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

TAY wee-beng zonexo at gmail.com
Thu Feb 22 00:23:04 CST 2018 

On 21/2/2018 11:44 AM, Smith, Barry F. wrote:
>    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
Ops sorry, indeed I didn't change that part. Got it compiled now.

However, I have got a new problem. Previously, I was using Intel 2016 
with PETSc 3.7.6. During compile, I used -O3 for all modules except one, 
which will give error (due to DMDAVecGetArrayF90 and 
DMDAVecRestoreArrayF90). Hence, I need to use -O1.

Now, I'm using Intel 2018 with PETSc 3.8.3 and I got the error:

M Diverged but why?, time =            2
  reason =           -9

I tried to change all *.F90 from using -O3 to -O1 and although there's 
no diverged err printed, my values are different:

1      0.01600000      0.46655767      0.46310378      1.42427154 
-0.81598016E+02 -0.11854431E-01  0.42046197E+06
        2      0.00956350      0.67395693      0.64698638 1.44166606 
-0.12828928E+03  0.12179394E-01  0.41961824E+06

vs

1      0.01600000      0.49096543      0.46259333      1.41828130 
-0.81561221E+02 -0.16146574E-01  0.42046335E+06
        2      0.00956310      0.68342495      0.63682485 1.44353571 
-0.12813998E+03  0.24226242E+00  0.41962121E+06

The latter values are obtained using the debug built and they compared 
correctly with another cluster, which use GNU.

What going on and how should I troubleshoot?
Thanks
>
>
>> 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
>>>>>>> ================================================
>>>>>>>
>>>>>>>
>>>>>>> ________________________________
>>>>>>>
>>>>>>> Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.

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