Re: [OMPI users] Simple question on GRID
Hi Shaandar, this is not a simple question! If you want to bring your cluster into the Grid, you first have to decide which Grid, because the different Grids use different Grid softwares. Having taken this decision, I would recommend to look onto the wen page of this Grid community, usually you can find here instructions on how to integrate your cluster into their Grid. Dependend on the Grid software used, these instructions can be really very different, therefore I cannot be more precise here and now. If you are deciding for a Grid which is using the Globus software, feel free to contact me for further question. In the case of Globus I can help you... Best wishes Alexander Hi I have two Beowulf clusters (both Ubuntu 10.10, one is OpenMPI, one is MPICH2). They run separately in their local network environment.I know there is a way to integrate them through Internet, presumably by Grid software, I guess. Is there any tutorial to do this? ___ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users
Re: [OMPI users] problems with parallel IO solved!
Hi Folks, the problem could be solved be using the same compiler settings for writung out and reading in. Writing out was done with -trace (Intel compiler), and the read in withou any supplemental options. Best wishes Alexander > Hi Folks, > > I have problems to retrieve my data thatI have written out with MPI > parallel IO. Ins tests everything works fine, but within an huger > environment, the data read in differ from those written out. > > Here the setup of my experiment: > > # the writer # > program parallel_io > > use mpi > > implicit none > > integer,parameter :: nx=1,ny=300,nz=256,nv=12 > integer ierr, i, myrank, comm_size, BUFSIZE, thefile, intsize > > parameter (BUFSIZE=1075200) > > real,dimension(nv+2,nx,ny,nz) :: v1 > > integer (kind=MPI_OFFSET_KIND) disp > integer ix, iy, iz, nn, counter > > character(6) cname > call mpi_init(ierr) > call mpi_comm_size(mpi_comm_world, comm_size, ierr) > call mpi_comm_rank(mpi_comm_world, myrank,ierr) > > counter=0 > do ix = 1,nz > do iy=1,ny > do iz=1,nx >do nn=1,nv+2 > v1(nn,ix,iy,iz) = counter*(myrank+20)/200. > counter=counter+1 >end do > end do > end do > end do > > call mpi_barrier(mpi_comm_world,ierr) > > call mpi_type_extent(mpi_real, intsize, ierr) > call mpi_file_open(mpi_comm_world, 'testfile', MPI_MODE_WRONLY + > MPI_MODE_CREATE, mpi_info_null, thefile, ierr) > call mpi_type_size(MPI_INTEGER, intsize, ierr) > > disp = myrank * BUFSIZE * intsize > > ! call mpi_file_set_view(thefile, disp, MPI_INTEGER, MPI_INTEGER, > 'native', mpi_info_null, ierr) > call mpi_file_write_at(thefile, disp, v1(1,1,1,1), BUFSIZE, MPI_REAL, > mpi_status_ignore, ierr) > > call mpi_file_close(thefile, ierr) > > ! print the data read in... > > open (12, file='out000.dat-parallel-write-0') > > if (myrank.eq.0) then > write (12,'(i4,e18.8)') myrank, > v1(nn,ix,iy,iz),nn=1,nv+2),ix=1,nx),iy=1,ny), iz=1,nz) > endif > > close (12) > > call mpi_finalize(ierr) > > > end program parallel_io > > ### > > and the reader... > > reader### > program parallel_read_io > > use mpi > > implicit none > integer,parameter :: nx=1,ny=300,nz=256,nv=12 > > integer ierr, i, myrank, comm_size, BUFSIZE, thefile, realsize > parameter (BUFSIZE=1075200) > > real,dimension(nv+2,nx,ny,nz) :: v1 > > integer (kind=MPI_OFFSET_KIND) disp > > integer ix, iy, iz, nn > > call mpi_init(ierr) > call mpi_comm_size(mpi_comm_world, comm_size, ierr) > call mpi_comm_rank(mpi_comm_world, myrank,ierr) > > ! do i=0,BUFSIZE > ! buf(i) = myrank*BUFSIZE + i > ! end do > > call mpi_type_extent(mpi_integer, realsize, ierr) > call mpi_file_open(mpi_comm_world, 'testfile', MPI_MODE_RDONLY, > mpi_info_null, thefile, ierr) > call mpi_type_size(MPI_REAL, realsize, ierr) > > disp = myrank * BUFSIZE * realsize > print*, 'myrank: ', myrank, ' disp: ', disp, ' realsize: ', realsize > > ! call mpi_file_set_view(thefile, disp, MPI_INTEGER, MPI_INTEGER, > 'native', mpi_info_null, ierr) > ! call mpi_file_read(thefile, buf, BUFSIZE, MPI_INTEGER, > mpi_status_ignore, ierr) > > call mpi_file_read_at(thefile, disp, v1(1,1,1,1), BUFSIZE, MPI_REAL, > mpi_status_ignore, ierr) > > call mpi_file_close(thefile, ierr) > > call mpi_barrier(mpi_comm_world,ierr) > > ! print the data read in... > > open (12, file='out000.dat-parallel-read-0') > > if (myrank.eq.0) then > write (12,'(i4,e18.8)') myrank, > v1(nn,ix,iy,iz),nn=1,nv+2),ix=1,nx),iy=1,ny), iz=1,nz) > endif > > close (12) > > call mpi_finalize(ierr) > > > end program parallel_read_io > ### > > Here everything is working fine. However integrating this into a huger > program, I get totally different data written out and read in. > > The setup up is the same as in the experiment, but I need some more > memory... > > What might be the reason for such problems, and if I have an MPI error, how > can I estimate this within a fortan program. I have only found examples for > the error handling of MPI errors in C or C++. I would need an example for > C. > > So any hints or ideas? > > Best wishes > > Alexander > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
[OMPI users] problems with parallel IO
Hi Folks, I have problems to retrieve my data thatI have written out with MPI parallel IO. Ins tests everything works fine, but within an huger environment, the data read in differ from those written out. Here the setup of my experiment: # the writer # program parallel_io use mpi implicit none integer,parameter :: nx=1,ny=300,nz=256,nv=12 integer ierr, i, myrank, comm_size, BUFSIZE, thefile, intsize parameter (BUFSIZE=1075200) real,dimension(nv+2,nx,ny,nz) :: v1 integer (kind=MPI_OFFSET_KIND) disp integer ix, iy, iz, nn, counter character(6) cname call mpi_init(ierr) call mpi_comm_size(mpi_comm_world, comm_size, ierr) call mpi_comm_rank(mpi_comm_world, myrank,ierr) counter=0 do ix = 1,nz do iy=1,ny do iz=1,nx do nn=1,nv+2 v1(nn,ix,iy,iz) = counter*(myrank+20)/200. counter=counter+1 end do end do end do end do call mpi_barrier(mpi_comm_world,ierr) call mpi_type_extent(mpi_real, intsize, ierr) call mpi_file_open(mpi_comm_world, 'testfile', MPI_MODE_WRONLY + MPI_MODE_CREATE, mpi_info_null, thefile, ierr) call mpi_type_size(MPI_INTEGER, intsize, ierr) disp = myrank * BUFSIZE * intsize ! call mpi_file_set_view(thefile, disp, MPI_INTEGER, MPI_INTEGER, 'native', mpi_info_null, ierr) call mpi_file_write_at(thefile, disp, v1(1,1,1,1), BUFSIZE, MPI_REAL, mpi_status_ignore, ierr) call mpi_file_close(thefile, ierr) ! print the data read in... open (12, file='out000.dat-parallel-write-0') if (myrank.eq.0) then write (12,'(i4,e18.8)') myrank, v1(nn,ix,iy,iz),nn=1,nv+2),ix=1,nx),iy=1,ny), iz=1,nz) endif close (12) call mpi_finalize(ierr) end program parallel_io ### and the reader... reader### program parallel_read_io use mpi implicit none integer,parameter :: nx=1,ny=300,nz=256,nv=12 integer ierr, i, myrank, comm_size, BUFSIZE, thefile, realsize parameter (BUFSIZE=1075200) real,dimension(nv+2,nx,ny,nz) :: v1 integer (kind=MPI_OFFSET_KIND) disp integer ix, iy, iz, nn call mpi_init(ierr) call mpi_comm_size(mpi_comm_world, comm_size, ierr) call mpi_comm_rank(mpi_comm_world, myrank,ierr) ! do i=0,BUFSIZE ! buf(i) = myrank*BUFSIZE + i ! end do call mpi_type_extent(mpi_integer, realsize, ierr) call mpi_file_open(mpi_comm_world, 'testfile', MPI_MODE_RDONLY, mpi_info_null, thefile, ierr) call mpi_type_size(MPI_REAL, realsize, ierr) disp = myrank * BUFSIZE * realsize print*, 'myrank: ', myrank, ' disp: ', disp, ' realsize: ', realsize ! call mpi_file_set_view(thefile, disp, MPI_INTEGER, MPI_INTEGER, 'native', mpi_info_null, ierr) ! call mpi_file_read(thefile, buf, BUFSIZE, MPI_INTEGER, mpi_status_ignore, ierr) call mpi_file_read_at(thefile, disp, v1(1,1,1,1), BUFSIZE, MPI_REAL, mpi_status_ignore, ierr) call mpi_file_close(thefile, ierr) call mpi_barrier(mpi_comm_world,ierr) ! print the data read in... open (12, file='out000.dat-parallel-read-0') if (myrank.eq.0) then write (12,'(i4,e18.8)') myrank, v1(nn,ix,iy,iz),nn=1,nv+2),ix=1,nx),iy=1,ny), iz=1,nz) endif close (12) call mpi_finalize(ierr) end program parallel_read_io ### Here everything is working fine. However integrating this into a huger program, I get totally different data written out and read in. The setup up is the same as in the experiment, but I need some more memory... What might be the reason for such problems, and if I have an MPI error, how can I estimate this within a fortan program. I have only found examples for the error handling of MPI errors in C or C++. I would need an example for C. So any hints or ideas? Best wishes Alexander
Re: [OMPI users] problems with parallel MPI-IO...
On Tuesday, July 19, 2011 16:13:38 Jonathan Dursi wrote: > On 19 Jul 9:02AM, Alexander Beck-Ratzka wrote: > >integer ierr, i, myrank, BUFSIZE, thefile, intsize > >parameter (BUFSIZE=100) > >integer buf(BUFSIZE) > > > >do i=0,BUFSIZE > > > > buf(i) = myrank*BUFSIZE + i > > print*, 'i =', i, 'myrank =', myrank, 'buf(i)=',buf(i) > > > >end do > > [...] > > > When I am reading the data in again and print them out, I always have: > > > > buf(0)=0 > > If you compile your code with -check bounds and run, you'll get an error > pointing out that buf(0) is an illegal access; in Fortran arrays start at > 1. > Thanks a lot, that solved the problem! Best wishes Alexander
[OMPI users] problems with parallel MPI-IO...
Hi Folks, I am using the following f90 example program for writing a file in parallel with MIP: [snip] program parallel_io use mpi implicit none integer ierr, i, myrank, BUFSIZE, thefile, intsize parameter (BUFSIZE=100) integer buf(BUFSIZE) ! integer (kind=MPI_OFFSET_KIND) disp integer*8 disp call mpi_init(ierr) call mpi_comm_rank(mpi_comm_world, myrank,ierr) do i=0,BUFSIZE buf(i) = myrank*BUFSIZE + i print*, 'i =', i, 'myrank =', myrank, 'buf(i)=',buf(i) end do call mpi_file_open(mpi_comm_world, 'testfile', MPI_MODE_WRONLY + MPI_MODE_CREATE, mpi_info_null, thefile, ierr) call mpi_type_size(MPI_INTEGER, intsize, ierr) disp = myrank * BUFSIZE * intsize ! call mpi_file_set_view(thefile, disp, MPI_INTEGER, MPI_INTEGER, 'native', mpi_info_null, ierr) call mpi_file_write_at(thefile, disp, buf, BUFSIZE, MPI_INTEGER, mpi_status_ignore, ierr) call mpi_file_close(thefile, ierr) call mpi_finalize(ierr) end program parallel_io [snip] And the follwoing program shall read all the data in again, and print them out [snip] program parallel_read_io use mpi implicit none integer ierr, i, myrank, BUFSIZE, thefile, intsize parameter (BUFSIZE=100) integer buf(BUFSIZE) ! integer (kind=MPI_OFFSET_KIND) disp integer*8 disp call mpi_init(ierr) call mpi_comm_rank(mpi_comm_world, myrank,ierr) ! do i=0,BUFSIZE ! buf(i) = myrank*BUFSIZE + i ! end do call mpi_file_open(mpi_comm_world, 'testfile', MPI_MODE_RDONLY, mpi_info_null, thefile, ierr) call mpi_type_size(MPI_INTEGER, intsize, ierr) disp = myrank * BUFSIZE * intsize ! call mpi_file_set_view(thefile, disp, MPI_INTEGER, MPI_INTEGER, 'native', mpi_info_null, ierr) ! call mpi_file_read(thefile, buf, BUFSIZE, MPI_INTEGER, mpi_status_ignore, ierr) call mpi_file_read_at(thefile, disp, buf, BUFSIZE, MPI_INTEGER, mpi_status_ignore, ierr) call mpi_file_close(thefile, ierr) ! print the data read in... if (myrank.eq.1) then do i = 0,BUFSIZE print*, 'i =', i, 'myrank =', myrank, 'buf(i)=', buf(i) end do endif call mpi_finalize(ierr) [snip] I have maid several tests, also with do loops only from 0 to (BUFSIZE-1), with MPI_FILE_SET_VIEW and MPI_FILE_READ, etc... When I am reading the data in again and print them out, I always have: buf(0)=0 for every rank, so I assume that something with the offset is wrong. I am using openmpi with an Intel f90 compiler. What am I doing wrong? Best wishes Alexander
