Re: [deal.II] Update of Ubuntu

2018-09-22 Thread Aquaman 
I tested MPI parallel using an example from
http://hamilton.nuigalway.ie/teaching/AOS/NINE/mpi-first-examples.html

MPI solver shows correct results..

Thanks a lot in advance!

Best regards,
Yaakov

On Fri, Sep 21, 2018 at 12:51 PM 'Maxi Miller' via deal.II User Group <
dealii@googlegroups.com> wrote:

> Are programs depending on MPI able to run in general (i.e. also without
> deal.II)? That should be the first thing to test
>
> Am Freitag, 21. September 2018 02:09:36 UTC+2 schrieb Aquaman:
>>
>> Dear Prof. Arndt,
>>
>> many thanks for your support!
>>
>> as you suggested, I have tested step-40, it works well.
>>
>> But in folder cracks, If I run mpirun -n 2 ./cracks
>> parameters_sneddon_2d.prm
>>
>> I received the same error infos
>>
>> Fatal error in PMPI_Init_thread: Other MPI error, error stack:
>> MPIR_Init_thread(474)...:
>> MPID_Init(190)..: channel initialization failed
>> MPIDI_CH3_Init(89)..:
>> MPID_nem_init(413)..:
>> MPIDI_nem_ckpt_init(170): BLCR kernel module not present
>> Fatal error in PMPI_Init_thread: Other MPI error, error stack:
>> MPIR_Init_thread(474)...:
>> MPID_Init(190)..: channel initialization failed
>> MPIDI_CH3_Init(89)..:
>> MPID_nem_init(413)..:
>> MPIDI_nem_ckpt_init(170): BLCR kernel module not present
>>
>> I really have no idea how to fix such kind of MPI's Bug.  (If I remove mpirun
>> -n 2, the phase-field model works...)
>>
>>
>> Kind regards,
>> Yaakov
>>
>> On Thursday, September 20, 2018 at 3:23:56 PM UTC+2, Daniel Arndt wrote:
>>>
>>> Yaakov,
>>>
>>>
 1. I use candi for the installation, I think I have to rebuilt deal.ii
 again.

>>> Yes, definitely!
>>>

 2.  The error should be related to MPI.

>>> What Jean-Paul meant to say is that there is nothing like "Dealii input
>>> files by Heister & Wick".
>>> You are probably referring to the crack propagation code that is built
>>> on top of deal.II and and parameter files for this application.
>>>
>>> If I were you, I would first make sure that your deal.II installation is
>>> working correctly, especially with respect to MPI, by
>>> compiling and running some example steps, e.g. step-40.
>>> Afer that you can have a look if the application code needs an update as
>>> well.
>>>
>>> Best,
>>> Daniel
>>>
>> --
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Re: [deal.II] Update of Ubuntu

2018-09-21 Thread 'Maxi Miller' via deal.II User Group 
Are programs depending on MPI able to run in general (i.e. also without 
deal.II)? That should be the first thing to test

Am Freitag, 21. September 2018 02:09:36 UTC+2 schrieb Aquaman:
>
> Dear Prof. Arndt,
>
> many thanks for your support!
>
> as you suggested, I have tested step-40, it works well.
>
> But in folder cracks, If I run mpirun -n 2 ./cracks 
> parameters_sneddon_2d.prm 
>
> I received the same error infos  
>
> Fatal error in PMPI_Init_thread: Other MPI error, error stack: 
> MPIR_Init_thread(474)...:  
> MPID_Init(190)..: channel initialization failed 
> MPIDI_CH3_Init(89)..:  
> MPID_nem_init(413)..:  
> MPIDI_nem_ckpt_init(170): BLCR kernel module not present 
> Fatal error in PMPI_Init_thread: Other MPI error, error stack: 
> MPIR_Init_thread(474)...:  
> MPID_Init(190)..: channel initialization failed 
> MPIDI_CH3_Init(89)..:  
> MPID_nem_init(413)..:  
> MPIDI_nem_ckpt_init(170): BLCR kernel module not present
>
> I really have no idea how to fix such kind of MPI's Bug.  (If I remove mpirun 
> -n 2, the phase-field model works...)
>
>
> Kind regards,
> Yaakov
>
> On Thursday, September 20, 2018 at 3:23:56 PM UTC+2, Daniel Arndt wrote:
>>
>> Yaakov,
>>  
>>
>>> 1. I use candi for the installation, I think I have to rebuilt deal.ii 
>>> again. 
>>>
>> Yes, definitely!
>>  
>>>
>>> 2.  The error should be related to MPI.
>>>
>> What Jean-Paul meant to say is that there is nothing like "Dealii input 
>> files by Heister & Wick".
>> You are probably referring to the crack propagation code that is built on 
>> top of deal.II and and parameter files for this application.
>>
>> If I were you, I would first make sure that your deal.II installation is 
>> working correctly, especially with respect to MPI, by
>> compiling and running some example steps, e.g. step-40.
>> Afer that you can have a look if the application code needs an update as 
>> well.
>>
>> Best,
>> Daniel
>>
>

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Re: [deal.II] Update of Ubuntu

2018-09-20 Thread Aquaman 
Dear Prof. Arndt,

many thanks for your support!

as you suggested, I have tested step-40, it works well.

But in folder cracks, If I run mpirun -n 2 ./cracks 
parameters_sneddon_2d.prm 

I received the same error infos  

Fatal error in PMPI_Init_thread: Other MPI error, error stack: 
MPIR_Init_thread(474)...:  
MPID_Init(190)..: channel initialization failed 
MPIDI_CH3_Init(89)..:  
MPID_nem_init(413)..:  
MPIDI_nem_ckpt_init(170): BLCR kernel module not present 
Fatal error in PMPI_Init_thread: Other MPI error, error stack: 
MPIR_Init_thread(474)...:  
MPID_Init(190)..: channel initialization failed 
MPIDI_CH3_Init(89)..:  
MPID_nem_init(413)..:  
MPIDI_nem_ckpt_init(170): BLCR kernel module not present

I really have no idea how to fix such kind of MPI's Bug.  (If I remove mpirun 
-n 2, the phase-field model works...)


Kind regards,
Yaakov

On Thursday, September 20, 2018 at 3:23:56 PM UTC+2, Daniel Arndt wrote:
>
> Yaakov,
>  
>
>> 1. I use candi for the installation, I think I have to rebuilt deal.ii 
>> again. 
>>
> Yes, definitely!
>  
>>
>> 2.  The error should be related to MPI.
>>
> What Jean-Paul meant to say is that there is nothing like "Dealii input 
> files by Heister & Wick".
> You are probably referring to the crack propagation code that is built on 
> top of deal.II and and parameter files for this application.
>
> If I were you, I would first make sure that your deal.II installation is 
> working correctly, especially with respect to MPI, by
> compiling and running some example steps, e.g. step-40.
> Afer that you can have a look if the application code needs an update as 
> well.
>
> Best,
> Daniel
>

-- 
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Re: [deal.II] Update of Ubuntu

2018-09-20 Thread Jean-Paul Pelteret 
Dear Yaakov,

> Thanks a lot for your answer!

You’re welcome. It was succinct, but at least I think that it might have helped 
identify the problem ;-)

> 1. I use candi for the installation, I think I have to rebuilt deal.ii again. 

Yes, I agree. Typically a major system upgrade would require this.

> 2.  The error should be related to MPI.

Thats useful to have confirmation that the error message specifically relates 
to MPI which I suspected. But what I was really questioning was you what you 
meant by some “dealii input files by Heister & Wick”. Anyway, I guess that this 
is largely unrelated, since any (MPI dependent)  deal.II program is likely to 
fail until you rebuilt deal.II and its dependencies.

I hope that you get this issue solved!

Best,
Jean-Paul

> On Thursday, September 20, 2018 at 3:02:08 PM UTC+2, Jean-Paul Pelteret wrote:
> Dear Yaakov,
> 
>> Recently, I have updated Ubuntu
> 
> Where does your deal.II installation come from? If you’ve compiled it 
> yourself, then have you rebuilt deal.II and its entries dependency list? With 
> a distribution update often comes an update in the compiler as well as other 
> dependencies.
> 
>> Dealii input files by Heister & Wick,
> 
> You’re really going to have to be more specific here. I guess that there are 
> only three people who might know what you’re referring to.
> 
> Best,
> Jean-Paul
> 
> -- 
> 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 
> 
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> .

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Re: [deal.II] Update of Ubuntu

2018-09-20 Thread Daniel Arndt 
Yaakov,
 

> 1. I use candi for the installation, I think I have to rebuilt deal.ii 
> again. 
>
Yes, definitely!
 
>
> 2.  The error should be related to MPI.
>
What Jean-Paul meant to say is that there is nothing like "Dealii input 
files by Heister & Wick".
You are probably referring to the crack propagation code that is built on 
top of deal.II and and parameter files for this application.

If I were you, I would first make sure that your deal.II installation is 
working correctly, especially with respect to MPI, by
compiling and running some example steps, e.g. step-40.
Afer that you can have a look if the application code needs an update as 
well.

Best,
Daniel

-- 
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https://groups.google.com/d/forum/dealii?hl=en
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Re: [deal.II] Update of Ubuntu

2018-09-20 Thread Aquaman 
Dear Dr. Pelteret,

Thanks a lot for your answer!

1. I use candi for the installation, I think I have to rebuilt deal.ii 
again. 

2.  The error should be related to MPI.

Kind regards,
Yaakov


On Thursday, September 20, 2018 at 3:02:08 PM UTC+2, Jean-Paul Pelteret 
wrote:
>
> Dear Yaakov,
>
> Recently, I have updated Ubuntu
>
>
> Where does your deal.II installation come from? If you’ve compiled it 
> yourself, then have you rebuilt deal.II and its entries dependency list? 
> With a distribution update often comes an update in the compiler as well as 
> other dependencies.
>
> Dealii input files by Heister & Wick,
>
>
> You’re really going to have to be more specific here. I guess that there 
> are only three people who might know what you’re referring to.
>
> Best,
> Jean-Paul
>

-- 
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Re: [deal.II] Update of Ubuntu

2018-09-20 Thread Jean-Paul Pelteret 
Dear Yaakov,

> Recently, I have updated Ubuntu

Where does your deal.II installation come from? If you’ve compiled it yourself, 
then have you rebuilt deal.II and its entries dependency list? With a 
distribution update often comes an update in the compiler as well as other 
dependencies.

> Dealii input files by Heister & Wick,

You’re really going to have to be more specific here. I guess that there are 
only three people who might know what you’re referring to.

Best,
Jean-Paul

-- 
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