[deal.II] Re: Parallel GridIn of large file - PETSC Error

2017-07-25 Thread Yi-Chung Chen 
Hi Mathias

Would you mind to check the memory usage? I guess you have about 3M DOFs 
right (based on the file size of msh)? My experience told me that 32GB can 
handle 10M DOFs(roughly). Your case is about 10GB memory based on the 
calculation.If you are using distributed mesh, which means you has a 
initial copy for each processor you assigned. Say you have 40 in a node and 
you use all of them, which indicates that your memory use is 10*40= 400 per 
node. I guess this is the reason. 

Another problem is int range (for index).

All best, 
YC Chen.

On Tuesday, May 9, 2017 at 11:40:22 AM UTC+1, Mathias Mentler wrote:
>
> Hi everybody, 
>
> I am currently trying to read in a large (~300MB) .msh mesh-file by using 
> the GridIn-workflow (described here 
> 
>  ). 
> My triangulation is of type parallel::distributed::Triangulation. I then 
> use four nodes (each with 64GB RAM and 40 processors) of a cluster, 
> accordingly spawn 160 processes and try to do my computations. However 
> while doing the ".read_msh()"-bit I get a PETSC-error I can't make sense 
> of. What I get from one process is:
>
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the 
> batch system) has told this process to end
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see 
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS 
> X to find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and 
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message 
> --
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html 
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.7.5, Jan, 01, 2017
> [0]PETSC ERROR: Configure options 
> --prefix=/home/woody/iwtm/iwtm002h/spack_dealii/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/petsc-3.7.5-6itsodseoiu5dr5aizwji7ki42p7gg7y
>  
> --with-ssl=0 --with-x=0 --download-c2$
> [0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>
>
> Could there be a problem with the needed memory? From what I read in a 
> related 
> question 
> ,
>  
> each process holds the coarsest mesh and since I don't refine the mesh any 
> further, each process will hold the entire mesh/triangulation. 
>
>
> Regards,
>
> Mathias 
>

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[deal.II] Re: Parallel GridIn of large file - PETSC Error

2017-05-09 Thread Denis Davydov 
p.s. could also be 
this https://groups.google.com/forum/#!topic/dealii/zSC33HFN9AA
 

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[deal.II] Re: Parallel GridIn of large file - PETSC Error

2017-05-09 Thread Denis Davydov 
It could be whatever. PETSc intercepts error and always print such things 
even when it happens outside of PETSc, which I find very inconvenient.
Try compiling and running in Debug mode.

On Tuesday, May 9, 2017 at 12:40:22 PM UTC+2, Mathias Mentler wrote:
>
> Hi everybody, 
>
> I am currently trying to read in a large (~300MB) .msh mesh-file by using 
> the GridIn-workflow (described here 
> 
>  ). 
> My triangulation is of type parallel::distributed::Triangulation. I then 
> use four nodes (each with 64GB RAM and 40 processors) of a cluster, 
> accordingly spawn 160 processes and try to do my computations. However 
> while doing the ".read_msh()"-bit I get a PETSC-error I can't make sense 
> of. What I get from one process is:
>
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the 
> batch system) has told this process to end
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see 
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS 
> X to find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and 
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message 
> --
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html 
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.7.5, Jan, 01, 2017
> [0]PETSC ERROR: Configure options 
> --prefix=/home/woody/iwtm/iwtm002h/spack_dealii/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/petsc-3.7.5-6itsodseoiu5dr5aizwji7ki42p7gg7y
>  
> --with-ssl=0 --with-x=0 --download-c2$
> [0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>
>
> Could there be a problem with the needed memory? From what I read in a 
> related 
> question 
> ,
>  
> each process holds the coarsest mesh and since I don't refine the mesh any 
> further, each process will hold the entire mesh/triangulation. 
>
>
> Regards,
>
> Mathias 
>

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