Re: [petsc-users] teething troubles / MatView() fails silently for transposed seqaij matrix

[Bryan Jurish]

hi Junchao,

thanks for the hint... I'll give it try when I'm back on my work machine on
Monday.

marmosets,
 Bryan

--
typed with my opposable thumbs!

On Fri, Apr 13, 2018, 15:46 Junchao Zhang  wrote:

> Looks like MatCreateTranspose does not form the transpose, See the notes
> here
> .
>  You
> may want to use MatTranspose
> 
> .
>
> --Junchao Zhang
>
> On Fri, Apr 13, 2018 at 7:25 AM, Bryan Jurish 
> wrote:
>
>> morning all,
>>
>> Apologies for what is very probably a boundlessly stupid question.  I've
>> just begun exploring PETSc, but find myself stumped by a pretty trivial
>> task.  I would like to load a real binary seqaij matrix and save its
>> transposition (also as a binary  seqaij matrix) to a different file.
>> I've tried PETSc v3.7.5 on debian stretch and v3.6.2 on ubuntu 16.04, both
>> with no joy.  In both cases the program runs to completion and exits
>> normally, but no output file ("INFILE.T") is written.  Stepping through
>> MatView() with the debugger, it seems that (mat->ops->view) is not set for
>> the transposition I created with MatCreateTranspose(). I suppose I could
>> always loop over the input indices and assemble a physical transposition
>> manually, but that rather defeats the purpose of the exercise... can anyone
>> here tell me what I'm doing wrong (almost certainly something fundamental
>> and obvious)?  Thanks in advance for any help you can provide.
>>
>> marmosets,
>>   Bryan
>>
>> ::: BEGIN MINIMUM BROKEN EXAMPLE :::
>> /*-*- Mode: C -*-*/
>>
>> static char help[] = "Transposes a matrix in BINARY format\n\
>> Input parameters are:\n\
>>   -file INFILE : input matrix in binary format\n\
>>   -out OUTFILE : write output to OUTFILE (default=INFILE.T)\n\
>> ";
>>
>>
>> #include 
>>
>> //-- handle v3.7 API change
>> #if PETSC_VERSION_MAJOR>3 || (PETSC_VERSION_MAJOR==3 &&
>> PETSC_VERSION_MINOR>=7)
>>   #define OPTIONS_NULL NULL,NULL
>> #else
>>   #define OPTIONS_NULL NULL
>> #endif
>>
>>
>> #undef __FUNCT__
>> #define __FUNCT__ "main"
>> int main(int argc,char **args)
>> {
>>   MatA,B;
>>   char   infile[PETSC_MAX_PATH_LEN], outfile[PETSC_MAX_PATH_LEN];
>>   PetscErrorCode ierr;
>>   PetscInt   m,n;
>>   PetscViewerview;
>>   PetscBool  flg_file,flg_out;
>>   PetscMPIIntsize;
>>
>>   PetscInitialize(,,(char*)0,help);
>>   ierr = MPI_Comm_size(PETSC_COMM_WORLD,);CHKERRQ(ierr);
>>   ierr = PetscPrintf(PETSC_COMM_WORLD," MPI_Comm_size reports %d
>> process(es) available.\n", size);CHKERRQ(ierr);
>>   if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This is a
>> uniprocessor operation only!");
>>
>>   /*-- Read in source matrix, binary --*/
>>   ierr =
>> PetscOptionsGetString(OPTIONS_NULL,"-file",infile,PETSC_MAX_PATH_LEN,_file);CHKERRQ(ierr);
>>   if (!flg_file) SETERRQ(PETSC_COMM_WORLD,1,"Must specify a file name
>> with the -file option");
>>
>> #if defined(PETSC_USE_COMPLEX)
>>   ierr = PetscPrintf(PETSC_COMM_WORLD," Reading COMPLEX matrix from
>> binary file `%s'...\n", infile);CHKERRQ(ierr);
>> #else
>>   ierr = PetscPrintf(PETSC_COMM_WORLD," Reading REAL matrix from binary
>> file `%s'...\n", infile);CHKERRQ(ierr);
>> #endif
>>   ierr =
>> PetscViewerBinaryOpen(PETSC_COMM_WORLD,infile,FILE_MODE_READ,);CHKERRQ(ierr);
>>   ierr = MatCreate(PETSC_COMM_WORLD,);CHKERRQ(ierr);
>>   ierr = MatSetFromOptions(A);CHKERRQ(ierr);
>>   ierr = MatLoad(A,view);CHKERRQ(ierr);
>>   ierr = PetscViewerDestroy();CHKERRQ(ierr);
>>   //
>>   ierr = MatGetSize(A,,);
>>   ierr = PetscPrintf(PETSC_COMM_WORLD," Read input matrix of size
>> (m=%D,n=%D)\n", m,n);CHKERRQ(ierr);
>>
>>   /*-- guts: transpose --*/
>>   ierr = PetscPrintf(PETSC_COMM_WORLD," Performing transposition
>> (constructive)\n");CHKERRQ(ierr);
>>   ierr = MatCreateTranspose(A,);CHKERRQ(ierr);
>>
>>   /*-- dump transposed matrix --*/
>>   ierr =
>> PetscOptionsGetString(OPTIONS_NULL,"-out",outfile,PETSC_MAX_PATH_LEN,_out);CHKERRQ(ierr);
>>   if (!flg_out) {
>> strcpy(outfile,infile);
>> strcat(outfile,".T");
>>   }
>>   ierr = PetscPrintf(PETSC_COMM_SELF," Writing transposed matrix in
>> binary format to '%s' ...\n", outfile);CHKERRQ(ierr);
>>   ierr =
>> PetscViewerBinaryOpen(PETSC_COMM_SELF,outfile,FILE_MODE_WRITE,);CHKERRQ(ierr);
>>   ierr = MatView(B,view);CHKERRQ(ierr);
>>
>>   /* !!!
>>* output file is not written: much wailing and gnashing of teeth
>>* !!!
>>*/
>>
>>   /*-- cleanup --*/
>>   ierr = MatDestroy();CHKERRQ(ierr);
>>   ierr = MatDestroy();CHKERRQ(ierr);
>>   ierr = PetscViewerDestroy();CHKERRQ(ierr);
>>   ierr = PetscFinalize();
>>   return 0;
>> }
>> ::: END MINIMUM BROKEN EXAMPLE :::
>>
>> --
>> 

Re: [petsc-users] teething troubles / MatView() fails silently for transposed seqaij matrix

[Junchao Zhang]

Looks like MatCreateTranspose does not form the transpose, See the notes
here
.
You
may want to use MatTranspose

.

--Junchao Zhang

On Fri, Apr 13, 2018 at 7:25 AM, Bryan Jurish 
wrote:

> morning all,
>
> Apologies for what is very probably a boundlessly stupid question.  I've
> just begun exploring PETSc, but find myself stumped by a pretty trivial
> task.  I would like to load a real binary seqaij matrix and save its
> transposition (also as a binary  seqaij matrix) to a different file.
> I've tried PETSc v3.7.5 on debian stretch and v3.6.2 on ubuntu 16.04, both
> with no joy.  In both cases the program runs to completion and exits
> normally, but no output file ("INFILE.T") is written.  Stepping through
> MatView() with the debugger, it seems that (mat->ops->view) is not set for
> the transposition I created with MatCreateTranspose(). I suppose I could
> always loop over the input indices and assemble a physical transposition
> manually, but that rather defeats the purpose of the exercise... can anyone
> here tell me what I'm doing wrong (almost certainly something fundamental
> and obvious)?  Thanks in advance for any help you can provide.
>
> marmosets,
>   Bryan
>
> ::: BEGIN MINIMUM BROKEN EXAMPLE :::
> /*-*- Mode: C -*-*/
>
> static char help[] = "Transposes a matrix in BINARY format\n\
> Input parameters are:\n\
>   -file INFILE : input matrix in binary format\n\
>   -out OUTFILE : write output to OUTFILE (default=INFILE.T)\n\
> ";
>
>
> #include 
>
> //-- handle v3.7 API change
> #if PETSC_VERSION_MAJOR>3 || (PETSC_VERSION_MAJOR==3 &&
> PETSC_VERSION_MINOR>=7)
>   #define OPTIONS_NULL NULL,NULL
> #else
>   #define OPTIONS_NULL NULL
> #endif
>
>
> #undef __FUNCT__
> #define __FUNCT__ "main"
> int main(int argc,char **args)
> {
>   MatA,B;
>   char   infile[PETSC_MAX_PATH_LEN], outfile[PETSC_MAX_PATH_LEN];
>   PetscErrorCode ierr;
>   PetscInt   m,n;
>   PetscViewerview;
>   PetscBool  flg_file,flg_out;
>   PetscMPIIntsize;
>
>   PetscInitialize(,,(char*)0,help);
>   ierr = MPI_Comm_size(PETSC_COMM_WORLD,);CHKERRQ(ierr);
>   ierr = PetscPrintf(PETSC_COMM_WORLD," MPI_Comm_size reports %d
> process(es) available.\n", size);CHKERRQ(ierr);
>   if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This is a
> uniprocessor operation only!");
>
>   /*-- Read in source matrix, binary --*/
>   ierr = PetscOptionsGetString(OPTIONS_NULL,"-file",infile,PETSC_MAX_
> PATH_LEN,_file);CHKERRQ(ierr);
>   if (!flg_file) SETERRQ(PETSC_COMM_WORLD,1,"Must specify a file name
> with the -file option");
>
> #if defined(PETSC_USE_COMPLEX)
>   ierr = PetscPrintf(PETSC_COMM_WORLD," Reading COMPLEX matrix from binary
> file `%s'...\n", infile);CHKERRQ(ierr);
> #else
>   ierr = PetscPrintf(PETSC_COMM_WORLD," Reading REAL matrix from binary
> file `%s'...\n", infile);CHKERRQ(ierr);
> #endif
>   ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,infile,FILE_MODE_
> READ,);CHKERRQ(ierr);
>   ierr = MatCreate(PETSC_COMM_WORLD,);CHKERRQ(ierr);
>   ierr = MatSetFromOptions(A);CHKERRQ(ierr);
>   ierr = MatLoad(A,view);CHKERRQ(ierr);
>   ierr = PetscViewerDestroy();CHKERRQ(ierr);
>   //
>   ierr = MatGetSize(A,,);
>   ierr = PetscPrintf(PETSC_COMM_WORLD," Read input matrix of size
> (m=%D,n=%D)\n", m,n);CHKERRQ(ierr);
>
>   /*-- guts: transpose --*/
>   ierr = PetscPrintf(PETSC_COMM_WORLD," Performing transposition
> (constructive)\n");CHKERRQ(ierr);
>   ierr = MatCreateTranspose(A,);CHKERRQ(ierr);
>
>   /*-- dump transposed matrix --*/
>   ierr = PetscOptionsGetString(OPTIONS_NULL,"-out",outfile,PETSC_MAX_
> PATH_LEN,_out);CHKERRQ(ierr);
>   if (!flg_out) {
> strcpy(outfile,infile);
> strcat(outfile,".T");
>   }
>   ierr = PetscPrintf(PETSC_COMM_SELF," Writing transposed matrix in binary
> format to '%s' ...\n", outfile);CHKERRQ(ierr);
>   ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,outfile,FILE_MODE_
> WRITE,);CHKERRQ(ierr);
>   ierr = MatView(B,view);CHKERRQ(ierr);
>
>   /* !!!
>* output file is not written: much wailing and gnashing of teeth
>* !!!
>*/
>
>   /*-- cleanup --*/
>   ierr = MatDestroy();CHKERRQ(ierr);
>   ierr = MatDestroy();CHKERRQ(ierr);
>   ierr = PetscViewerDestroy();CHKERRQ(ierr);
>   ierr = PetscFinalize();
>   return 0;
> }
> ::: END MINIMUM BROKEN EXAMPLE :::
>
> --
> Bryan Jurish   "There is *always* one more bug."
> moocow.bov...@gmail.com -Lubarsky's Law of Cybernetic Entomology
>

[petsc-users] teething troubles / MatView() fails silently for transposed seqaij matrix

[Bryan Jurish]

morning all,

Apologies for what is very probably a boundlessly stupid question.  I've
just begun exploring PETSc, but find myself stumped by a pretty trivial
task.  I would like to load a real binary seqaij matrix and save its
transposition (also as a binary  seqaij matrix) to a different file.  I've
tried PETSc v3.7.5 on debian stretch and v3.6.2 on ubuntu 16.04, both with
no joy.  In both cases the program runs to completion and exits normally,
but no output file ("INFILE.T") is written.  Stepping through MatView()
with the debugger, it seems that (mat->ops->view) is not set for the
transposition I created with MatCreateTranspose(). I suppose I could always
loop over the input indices and assemble a physical transposition manually,
but that rather defeats the purpose of the exercise... can anyone here tell
me what I'm doing wrong (almost certainly something fundamental and
obvious)?  Thanks in advance for any help you can provide.

marmosets,
  Bryan

::: BEGIN MINIMUM BROKEN EXAMPLE :::
/*-*- Mode: C -*-*/

static char help[] = "Transposes a matrix in BINARY format\n\
Input parameters are:\n\
  -file INFILE : input matrix in binary format\n\
  -out OUTFILE : write output to OUTFILE (default=INFILE.T)\n\
";


#include 

//-- handle v3.7 API change
#if PETSC_VERSION_MAJOR>3 || (PETSC_VERSION_MAJOR==3 &&
PETSC_VERSION_MINOR>=7)
  #define OPTIONS_NULL NULL,NULL
#else
  #define OPTIONS_NULL NULL
#endif


#undef __FUNCT__
#define __FUNCT__ "main"
int main(int argc,char **args)
{
  MatA,B;
  char   infile[PETSC_MAX_PATH_LEN], outfile[PETSC_MAX_PATH_LEN];
  PetscErrorCode ierr;
  PetscInt   m,n;
  PetscViewerview;
  PetscBool  flg_file,flg_out;
  PetscMPIIntsize;

  PetscInitialize(,,(char*)0,help);
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD," MPI_Comm_size reports %d
process(es) available.\n", size);CHKERRQ(ierr);
  if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This is a
uniprocessor operation only!");

  /*-- Read in source matrix, binary --*/
  ierr =
PetscOptionsGetString(OPTIONS_NULL,"-file",infile,PETSC_MAX_PATH_LEN,_file);CHKERRQ(ierr);
  if (!flg_file) SETERRQ(PETSC_COMM_WORLD,1,"Must specify a file name with
the -file option");

#if defined(PETSC_USE_COMPLEX)
  ierr = PetscPrintf(PETSC_COMM_WORLD," Reading COMPLEX matrix from binary
file `%s'...\n", infile);CHKERRQ(ierr);
#else
  ierr = PetscPrintf(PETSC_COMM_WORLD," Reading REAL matrix from binary
file `%s'...\n", infile);CHKERRQ(ierr);
#endif
  ierr =
PetscViewerBinaryOpen(PETSC_COMM_WORLD,infile,FILE_MODE_READ,);CHKERRQ(ierr);
  ierr = MatCreate(PETSC_COMM_WORLD,);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatLoad(A,view);CHKERRQ(ierr);
  ierr = PetscViewerDestroy();CHKERRQ(ierr);
  //
  ierr = MatGetSize(A,,);
  ierr = PetscPrintf(PETSC_COMM_WORLD," Read input matrix of size
(m=%D,n=%D)\n", m,n);CHKERRQ(ierr);

  /*-- guts: transpose --*/
  ierr = PetscPrintf(PETSC_COMM_WORLD," Performing transposition
(constructive)\n");CHKERRQ(ierr);
  ierr = MatCreateTranspose(A,);CHKERRQ(ierr);

  /*-- dump transposed matrix --*/
  ierr =
PetscOptionsGetString(OPTIONS_NULL,"-out",outfile,PETSC_MAX_PATH_LEN,_out);CHKERRQ(ierr);
  if (!flg_out) {
strcpy(outfile,infile);
strcat(outfile,".T");
  }
  ierr = PetscPrintf(PETSC_COMM_SELF," Writing transposed matrix in binary
format to '%s' ...\n", outfile);CHKERRQ(ierr);
  ierr =
PetscViewerBinaryOpen(PETSC_COMM_SELF,outfile,FILE_MODE_WRITE,);CHKERRQ(ierr);
  ierr = MatView(B,view);CHKERRQ(ierr);

  /* !!!
   * output file is not written: much wailing and gnashing of teeth
   * !!!
   */

  /*-- cleanup --*/
  ierr = MatDestroy();CHKERRQ(ierr);
  ierr = MatDestroy();CHKERRQ(ierr);
  ierr = PetscViewerDestroy();CHKERRQ(ierr);
  ierr = PetscFinalize();
  return 0;
}
::: END MINIMUM BROKEN EXAMPLE :::

-- 
Bryan Jurish   "There is *always* one more bug."
moocow.bov...@gmail.com -Lubarsky's Law of Cybernetic Entomology