[petsc-users] Problem compiling with 64bit PETSc
TAY wee-beng
zonexo at gmail.com
Fri Sep 7 01:36:59 CDT 2018
Hi,
Thank you very much. I got it working now.
Yours sincerely,
================================================
TAY Wee-Beng (Zheng Weiming) 郑伟明
Personal research webpage: http://tayweebeng.wixsite.com/website
Youtube research showcase: https://www.youtube.com/channel/UC72ZHtvQNMpNs2uRTSToiLA
linkedin: www.linkedin.com/in/tay-weebeng
================================================
On 7/9/2018 8:17 AM, Smith, Barry F. wrote:
> Ignore this message; MPIU_INTEGER already exists you can just use it to replace MPI_INTEGER for places where you are passing PetscInt through MPI calls.
>
> Barry
>
>
>> On Sep 6, 2018, at 5:46 PM, Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
>>
>>
>> I have added MPIU_INTEGER to the branch barry/add-mpiu_integer so you can make your MPI calls portable between 32 and 64 bit indices in Fortran.
>>
>> Please let me know if you have any difficulties.
>>
>> Barry
>>
>>
>>> On Sep 5, 2018, at 11:58 PM, TAY wee-beng <zonexo at gmail.com> wrote:
>>>
>>>
>>> On 6/9/2018 12:09 PM, Smith, Barry F. wrote:
>>>>> On Sep 5, 2018, at 11:01 PM, Randall Mackie <rlmackie862 at gmail.com> wrote:
>>>>>
>>>>> You can use PetscMPIInt for integers in MPI calls.
>>>>>
>>>>> Check petscsys.h for definitions of all of these.
>>>> This is true but can be cumbersome because one may need to convert arrays of PetscInt to PetscMPIInt for MPI and then convert back after (with possible loss of precision).
>>>>
>>>> In C we have macros MPIU_INT that we use to indicate that the integer argument to the MPI call is 64 bit when 64 bit indices are used and 32 bit otherwise allowing users to write portable code that can just be reconfigured for 32 or 64 bit integers. I see we do not provide such a thing for Fortran; we should provide it. Unless Karl has coding time today we won't be able to get to it until tomorrow US time since it is already late in the US.
>>>>
>>>> Barry
>>> Hi,
>>>
>>> That would be great! I've no problem waiting a few days. Does it mean that I can then use：
>>>
>>> call MPI_ALLGATHER(counter,1,MPIU_INT,counter_global,1,MPIU_INT,MPI_COMM_WORLD,ierr)
>>>
>>> Thanks!
>>>>> Randy
>>>>>
>>>>>
>>>>>> On Sep 5, 2018, at 8:56 PM, TAY wee-beng <zonexo at gmail.com> wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> My code has some problems now after converting to 64bit indices.
>>>>>>
>>>>>> After debugging, I realised that I'm using:
>>>>>>
>>>>>> call MPI_ALLGATHER(counter,1,MPI_INTEGER,counter_global,1,MPI_INTEGER,MPI_COMM_WORLD,ierr)
>>>>>>
>>>>>> but now counter and counter_global are both 64bit integers. So should I change all mpi routine from MPI_INTEGER to MPI_INTEGER8?
>>>>>>
>>>>>> But if I switch back to using the 32bit PETSc, do I have to switch back again? In that case, does it mean I need to have 2 copies of my code - one to compile with PETSc 32, another to compile with PETSc 64?
>>>>>>
>>>>>> Is there an easier way?
>>>>>> Thank you very much.
>>>>>>
>>>>>> Yours sincerely,
>>>>>>
>>>>>> ================================================
>>>>>> TAY Wee-Beng (Zheng Weiming) 郑伟明
>>>>>> Personal research webpage:
>>>>>> http://tayweebeng.wixsite.com/website
>>>>>>
>>>>>> Youtube research showcase:
>>>>>> https://www.youtube.com/channel/UC72ZHtvQNMpNs2uRTSToiLA
>>>>>>
>>>>>> linkedin:
>>>>>> www.linkedin.com/in/tay-weebeng
>>>>>>
>>>>>> ================================================
>>>>>>
>>>>>> On 5/9/2018 6:25 PM, Matthew Knepley wrote:
>>>>>>> On Wed, Sep 5, 2018 at 3:27 AM TAY wee-beng <zonexo at gmail.com> wrote:
>>>>>>>
>>>>>>> On 31/8/2018 10:43 AM, Smith, Barry F. wrote:
>>>>>>>>> On Aug 30, 2018, at 9:40 PM, TAY wee-beng <zonexo at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 31/8/2018 10:38 AM, Smith, Barry F. wrote:
>>>>>>>>>> PetscReal is by default real(8) you can leave those alone
>>>>>>>>>>
>>>>>>>>>> Any integer you pass to a PETSc routine needs to be declared as PetscInt (not integer) otherwise the 64 bit indices stuff won't work.
>>>>>>>>>>
>>>>>>>>>> Barry
>>>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> ok, I got it. Btw, is it advisable to change all integer in my code to PetscInt?
>>>>>>>>>
>>>>>>>>> Will it cause any conflict or waste a lot of memory?
>>>>>>>>>
>>>>>>>>> Or should I only change those related to PETSc?
>>>>>>>> That is up to you. Since you probably pass the values between PETSc and non-PETSc part of the code it is probably easier just to make all the integer PetscInt instead. No performance difference that you can measure by keeping a few integer around.
>>>>>>>>
>>>>>>>> Barry
>>>>>>> Hi,
>>>>>>>
>>>>>>> For some small parts of the code, it is preferred to use integer
>>>>>>> instead. Btw, to force variable as integer, I can use int(aa). However,
>>>>>>> I tried to force variable as PetscInt using PetscInt(aa) but it can't work.
>>>>>>>
>>>>>>> Is there any way I can make it work?
>>>>>>>
>>>>>>> I think you just define a PetscInt variable and use assignment.
>>>>>>>
>>>>>>> Matt
>>>>>>> Thanks.
>>>>>>>>> Thanks!
>>>>>>>>>>> On Aug 30, 2018, at 9:35 PM, TAY wee-beng <zonexo at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 31/8/2018 10:21 AM, Matthew Knepley wrote:
>>>>>>>>>>>> On Thu, Aug 30, 2018 at 10:17 PM TAY wee-beng <zonexo at gmail.com> wrote:
>>>>>>>>>>>> Hi,
>>>>>>>>>>>>
>>>>>>>>>>>> Due to my increase grid size, I have to go 64bit. I compiled the 64bit
>>>>>>>>>>>> PETSc w/o error. However, when I tried to compile my code using the
>>>>>>>>>>>> 64bit PETSc, I got the error below. May I know why is this so?
>>>>>>>>>>>>
>>>>>>>>>>>> What changes should I make?
>>>>>>>>>>>>
>>>>>>>>>>>> Is it possible that you did not declare some inputs as PetscInt, so the interface check is failing?
>>>>>>>>>>>>
>>>>>>>>>>>> Matt
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> I'm using the standard
>>>>>>>>>>>
>>>>>>>>>>> integer ::
>>>>>>>>>>>
>>>>>>>>>>> real(8) ::
>>>>>>>>>>>
>>>>>>>>>>> for some variables. For some others relating to PETSc, I use PetscInt.
>>>>>>>>>>>
>>>>>>>>>>> Should I change all to PetscInt and PetscReal?
>>>>>>>>>>>
>>>>>>>>>>> Currently, I use real(8) for all real values. If I change all to PetscReal, will PetscReal be real or real(8) by default?
>>>>>>>>>>>
>>>>>>>>>>> Thanks!
>>>>>>>>>>>> [tsltaywb at nus02 ibm3d_IIB_mpi]$ make -f makefile_2018
>>>>>>>>>>>> /app/intel/xe2018/compilers_and_libraries_2018.0.128/linux/mpi/intel64/bin/mpif90
>>>>>>>>>>>> -g -ip -ipo -O3 -c -fPIC -save kinefunc.F90
>>>>>>>>>>>> /app/intel/xe2018/compilers_and_libraries_2018.0.128/linux/mpi/intel64/bin/mpif90
>>>>>>>>>>>> -g -ip -ipo -O3 -c -fPIC -save -w
>>>>>>>>>>>> -I/home/users/nus/tsltaywb/propeller/lib/petsc-3.9.3_intel_2018_64bit_rel/include
>>>>>>>>>>>> -I/app/intel/xe2018/compilers_and_libraries_2018.0.128/linux/mpi/intel64/include
>>>>>>>>>>>> global.F90
>>>>>>>>>>>> global.F90(979): error #6285: There is no matching specific subroutine
>>>>>>>>>>>> for this generic subroutine call. [DMDACREATE3D]
>>>>>>>>>>>> call
>>>>>>>>>>>> DMDACreate3d(MPI_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,size_x,size_y,&
>>>>>>>>>>>> -----^
>>>>>>>>>>>> global.F90(989): error #6285: There is no matching specific subroutine
>>>>>>>>>>>> for this generic subroutine call. [DMDACREATE3D]
>>>>>>>>>>>> call
>>>>>>>>>>>> DMDACreate3d(MPI_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,size_x,size_y,&
>>>>>>>>>>>> ---------^
>>>>>>>>>>>> global.F90(997): error #6285: There is no matching specific subroutine
>>>>>>>>>>>> for this generic subroutine call. [DMDACREATE3D]
>>>>>>>>>>>> call
>>>>>>>>>>>> DMDACreate3d(MPI_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,size_x,size_y,&
>>>>>>>>>>>> ---------^
>>>>>>>>>>>> global.F90(1005): error #6285: There is no matching specific subroutine
>>>>>>>>>>>> for this generic subroutine call. [DMDACREATE3D]
>>>>>>>>>>>> call
>>>>>>>>>>>> DMDACreate3d(MPI_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,size_x,size_y,&
>>>>>>>>>>>> ---------^
>>>>>>>>>>>> global.F90(1013): error #6285: There is no matching specific subroutine
>>>>>>>>>>>> for this generic subroutine call. [DMDACREATE3D]
>>>>>>>>>>>> call
>>>>>>>>>>>> DMDACreate3d(MPI_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,size_x,size_y,&
>>>>>>>>>>>> ---------^
>>>>>>>>>>>> global.F90(1021): error #6285: There is no matching specific subroutine
>>>>>>>>>>>> for this generic subroutine call. [DMDACREATE3D]
>>>>>>>>>>>> call
>>>>>>>>>>>> DMDACreate3d(MPI_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,size_x,size_y,&
>>>>>>>>>>>> ---------^
>>>>>>>>>>>> global.F90(1029): error #6285: There is no matching specific subroutine
>>>>>>>>>>>> for this generic subroutine call. [DMDACREATE3D]
>>>>>>>>>>>> call
>>>>>>>>>>>> DMDACreate3d(MPI_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,size_x,size_y,&
>>>>>>>>>>>> ---------^
>>>>>>>>>>>> compilation aborted for global.F90 (code 1)
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Thank you very much.
>>>>>>>>>>>>
>>>>>>>>>>>> Yours sincerely,
>>>>>>>>>>>>
>>>>>>>>>>>> ================================================
>>>>>>>>>>>> TAY Wee-Beng (Zheng Weiming) 郑伟明
>>>>>>>>>>>> Personal research webpage: http://tayweebeng.wixsite.com/website
>>>>>>>>>>>> Youtube research showcase: https://www.youtube.com/channel/UC72ZHtvQNMpNs2uRTSToiLA
>>>>>>>>>>>> linkedin: www.linkedin.com/in/tay-weebeng
>>>>>>>>>>>> ================================================
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
>>>>>>>>>>>> -- Norbert Wiener
>>>>>>>>>>>>
>>>>>>>>>>>> https://www.cse.buffalo.edu/~knepley/
>>>>>>>
>>>>>>> --
>>>>>>> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
>>>>>>> -- Norbert Wiener
>>>>>>>
>>>>>>> https://www.cse.buffalo.edu/~knepley/
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