March 2013 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] MPI IO, reading MPI Writes without MPI read
by Ryan Crocker 28 Mar '13

28 Mar '13

Yes. On Mar 28, 2013, at 12:11 PM, Rajeev Thakur wrote: > Have you declared disp as integer (kind=MPI_OFFSET_KIND) instead of just integer? > > On Mar 28, 2013, at 1:33 PM, Ryan Crocker wrote: > >> Okay, so i coded the MPI IO. All the characters and stuff show up, but when i try to read in my data buffers i just get the same number for the whole vector. All the characters in the header read in and are what they'er supposed to be, and the program finishes without any errors. >> >> my write is: >> >> call MPI_FILE_OPEN(comm,file,IOR(MPI_MODE_WRONLY,MPI_MODE_CREATE),mpi_info,iunit,ierr) >> >> ! Write header (only root) >> if (irank.eq.iroot) then >> buffer = trim(adjustl(name)) >> size = 80 >> call MPI_FILE_WRITE(iunit,buffer,size,MPI_CHARACTER,status,ierr) >> buffer = 'part' >> size = 80 >> call MPI_FILE_WRITE(iunit,buffer,size,MPI_CHARACTER,status,ierr) >> ibuffer = 1 >> size = 1 >> call MPI_FILE_WRITE(iunit,ibuffer,size,MPI_INTEGER,status,ierr) >> buffer = 'hexa8' >> size = 80 >> call MPI_FILE_WRITE(iunit,buffer,size,MPI_CHARACTER,status,ierr) >> end if >> >> ! Write the data >> disp = 3*80+4+0*ncells_hexa*4 >> call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) >> call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,1),ncells_hexa_,MPI_REAL_SP,status,ierr) >> disp = 3*80+4+1*ncells_hexa*4 >> call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) >> call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,2),ncells_hexa_,MPI_REAL_SP,status,ierr) >> disp = 3*80+4+2*ncells_hexa*4 >> call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) >> call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,3),ncells_hexa_,MPI_REAL_SP,status,ierr) >> >> ! Close the file >> call MPI_FILE_CLOSE(iunit,ierr) >> >> and the read is: >> >> ncells = parallel_sum(ncells_hexa_,ncells) >> >> allocate(buffer3(ncells,3)) >> >> openfile=trim(workdir)//'/'//'V/V.000002' >> call MPI_FILE_OPEN(comm,openfile,MPI_MODE_RDONLY,mpi_info,iunit,ierr) >> >> ! Read header >> bsize = 80 >> call MPI_FILE_READ(iunit,cbuffer,bsize,MPI_CHARACTER,status,ierr) >> print*,trim(cbuffer) >> bsize = 80 >> call MPI_FILE_READ(iunit,cbuffer,bsize,MPI_CHARACTER,status,ierr) >> print*,trim(cbuffer) >> bsize = 1 >> call MPI_FILE_READ(iunit,ibuffer,bsize,MPI_INTEGER,status,ierr) >> print*,ibuffer >> bsize = 80 >> call MPI_FILE_READ(iunit,cbuffer,bsize,MPI_CHARACTER,status,ierr) >> print*,trim(cbuffer),ncells >> >> ! Read the data >> disp = 3*80+4+0*ncells*4 >> call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) >> call MPI_FILE_READ_ALL(iunit,buffer3(:,1),ncells,MPI_REAL_SP,status,ierr) >> disp = 3*80+4+1*ncells*4 >> call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) >> call MPI_FILE_READ_ALL(iunit,buffer3(:,2),ncells,MPI_REAL_SP,status,ierr) >> disp = 3*80+4+2*ncells*4 >> call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) >> call MPI_FILE_READ_ALL(iunit,buffer3(:,3),ncells,MPI_REAL_SP,status,ierr) >> >> ! Close the file >> call MPI_FILE_CLOSE(iunit,ierr) >> >> On Mar 28, 2013, at 8:48 AM, Rob Latham wrote: >> >>> On Thu, Mar 28, 2013 at 08:19:23AM -0700, Ryan Crocker wrote: >>>> from the file those points are most definitely not in the same spot. We're using a set view so the memory is stored non-contiguously so you can't just read it back in, and i can see the offset in the data blocks. >>> >>> If you write the data with MPI_File_write_at, then you should read it >>> back with MPI_File_read_at. Fortran I/O will expect the input to have various >>> compiler-specific padding or ... well I don't properly know the >>> details, other than it's a mess. >>> >>> ==rob >>> >>> >>>> >>>> On Mar 28, 2013, at 6:47 AM, Rajeev Thakur wrote: >>>> >>>>> Most MPI-IO implementations write plain binary files without any additional information. So the data should be exactly what you wrote and at the locations you specified. The disp is not stored in the file. It is just used to offset to the right location. The file won't be portable with the default "native" file format used for writing. In other words, it will be readable only on the same type of machine architecture. >>>>> >>>>> Try writing a simple MPI-IO program to write a file and then read it back using POSIX I/O calls (lseek, read) from a C program. I don't know if Fortran I/O expects files to be formatted in a particular way, which could cause a problem when reading from Fortran. >>>>> >>>>> Rajeev >>>>> >>>>> >>>>> On Mar 28, 2013, at 2:00 AM, Ryan Crocker wrote: >>>>> >>>>>> So i'm not sure if this is crazy or not, but i have file outputs from my code that write ensight gold files in MPI. Here is the write, >>>>>> >>>>>> disp = 3*80+4+0*ncells_hexa*4 >>>>>> call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) >>>>>> call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,1),ncells_hexa_,MPI_REAL_SP,status,ierr) >>>>>> >>>>>> if i wanted to read that in binary in fortran, or C (preferably fortran) what exactly would i need to do? I can't seem to write code that reads these in and produces anything that looks like the plot i get in paraview. I know that MPI write puts out each processor data vector with that disp in between them, but i just can't make that structure make sense to me when i try to read it in. >>>>>> >>>>>> Thanks for the help, >>>>>> >>>>>> Ryan Crocker >>>>>> University of Vermont, School of Engineering >>>>>> Mechanical Engineering Department >>>>>> rcrocker(a)uvm.edu >>>>>> 315-212-7331 >>>>>> >>>>>> _______________________________________________ >>>>>> discuss mailing list discuss(a)mpich.org >>>>>> To manage subscription options or unsubscribe: >>>>>> https://lists.mpich.org/mailman/listinfo/discuss >>>>> >>>>> _______________________________________________ >>>>> discuss mailing list discuss(a)mpich.org >>>>> To manage subscription options or unsubscribe: >>>>> https://lists.mpich.org/mailman/listinfo/discuss >>>> >>>> Ryan Crocker >>>> University of Vermont, School of Engineering >>>> Mechanical Engineering Department >>>> rcrocker(a)uvm.edu >>>> 315-212-7331 >>>> >>>> _______________________________________________ >>>> discuss mailing list discuss(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>> >>> -- >>> Rob Latham >>> Mathematics and Computer Science Division >>> Argonne National Lab, IL USA >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >> >> Ryan Crocker >> University of Vermont, School of Engineering >> Mechanical Engineering Department >> rcrocker(a)uvm.edu >> 315-212-7331 >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss Ryan Crocker University of Vermont, School of Engineering Mechanical Engineering Department rcrocker(a)uvm.edu 315-212-7331

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Re: [mpich-discuss] MPI IO, reading MPI Writes without MPI read
by Rajeev Thakur 28 Mar '13

28 Mar '13

Have you declared disp as integer (kind=MPI_OFFSET_KIND) instead of just integer? On Mar 28, 2013, at 1:33 PM, Ryan Crocker wrote: > Okay, so i coded the MPI IO. All the characters and stuff show up, but when i try to read in my data buffers i just get the same number for the whole vector. All the characters in the header read in and are what they'er supposed to be, and the program finishes without any errors. > > my write is: > > call MPI_FILE_OPEN(comm,file,IOR(MPI_MODE_WRONLY,MPI_MODE_CREATE),mpi_info,iunit,ierr) > > ! Write header (only root) > if (irank.eq.iroot) then > buffer = trim(adjustl(name)) > size = 80 > call MPI_FILE_WRITE(iunit,buffer,size,MPI_CHARACTER,status,ierr) > buffer = 'part' > size = 80 > call MPI_FILE_WRITE(iunit,buffer,size,MPI_CHARACTER,status,ierr) > ibuffer = 1 > size = 1 > call MPI_FILE_WRITE(iunit,ibuffer,size,MPI_INTEGER,status,ierr) > buffer = 'hexa8' > size = 80 > call MPI_FILE_WRITE(iunit,buffer,size,MPI_CHARACTER,status,ierr) > end if > > ! Write the data > disp = 3*80+4+0*ncells_hexa*4 > call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) > call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,1),ncells_hexa_,MPI_REAL_SP,status,ierr) > disp = 3*80+4+1*ncells_hexa*4 > call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) > call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,2),ncells_hexa_,MPI_REAL_SP,status,ierr) > disp = 3*80+4+2*ncells_hexa*4 > call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) > call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,3),ncells_hexa_,MPI_REAL_SP,status,ierr) > > ! Close the file > call MPI_FILE_CLOSE(iunit,ierr) > > and the read is: > > ncells = parallel_sum(ncells_hexa_,ncells) > > allocate(buffer3(ncells,3)) > > openfile=trim(workdir)//'/'//'V/V.000002' > call MPI_FILE_OPEN(comm,openfile,MPI_MODE_RDONLY,mpi_info,iunit,ierr) > > ! Read header > bsize = 80 > call MPI_FILE_READ(iunit,cbuffer,bsize,MPI_CHARACTER,status,ierr) > print*,trim(cbuffer) > bsize = 80 > call MPI_FILE_READ(iunit,cbuffer,bsize,MPI_CHARACTER,status,ierr) > print*,trim(cbuffer) > bsize = 1 > call MPI_FILE_READ(iunit,ibuffer,bsize,MPI_INTEGER,status,ierr) > print*,ibuffer > bsize = 80 > call MPI_FILE_READ(iunit,cbuffer,bsize,MPI_CHARACTER,status,ierr) > print*,trim(cbuffer),ncells > > ! Read the data > disp = 3*80+4+0*ncells*4 > call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) > call MPI_FILE_READ_ALL(iunit,buffer3(:,1),ncells,MPI_REAL_SP,status,ierr) > disp = 3*80+4+1*ncells*4 > call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) > call MPI_FILE_READ_ALL(iunit,buffer3(:,2),ncells,MPI_REAL_SP,status,ierr) > disp = 3*80+4+2*ncells*4 > call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) > call MPI_FILE_READ_ALL(iunit,buffer3(:,3),ncells,MPI_REAL_SP,status,ierr) > > ! Close the file > call MPI_FILE_CLOSE(iunit,ierr) > > On Mar 28, 2013, at 8:48 AM, Rob Latham wrote: > >> On Thu, Mar 28, 2013 at 08:19:23AM -0700, Ryan Crocker wrote: >>> from the file those points are most definitely not in the same spot. We're using a set view so the memory is stored non-contiguously so you can't just read it back in, and i can see the offset in the data blocks. >> >> If you write the data with MPI_File_write_at, then you should read it >> back with MPI_File_read_at. Fortran I/O will expect the input to have various >> compiler-specific padding or ... well I don't properly know the >> details, other than it's a mess. >> >> ==rob >> >> >>> >>> On Mar 28, 2013, at 6:47 AM, Rajeev Thakur wrote: >>> >>>> Most MPI-IO implementations write plain binary files without any additional information. So the data should be exactly what you wrote and at the locations you specified. The disp is not stored in the file. It is just used to offset to the right location. The file won't be portable with the default "native" file format used for writing. In other words, it will be readable only on the same type of machine architecture. >>>> >>>> Try writing a simple MPI-IO program to write a file and then read it back using POSIX I/O calls (lseek, read) from a C program. I don't know if Fortran I/O expects files to be formatted in a particular way, which could cause a problem when reading from Fortran. >>>> >>>> Rajeev >>>> >>>> >>>> On Mar 28, 2013, at 2:00 AM, Ryan Crocker wrote: >>>> >>>>> So i'm not sure if this is crazy or not, but i have file outputs from my code that write ensight gold files in MPI. Here is the write, >>>>> >>>>> disp = 3*80+4+0*ncells_hexa*4 >>>>> call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) >>>>> call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,1),ncells_hexa_,MPI_REAL_SP,status,ierr) >>>>> >>>>> if i wanted to read that in binary in fortran, or C (preferably fortran) what exactly would i need to do? I can't seem to write code that reads these in and produces anything that looks like the plot i get in paraview. I know that MPI write puts out each processor data vector with that disp in between them, but i just can't make that structure make sense to me when i try to read it in. >>>>> >>>>> Thanks for the help, >>>>> >>>>> Ryan Crocker >>>>> University of Vermont, School of Engineering >>>>> Mechanical Engineering Department >>>>> rcrocker(a)uvm.edu >>>>> 315-212-7331 >>>>> >>>>> _______________________________________________ >>>>> discuss mailing list discuss(a)mpich.org >>>>> To manage subscription options or unsubscribe: >>>>> https://lists.mpich.org/mailman/listinfo/discuss >>>> >>>> _______________________________________________ >>>> discuss mailing list discuss(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>> >>> Ryan Crocker >>> University of Vermont, School of Engineering >>> Mechanical Engineering Department >>> rcrocker(a)uvm.edu >>> 315-212-7331 >>> >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >> >> -- >> Rob Latham >> Mathematics and Computer Science Division >> Argonne National Lab, IL USA >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > Ryan Crocker > University of Vermont, School of Engineering > Mechanical Engineering Department > rcrocker(a)uvm.edu > 315-212-7331 > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPI IO, reading MPI Writes without MPI read
by Ryan Crocker 28 Mar '13

28 Mar '13

Okay, so i coded the MPI IO. All the characters and stuff show up, but when i try to read in my data buffers i just get the same number for the whole vector. All the characters in the header read in and are what they'er supposed to be, and the program finishes without any errors. my write is: call MPI_FILE_OPEN(comm,file,IOR(MPI_MODE_WRONLY,MPI_MODE_CREATE),mpi_info,iunit,ierr) ! Write header (only root) if (irank.eq.iroot) then buffer = trim(adjustl(name)) size = 80 call MPI_FILE_WRITE(iunit,buffer,size,MPI_CHARACTER,status,ierr) buffer = 'part' size = 80 call MPI_FILE_WRITE(iunit,buffer,size,MPI_CHARACTER,status,ierr) ibuffer = 1 size = 1 call MPI_FILE_WRITE(iunit,ibuffer,size,MPI_INTEGER,status,ierr) buffer = 'hexa8' size = 80 call MPI_FILE_WRITE(iunit,buffer,size,MPI_CHARACTER,status,ierr) end if ! Write the data disp = 3*80+4+0*ncells_hexa*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,1),ncells_hexa_,MPI_REAL_SP,status,ierr) disp = 3*80+4+1*ncells_hexa*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,2),ncells_hexa_,MPI_REAL_SP,status,ierr) disp = 3*80+4+2*ncells_hexa*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,3),ncells_hexa_,MPI_REAL_SP,status,ierr) ! Close the file call MPI_FILE_CLOSE(iunit,ierr) and the read is: ncells = parallel_sum(ncells_hexa_,ncells) allocate(buffer3(ncells,3)) openfile=trim(workdir)//'/'//'V/V.000002' call MPI_FILE_OPEN(comm,openfile,MPI_MODE_RDONLY,mpi_info,iunit,ierr) ! Read header bsize = 80 call MPI_FILE_READ(iunit,cbuffer,bsize,MPI_CHARACTER,status,ierr) print*,trim(cbuffer) bsize = 80 call MPI_FILE_READ(iunit,cbuffer,bsize,MPI_CHARACTER,status,ierr) print*,trim(cbuffer) bsize = 1 call MPI_FILE_READ(iunit,ibuffer,bsize,MPI_INTEGER,status,ierr) print*,ibuffer bsize = 80 call MPI_FILE_READ(iunit,cbuffer,bsize,MPI_CHARACTER,status,ierr) print*,trim(cbuffer),ncells ! Read the data disp = 3*80+4+0*ncells*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) call MPI_FILE_READ_ALL(iunit,buffer3(:,1),ncells,MPI_REAL_SP,status,ierr) disp = 3*80+4+1*ncells*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) call MPI_FILE_READ_ALL(iunit,buffer3(:,2),ncells,MPI_REAL_SP,status,ierr) disp = 3*80+4+2*ncells*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) call MPI_FILE_READ_ALL(iunit,buffer3(:,3),ncells,MPI_REAL_SP,status,ierr) ! Close the file call MPI_FILE_CLOSE(iunit,ierr) On Mar 28, 2013, at 8:48 AM, Rob Latham wrote: > On Thu, Mar 28, 2013 at 08:19:23AM -0700, Ryan Crocker wrote: >> from the file those points are most definitely not in the same spot. We're using a set view so the memory is stored non-contiguously so you can't just read it back in, and i can see the offset in the data blocks. > > If you write the data with MPI_File_write_at, then you should read it > back with MPI_File_read_at. Fortran I/O will expect the input to have various > compiler-specific padding or ... well I don't properly know the > details, other than it's a mess. > > ==rob > > >> >> On Mar 28, 2013, at 6:47 AM, Rajeev Thakur wrote: >> >>> Most MPI-IO implementations write plain binary files without any additional information. So the data should be exactly what you wrote and at the locations you specified. The disp is not stored in the file. It is just used to offset to the right location. The file won't be portable with the default "native" file format used for writing. In other words, it will be readable only on the same type of machine architecture. >>> >>> Try writing a simple MPI-IO program to write a file and then read it back using POSIX I/O calls (lseek, read) from a C program. I don't know if Fortran I/O expects files to be formatted in a particular way, which could cause a problem when reading from Fortran. >>> >>> Rajeev >>> >>> >>> On Mar 28, 2013, at 2:00 AM, Ryan Crocker wrote: >>> >>>> So i'm not sure if this is crazy or not, but i have file outputs from my code that write ensight gold files in MPI. Here is the write, >>>> >>>> disp = 3*80+4+0*ncells_hexa*4 >>>> call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) >>>> call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,1),ncells_hexa_,MPI_REAL_SP,status,ierr) >>>> >>>> if i wanted to read that in binary in fortran, or C (preferably fortran) what exactly would i need to do? I can't seem to write code that reads these in and produces anything that looks like the plot i get in paraview. I know that MPI write puts out each processor data vector with that disp in between them, but i just can't make that structure make sense to me when i try to read it in. >>>> >>>> Thanks for the help, >>>> >>>> Ryan Crocker >>>> University of Vermont, School of Engineering >>>> Mechanical Engineering Department >>>> rcrocker(a)uvm.edu >>>> 315-212-7331 >>>> >>>> _______________________________________________ >>>> discuss mailing list discuss(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>> >>> _______________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/mailman/listinfo/discuss >> >> Ryan Crocker >> University of Vermont, School of Engineering >> Mechanical Engineering Department >> rcrocker(a)uvm.edu >> 315-212-7331 >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > -- > Rob Latham > Mathematics and Computer Science Division > Argonne National Lab, IL USA > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss Ryan Crocker University of Vermont, School of Engineering Mechanical Engineering Department rcrocker(a)uvm.edu 315-212-7331

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Re: [mpich-discuss] MPI error, help needed
by Jayesh Krishna 28 Mar '13

28 Mar '13

Hi, The first error message indicates that the parameters specified to the program when running through VS is incorrect (Likely a VS configuration issue when running your code - I am assuming you are running your code as a singleton process here). In the second case (error message when running via command prompt), the error message indicates that you have specified a negative (or too large for an integer) count in the MPI_Scatter() call. The address of the receive buffer also looks to be NULL. You might have to debug your code or provide us more information so that we can help you. Regards, Jayesh ----- Original Message ----- From: "Suvarna Arakh" <arakhs(a)cwu.EDU> To: discuss(a)mpich.org Sent: Wednesday, March 27, 2013 2:48:54 PM Subject: [mpich-discuss] MPI error, help needed Hi, I am trying to run my MPI program on multiple processes, but I get the below errors, attached is the code. The code runs fine on 1 process. When running through Visual studio 2008: buffer provided too short for path: 4096 provided, 0 needed launch failed: CreateProcess(""ABC-HP c:\Users\ABC\Desktop\BS\Debug\BS.e xe) on 'ABC-HP' failed, error 87 - The parameter is incorrect. When running through command prompt: Fatal error in PMPI_Scatter: Invalid count, error stack: PMPI_Scatter(791): MPI_Scatter(sbuf=10030040, scount=-858993460, MPI_INT, rbuf=0 0000000, rcount=-858993460, MPI_INT, root=0, MPI_COMM_WORLD) failed PMPI_Scatter(728): Negative count, value is -858993460 Enter number of elements to be sorted job aborted: rank: node: exit code[: error message] 0: ABC-HP: 1: process 0 exited without calling finalize Please help. Regards. _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPI IO, reading MPI Writes without MPI read
by Rob Latham 28 Mar '13

28 Mar '13

On Thu, Mar 28, 2013 at 08:19:23AM -0700, Ryan Crocker wrote: > from the file those points are most definitely not in the same spot. We're using a set view so the memory is stored non-contiguously so you can't just read it back in, and i can see the offset in the data blocks. If you write the data with MPI_File_write_at, then you should read it back with MPI_File_read_at. Fortran I/O will expect the input to have various compiler-specific padding or ... well I don't properly know the details, other than it's a mess. ==rob > > On Mar 28, 2013, at 6:47 AM, Rajeev Thakur wrote: > > > Most MPI-IO implementations write plain binary files without any additional information. So the data should be exactly what you wrote and at the locations you specified. The disp is not stored in the file. It is just used to offset to the right location. The file won't be portable with the default "native" file format used for writing. In other words, it will be readable only on the same type of machine architecture. > > > > Try writing a simple MPI-IO program to write a file and then read it back using POSIX I/O calls (lseek, read) from a C program. I don't know if Fortran I/O expects files to be formatted in a particular way, which could cause a problem when reading from Fortran. > > > > Rajeev > > > > > > On Mar 28, 2013, at 2:00 AM, Ryan Crocker wrote: > > > >> So i'm not sure if this is crazy or not, but i have file outputs from my code that write ensight gold files in MPI. Here is the write, > >> > >> disp = 3*80+4+0*ncells_hexa*4 > >> call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) > >> call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,1),ncells_hexa_,MPI_REAL_SP,status,ierr) > >> > >> if i wanted to read that in binary in fortran, or C (preferably fortran) what exactly would i need to do? I can't seem to write code that reads these in and produces anything that looks like the plot i get in paraview. I know that MPI write puts out each processor data vector with that disp in between them, but i just can't make that structure make sense to me when i try to read it in. > >> > >> Thanks for the help, > >> > >> Ryan Crocker > >> University of Vermont, School of Engineering > >> Mechanical Engineering Department > >> rcrocker(a)uvm.edu > >> 315-212-7331 > >> > >> _______________________________________________ > >> discuss mailing list discuss(a)mpich.org > >> To manage subscription options or unsubscribe: > >> https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > Ryan Crocker > University of Vermont, School of Engineering > Mechanical Engineering Department > rcrocker(a)uvm.edu > 315-212-7331 > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Rob Latham Mathematics and Computer Science Division Argonne National Lab, IL USA

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Re: [mpich-discuss] MPI IO, reading MPI Writes without MPI read
by Ryan Crocker 28 Mar '13

28 Mar '13

So write the vector to be written counter = 0 do k do j do i counter = counter +1 buffer(counter) = U(i,j,k) end do end do end do when i read that back in: counter = 0 do k do j do i counter = counter +1 U(i,j,k) = buffer(counter) end do end do end do from the file those points are most definitely not in the same spot. We're using a set view so the memory is stored non-contiguously so you can't just read it back in, and i can see the offset in the data blocks. On Mar 28, 2013, at 6:47 AM, Rajeev Thakur wrote: > Most MPI-IO implementations write plain binary files without any additional information. So the data should be exactly what you wrote and at the locations you specified. The disp is not stored in the file. It is just used to offset to the right location. The file won't be portable with the default "native" file format used for writing. In other words, it will be readable only on the same type of machine architecture. > > Try writing a simple MPI-IO program to write a file and then read it back using POSIX I/O calls (lseek, read) from a C program. I don't know if Fortran I/O expects files to be formatted in a particular way, which could cause a problem when reading from Fortran. > > Rajeev > > > On Mar 28, 2013, at 2:00 AM, Ryan Crocker wrote: > >> So i'm not sure if this is crazy or not, but i have file outputs from my code that write ensight gold files in MPI. Here is the write, >> >> disp = 3*80+4+0*ncells_hexa*4 >> call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) >> call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,1),ncells_hexa_,MPI_REAL_SP,status,ierr) >> >> if i wanted to read that in binary in fortran, or C (preferably fortran) what exactly would i need to do? I can't seem to write code that reads these in and produces anything that looks like the plot i get in paraview. I know that MPI write puts out each processor data vector with that disp in between them, but i just can't make that structure make sense to me when i try to read it in. >> >> Thanks for the help, >> >> Ryan Crocker >> University of Vermont, School of Engineering >> Mechanical Engineering Department >> rcrocker(a)uvm.edu >> 315-212-7331 >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss Ryan Crocker University of Vermont, School of Engineering Mechanical Engineering Department rcrocker(a)uvm.edu 315-212-7331

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Re: [mpich-discuss] MPI IO, reading MPI Writes without MPI read
by Rajeev Thakur 28 Mar '13

28 Mar '13

Most MPI-IO implementations write plain binary files without any additional information. So the data should be exactly what you wrote and at the locations you specified. The disp is not stored in the file. It is just used to offset to the right location. The file won't be portable with the default "native" file format used for writing. In other words, it will be readable only on the same type of machine architecture. Try writing a simple MPI-IO program to write a file and then read it back using POSIX I/O calls (lseek, read) from a C program. I don't know if Fortran I/O expects files to be formatted in a particular way, which could cause a problem when reading from Fortran. Rajeev On Mar 28, 2013, at 2:00 AM, Ryan Crocker wrote: > So i'm not sure if this is crazy or not, but i have file outputs from my code that write ensight gold files in MPI. Here is the write, > > disp = 3*80+4+0*ncells_hexa*4 > call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) > call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,1),ncells_hexa_,MPI_REAL_SP,status,ierr) > > if i wanted to read that in binary in fortran, or C (preferably fortran) what exactly would i need to do? I can't seem to write code that reads these in and produces anything that looks like the plot i get in paraview. I know that MPI write puts out each processor data vector with that disp in between them, but i just can't make that structure make sense to me when i try to read it in. > > Thanks for the help, > > Ryan Crocker > University of Vermont, School of Engineering > Mechanical Engineering Department > rcrocker(a)uvm.edu > 315-212-7331 > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPI IO, reading MPI Writes without MPI read
by Ryan Crocker 28 Mar '13

28 Mar '13

Here is the whole code snippet for writing a vector, it will probably help: inquire(file=file,exist=file_is_there) if (file_is_there .and. irank.eq.iroot) call MPI_FILE_DELETE(file,mpi_info,ierr) call MPI_FILE_OPEN(comm,file,IOR(MPI_MODE_WRONLY,MPI_MODE_CREATE),mpi_info,iunit,ierr) ! Write header (only root) if (irank.eq.iroot) then buffer = trim(adjustl(name)) size = 80 call MPI_FILE_WRITE(iunit,buffer,size,MPI_CHARACTER,status,ierr) buffer = 'part' size = 80 call MPI_FILE_WRITE(iunit,buffer,size,MPI_CHARACTER,status,ierr) ibuffer = 1 size = 1 call MPI_FILE_WRITE(iunit,ibuffer,size,MPI_INTEGER,status,ierr) buffer = 'hexa8' size = 80 call MPI_FILE_WRITE(iunit,buffer,size,MPI_CHARACTER,status,ierr) end if ! Write the data disp = 3*80+4+0*ncells_hexa*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,1),ncells_hexa_,MPI_REAL_SP,status,ierr) disp = 3*80+4+1*ncells_hexa*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,2),ncells_hexa_,MPI_REAL_SP,status,ierr) disp = 3*80+4+2*ncells_hexa*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,3),ncells_hexa_,MPI_REAL_SP,status,ierr) ! Write the file - wedge if (ncells_wedge.gt.0) then disp = 3*80+4+3*ncells_hexa*4+0*ncells_wedge*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_CHARACTER,MPI_CHARACTER,"native",mpi_info,ierr) if (irank.eq.iroot) then buffer = 'penta6' size = 80 call MPI_FILE_WRITE(iunit,buffer,size,MPI_CHARACTER,status,ierr) end if disp = 3*80+4+3*ncells_hexa*4+80+0*ncells_wedge*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_wedge,"native",mpi_info,ierr) call MPI_FILE_WRITE_ALL(iunit,buffer3_wedge(:,1),ncells_wedge_,MPI_REAL_SP,status,ierr) disp = 3*80+4+3*ncells_hexa*4+80+1*ncells_wedge*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_wedge,"native",mpi_info,ierr) call MPI_FILE_WRITE_ALL(iunit,buffer3_wedge(:,2),ncells_wedge_,MPI_REAL_SP,status,ierr) disp = 3*80+4+3*ncells_hexa*4+80+2*ncells_wedge*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_wedge,"native",mpi_info,ierr) call MPI_FILE_WRITE_ALL(iunit,buffer3_wedge(:,3),ncells_wedge_,MPI_REAL_SP,status,ierr) end if ! Close the file call MPI_FILE_CLOSE(iunit,ierr) On Mar 28, 2013, at 12:00 AM, Ryan Crocker wrote: > So i'm not sure if this is crazy or not, but i have file outputs from my code that write ensight gold files in MPI. Here is the write, > > disp = 3*80+4+0*ncells_hexa*4 > call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) > call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,1),ncells_hexa_,MPI_REAL_SP,status,ierr) > > if i wanted to read that in binary in fortran, or C (preferably fortran) what exactly would i need to do? I can't seem to write code that reads these in and produces anything that looks like the plot i get in paraview. I know that MPI write puts out each processor data vector with that disp in between them, but i just can't make that structure make sense to me when i try to read it in. > > Thanks for the help, > > Ryan Crocker > University of Vermont, School of Engineering > Mechanical Engineering Department > rcrocker(a)uvm.edu > 315-212-7331 > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss Ryan Crocker University of Vermont, School of Engineering Mechanical Engineering Department rcrocker(a)uvm.edu 315-212-7331

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MPI IO, reading MPI Writes without MPI read
by Ryan Crocker 28 Mar '13

28 Mar '13

So i'm not sure if this is crazy or not, but i have file outputs from my code that write ensight gold files in MPI. Here is the write, disp = 3*80+4+0*ncells_hexa*4 call MPI_FILE_SET_VIEW(iunit,disp,MPI_REAL_SP,fileview_hexa,"native",mpi_info,ierr) call MPI_FILE_WRITE_ALL(iunit,buffer3_hexa(:,1),ncells_hexa_,MPI_REAL_SP,status,ierr) if i wanted to read that in binary in fortran, or C (preferably fortran) what exactly would i need to do? I can't seem to write code that reads these in and produces anything that looks like the plot i get in paraview. I know that MPI write puts out each processor data vector with that disp in between them, but i just can't make that structure make sense to me when i try to read it in. Thanks for the help, Ryan Crocker University of Vermont, School of Engineering Mechanical Engineering Department rcrocker(a)uvm.edu 315-212-7331

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MPI error, help needed
by Suvarna Arakh 27 Mar '13

27 Mar '13

Hi, I am trying to run my MPI program on multiple processes, but I get the below errors, attached is the code. The code runs fine on 1 process. When running through Visual studio 2008: buffer provided too short for path: 4096 provided, 0 needed launch failed: CreateProcess(""ABC-HP c:\Users\ABC\Desktop\BS\Debug\BS.e xe) on 'ABC-HP' failed, error 87 - The parameter is incorrect. When running through command prompt: Fatal error in PMPI_Scatter: Invalid count, error stack: PMPI_Scatter(791): MPI_Scatter(sbuf=10030040, scount=-858993460, MPI_INT, rbuf=0 0000000, rcount=-858993460, MPI_INT, root=0, MPI_COMM_WORLD) failed PMPI_Scatter(728): Negative count, value is -858993460 Enter number of elements to be sorted job aborted: rank: node: exit code[: error message] 0: ABC-HP: 1: process 0 exited without calling finalize Please help. Regards.

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