Update of Ubuntu

[Aquaman]

Dear All,

Recently, I have updated Ubuntu, after that, when I test Dealii input files by Heister & Wick, I get the following error:

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

How can I remove this bug (Easy method...)?

Best regards,

Yaakov

[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

[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

[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

[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

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[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

[Maxi Miller]

Are programs depending on MPI able to run in general (i.e. also without deal.II)? That should be the first thing to test

[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

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