subject:"Re\: \[petsc\-users\] \[petsc\-maint\] how to check if cell is local owned in DMPlex"

Re: [petsc-users] [petsc-maint] how to check if cell is local owned in DMPlex

2018-03-08 Thread Danyang Su


On 18-03-07 03:54 PM, Jed Brown wrote:

Danyang Su  writes:


Based on my test, this function works fine using current PETSc-dev
version, but I cannot get it compiled correctly using other versions for
Fortran code, as mentioned in the previous emails. I asked this question
because some of the clusters we use do not have the PETSc-dev version
and it takes time get staff reinstall another version.

You can install PETSc yourself as a normal user.

Thanks, Jed. This is the way I will follow.

Danyang

Re: [petsc-users] [petsc-maint] how to check if cell is local owned in DMPlex

2018-03-07 Thread Danyang Su


Hi All,

Thanks again for all your help during my code development and it turns 
out the DMPlex for unstructured grid works pretty well. I have another 
question.


 Is there any alternative method to get number of leaves without using 
PetscSFGetGraph?


Based on my test, this function works fine using current PETSc-dev 
version, but I cannot get it compiled correctly using other versions for 
Fortran code, as mentioned in the previous emails. I asked this question 
because some of the clusters we use do not have the PETSc-dev version 
and it takes time get staff reinstall another version.


Thanks,

Danyang

On 18-03-05 11:50 AM, Smith, Barry F. wrote:

MatSolverPackage

became MatSolverType




On Mar 5, 2018, at 1:35 PM, Danyang Su  wrote:

Hi Barry and Matt,

The compiling problem should be caused by the PETSc version installed on my 
computer. When updated to PETSc-Dev version, the ex1f example works fine. 
However, I cannot compile this example under PETSc-3.8.3 version.

After updating to PETSc-Dev verison, I encounter another compiling problem in 
my code.

 MatSolverPackage :: solver_pkg_flow
 1
Error: Unclassifiable statement at (1)

Including petscmat.h or petscpc.h does not help to solve this problem. I can 
rewrite this part to get rid of this. But I would rather to keep this if there 
is alternative way to go. What is the head file should I include in order to 
use MatSolverPackage?

Thanks,

Danyang


On 18-03-04 11:15 AM, Smith, Barry F. wrote:

   See src/vec/is/sf/examples/tutorials/ex1f.F90 in the master branch of the 
PETSc git repository

   BTW:

git grep -i petscsfgetgraph

will show every use of the function in the source code. Very useful tool

Barry



On Mar 4, 2018, at 1:05 PM, Danyang Su  wrote:



On 18-03-04 08:08 AM, Matthew Knepley wrote:

On Fri, Mar 2, 2018 at 3:22 PM, Danyang Su  wrote:
Hi Matt,
I use the latest Fortran style in PETSc 3.8. Enclosed are the PETSc 
configuration, code compiling log and the function that causes compiling error. 
The compiling error happens after I include petscsf.h in the following section. 
I didn't find petscsf.h in petsc/finclude/ folder so I use the head file in the 
'include' folder and this seems not allowed.

I apologize for taking so long. The PetscSF definitions are in

#include 

Hi Matt,

After including
#include 
   use petscis

I still get error saying undefined reference to `petscsfgetgraph_'

Did I miss any other head file?

Thanks,

Danyang

You are correct that they should be moved out.

   Thanks,

  Matt

#ifdef PETSC_V3_8_X

#include 
#include 
#include 
#include 
   use petscsys
   use petscdmplex
   use petscsf

#endif

Thanks,

Danyang


On 18-03-02 12:08 PM, Matthew Knepley wrote:

On Fri, Mar 2, 2018 at 3:00 PM, Danyang Su  wrote:
On 18-03-02 10:58 AM, Matthew Knepley wrote:

On Fri, Mar 2, 2018 at 1:41 PM, Danyang Su  wrote:

On 18-02-19 03:30 PM, Matthew Knepley wrote:

On Mon, Feb 19, 2018 at 3:11 PM, Danyang Su  wrote:
Hi Matt,

Would you please let me know how to check if a cell is local owned? When overlap 
is 0 in DMPlexDistribute, all the cells are local owned. How about overlap > 0? 
It sounds like impossible to check by node because a cell can be local owned even 
if none of the nodes in this cell is local owned.

If a cell is in the PetscSF, then it is not locally owned. The local nodes in 
the SF are sorted, so I use
PetscFindInt 
(http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscFindInt.html).

Hi Matt,

Would you please give me a little more about how to mark the ghost cells when 
overlap > 0? What do you mean a cell is in the PetscSF? I use PetscSFView to 
export the graph (original mesh file pile.vtk) and it exports all the cells, 
including the ghost cells (PETScSFView.txt).

Yes, I will send you some sample code when I get time. The first problem is 
that you are looking at a different PetscSF. This looks like the
one returned by DMPlexDistribute(). This is mapping the serial mesh to the 
parallel mesh. You want

   
http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMGetPointSF.html

Then you can look at

   
https://bitbucket.org/petsc/petsc/src/1788fc36644e622df8cb1a0de85676ccc5af0239/src/dm/impls/plex/plexsubmesh.c?at=master=file-view-default#plexsubmesh.c-683

I get the pointSF, get out the list of leaves, and find points in it using 
PetscFindInt()

Hi Matt,
By using the local dm, I can get the PetscSF I want, as shown below. Now I need to get the number 
of ghost cells or local cells (here 4944) or number of leaves (here 825) for each processor. I try 
to use PetscSFGetGraph to get number of leaves in Fortran. After including "petscsf.h", I 
got compilation error saying "You need a ISO C conforming compiler to use the glibc 
headers". Is there any alternative way to do this? I do not

Re: [petsc-users] [petsc-maint] how to check if cell is local owned in DMPlex

2018-03-05 Thread Smith, Barry F.


> MatSolverPackage

became MatSolverType



> On Mar 5, 2018, at 1:35 PM, Danyang Su  wrote:
> 
> Hi Barry and Matt,
> 
> The compiling problem should be caused by the PETSc version installed on my 
> computer. When updated to PETSc-Dev version, the ex1f example works fine. 
> However, I cannot compile this example under PETSc-3.8.3 version.
> 
> After updating to PETSc-Dev verison, I encounter another compiling problem in 
> my code.
> 
> MatSolverPackage :: solver_pkg_flow
> 1
> Error: Unclassifiable statement at (1)
> 
> Including petscmat.h or petscpc.h does not help to solve this problem. I can 
> rewrite this part to get rid of this. But I would rather to keep this if 
> there is alternative way to go. What is the head file should I include in 
> order to use MatSolverPackage?
> 
> Thanks,
> 
> Danyang
> 
> 
> On 18-03-04 11:15 AM, Smith, Barry F. wrote:
>>   See src/vec/is/sf/examples/tutorials/ex1f.F90 in the master branch of the 
>> PETSc git repository
>> 
>>   BTW:
>> 
>>git grep -i petscsfgetgraph
>> 
>> will show every use of the function in the source code. Very useful tool
>> 
>>Barry
>> 
>> 
>>> On Mar 4, 2018, at 1:05 PM, Danyang Su  wrote:
>>> 
>>> 
>>> 
>>> On 18-03-04 08:08 AM, Matthew Knepley wrote:
 On Fri, Mar 2, 2018 at 3:22 PM, Danyang Su  wrote:
 Hi Matt,
 I use the latest Fortran style in PETSc 3.8. Enclosed are the PETSc 
 configuration, code compiling log and the function that causes compiling 
 error. The compiling error happens after I include petscsf.h in the 
 following section. I didn't find petscsf.h in petsc/finclude/ folder so I 
 use the head file in the 'include' folder and this seems not allowed.
 
 I apologize for taking so long. The PetscSF definitions are in
 
 #include 
>>> Hi Matt,
>>> 
>>> After including
>>> #include 
>>>   use petscis
>>> 
>>> I still get error saying undefined reference to `petscsfgetgraph_'
>>> 
>>> Did I miss any other head file?
>>> 
>>> Thanks,
>>> 
>>> Danyang
 You are correct that they should be moved out.
 
   Thanks,
 
  Matt
 
 #ifdef PETSC_V3_8_X
 
 #include 
 #include 
 #include 
 #include 
   use petscsys
   use petscdmplex
   use petscsf
 
 #endif
 
 Thanks,
 
 Danyang
 
 
 On 18-03-02 12:08 PM, Matthew Knepley wrote:
> On Fri, Mar 2, 2018 at 3:00 PM, Danyang Su  wrote:
> On 18-03-02 10:58 AM, Matthew Knepley wrote:
>> On Fri, Mar 2, 2018 at 1:41 PM, Danyang Su  wrote:
>> 
>> On 18-02-19 03:30 PM, Matthew Knepley wrote:
>>> On Mon, Feb 19, 2018 at 3:11 PM, Danyang Su  
>>> wrote:
>>> Hi Matt,
>>> 
>>> Would you please let me know how to check if a cell is local owned? 
>>> When overlap is 0 in DMPlexDistribute, all the cells are local owned. 
>>> How about overlap > 0? It sounds like impossible to check by node 
>>> because a cell can be local owned even if none of the nodes in this 
>>> cell is local owned.
>>> 
>>> If a cell is in the PetscSF, then it is not locally owned. The local 
>>> nodes in the SF are sorted, so I use
>>> PetscFindInt 
>>> (http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscFindInt.html).
>> Hi Matt,
>> 
>> Would you please give me a little more about how to mark the ghost cells 
>> when overlap > 0? What do you mean a cell is in the PetscSF? I use 
>> PetscSFView to export the graph (original mesh file pile.vtk) and it 
>> exports all the cells, including the ghost cells (PETScSFView.txt).
>> 
>> Yes, I will send you some sample code when I get time. The first problem 
>> is that you are looking at a different PetscSF. This looks like the
>> one returned by DMPlexDistribute(). This is mapping the serial mesh to 
>> the parallel mesh. You want
>> 
>>   
>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMGetPointSF.html
>> 
>> Then you can look at
>> 
>>   
>> https://bitbucket.org/petsc/petsc/src/1788fc36644e622df8cb1a0de85676ccc5af0239/src/dm/impls/plex/plexsubmesh.c?at=master=file-view-default#plexsubmesh.c-683
>> 
>> I get the pointSF, get out the list of leaves, and find points in it 
>> using PetscFindInt()
> Hi Matt,
> By using the local dm, I can get the PetscSF I want, as shown below. Now 
> I need to get the number of ghost cells or local cells (here 4944) or 
> number of leaves (here 825) for each processor. I try to use 
> PetscSFGetGraph to get number of leaves in Fortran. After including 
> "petscsf.h", I got compilation error saying "You need a ISO C conforming 
> compiler to use the glibc headers". Is there any alternative way to do 
> this? I do

Re: [petsc-users] [petsc-maint] how to check if cell is local owned in DMPlex

2018-03-05 Thread Danyang Su

Hi Barry and Matt,

The compiling problem should be caused by the PETSc version installed on
my computer. When updated to PETSc-Dev version, the ex1f example works
fine. However, I cannot compile this example under PETSc-3.8.3 version.

After updating to PETSc-Dev verison, I encounter another compiling
problem in my code.

MatSolverPackage :: solver_pkg_flow
1
Error: Unclassifiable statement at (1)

Including petscmat.h or petscpc.h does not help to solve this problem. I
can rewrite this part to get rid of this. But I would rather to keep
this if there is alternative way to go. What is the head file should I
include in order to use MatSolverPackage?

Thanks,

Danyang

On 18-03-04 11:15 AM, Smith, Barry F. wrote:

See src/vec/is/sf/examples/tutorials/ex1f.F90 in the master branch of the
PETSc git repository

BTW:

git grep -i petscsfgetgraph

will show every use of the function in the source code. Very useful tool

Barry

On Mar 4, 2018, at 1:05 PM, Danyang Su wrote:

On 18-03-04 08:08 AM, Matthew Knepley wrote:

On Fri, Mar 2, 2018 at 3:22 PM, Danyang Su wrote:
Hi Matt,
I use the latest Fortran style in PETSc 3.8. Enclosed are the PETSc
configuration, code compiling log and the function that causes compiling error.
The compiling error happens after I include petscsf.h in the following section.
I didn't find petscsf.h in petsc/finclude/ folder so I use the head file in the
'include' folder and this seems not allowed.

I apologize for taking so long. The PetscSF definitions are in

#include

Hi Matt,

After including
#include
use petscis

I still get error saying undefined reference to `petscsfgetgraph_'

Did I miss any other head file?

Thanks,

Danyang

You are correct that they should be moved out.

Thanks,

Matt

#ifdef PETSC_V3_8_X

#include
#include
#include
#include
use petscsys
use petscdmplex
use petscsf

#endif

Thanks,

Danyang

On 18-03-02 12:08 PM, Matthew Knepley wrote:

On Fri, Mar 2, 2018 at 3:00 PM, Danyang Su wrote:
On 18-03-02 10:58 AM, Matthew Knepley wrote:

On Fri, Mar 2, 2018 at 1:41 PM, Danyang Su wrote:

On 18-02-19 03:30 PM, Matthew Knepley wrote:

On Mon, Feb 19, 2018 at 3:11 PM, Danyang Su wrote:
Hi Matt,

Would you please let me know how to check if a cell is local owned? When overlap
is 0 in DMPlexDistribute, all the cells are local owned. How about overlap > 0?
It sounds like impossible to check by node because a cell can be local owned even
if none of the nodes in this cell is local owned.

If a cell is in the PetscSF, then it is not locally owned. The local nodes in
the SF are sorted, so I use
PetscFindInt
(http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscFindInt.html).

Hi Matt,

Would you please give me a little more about how to mark the ghost cells when
overlap > 0? What do you mean a cell is in the PetscSF? I use PetscSFView to
export the graph (original mesh file pile.vtk) and it exports all the cells,
including the ghost cells (PETScSFView.txt).

Yes, I will send you some sample code when I get time. The first problem is
that you are looking at a different PetscSF. This looks like the
one returned by DMPlexDistribute(). This is mapping the serial mesh to the
parallel mesh. You want

http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMGetPointSF.html

Then you can look at

https://bitbucket.org/petsc/petsc/src/1788fc36644e622df8cb1a0de85676ccc5af0239/src/dm/impls/plex/plexsubmesh.c?at=master=file-view-default#plexsubmesh.c-683

I get the pointSF, get out the list of leaves, and find points in it using
PetscFindInt()

Hi Matt,
By using the local dm, I can get the PetscSF I want, as shown below. Now I need to get the number
of ghost cells or local cells (here 4944) or number of leaves (here 825) for each processor. I try
to use PetscSFGetGraph to get number of leaves in Fortran. After including "petscsf.h", I
got compilation error saying "You need a ISO C conforming compiler to use the glibc
headers". Is there any alternative way to do this? I do not need the ghost-neighbor mapping,
but just the number of local owned cells.

Also, make sure you are using the latest Fortran style for PETSc:

http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/UsingFortran.html

[0] Number of roots=11449, leaves=825, remote ranks=1

[0] 4944 <- (1,0)
[0] 4945 <- (1,28)
[0] 4946 <- (1,56)
...
[1] Number of roots=11695, leaves=538, remote ranks=1
[1] 5056 <- (0,21)
[1] 5057 <- (0,43)
[1] 5058 <- (0,65)
[1] 5059 <- (0,87)

In file included from /usr/include/features.h:375:0,
from /usr/include/stdio.h:28,
from /home/dsu/Soft/PETSc/petsc-3.8.3/include/petscsys.h:175,
from /home/dsu/Soft/PETSc/petsc-3.8.3/include/petscsf.h:7,

Re: [petsc-users] [petsc-maint] how to check if cell is local owned in DMPlex

2018-03-04 Thread Smith, Barry F.


  See src/vec/is/sf/examples/tutorials/ex1f.F90 in the master branch of the 
PETSc git repository

  BTW: 

   git grep -i petscsfgetgraph 

will show every use of the function in the source code. Very useful tool

   Barry


> On Mar 4, 2018, at 1:05 PM, Danyang Su  wrote:
> 
> 
> 
> On 18-03-04 08:08 AM, Matthew Knepley wrote:
>> On Fri, Mar 2, 2018 at 3:22 PM, Danyang Su  wrote:
>> Hi Matt,
>> I use the latest Fortran style in PETSc 3.8. Enclosed are the PETSc 
>> configuration, code compiling log and the function that causes compiling 
>> error. The compiling error happens after I include petscsf.h in the 
>> following section. I didn't find petscsf.h in petsc/finclude/ folder so I 
>> use the head file in the 'include' folder and this seems not allowed.
>> 
>> I apologize for taking so long. The PetscSF definitions are in
>> 
>> #include 
> Hi Matt,
> 
> After including 
> #include 
>   use petscis
> 
> I still get error saying undefined reference to `petscsfgetgraph_'
> 
> Did I miss any other head file?
> 
> Thanks,
> 
> Danyang
>> 
>> You are correct that they should be moved out.
>> 
>>   Thanks,
>> 
>>  Matt
>> 
>> #ifdef PETSC_V3_8_X
>> 
>> #include 
>> #include 
>> #include 
>> #include 
>>   use petscsys
>>   use petscdmplex
>>   use petscsf
>> 
>> #endif
>> 
>> Thanks,
>> 
>> Danyang
>> 
>> 
>> On 18-03-02 12:08 PM, Matthew Knepley wrote:
>>> On Fri, Mar 2, 2018 at 3:00 PM, Danyang Su  wrote:
>>> On 18-03-02 10:58 AM, Matthew Knepley wrote:
 On Fri, Mar 2, 2018 at 1:41 PM, Danyang Su  wrote:
 
 On 18-02-19 03:30 PM, Matthew Knepley wrote:
> On Mon, Feb 19, 2018 at 3:11 PM, Danyang Su  wrote:
> Hi Matt,
> 
> Would you please let me know how to check if a cell is local owned? When 
> overlap is 0 in DMPlexDistribute, all the cells are local owned. How 
> about overlap > 0? It sounds like impossible to check by node because a 
> cell can be local owned even if none of the nodes in this cell is local 
> owned.
> 
> If a cell is in the PetscSF, then it is not locally owned. The local 
> nodes in the SF are sorted, so I use
> PetscFindInt 
> (http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscFindInt.html).
 Hi Matt,
 
 Would you please give me a little more about how to mark the ghost cells 
 when overlap > 0? What do you mean a cell is in the PetscSF? I use 
 PetscSFView to export the graph (original mesh file pile.vtk) and it 
 exports all the cells, including the ghost cells (PETScSFView.txt).
 
 Yes, I will send you some sample code when I get time. The first problem 
 is that you are looking at a different PetscSF. This looks like the
 one returned by DMPlexDistribute(). This is mapping the serial mesh to the 
 parallel mesh. You want
 
   
 http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/DM/DMGetPointSF.html
 
 Then you can look at
 
   
 https://bitbucket.org/petsc/petsc/src/1788fc36644e622df8cb1a0de85676ccc5af0239/src/dm/impls/plex/plexsubmesh.c?at=master=file-view-default#plexsubmesh.c-683
 
 I get the pointSF, get out the list of leaves, and find points in it using 
 PetscFindInt()
>>> Hi Matt,
>>> By using the local dm, I can get the PetscSF I want, as shown below. Now I 
>>> need to get the number of ghost cells or local cells (here 4944) or number 
>>> of leaves (here 825) for each processor. I try to use PetscSFGetGraph to 
>>> get number of leaves in Fortran. After including "petscsf.h", I got 
>>> compilation error saying "You need a ISO C conforming compiler to use the 
>>> glibc headers". Is there any alternative way to do this? I do not need the 
>>> ghost-neighbor mapping, but just the number of local owned cells.
>>> 
>>> Also, make sure you are using the latest Fortran style for PETSc:
>>> 
>>>   
>>> http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/UsingFortran.html
>>>  
>>>   [0] Number of roots=11449, leaves=825, remote ranks=1
>>>   [0] 4944 <- (1,0)
>>>   [0] 4945 <- (1,28)
>>>   [0] 4946 <- (1,56)
>>> ...
>>>   [1] Number of roots=11695, leaves=538, remote ranks=1
>>>   [1] 5056 <- (0,21)
>>>   [1] 5057 <- (0,43)
>>>   [1] 5058 <- (0,65)
>>>   [1] 5059 <- (0,87)
>>> 
>>> In file included from /usr/include/features.h:375:0,
>>>  from /usr/include/stdio.h:28,
>>>  from 
>>> /home/dsu/Soft/PETSc/petsc-3.8.3/include/petscsys.h:175,
>>>  from /home/dsu/Soft/PETSc/petsc-3.8.3/include/petscsf.h:7,
>>>  from ../../solver/solver_ddmethod.F90:4837:
>>> /usr/include/x86_64-linux-gnu/sys/cdefs.h:30:3: error: #error "You need a 
>>> ISO C conforming compile\
>>> r to use the glibc headers"
>>>  # error "You need a ISO C conforming compiler to use the glibc headers"
>>> 
>>> Can you send this to

Re: [petsc-users] [petsc-maint] how to check if cell is local owned in DMPlex

Re: [petsc-users] [petsc-maint] how to check if cell is local owned in DMPlex

Re: [petsc-users] [petsc-maint] how to check if cell is local owned in DMPlex

Re: [petsc-users] [petsc-maint] how to check if cell is local owned in DMPlex

Re: [petsc-users] [petsc-maint] how to check if cell is local owned in DMPlex

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