[petsc-users] Compiling problem after upgrading to PETSc 3.8.3

Smith, Barry F. bsmith at mcs.anl.gov
Tue Feb 20 21:44:36 CST 2018 

  Did you follow the directions in the changes file for 3.8?

<li>Replace calls to DMDACreateXd() with DMDACreateXd(), [DMSetFromOptions()] DMSetUp()</li>
        <li>DMDACreateXd() no longer can take negative values for dimensons, instead pass positive values and call DMSetFromOptions() immediately after</li>

I suspect you are not calling DMSetUp() and this is causing the problem.

  Barry


> On Feb 20, 2018, at 7:35 PM, TAY wee-beng <zonexo at gmail.com> wrote:
> 
> 
> On 21/2/2018 10:47 AM, Smith, Barry F. wrote:
>>   Try setting
>> 
>>   u_global = tVec(1)
>> 
>>   immediately before the call to DMCreateGlobalVector()
>> 
>> 
> Hi,
> 
> I added the line in but still got the same error below. Btw, my code is organised as:
> 
> module global_data
> 
> #include "petsc/finclude/petsc.h"
> use petsc
> use kdtree2_module
> implicit none
> save
> ...
> Vec u_local,u_global ...
> ...
> contains
> 
> subroutine allo_var
> ...
> u_global = tVec(1)
> call DMCreateGlobalVector(da_u,u_global,ierr)
> ...
> 
> 
> 
> 
> [0]PETSC ERROR: --------------------- Error Message ----------------------------
> ----------------------------------
> [0]PETSC ERROR: Null argument, when expecting valid pointer
> [0]PETSC ERROR: Null Object: Parameter # 2
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trou
> ble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> [0]PETSC ERROR: C:\Obj_tmp\ibm3d_IIB_mpi\Debug\ibm3d_IIB_mpi.exe on a petsc-3.8.
> 3_win64_msmpi_vs2008 named 1C3YYY1-PC by tsltaywb Wed Feb 21 11:18:20 2018
> [0]PETSC ERROR: Configure options --with-cc="win32fe icl" --with-fc="win32fe ifo
> rt" --with-cxx="win32fe icl" --download-fblaslapack --with-mpi-include="[/cygdri
> ve/c/Program Files (x86)/Microsoft SDKs/MPI/Include,/cygdrive/c/Program Files (x
> 86)/Microsoft SDKs/MPI/Include/x64]" --with-mpi-mpiexec="/cygdrive/c/Program Fil
> es/Microsoft MPI/Bin/mpiexec.exe" --with-debugging=1 --with-file-create-pause=1
> --prefix=/cygdrive/c/wtay/Lib/petsc-3.8.3_win64_msmpi_vs2008 --with-mpi-lib="[/c
> ygdrive/c/Program Files (x86)/Microsoft SDKs/MPI/Lib/x64/msmpifec.lib,/cygdrive/
> c/Program Files (x86)/Microsoft SDKs/MPI/Lib/x64/msmpi.lib]" --with-shared-libra
> ries=0
> [0]PETSC ERROR: #1 VecSetLocalToGlobalMapping() line 78 in C:\Source\PETSC-~2.3\
> src\vec\vec\INTERF~1\vector.c
> [0]PETSC ERROR: #2 DMCreateGlobalVector_DA() line 41 in C:\Source\PETSC-~2.3\src
> \dm\impls\da\dadist.c
> [0]PETSC ERROR: #3 DMCreateGlobalVector() line 844 in C:\Source\PETSC-~2.3\src\d
> m\INTERF~1\dm.c
> 
> Thanks.
>>> On Feb 20, 2018, at 6:40 PM, TAY wee-beng <zonexo at gmail.com> wrote:
>>> 
>>> Hi,
>>> 
>>> Indeed, replacing tvec with t_vec solves the problem. Now I'm trying to debug step by step. I got into problem when calling:
>>> 
>>> call DMCreateGlobalVector(da_u,u_global,ierr)
>>> 
>>> The error is:
>>> 
>>> [0]PETSC ERROR: --------------------- Error Message ----------------------------
>>> ----------------------------------
>>> [0]PETSC ERROR: Null argument, when expecting valid pointer
>>> [0]PETSC ERROR: Null Object: Parameter # 2
>>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trou
>>> ble shooting.
>>> [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
>>> [0]PETSC ERROR: C:\Obj_tmp\ibm3d_IIB_mpi\Debug\ibm3d_IIB_mpi.exe on a petsc-3.8.
>>> 3_win64_msmpi_vs2008 named 1C3YYY1-PC by tsltaywb Wed Feb 21 10:20:20 2018
>>> [0]PETSC ERROR: Configure options --with-cc="win32fe icl" --with-fc="win32fe ifo
>>> rt" --with-cxx="win32fe icl" --download-fblaslapack --with-mpi-include="[/cygdri
>>> ve/c/Program Files (x86)/Microsoft SDKs/MPI/Include,/cygdrive/c/Program Files (x....
>>> 
>>> But all I changed is from:
>>> 
>>> module global_data
>>> #include "petsc/finclude/petsc.h"
>>> use petsc
>>> use kdtree2_module
>>> implicit none
>>> save
>>> !grid variables
>>> 
>>> integer :: size_x,s....
>>> 
>>> ...
>>> 
>>> to
>>> 
>>> module global_data
>>> use kdtree2_module
>>> implicit none
>>> save
>>> #include "petsc/finclude/petsc.h90"
>>> !grid variables
>>> integer :: size_x,s...
>>> 
>>> ...
>>> 
>>> da_u, u_global were declared thru:
>>> 
>>> DM  da_u,da_v,...
>>> DM  da_cu_types ...
>>> Vec u_local,u_global,v_local...
>>> 
>>> So what could be the problem?
>>> 
>>> 
>>> 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 20/2/2018 10:46 PM, Jose E. Roman wrote:
>>>> Probably the first error is produced by using a variable (mpi_comm) with the same name as an MPI type.
>>>> 
>>>> The second error I guess is due to variable tvec, since a Fortran type tVec is now being defined in src/vec/f90-mod/petscvec.h
>>>> 
>>>> Jose
>>>> 
>>>> 
>>>>> El 20 feb 2018, a las 15:35, Smith, Barry F. <bsmith at mcs.anl.gov> escribió:
>>>>> 
>>>>> 
>>>>>   Please run a clean compile of everything and cut and paste all the output. This will make it much easier to debug than trying to understand your snippets of what is going wrong.
>>>>> 
>>>>>> On Feb 20, 2018, at 1:56 AM, TAY Wee Beng <tsltaywb at nus.edu.sg> wrote:
>>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I was previously using PETSc 3.7.6 on different clusters with both Intel
>>>>>> Fortran and GNU Fortran. After upgrading, I met some problems when
>>>>>> trying to compile:
>>>>>> 
>>>>>> On Intel Fortran:
>>>>>> 
>>>>>> Previously, I was using:
>>>>>> 
>>>>>> #include "petsc/finclude/petsc.h90"
>>>>>> 
>>>>>> in *.F90 when requires the use of PETSc
>>>>>> 
>>>>>> I read in the change log that h90 is no longer there and so I replaced
>>>>>> with #include "petsc/finclude/petsc.h"
>>>>>> 
>>>>>> It worked. But I also have some *.F90 which do not use PETSc. However,
>>>>>> they use some modules which uses PETSc.
>>>>>> 
>>>>>> Now I can't compile them. The error is :
>>>>>> 
>>>>>> math_routine.f90(3): error #7002: Error in opening the compiled module
>>>>>> file.  Check INCLUDE paths.   [PETSC]
>>>>>> use mpi_subroutines
>>>>>> 
>>>>>> mpi_subroutines is a module which uses PETSc, and it compiled w/o problem.
>>>>>> 
>>>>>> The solution is that I have to compile e.g.  math_routine.F90 as if they
>>>>>> use PETSc, by including PETSc include and lib files.
>>>>>> 
>>>>>> May I know why this is so? It was not necessary before.
>>>>>> 
>>>>>> Anyway, it managed to compile until it reached hypre.F90.
>>>>>> 
>>>>>> Previously, due to some bugs, I have to compile hypre with the -r8
>>>>>> option. Also, I have to use:
>>>>>> 
>>>>>> integer(8) mpi_comm
>>>>>> 
>>>>>> mpi_comm = MPI_COMM_WORLD
>>>>>> 
>>>>>> to make my codes work with HYPRE.
>>>>>> 
>>>>>> But now, compiling gives the error:
>>>>>> 
>>>>>> hypre.F90(11): error #6401: The attributes of this name conflict with
>>>>>> those made accessible by a USE statement.   [MPI_COMM]
>>>>>> integer(8) mpi_comm
>>>>>> --------------------------------------^
>>>>>> hypre.F90(84): error #6478: A type-name must not be used as a
>>>>>> variable.   [MPI_COMM]
>>>>>>   mpi_comm = MPI_COMM_WORLD
>>>>>> ----^
>>>>>> hypre.F90(84): error #6303: The assignment operation or the binary
>>>>>> expression operation is invalid for the data types of the two
>>>>>> operands.   [1140850688]
>>>>>>   mpi_comm = MPI_COMM_WORLD
>>>>>> ---------------^
>>>>>> hypre.F90(100): error #6478: A type-name must not be used as a
>>>>>> variable.   [MPI_COMM]
>>>>>>       call HYPRE_StructGridCreate(mpi_comm, 3, grid_hypre, ierr)
>>>>>> ...
>>>>>> 
>>>>>> What's actually happening? Why can't I compile now?
>>>>>> 
>>>>>> On GNU gfortran:
>>>>>> 
>>>>>> I tried to use similar tactics as above here. However, when compiling
>>>>>> math_routine.F90, I got the error:
>>>>>> 
>>>>>> math_routine.F90:1333:21:
>>>>>> 
>>>>>> call subb(orig,vert1,tvec)
>>>>>>                    1
>>>>>> Error: Invalid procedure argument at (1)
>>>>>> math_routine.F90:1339:18:
>>>>>> 
>>>>>> qvec = cross_pdt2(tvec,edge1)
>>>>>>                 1
>>>>>> Error: Invalid procedure argument at (1)
>>>>>> math_routine.F90:1345:21:
>>>>>> 
>>>>>>    uu = dot_product(tvec,pvec)
>>>>>>                    1
>>>>>> Error: ‘vector_a’ argument of ‘dot_product’ intrinsic at (1) must be
>>>>>> numeric or LOGICAL
>>>>>> math_routine.F90:1371:21:
>>>>>> 
>>>>>>    uu = dot_product(tvec,pvec)
>>>>>> 
>>>>>> These errors were not present before. My variables are mostly vectors:
>>>>>> 
>>>>>> real(8), intent(in) ::
>>>>>> orig(3),infinity(3),vert1(3),vert2(3),vert3(3),normal(3)
>>>>>> 
>>>>>> real(8) :: uu,vv,dir(3)
>>>>>> 
>>>>>> real(8) :: edge1(3),edge2(3),tvec(3),pvec(3),qvec(3),det,inv_det,epsilon,d,t
>>>>>> 
>>>>>> I wonder what happened?
>>>>>> 
>>>>>> Please advice.
>>>>>> 
>>>>>> 
>>>>>> --
>>>>>> Thank you very much.
>>>>>> 
>>>>>> Yours sincerely,
>>>>>> 
>>>>>> ================================================
>>>>>> TAY Wee-Beng 郑伟明
>>>>>> Research Scientist
>>>>>> Experimental AeroScience Group
>>>>>> Temasek Laboratories
>>>>>> National University of Singapore
>>>>>> T-Lab Building
>>>>>> 5A, Engineering Drive 1, #02-02
>>>>>> Singapore 117411
>>>>>> Phone: +65 65167330
>>>>>> E-mail: tsltaywb at nus.edu.sg
>>>>>> http://www.temasek-labs.nus.edu.sg/program/program_aeroexperimental_tsltaywb.php
>>>>>> Personal research webpage: http://tayweebeng.wixsite.com/website
>>>>>> Youtube research showcase: https://www.youtube.com/channel/UC72ZHtvQNMpNs2uRTSToiLA
>>>>>> linkedin: www.linkedin.com/in/tay-weebeng
>>>>>> ================================================
>>>>>> 
>>>>>> 
>>>>>> ________________________________
>>>>>> 
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>

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