Re: [petsc-users] Is it possible to start MPI with n processes from within the code so it takes only effect on the petsc code?

2018-12-04 Thread Jed Brown via petsc-users
See MPI_Comm_spawn(). https://www.mpi-forum.org/docs/mpi-3.1/mpi31-report/node240.htm#Node240 Note that it may interact poorly (or not at all) with resource managers and other HPC infrastructure (relative to using mpiexec or similar to spawn the jobs, which does not give you the

Re: [petsc-users] Is it possible to start MPI with n processes from within the code so it takes only effect on the petsc code?

2018-12-04 Thread Smith, Barry F. via petsc-users
If you want to run PETSc on a subset of the processes the original program started with, this is easy. Simply use the MPI communicator routines to create a communicator that contains the processes you want PETSc run on. Then on that subset of processes set PETSC_COMM_WORLD to that

Re: [petsc-users] VecLoad hdf5

2018-12-04 Thread Smith, Barry F. via petsc-users
> On Dec 4, 2018, at 4:09 PM, Josh L wrote: > > I haven't figured out what causes it. I just use binaryopen instead of HDF5, > and everything works fine. Did you originally save the data into the file with HDF5 format? > > > > Josh L 於 2018年12月4日 週二 下午2:55寫道: > The first error comes

[petsc-users] Is it possible to start MPI with n processes from within the code so it takes only effect on the petsc code?

2018-12-04 Thread Klaus Burkart via petsc-users
Hello, I try to integrate petsc into an application and I think it would be much simpler if I could bypass the applications original MPI functionality by starting MPI with n processes when initializing Petsc and stopping it when PetscFinalize(); is called. The standard  mpirun -np 4

Re: [petsc-users] PETSc binary write format

2018-12-04 Thread Sajid Ali via petsc-users
For future reference, the numbers do look like they're stored as per IEEE 754 64-bit convention. I don't know what the special characters in the xxd output are but the size of the file is consistent with 2*int_32+num_elements*dobule_64. Thank you ! Sajid Ali Applied Physics Northwestern

Re: [petsc-users] VecLoad hdf5

2018-12-04 Thread Josh L via petsc-users
I just found out that I missed that note in VecLoad manual page, and I am trying it now. Thanks. Smith, Barry F. 於 2018年12月4日 週二 下午2:00寫道: > >Hmm, this is a guess. HDF5 files read in objects based on their names. > Are you sure that the vector you saved and the vector you later try to

Re: [petsc-users] VecLoad hdf5

2018-12-04 Thread Smith, Barry F. via petsc-users
Hmm, this is a guess. HDF5 files read in objects based on their names. Are you sure that the vector you saved and the vector you later try to read in have the same name? You can set the name of the loaded vector with PetscObjectSetName((PetscObject)nv,"name") after you create it to match

Re: [petsc-users] RAW binary write

2018-12-04 Thread Jed Brown via petsc-users
Matthew Knepley via petsc-users writes: > On Tue, Dec 4, 2018 at 11:11 AM Lisandro Dalcin via petsc-users < > petsc-users@mcs.anl.gov> wrote: > >> PetscByteSwap ? But be careful, you should (1) vec get array, byteswap, >> vec restore array, (2) view, (3) vec get array, byteswap, vec restore >>