why is it 
not multicore compatible?


Kind Regards,
S. A. Mohseni

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[deal.II] Synchronization issue for parallel computation of material forces

['Seyed Ali Mohseni' via deal.II User Group]

Hi,

With regard to the approach which was recently discussed in: 
https://groups.google.com/d/msg/dealii/25C57MYvfpg/JFB8aXKoAgAJ

There is a little problem when computing the material forces in a parallel 
setting.


  
  



I assume it has something to do with the synchronization. 

The computation of material forces is done similar to the system_rhs vector.



Vector cell_cf(dofs_per_cell); // Cell Configurational forces

typename DoFHandler::active_cell_iterator cell = 
dof_handler.begin_active(), endc = dof_handler.end();
for (; cell != endc; ++cell)
{
if ( cell->is_locally_owned() )
{
fe_values.reinit(cell);

cell_cf = 0;

...

// Configurational force computation ...

...

cell->get_dof_indices(local_dof_indices);

constraints.distribute_local_to_global(cell_cf, 
local_dof_indices, configurational_forces);
}
}

configurational_forces.compress(VectorOperation::add);


For a single core computation it is validated and correct.


What could be possibly wrong when going to parallel?



Best regards,

Seyed Ali Mohseni  




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[deal.II] Re: Source of a constant residual error when a triangulation has hanging nodes

[amir . pasha . beh]

 

Dear Daniel


After solving constraints_update.distribute is called. In addition, after 
assembling the system matrix and residual vector using the first method, 
constraints_update.condense is called before solving the system. After that 
the solution is updated and the new residual is calculated based on the 
first method, so in error calculation the constraints are considered as,


BlockVector 
 
error_res(dofs_per_block);

for (unsigned int i = 0; i < dof_handler.n_dofs 
();
 
++i)

if (!constraints_update.is_constrained 

(i))

error_res(i) = system_rhs(i);

error_residual.norm = error_res.l2_norm();



constraints update 

1 = 0

3 = 0

11 = 0

21 = 0

22 10: 5.0e-01

22 14: 5.0e-01

23 15: 5.0e-01

24 14: 5.0e-01

24 16: 5.0e-01

25 15: 5.0e-01

25 17: 5.0e-01

26 16: 5.0e-01

26 40: 5.0e-01

27 17: 5.0e-01

27 41: 5.0e-01

42 = 0

43 = 1.0e-04

45 = 1.0e-04

46 = 0

49 = 1.0e-04

51 = 1.0e-04

53 = 1.0e-04

55 = 0

56 40: 5.0e-01

57 41: 5.0e-01

57 59: 5.0e-01

58 = 0

69 = 0

70 = 0

72 = 0

78 = 0

79 = 0

80 = 0

93 87: 5.0e-01

93 89: 5.0e-01

94 89: 5.0e-01

94 90: 5.0e-01

95 90: 5.0e-01

95 102: 5.0e-01

110 102: 5.0e-01

110 111: 5.0e-01


constraints hanging nodes 

22 10: 5.0e-01

22 14: 5.0e-01

23 11: 5.0e-01

23 15: 5.0e-01

24 14: 5.0e-01

24 16: 5.0e-01

25 15: 5.0e-01

25 17: 5.0e-01

26 16: 5.0e-01

26 40: 5.0e-01

27 17: 5.0e-01

27 41: 5.0e-01

56 40: 5.0e-01

56 58: 5.0e-01

57 41: 5.0e-01

57 59: 5.0e-01

93 87: 5.0e-01

93 89: 5.0e-01

94 89: 5.0e-01

94 90: 5.0e-01

95 90: 5.0e-01

95 102: 5.0e-01

110 102: 5.0e-01

110 111: 5.0e-01



Thank you.

Pasha

On Thursday, February 2, 2017 at 2:14:34 PM UTC+3:30, Daniel Arndt wrote:
>
> Pasha,
>  
>
>> I checked the the system residual assembly process. For a triangulation 
>> with 28 cells, the dof index 17 is belong to cells 2, 5, 8 and 27. The 
>> corresponding cell_rhs values for this index are,
>>
>>
>> cellcell_rhs value
>>
>> 22.88462e+00
>>
>> 52.88462e+00
>>
>> 8   -2.88462e+00
>>
>> 27 -1.44231e+00
>>
>>
>> This dof is not constrained. When the following assembly method is used:
>>
>>
>> *for* (*unsigned* *int* i = 0; i < dofs_per_cell; ++i)
>>
>> system_rhs(data.local_dof_indices[i]) += data.cell_rhs(i);
>>
>>
>> the system_rhs(17) = 1.4423076, however, using the following method,
>>
>>
>> constraints_update.distribute_local_to_global(data.cell_rhs,
>>
>> data.local_dof_indices, system_rhs);
>>
>>
>>
>> the system_rhs(17) = -1.33e-15. This is the source of the problem because 
>> I have used the second method in the previous code and the first one 
>> (similar to step-44) in the new code. I cant understand why the results are 
>> different.
>>
> This looks like DoF 17 is constrained, possibly by hanging node 
> constraints. Can you recheck the constraints stored in `constraints_update` 
> via `constraints_update.print(std::cout)`?
> In any case, you need to use a ConstraintMatrix for assembling the 
> right-hand side either via calling `distribute_local_to_global` on each 
> cell or calling `condense` after the loop over all cells. After solving you 
> would call `constraints.distribute`.
> Otherwise, you would not take the hanging node constraints into account.
> Are you missing the call to `constraints.condense(system_matrix, 
> system_rhs);` in the first approach?
>
> Best,
> Daniel
>

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Re: [deal.II] using VectorTools::interpolate_boundary_values :Simple verification of Stokes system with zero velocity (using step-22)

[Jane Lee]

Thanks Wolfgang, very silly of me. Have sorted the other problem too which 
didn't have anything to do with the way i was interpolating boundaries. 

On Wednesday, February 1, 2017 at 6:30:00 PM UTC, Wolfgang Bangerth wrote:
>
> On 02/01/2017 11:24 AM, Jane Lee wrote: 
> > 
> > where the boundary values are just 1.0 so that u is a constant vector 
> field. 
> > this still gives me the bizarre 22 factor in my pressures solution 
> > (which is just linear in z - the resulting pressure solution is atleast 
> > linear), but the pressure solution aside, both the x and y components of 
> > the velocity are 0.0 ON the boundaries and 1.0 everywhere else. 
>
> Are you calling constraints.distribute on the solution vector after 
> solving your linear system? 
>
> Best 
>   W. 
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>

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[deal.II] Re: Source of a constant residual error when a triangulation has hanging nodes

[amir . pasha . beh]

 

Dear Denis


I checked the the system residual assembly process. For a triangulation 
with 28 cells, the dof index 17 is belong to cells 2, 5, 8 and 27. The 
corresponding cell_rhs values for this index are,


cellcell_rhs value

22.88462e+00

52.88462e+00

8   -2.88462e+00

27 -1.44231e+00


This dof is not constrained. When the following assembly method is used:


*for* (*unsigned* *int* i = 0; i < dofs_per_cell; ++i)

system_rhs(data.local_dof_indices[i]) += data.cell_rhs(i);


the system_rhs(17) = 1.4423076, however, using the following method,


constraints_update.distribute_local_to_global(data.cell_rhs,

data.local_dof_indices, system_rhs);



the system_rhs(17) = -1.33e-15. This is the source of the problem because I 
have used the second method in the previous code and the first one (similar 
to step-44) in the new code. I cant understand why the results are 
different.


Regards

P.

On Wednesday, February 1, 2017 at 8:24:51 PM UTC+3:30, Daniel Arndt wrote:
>
> Pasha,
>
> I have a code that works fine. Now, I am working to change the code 
>> structure to use “workstream”. The new code works fine without adaptive 
>> refinement. However, when the mesh is refined and the triangulation has 
>> hanging node, a constant residual error remains during Newton iteration. I 
>> cant find source of the problem
>>
> You are providing way too few information to expect useful answers. What 
> are you doing in your code?
> For which part in your code do you want to change to WorkStream? 
> What exactly did you change? How is this related to whether you are doing 
> adaptive refinement or not?
>
> Best,
> Daniel
>

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