<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial, helvetica, sans-serif;font-size:12pt"><div>Thanks Jed and Barry. It works fine now.</div><div><br></div><div>Khalid</div><div style="font-family:arial, helvetica, sans-serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> "petsc-users-request@mcs.anl.gov" <petsc-users-request@mcs.anl.gov><br><b><span style="font-weight: bold;">To:</span></b> petsc-users@mcs.anl.gov<br><b><span style="font-weight: bold;">Sent:</span></b> Fri, November 26, 2010 10:00:19 AM<br><b><span style="font-weight: bold;">Subject:</span></b> petsc-users Digest, Vol 23, Issue 29<br></font><br>
Send petsc-users mailing list submissions to<br> <a ymailto="mailto:petsc-users@mcs.anl.gov" href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="https://lists.mcs.anl.gov/mailman/listinfo/petsc-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/petsc-users</a><br>or, via email, send a message with subject or body 'help' to<br> <a ymailto="mailto:petsc-users-request@mcs.anl.gov" href="mailto:petsc-users-request@mcs.anl.gov">petsc-users-request@mcs.anl.gov</a><br><br>You can reach the person managing the list at<br> <a ymailto="mailto:petsc-users-owner@mcs.anl.gov" href="mailto:petsc-users-owner@mcs.anl.gov">petsc-users-owner@mcs.anl.gov</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of petsc-users digest..."<br><br><br>Today's
Topics:<br><br> 1. Global DA index using DAGetCorners (khalid ashraf)<br> 2. Re: Global DA index using DAGetCorners (Barry Smith)<br> 3. Re: Printing parallel Vector in VTK format (khalid ashraf)<br> 4. Re: Printing parallel Vector in VTK format (Jed Brown)<br> 5. Re: Printing parallel Vector in VTK format (Barry Smith)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Thu, 25 Nov 2010 17:50:21 -0800 (PST)<br>From: khalid ashraf <<a ymailto="mailto:khalid_eee@yahoo.com" href="mailto:khalid_eee@yahoo.com">khalid_eee@yahoo.com</a>><br>Subject: [petsc-users] Global DA index using DAGetCorners<br>To: <a ymailto="mailto:petsc-users@mcs.anl.gov" href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a><br>Message-ID: <<a ymailto="mailto:113982.45603.qm@web112617.mail.gq1.yahoo.com"
href="mailto:113982.45603.qm@web112617.mail.gq1.yahoo.com">113982.45603.qm@web112617.mail.gq1.yahoo.com</a>><br>Content-Type: text/plain; charset="us-ascii"<br><br>It doesn't seem like the problem is with the natural ordering. Since in Fig.9 of <br>the manual,<br>the highest number of the grid should be the same(30 in fig. 9) for natural and <br>petsc ordering.<br>But I get a lower number when I print it. <br><br>I also tried the petsc to natural conversion using the following code, <br> {<br> ia[0]=(PetscInt)((k)*(my)*(mx)+(j)*(mx)+(i));<br> AOPetscToApplication(ao,1,ia);<br> w_localptr[k][j][i] = ia[0];<br>PetscPrintf(PETSC_COMM_WORLD,"%d\n",ia[0]);<br>}<br>But this gives even lower number for the highest index.<br><br>Anyway my goal is to be able to determine the global natural index of the <br>grid within the for loops in the following way:<br>for (k=zs; k<zs+zm; k++) {<br> for (j=ys;
j<ys+ym; j++) {<br> for (i=xs; i<xs+xm; i++) {<br>natural_global_coordinate(k',j',i')=f(k,j,i);<br>if natural_global_coord[k'][j'][i'] > half of the grid along x {Do something}<br>if natural_global_coord[k'][j'][i'] > half of the grid along y {Do something}<br>etc..<br>}}} <br>Could you please suggest what would be the simplest way to achieve this. <br>Thanks in advance.<br><br><br> <br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br><span>URL: <<a target="_blank" href="http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20101125/ff463aaa/attachment-0001.htm">http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20101125/ff463aaa/attachment-0001.htm</a>></span><br><br>------------------------------<br><br>Message: 2<br>Date: Thu, 25 Nov 2010 20:31:17 -0600<br>From: Barry Smith <<a ymailto="mailto:bsmith@mcs.anl.gov"
href="mailto:bsmith@mcs.anl.gov">bsmith@mcs.anl.gov</a>><br>Subject: Re: [petsc-users] Global DA index using DAGetCorners<br>To: PETSc users list <<a ymailto="mailto:petsc-users@mcs.anl.gov" href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>><br>Message-ID: <<a ymailto="mailto:B39F8696-63EC-4C5B-83D2-AA0ECAA6A073@mcs.anl.gov" href="mailto:B39F8696-63EC-4C5B-83D2-AA0ECAA6A073@mcs.anl.gov">B39F8696-63EC-4C5B-83D2-AA0ECAA6A073@mcs.anl.gov</a>><br>Content-Type: text/plain; charset=us-ascii<br><br><br>On Nov 25, 2010, at 7:50 PM, khalid ashraf wrote:<br><br>> It doesn't seem like the problem is with the natural ordering. Since in Fig.9 of the manual,<br>> the highest number of the grid should be the same(30 in fig. 9) for natural and petsc ordering.<br>> But I get a lower number when I print it. <br>> <br>> I also tried the petsc to natural conversion using the following code, <br>>
{<br>> ia[0]=(PetscInt)((k)*(my)*(mx)+(j)*(mx)+(i));<br> <br> This give the natural number of the location in ia[0]<br>> AOPetscToApplication(ao,1,ia);<br><br> So it makes no sense to call AOPetscToApplication() to map it to something else. It is already in the natural (i.e. application ordering)<br><br>> w_localptr[k][j][i] = ia[0];<br>> PetscPrintf(PETSC_COMM_WORLD,"%d\n",ia[0]);<br>> }<br>> But this gives even lower number for the highest index.<br>> <br>> Anyway my goal is to be able to determine the global natural index of the <br>> grid within the for loops in the following way:<br>> for (k=zs; k<zs+zm; k++) {<br>> for (j=ys; j<ys+ym; j++) {<br>> for (i=xs; i<xs+xm; i++) {<br>> natural_global_coordinate(k',j',i')=f(k,j,i);<br>> if natural_global_coord[k'][j'][i'] > half of the grid along x {Do
something}<br>> if natural_global_coord[k'][j'][i'] > half of the grid along y {Do something}<br><br> i > m/2 means means it is in the right half of the grid along x (where m is the number of grid points in the x direction).<br><br> To determine these things you don't need to do anything about mapping between orderings.<br><br> You are chasing yourself in circles to do something that is essentially trivial. With the loop structure you have above, the i,j,k ARE exactly the logical locations in the global X, Y, Z grid. It couldn't be simplier.<br> <br> Barry<br><br>> etc..<br>> }}} <br>> Could you please suggest what would be the simplest way to achieve this. <br>> Thanks in advance.<br>> <br>> <br>> <br>> <br>> <br><br><br><br>------------------------------<br><br>Message: 3<br>Date: Thu, 25 Nov 2010 21:36:08 -0800
(PST)<br>From: khalid ashraf <<a ymailto="mailto:khalid_eee@yahoo.com" href="mailto:khalid_eee@yahoo.com">khalid_eee@yahoo.com</a>><br>Subject: Re: [petsc-users] Printing parallel Vector in VTK format<br>To: <a ymailto="mailto:petsc-users@mcs.anl.gov" href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a><br>Message-ID: <<a ymailto="mailto:804366.55079.qm@web112616.mail.gq1.yahoo.com" href="mailto:804366.55079.qm@web112616.mail.gq1.yahoo.com">804366.55079.qm@web112616.mail.gq1.yahoo.com</a>><br>Content-Type: text/plain; charset="us-ascii"<br><br>Thanks Barry. I get the correct output when I use <br>VecView(w,PETSC_VIEWER_STDOUT_WORLD)<br><br>But if I use the VecView_VTK function from the file<br>ksp/ksp/examples/tutorials/ex29.c<br><br>then I get different results.<br><br>For the code:<br>if (i<m/2) vec=0.001 else vec=-0.001;<br><br>Output with VecView: 0.001 for half of the grid<br>
-0.001 for rest half of the grid<br>Output with VecView_VTK:<br> 0.001 for the full grid.<br><br><br>Date: Thu, 25 Nov 2010 02:24:52 -0800 (PST)<br>From: khalid ashraf <<a ymailto="mailto:khalid_eee@yahoo.com" href="mailto:khalid_eee@yahoo.com">khalid_eee@yahoo.com</a>><br>Subject: [petsc-users] DAGetCorners; xs,ys,zs return 0 for all the<br> processors<br>To: <a ymailto="mailto:petsc-users@mcs.anl.gov" href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a><br>Message-ID: <<a ymailto="mailto:588844.78157.qm@web112619.mail.gq1.yahoo.com" href="mailto:588844.78157.qm@web112619.mail.gq1.yahoo.com">588844.78157.qm@web112619.mail.gq1.yahoo.com</a>><br>Content-Type: text/plain; charset="us-ascii"<br><br>Here is the
call to DA creation:<br><br>ierr = <br>DACreate3d(PETSC_COMM_WORLD,DA_NONPERIODIC,DA_STENCIL_BOX,appctx.l,appctx.m,appctx.n,<br><br><br> <br>PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,PETSC_NULL,<br> &appctx.da);CHKERRQ(ierr);<br><br>Khalid<br><br><br> <br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <br><span><<a target="_blank" href="http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20101125/d0590ec8/attachment-0001.htm">http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20101125/d0590ec8/attachment-0001.htm</a>></span><br><br><br>------------------------------<br><br>Message: 2<br>Date: Thu, 25 Nov 2010 11:35:43 +0100<br>From: Jed Brown <<a ymailto="mailto:jed@59A2.org"
href="mailto:jed@59A2.org">jed@59A2.org</a>><br>Subject: Re: [petsc-users] DAGetCorners; xs,ys,zs return 0 for all the<br> processors<br>To: PETSc users list <<a ymailto="mailto:petsc-users@mcs.anl.gov" href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>><br>Message-ID:<br> <AANLkTineq3bTG=<a ymailto="mailto:iRsjkdoY2ZhZ9ac7r8vBmSUqEpOvu5@mail.gmail.com" href="mailto:iRsjkdoY2ZhZ9ac7r8vBmSUqEpOvu5@mail.gmail.com">iRsjkdoY2ZhZ9ac7r8vBmSUqEpOvu5@mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>On Thu, Nov 25, 2010 at 11:24, khalid ashraf <<a ymailto="mailto:khalid_eee@yahoo.com" href="mailto:khalid_eee@yahoo.com">khalid_eee@yahoo.com</a>> wrote:<br><br>> Here is the call to DA creation:<br>><br>> ierr =<br>>DACreate3d(PETSC_COMM_WORLD,DA_NONPERIODIC,DA_STENCIL_BOX,appctx.l,appctx.m,appctx.n,<br>>,<br>><br>>
PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,PETSC_NULL,<br>> &appctx.da);CHKERRQ(ierr);<br>><br><br>If you created the DA as above and then call<br><br> DAGetCorners(appctx.da,&xs,&ys,&zs,&xm,&ym,&zm);<br><br>then only on rank=0 will xs,ys,zs all be equal to zero. Your other message<br>about PETSc versus natural ordering indicates that this is working<br>correctly. Is it working now? If not, please send more context, including<br>whatever code you are using to print output.<br><br>Jed<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <br><span><<a target="_blank"
href="http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20101125/6da538a3/attachment-0001.htm">http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20101125/6da538a3/attachment-0001.htm</a>></span><br><br><br>------------------------------<br><br>_______________________________________________<br>petsc-users mailing list<br><a ymailto="mailto:petsc-users@mcs.anl.gov" href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a><br><a href="https://lists.mcs.anl.gov/mailman/listinfo/petsc-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/petsc-users</a><br><br><br>End of petsc-users Digest, Vol 23, Issue 28<br>*******************************************<br><br><br><br> <br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br><span>URL: <<a target="_blank"
href="http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20101125/d2817c38/attachment-0001.htm">http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20101125/d2817c38/attachment-0001.htm</a>></span><br><br>------------------------------<br><br>Message: 4<br>Date: Fri, 26 Nov 2010 10:13:31 +0100<br>From: Jed Brown <<a ymailto="mailto:jed@59A2.org" href="mailto:jed@59A2.org">jed@59A2.org</a>><br>Subject: Re: [petsc-users] Printing parallel Vector in VTK format<br>To: PETSc users list <<a ymailto="mailto:petsc-users@mcs.anl.gov" href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>><br>Message-ID:<br> <<a ymailto="mailto:AANLkTikLk3g3xgGnVbDTtB4Wcr7HcuJeLyn9ejWuMBEg@mail.gmail.com" href="mailto:AANLkTikLk3g3xgGnVbDTtB4Wcr7HcuJeLyn9ejWuMBEg@mail.gmail.com">AANLkTikLk3g3xgGnVbDTtB4Wcr7HcuJeLyn9ejWuMBEg@mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>On Fri, Nov 26, 2010
at 06:36, khalid ashraf <<a ymailto="mailto:khalid_eee@yahoo.com" href="mailto:khalid_eee@yahoo.com">khalid_eee@yahoo.com</a>> wrote:<br><br>> Thanks Barry. I get the correct output when I use<br>> VecView(w,PETSC_VIEWER_STDOUT_WORLD)<br>><br>> But if I use the VecView_VTK function from the file<br>> ksp/ksp/examples/tutorials/ex29.c<br>><br>> then I get different results.<br>><br><br>This is a crucial piece of information, if you stated this in the first<br>email, you would have gotten a good answer to your first email.<br><br>The problem is that this function and the copy in ex50.c, never worked in<br>parallel. Clearly the person who wrote it misunderstood the VTK legacy<br>format because nothing similar can work in parallel. See<br>src/snes/examples/tutorials/ex5.c for the correct way to do it:<br><br> PetscViewer viewer;<br> ierr = PetscViewerCreate(PETSC_COMM_WORLD,
&viewer);CHKERRQ(ierr);<br> ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr);<br> ierr = PetscViewerFileSetName(viewer, "ex5_sol.vtk");CHKERRQ(ierr);<br> ierr = PetscViewerSetFormat(viewer,<br>PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);<br> ierr = DAView(user.da, viewer);CHKERRQ(ierr);<br> ierr = VecView(x, viewer);CHKERRQ(ierr);<br> ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);<br><br>Jed<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br><span>URL: <<a target="_blank" href="http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20101126/31c1b6cf/attachment-0001.htm">http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20101126/31c1b6cf/attachment-0001.htm</a>></span><br><br>------------------------------<br><br>Message: 5<br>Date: Fri, 26 Nov 2010 10:42:04 -0600<br>From: Barry Smith <<a
ymailto="mailto:bsmith@mcs.anl.gov" href="mailto:bsmith@mcs.anl.gov">bsmith@mcs.anl.gov</a>><br>Subject: Re: [petsc-users] Printing parallel Vector in VTK format<br>To: PETSc users list <<a ymailto="mailto:petsc-users@mcs.anl.gov" href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a>><br>Message-ID: <<a ymailto="mailto:8A1D2053-2CC5-44E6-AC92-AAE60D7CF966@mcs.anl.gov" href="mailto:8A1D2053-2CC5-44E6-AC92-AAE60D7CF966@mcs.anl.gov">8A1D2053-2CC5-44E6-AC92-AAE60D7CF966@mcs.anl.gov</a>><br>Content-Type: text/plain; charset=us-ascii<br><br><br> Jed,<br><br> Can you please remove that bad code from those two examples if you haven't yet.<br><br> Thanks<br><br> Barry<br><br>On Nov 26, 2010, at 3:13 AM, Jed Brown wrote:<br><br>> On Fri, Nov 26, 2010 at 06:36, khalid ashraf <<a ymailto="mailto:khalid_eee@yahoo.com" href="mailto:khalid_eee@yahoo.com">khalid_eee@yahoo.com</a>> wrote:<br>>
Thanks Barry. I get the correct output when I use <br>> VecView(w,PETSC_VIEWER_STDOUT_WORLD)<br>> <br>> But if I use the VecView_VTK function from the file<br>> ksp/ksp/examples/tutorials/ex29.c<br>> <br>> then I get different results.<br>> <br>> This is a crucial piece of information, if you stated this in the first email, you would have gotten a good answer to your first email.<br>> <br>> The problem is that this function and the copy in ex50.c, never worked in parallel. Clearly the person who wrote it misunderstood the VTK legacy format because nothing similar can work in parallel. See src/snes/examples/tutorials/ex5.c for the correct way to do it:<br>> <br>> PetscViewer viewer;<br>> ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);<br>> ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr);<br>> ierr =
PetscViewerFileSetName(viewer, "ex5_sol.vtk");CHKERRQ(ierr);<br>> ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);<br>> ierr = DAView(user.da, viewer);CHKERRQ(ierr);<br>> ierr = VecView(x, viewer);CHKERRQ(ierr);<br>> ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);<br>> <br>> Jed<br><br><br><br>------------------------------<br><br>_______________________________________________<br>petsc-users mailing list<br><a ymailto="mailto:petsc-users@mcs.anl.gov" href="mailto:petsc-users@mcs.anl.gov">petsc-users@mcs.anl.gov</a><br><a href="https://lists.mcs.anl.gov/mailman/listinfo/petsc-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/petsc-users</a><br><br><br>End of petsc-users Digest, Vol 23, Issue 29<br>*******************************************<br></div></div><div style="position:fixed"></div>
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