I ran the modified program using mpich 3.1 instead and it fixes the problem on 32 bit, so it seems to work everywhere using mpich 3.1 Thanks, Scot On Mar 11, 2014, at 2:51 PM, Rajeev Thakur <[email protected]> wrote:
I ran it on a Mac. 64 bit.
Rajeev
On Mar 11, 2014, at 2:49 PM, Scot Breitenfeld <[email protected]> wrote:
I could also get it to work on
Linux 2.6.32-431.5.1.el6.x86_64 #1 SMP Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
which is probably what your laptop is running?
Maybe it’s a 32-bit version issue?
The comment about documentation was geared toward the people in charge of mpich.org, since they run the mailing list and I’m assuming they are in charge of the Documentation Manpages on mpich.org. I just gravitate to an html document rather then scanning a pdf :)
Thanks, Scot
On Mar 11, 2014, at 2:13 PM, Rajeev Thakur <[email protected]> wrote:
The modified program works correctly on my laptop.
Also, the documentation for MPI_Type_create_struct leads one to think that all MPI objects (that includes MPI_Aint) in fortran are of type integer.
http://www.mpich.org/static/docs/v3.0.x/www3/MPI_Type_create_struct.html
That page provides the C binding and generic description of arguments identical to the one provided on pg 93 of the MPI 3.0 standard. In any case, the definitive source for function bindings should be the MPI 3.0 standard available at www.mpi-forum.org, not any other web site.
Rajeev
On Mar 11, 2014, at 1:39 PM, Scot Breitenfeld <[email protected]> wrote:
I checked the original program and the suggested version on another machine using
mpif90 for MPICH2 version 1.5 exec: export(export,XL_CONFIG=/soft/compilers/ibmcmp-aug2013/xlf/bg/14.1/etc/xlf.cfg.rhel6.5.gcc447:bgxlf90,NULL) exec: export(export,XLF_USR_CONFIG=/soft/compilers/ibmcmp-aug2013/xlf/bg/14.1/etc/V1R2M1.xlf.cfg.rhel6.5.gcc447,NULL)
And both methods of reading the file worked correctly for both programs. However, the suggested changes do not work on the original system. Also, the documentation for MPI_Type_create_struct leads one to think that all MPI objects (that includes MPI_Aint) in fortran are of type integer.
http://www.mpich.org/static/docs/v3.0.x/www3/MPI_Type_create_struct.html
I think elsewhere in the documentation it says MPI_Aint is kind=MPI_ADDRESS_KIND, but it would be nice to have note that on the man page.
Scot
Updated program:
PROGRAM struct
USE mpi USE iso_c_binding
IMPLICIT NONE
INTEGER, PARAMETER :: NELEM = 2 INTEGER :: numtasks, rank, source, dest, tag, i, ierr INTEGER :: stat(MPI_STATUS_SIZE) INTEGER :: fh INTEGER :: status INTEGER(kind=MPI_OFFSET_KIND) :: disp
INTEGER, DIMENSION(1:3) :: iiaux
TYPE Particle SEQUENCE INTEGER, DIMENSION(1:3) :: indx END TYPE Particle
TYPE(Particle), DIMENSION(1:nelem), TARGET :: particles INTEGER particletype, oldtypes(1:1), blockcounts(1:1), extent INTEGER(kind=MPI_ADDRESS_KIND), DIMENSION(1:1) :: offsets TYPE(C_PTR) :: fptr
CALL MPI_INIT(ierr) CALL MPI_COMM_RANK(MPI_COMM_WORLD, rank, ierr) CALL MPI_COMM_SIZE(MPI_COMM_WORLD, numtasks, ierr)
! Setup description of the 3 MPI_INTEGERS fields x, y, z offsets(1) = 0 oldtypes(1) = MPI_INTEGER blockcounts(1) = 3
! Now define structured TYPE and commit it CALL MPI_Type_create_struct(1, blockcounts, offsets, oldtypes, particletype, ierr) CALL MPI_TYPE_COMMIT(particletype, ierr)
CALL MPI_File_open(MPI_COMM_WORLD, "ustream.demo", MPI_MODE_RDONLY, MPI_INFO_NULL, fh, ierr)
disp = 0
CALL MPI_File_set_view(fh, disp, MPI_INTEGER, particletype, "native", MPI_INFO_NULL, ierr)
particles(1)%indx = -1
fptr = C_LOC( particles(1)%indx(1))
CALL MPI_File_read(fh, particles, nelem, particletype, status, ierr)
PRINT*,"Derived type" DO i=1,nelem PRINT*,particles(i)%indx ENDDO
CALL MPI_File_close(fh, ierr)
CALL MPI_File_open(MPI_COMM_WORLD, "ustream.demo", MPI_MODE_RDONLY, & MPI_INFO_NULL, fh, ierr)
CALL MPI_FILE_read(fh,iiaux,3,MPI_INTEGER,status,ierr)
PRINT*,"No derived type"
PRINT*,iiaux CALL MPI_FILE_read(fh,iiaux,3,MPI_INTEGER,status,ierr) PRINT*,iiaux
CALL MPI_File_close(fh, ierr)
CALL MPI_FINALIZE(ierr) END PROGRAM struct
On Mar 11, 2014, at 11:25 AM, Scot Breitenfeld <[email protected]> wrote:
Hi,
I created a file in fortran using (which I compiled with mpif90):
PROGRAM writeUstream
IMPLICIT NONE INTEGER :: i, ii INTEGER, DIMENSION(1:3,1:25) :: buf
OPEN(UNIT=11, FILE="ustream.demo", FORM="unformatted", STATUS="UNKNOWN", ACCESS="STREAM")
ii = 1
DO i=1, 25 buf(1,i) = ii buf(2,i) = ii+1 buf(3,i) = ii+2 WRITE(11) buf(1:3,i) ii = ii + 3 ENDDO CLOSE(UNIT=11)
END PROGRAM writeUstream
And I’ve made a simple program to read the file (on the same machine) using MPI_FILE_read:
PROGRAM struct
USE mpi
IMPLICIT NONE
INTEGER, PARAMETER :: NELEM = 2 INTEGER :: numtasks, rank, source, dest, tag, i, ierr INTEGER :: stat(MPI_STATUS_SIZE) INTEGER :: fh INTEGER :: status INTEGER(kind=MPI_OFFSET_KIND) :: disp
INTEGER, DIMENSION(1:3) :: iiaux
TYPE Particle SEQUENCE INTEGER, DIMENSION(1:3) :: indx END TYPE Particle
TYPE(Particle), DIMENSION(1:nelem) :: particles INTEGER particletype, oldtypes(1:1), blockcounts(1:1), offsets(1:1), extent
CALL MPI_INIT(ierr) CALL MPI_COMM_RANK(MPI_COMM_WORLD, rank, ierr) CALL MPI_COMM_SIZE(MPI_COMM_WORLD, numtasks, ierr)
! Setup description of the 3 MPI_INTEGERS fields x, y, z offsets(1) = 0 oldtypes(1) = MPI_INTEGER blockcounts(1) = 3
! Now define structured TYPE and commit it CALL MPI_TYPE_STRUCT(1, blockcounts, offsets, oldtypes, particletype, ierr) CALL MPI_TYPE_COMMIT(particletype, ierr)
CALL MPI_File_open(MPI_COMM_WORLD, "ustream.demo", MPI_MODE_RDONLY, MPI_INFO_NULL, fh, ierr)
disp = 0
CALL MPI_File_set_view(fh, disp, MPI_INTEGER, particletype, "native", MPI_INFO_NULL, ierr)
particles(1:nelem)%indx = -1
CALL MPI_File_read(fh, particles, nelem, particletype, status, ierr)
PRINT*,"derived type" DO i=1,nelem PRINT*,particles(i)%indx ENDDO
CALL MPI_File_close(fh, ierr)
CALL MPI_File_open(MPI_COMM_WORLD, "ustream.demo", MPI_MODE_RDONLY, & MPI_INFO_NULL, fh, ierr)
CALL MPI_FILE_read(fh,iiaux,3,MPI_INTEGER,status,ierr)
PRINT*,"No derived type"
PRINT*,iiaux CALL MPI_FILE_read(fh,iiaux,3,MPI_INTEGER,status,ierr) PRINT*,iiaux
CALL MPI_File_close(fh, ierr)
CALL MPI_FINALIZE(ierr) END PROGRAM struct
When I run this program to read the file using just one process, the first two integers of the derived type are not correct, but all the remaining values are correct. All the values when reading them into an integer array is correct. Here is the output:
derived type 24 0 3 4 5 6 No derived type 1 2 3 4 5 6
I don’t get any error from the MPI calls and I used gcc 4.8.1 to compile mpich 3.0.4 on Linux 2.6.18-308.13.1.el5PAE #1 SMP Tue Aug 21 17:50:26 EDT 2012 i686 i686 i386 GNU/Linux I not exactly sure what is going on.
Thanks, Scot
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