[deal.II] Re: Installation on cray XC50 | linking to petsc, lapack and blas libraries with different names

[vachan potluri]

I have found few reports of glibc version 2.28 causing such behaviour (e.g. 
see here ). It might be possible 
that /lib64/ld-linux-x86-64.so.2 on our system "links" to this version of 
glibc. But it actually is a static library:
$ ldd -v ld-linux-x86-64.so.2
statically linked
So there is probably no way to ascertain this. If it infact is so (linked 
to glibc 2.28), then I don't think there is anyway I can get working. With 
a simple code from here ,  I 
have found that my compiler links to glibc version 2.22 both during compile 
and run time. So there is no issue with the compiler.

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[deal.II] Re: Installation on cray XC50 | linking to petsc, lapack and blas libraries with different names

[vachan potluri]

This is the full backtrace with gdb.
(gdb) bt
#0  __static_initialization_and_destruction_0 (__initialize_p=1, 
__priority=65535)
at 
/home/ComptGasDynLab/vachanpotluri/source/dealii-9.1.1/source/numerics/time_dependent.cc:1196
#1  0x7fffec1aa6f8 in _GLOBAL__sub_I_time_dependent.cc(void) () at 
/home/ComptGasDynLab/vachanpotluri/source/dealii-9.1.1/source/numerics/time_dependent.cc:1275
#2  0x77deacba in call_init.part () from /lib64/ld-linux-x86-64.so.2
#3  0x77deada3 in _dl_init () from /lib64/ld-linux-x86-64.so.2
#4  0x77ddd22a in _dl_start_user () from /lib64/ld-linux-x86-64.so.2
#5  0x0001 in ?? ()
#6  0x7fff729e in ?? ()
#7  0x in ?? ()
Unfortunately, gdb is probably not configured properly. Cray has its own 
debuggers, most of them GUIs (and hence cannot be used) and all of them 
require submitting a job interactively which I am currently unable to do. I 
will post the bt with one of those when the queue is empty.

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Re: [deal.II] Running multiple programs at the same time

[Wolfgang Bangerth]

On 2/12/20 3:13 AM, Toni Vidal wrote:

- Matrix-free methods would have this problems minimised?


Maybe. Probably.


- Will this affect also to MPI parallelization scalability in this computer?


Yes. That's one of the issues with having modern many-core chips and running 
lots of MPI processes on them.


Best
 W.


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[deal.II] Re: Installation on cray XC50 | linking to petsc, lapack and blas libraries with different names

[Bruno Turcksin]

Vachan,

On Wednesday, February 12, 2020 at 12:24:38 AM UTC-5, vachan potluri wrote:
>
> Step-1 aborts with Illegal Instruction (core dumped). The error msg gdb 
> prints is the following.
> Program received signal SIGILL, Illegal instruction.
> __static_initialization_and_destruction_0 (__initialize_p=1, 
> __priority=65535)
> at 
> /home/ComptGasDynLab/vachanpotluri/source/dealii-9.1.1/source/numerics/time_dependent.cc:1196
> 1196  std::make_pair(0U, 
> 0.)));
> When I backtrace the error, it leads to this.
> template  
> typename 
> TimeStepBase_Tria_Flags::RefinementFlags::CorrectionRelaxations
>   
> TimeStepBase_Tria_Flags::RefinementFlags::default_correction_relaxations(
> 1, // one element, denoting the first and all subsequent sweeps
> std::vector>(1, // one element, 
> denoting the
> // upper bound for the
> // following relaxation
>  std::make_pair(0U, 0.)));
> Not just step-1, but step.debug, affinity.debug and mpi.debug (and 
> possibly other debug tests may) also terminate with the same error and bt. 
> Can someone explain why this is happening?
>

I am not sure why you have this error. Can you show the whole backtrace? 

Best,

Bruno

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Re: [deal.II] Re: Problem installing Dealii-9.0.0

[Felipe Orellana]

 Hi Bruno, and Dan,

Great !  I successfully installed dealii 9.0.0. on my cluster.
I paste below the finishing line and the tests it passed.

  Thanks a lot for your crucial support.

  Thanks Bruno for your specific instructions.

 I guess any subsequent potential issues could be just due to linking and
pointing to this library software.

cheers many,
Felipe
-- Installing:
/home/Felipe/BIGSOFTWARE/dealii-9.0.0/examples/step-9/step-9.release
-- Set runtime path of
"/home/Felipe/BIGSOFTWARE/dealii-9.0.0/examples/step-9/step-9.release" to
"/home/Felipe/BIGSOFTWARE/dealii-9.0.0/lib"

   [Felipe@mu01 build]$ make test
Scanning dependencies of target test
[100%] Running quicktests...
Test project /home/Felipe/BIGSOFTWARE/dealii-9.0.0/build/tests/quick_tests
Start 1: step.debug
1/5 Test #1: step.debug ...   Passed   21.94 sec
Start 2: step.release
2/5 Test #2: step.release .   Passed   19.10 sec
Start 3: affinity.debug
3/5 Test #3: affinity.debug ...   Passed   13.06 sec
Start 4: tbb.debug
4/5 Test #4: tbb.debug    Passed   11.88 sec
Start 5: boost_zlib.debug
5/5 Test #5: boost_zlib.debug .   Passed   13.69 sec

100% tests passed, 0 tests failed out of 5

Total Test time (real) =  79.67 sec
Built target test



On Tue, 11 Feb 2020 at 22:13, Bruno Turcksin 
wrote:

> Le mar. 11 févr. 2020 à 09:03, Felipe Orellana <
> felipeorellanarovir...@gmail.com> a écrit :
>
>>
>>   2)  I am not understanding well here:
>>
>> YW:  Why didn't you copy/paste the patch?
>>
>> What is 'the patch'  ..how can access that text?,
>>
>>   if I click on Tamiko's post, the web cannot find the site,
>> cannot find the commit.
>>
> Here it is
> https://github.com/dealii/dealii/commit/336319966b484889bbdd1da58623293b93980628.patch
>
> Bruno
>
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> 
> .
>

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Re: [deal.II] Running multiple programs at the same time

[Toni Vidal]

Hello Wolfgang,

The memory bus bandwidth seems the most reliable answer. But two more 
questions arise:
- Matrix-free methods would have this problems minimised?
- Will this affect also to MPI parallelization scalability in this computer?

Regards,
Toni
 

El dimarts, 11 febrer de 2020 22:37:31 UTC+1, Wolfgang Bangerth va escriure:
>
> On 2/11/20 2:27 PM, Toni Vidal wrote: 
> > 
> > That did not solve the problem with step 6. I got the same times. 
> > 
> > Indeed I have installed deal.II without  threads (DEAL_II_WITH_THREADS = 
> > OFF) and I set in my .basrc OMP_NUM_THREADS=1. 
>
> There are many other possible reasons for contention. For example, most 
> finite element programs are limited by the transfer of data from memory 
> to the processor. If you have just one program running, then only one 
> program is using the memory bus and is getting its full speed. But if 
> you have multiple programs running, then they are all competing for the 
> same bandwidth on the memory bus, and they will also be slowed down by 
> more than a single program would be. 
>
> It could also be that you have, say, 4 cores on your processor but 3 
> other programs currently running. Then running one instance of your code 
> will get a full core, but if you ran four, the total of 7 codes would 
> have to compete for 4 cores, and all would be slowed down. 
>
> By the way, to see whether your program really is using only one thread, 
> you can run the program 'top' in a separate command line window. It will 
> show you which percentage of a processor each running job takes up. 
>
> Best 
>   W. 
>
>
> -- 
>  
> Wolfgang Bangerth  email: bang...@colostate.edu 
>  
> www: http://www.math.colostate.edu/~bangerth/ 
>

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Re: [deal.II] Running multiple programs at the same time

[Toni Vidal]

Hi Ahmad,

I commented the output results method but it is the times did not change 
significantly.

Toni

El dimarts, 11 febrer de 2020 22:40:42 UTC+1, Ahmad Shahba va escriure:
>
> I was just wondering how much I/O operations contribute to your timings. 
> What would happen if you minimize the I/O activities, maybe comment out 
> output_results method and see if anything changes?
>
> Regards 
> Ahmad
>
> On Tue, Feb 11, 2020 at 16:27 Toni Vidal  > wrote:
>
>> Hi David,
>>
>> That did not solve the problem with step 6. I got the same times.
>>
>> Indeed I have installed deal.II without  threads (DEAL_II_WITH_THREADS = 
>> OFF) and I set in my .basrc OMP_NUM_THREADS=1.
>>
>> Any other idea?
>>
>>
>> El dimarts, 11 febrer de 2020 17:53:53 UTC+1, David Wells va escriure:
>>>
>>> Hi Toni, 
>>>
>>> I think that this is due to each individual program creating the same 
>>> number of threads as you have physical processors. Try adding 
>>>
>>> MultithreadInfo::set_thread_limit(1); 
>>>
>>> at the top of your code to prevent this from happening. Let us know if 
>>> this works! 
>>>
>>> Thanks, 
>>> David 
>>>
>>> On Tue, Feb 11, 2020 at 11:45 AM Toni Vidal  
>>> wrote: 
>>> > 
>>> > 
>>> > Dear deal.ii users and developers, 
>>> > 
>>> > I am currently running a deal.II based code thousands of times with 
>>> different input parameters. Each  simulation takes about 30 seconds in a 
>>> single processor. To do this, I have made a python script that runs 4 
>>> simulations at a time (using the multiprocessing module). However, each 
>>> simulation takes about 60 seconds and my have 8 cores (Intel® Core™ 
>>> i7-9700K CPU @ 3.60GHz × 8).  Is it not supposed to take approximately the 
>>> same amount of because the processors are independent? Am I 
>>> > 
>>> > In order to isolate the problem I have executed deal.II's step 6 (with 
>>> 12 cycles and 1e5 maximum solver steps) 1, 2 and 4 times at the same (using 
>>> different terminals). 
>>> > 
>>> > 1 running programs ~ 32 s user time 
>>> > 2 running programs ~ 44 s user time 
>>> > 4 running programs ~ 80 s user time 
>>> > 
>>> > Why the programs does not take the same time even though my computer 
>>> have 8 cores? 
>>> > Any idea? Am I missing something obvious? 
>>> > 
>>> > Ton Vidal 
>>> > 
>>> > -- 
>>> > The deal.II project is located at http://www.dealii.org/ 
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>>>  
>>>
>>>
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>>  
>> 
>> .
>>
>

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