[petsc-users] upgrading to 3.22.4
Sanjay Govindjee
s_g at berkeley.edu
Sun Mar 23 02:52:46 CDT 2025
Here is what I have right now:
call MatMPIBAIJSetPreallocation(Mmat,nsbk,
& PETSC_NULL_INTEGER,mr(np(246)),
& PETSC_NULL_INTEGER,mr(np(247)),
& ierr)
call MatSeqBAIJSetPreallocation(Mmat,nsbk,
& PETSC_DEFAULT_INTEGER,mr(np(246)),
& ierr)
else
call MatSetType(Mmat,MATAIJ,ierr)
call MatMPIAIJSetPreallocation(Mmat,
& PETSC_NULL_INTEGER_ARRAY,mr(np(246)),
& PETSC_NULL_INTEGER_ARRAY,mr(np(247)),
& ierr)
call MatSeqAIJSetPreallocation(Mmat,
& PETSC_NULL_INTEGER_ARRAY,mr(np(246)),
& ierr)
Before with prior versions of petsc I had
call MatMPIBAIJSetPreallocation(Mmat,nsbk,
& PETSC_NULL_INTEGER,mr(np(246)),
& PETSC_NULL_INTEGER,mr(np(247)),
& ierr)
call MatSeqBAIJSetPreallocation(Mmat,nsbk,
& PETSC_DEFAULT_INTEGER,mr(np(246)),
& ierr)
else
call MatSetType(Mmat,MATAIJ,ierr)
call MatMPIAIJSetPreallocation(Mmat,
& PETSC_NULL_INTEGER(1),mr(np(246)),
& PETSC_NULL_INTEGER(1),mr(np(247)),
& ierr)
call MatSeqAIJSetPreallocation(Mmat,
& PETSC_NULL_INTEGER(1),mr(np(246)),
& ierr)
N.B. I wrote this decades ago...
-------------------------------------------------------------------
Sanjay Govindjee, PhD, PE
Horace, Dorothy, and Katherine Johnson Professor in Engineering
Distinguished Professor of Civil and Environmental Engineering
779 Davis Hall
University of California
Berkeley, CA 94720-1710
Voice: +1 510 642 6060
FAX: +1 510 643 5264
s_g at berkeley.edu
https://urldefense.us/v3/__http://faculty.ce.berkeley.edu/sanjay__;!!G_uCfscf7eWS!bt6E7YD1LcI-TwFlsTEukfgnddGYNt7h4xMMAJWHrDwwawBGGixIG0Y3GlzVgrc5tbcz99GRwLp7rNWRMRlaRQ$
-------------------------------------------------------------------
Books:
Introduction to Mechanics of Solid Materials
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Continuum Mechanics of Solids
https://urldefense.us/v3/__https://global.oup.com/academic/product/continuum-mechanics-of-solids-9780198864721__;!!G_uCfscf7eWS!bt6E7YD1LcI-TwFlsTEukfgnddGYNt7h4xMMAJWHrDwwawBGGixIG0Y3GlzVgrc5tbcz99GRwLp7rNUAfx_NXw$
Example Problems for Continuum Mechanics of Solids
https://urldefense.us/v3/__https://www.amazon.com/dp/1083047361/__;!!G_uCfscf7eWS!bt6E7YD1LcI-TwFlsTEukfgnddGYNt7h4xMMAJWHrDwwawBGGixIG0Y3GlzVgrc5tbcz99GRwLp7rNXmFjJvVw$
Engineering Mechanics of Deformable Solids
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Engineering Mechanics 3 (Dynamics) 2nd Edition
https://urldefense.us/v3/__http://www.amazon.com/dp/3642537111__;!!G_uCfscf7eWS!bt6E7YD1LcI-TwFlsTEukfgnddGYNt7h4xMMAJWHrDwwawBGGixIG0Y3GlzVgrc5tbcz99GRwLp7rNVKDd03jQ$
Engineering Mechanics 3, Supplementary Problems: Dynamics
https://urldefense.us/v3/__http://www.amzn.com/B00SOXN8JU__;!!G_uCfscf7eWS!bt6E7YD1LcI-TwFlsTEukfgnddGYNt7h4xMMAJWHrDwwawBGGixIG0Y3GlzVgrc5tbcz99GRwLp7rNXURaBrxQ$
-------------------------------------------------------------------
NSF NHERI SimCenter
https://urldefense.us/v3/__https://simcenter.designsafe-ci.org/__;!!G_uCfscf7eWS!bt6E7YD1LcI-TwFlsTEukfgnddGYNt7h4xMMAJWHrDwwawBGGixIG0Y3GlzVgrc5tbcz99GRwLp7rNU3AIDj7w$
-------------------------------------------------------------------
On 3/23/25 12:42 AM, Jose E. Roman wrote:
> The Fortran interfaces for those functions are generated correctly, see $PETSC_ARCH/ftn/mat/petscmat.h90
>
> For instance:
>
> interface MatMPIBAIJSetPreallocation
> subroutine MatMPIBAIJSetPreallocation(a,b,c,d,e,f, z)
> import tMat
> Mat :: a
> PetscInt :: b
> PetscInt :: c
> PetscInt :: d(*)
> PetscInt :: e
> PetscInt :: f(*)
> PetscErrorCode z
> end subroutine
> end interface
>
> The compiler message is probably due to the type of an argument not matching the expected one. In particular, if you are passing NULL in one of the array arguments, you should use PETSC_NULL_INTEGER_ARRAY and not PETSC_NULL_INTEGER.
>
> Jose
>
>
>> El 23 mar 2025, a las 8:25, Sanjay Govindjee via petsc-users<petsc-users at mcs.anl.gov> escribió:
>>
>> Small update. I managed to eliminate all the errors associated with PetscViewer and below (it had to do with the fact that I had not yet built a module that was needed). The errors related to the preallocation routines still persists.
>> -sanjay
>>
>> On 3/23/25 12:19 AM, Sanjay Govindjee wrote:
>>> Hi Barry,
>>> I have moved to main and rebuilt the PETSc libraries etc. Right now I am having trouble just getting my source code to compile. Plenty of subroutines with PETSc calls compile but a few are throwing errors and killing my compile. I suspect there will be more but if I can figure these hopefully I can debug the ones that will follow.
>>> -sanjay
>>> Error: There is no specific subroutine for the generic 'matmpibaijsetpreallocation' at (1)
>>> upremas.F:68:72:
>>>
>>> 68 | & ierr)
>>> | 1
>>> Error: There is no specific subroutine for the generic 'matseqbaijsetpreallocation' at (1)
>>> upremas.F:74:72:
>>>
>>> 74 | & ierr)
>>> | 1
>>> Error: There is no specific subroutine for the generic 'matmpiaijsetpreallocation' at (1)
>>> upremas.F:77:72:
>>>
>>> 77 | & ierr)
>>> | 1
>>> Error: There is no specific subroutine for the generic 'matseqaijsetpreallocation' at (1)
>>>
>>> parkv.F:58:25:
>>>
>>> 58 | PetscViewer Y_view
>>> | 1
>>> Error: Type name 'tpetscviewer' at (1) is ambiguous
>>> parkv.F:69:9:
>>>
>>> 69 | endif
>>> | 1
>>> Error: Expecting END SUBROUTINE statement at (1)
>>> parkv.F:72:9:
>>>
>>> 72 | endif
>>> | 1
>>> Error: Expecting END SUBROUTINE statement at (1)
>>> parkv.F:91:66:
>>>
>>> 91 | call PetscViewerASCIIOpen(PETSC_COMM_WORLD,"yvec.m",Y_view,
>>> | 1
>>> Error: Symbol 'y_view' at (1) has no IMPLICIT type; did you mean 'yvec'?
>>> parkv.F:65:72:
>>>
>>> 65 | call VecCreate (PETSC_COMM_WORLD, xvec, ierr)
>>> | 1
>>> Error: There is no specific subroutine for the generic 'veccreate' at (1)
>>> parkv.F:67:72:
>>>
>>> 67 | call VecSetFromOptions(xvec, ierr)
>>> | 1
>>> Error: There is no specific subroutine for the generic 'vecsetfromoptions' at (1)
>>> parkv.F:68:72:
>>>
>>> 68 | call VecDuplicate (xvec, yvec, ierr)
>>> | 1
>>> Error: There is no specific subroutine for the generic 'vecduplicate' at (1)
>>> parkv.F:71:72:
>>>
>>> 71 | call VecDuplicate (xvec, yvec, ierr)
>>> | 1
>>> Error: There is no specific subroutine for the generic 'vecduplicate' at (1)
>>> parkv.F:85:72:
>>>
>>> 85 | call VecAssemblyBegin(xvec, ierr)
>>> | 1
>>> Error: There is no specific subroutine for the generic 'vecassemblybegin' at (1)
>>> parkv.F:86:72:
>>>
>>> 86 | call VecAssemblyEnd (xvec, ierr)
>>> | 1
>>> Error: There is no specific subroutine for the generic 'vecassemblyend' at (1)
>>> parkv.F:88:72:
>>>
>>> 88 | call MatMult (Kmat, xvec, yvec, ierr)
>>> | 1
>>> Error: There is no specific subroutine for the generic 'matmult' at (1)
>>> parkv.F:101:72:
>>>
>>> 101 | call VecGetOwnershipRange(yvec, starti, endi, ierr)
>>> | 1
>>> Error: There is no specific subroutine for the generic 'vecgetownershiprange' at (1)
>>>
>>>
>>> -
>>>
>>>
>>> On 3/21/25 7:17 AM, Barry Smith wrote:
>>>> I have just pushed a major update to the Fortran interface to the main PETSc git branch. Could you please try to work with main (to become release in a couple of weeks) with your Fortran code as we debug the problem? This will save you a lot of work and hopefully make the debugging more straightforward.
>>>>
>>>> You can send the same output with the debugger if it crashes in the main branch and I can try to track down what is going wrong.
>>>>
>>>> Barry
>>>>
>>>>
>>>>
>>>>
>>>>> On Mar 21, 2025, at 12:37 AM, Sanjay Govindjee via petsc-users<petsc-users at mcs.anl.gov> wrote:
>>>>>
>>>>> I am trying to upgrade my code to PETSc 3.22.4 (the code was last updated to 3.19.4 or perhaps 3.18.1, I've lost track). I've been using this code with PETSc for over 20 years.
>>>>>
>>>>> To get my code to compile and link during this update, I only need to make two changes; one was to use PetscViewerPushFormat instead of PetscViewerSetFormat and the other was to use PETSC_NULL_INTEGER_ARRAY in a spot or two.
>>>>>
>>>>> When I run the code however, I am getting an error very early on during a call to MatCreate near the beginning of the code. The screen output says:
>>>>> [3]PETSC ERROR: matcreate_() at /Users/sg/petsc-3.22.4/gnug/src/mat/utils/ftn-auto/gcreatef.c:101 Cannot create PETSC_NULL_XXX object
>>>>> [0]PETSC ERROR: matcreate_() at /Users/sg/petsc-3.22.4/gnug/src/mat/utils/ftn-auto/gcreatef.c:101 Cannot create PETSC_NULL_XXX object
>>>>> [1]PETSC ERROR: matcreate_() at /Users/sg/petsc-3.22.4/gnug/src/mat/utils/ftn-auto/gcreatef.c:101 Cannot create PETSC_NULL_XXX object
>>>>> [2]PETSC ERROR: matcreate_() at /Users/sg/petsc-3.22.4/gnug/src/mat/utils/ftn-auto/gcreatef.c:101 Cannot create PETSC_NULL_XXX object
>>>>> I have a 4 processor run going. I am running with -on_error_attach_debugger but the debugger is giving me cryptic (at least to me) output (the same for all 4 processes modulo the PID). Stack traces seem to be unavailable :(
>>>>> lldb -p 71963
>>>>> (lldb) process attach --pid 71963
>>>>> Process 71963 stopped
>>>>> * thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGSTOP
>>>>> frame #0: 0x00007fff69d92746 libsystem_kernel.dylib`__semwait_signal + 10
>>>>> libsystem_kernel.dylib`__semwait_signal:
>>>>> -> 0x7fff69d92746 <+10>: jae 0x7fff69d92750 ; <+20>
>>>>> 0x7fff69d92748 <+12>: movq %rax, %rdi
>>>>> 0x7fff69d9274b <+15>: jmp 0x7fff69d9121d ; cerror
>>>>> 0x7fff69d92750 <+20>: retq
>>>>> Target 0: (feap) stopped.
>>>>>
>>>>> Executable module set to "/Users/sg/Feap/ver87/parfeap/feap".
>>>>> Architecture set to: x86_64h-apple-macosx-.
>>>>> Does anyone have any hints as to what may be going on? Note the program starts normally and i can do stuff with the interactive interface for the code -- even plotting the mesh etc. so I believe the input data has been read in correctly. The crash only occurs when I initiate the formation of the matrix.
>>>>>
>>>>> I am attaching the /Users/sg/petsc-3.22.4/gnug/src/mat/utils/ftn-auto/gcreatef.c file in case that offers some insight.
>>>>>
>>>>> Note, I have been
>>>>> -sanjay
>>>>> --
>>>>>
>>>>> <gcreatef.c>
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