[mpich-discuss] MPI_FILE_read and derived types in fortran.

Rajeev Thakur thakur at mcs.anl.gov
Tue Mar 11 14:54:28 CDT 2014 

>> 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 :)

I meant to say the documentation on that page is correct. It is exactly as it is in the MPI standard. The description of arguments is a generic description, where integer does not refer to a particular size of integer.

Rajeev



On Mar 11, 2014, at 2:51 PM, Rajeev Thakur <thakur at mcs.anl.gov>
 wrote:

> I ran it on a Mac. 64 bit.
> 
> Rajeev
> 
> On Mar 11, 2014, at 2:49 PM, Scot Breitenfeld <brtnfld at hdfgroup.org>
> 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 <thakur at mcs.anl.gov> 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 <brtnfld at hdfgroup.org> 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 <brtnfld at hdfgroup.org> 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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