[mpich-discuss] Bcast question?

[Rajeev Thakur]

You can simply have each process read the entire file using a single MPI_File_read_all. No need for Gather or Gatherv.

Rajeev

On Aug 11, 2012, at 5:47 AM, John Chludzinski wrote:

> I followed up on your suggestion to look into MPI-IO - GREAT suggestion.
> 
> I found an example at http://beige.ucs.indiana.edu/I590/node92.html and added code to gather the pieces of the file read in by each process:  
> 
> MPI_Gather( read_buffer, number_of_bytes, MPI_BYTE, rbuf, number_of_bytes, MPI_BYTE, MASTER_RANK, MPI_COMM_WORLD);
> 
> All process execute this line.  The problem is that number_of_bytes maybe different for the last process if  total_number_of_bytes is not a multiple of pool_size (i.e., total_number_of_bytes % pool_size != 0).  And if the value isn't the same for all processes, you get:
> 
> Fatal error in PMPI_Gather: Message truncated
> 
> If I set pool_size (the number of processes) so that total_number_of_bytes is a multiple of it (i.e., total_number_of_bytes % pool_size == 0), the code executes without error.
> 
> I thought I read in Peter Pacheco's book that this need not necessarily be required?
> 
> ---John
> 
> 
> On Fri, Aug 10, 2012 at 9:58 AM, William Gropp <wgropp at illinois.edu> wrote:
> The most likely newbe mistake is that you are timing the time time that the MPI_Bcast is waiting - for example, if your code looks like this:
> 
> if (rank == 0) { tr = MPI_Wtime(); read data tr = MPI_Wtime()-tr; }
> tb = MPI_Wtime(): MPI_Bcast(…); tb = MPI_Wtime() - tb;
> 
> then on all but rank 0, you are timing the time that MPI_Bcast is waiting for the read data step to finish.  Instead, consider adding an MPI_Barrier before the MPI_Bcast:
> 
> if (rank == 0) { tr = MPI_Wtime(); read data tr = MPI_Wtime()-tr; }
> MPI_Barrier();
> tb = MPI_Wtime(): MPI_Bcast(…); tb = MPI_Wtime() - tb;
> 
> *Only* do this when you are trying to answer such timing questions.
> 
> You may also want to consider using MPI-IO to parallelize the read step.
> 
> Bill
> 
> William Gropp
> Director, Parallel Computing Institute
> Deputy Director for Research
> Institute for Advanced Computing Applications and Technologies
> Paul and Cynthia Saylor Professor of Computer Science
> University of Illinois Urbana-Champaign
> 
> 
> 
> On Aug 10, 2012, at 3:03 AM, John Chludzinski wrote:
> 
> > I have a problem which requires all process to have a copy of an array of data that is read in from a file (process 0).  I Bcast the array to all processes (using MPI_COMM_WORLD).
> >
> > I instrumented the code with some calls to Wtime to find the time consumed for different actions.  In particular, I was interested in comparing the time required for Bcast's vs. fread's.  The size of the array is 1,200,000 of type MPI_DOUBLE.
> >
> > For a 3 process run:
> >
> > RANK = 0      fread_time = 2.323575
> >
> > vs.
> >
> > RANK = 2      bcast_time = 2.361233
> > RANK = 0      bcast_time = 0.081910
> > RANK = 1      bcast_time = 2.399790
> >
> > These numbers seem to indicate that Bcast-ing the data is as slow as reading the data from a file (on my Western Digital Passport USB drive).  Am I making a newbie mistake?
> >
> > ---John
> >
> > PS> I'm using Fedora 16 (32 bit) notebook with a dual core AMD Phenom processor.
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