<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>and the second application I have in mind is solving a system of the from AX=B where A and B are sparse and B is given by a block matrix of the form B=[B1 0, 0 0] where B1 is dense but the dimension is (much) smaller than that of the whole matrix B.
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<div class="gmail_quote">Marius:</div>
<div class="gmail_quote">Current PETSc interface supports sequential sparse <span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: small;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;">multiple right-hand side, but not distributed.</span></div>
<div class="gmail_quote">It turns out that mumps does not support <span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;">distributed sparse multiple right-hand sides at</span><br style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);"/>
<span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;">the moment (see attached email). </span></div>
<div class="gmail_quote"> </div>
<div class="gmail_quote"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;">Jean-Yves invites you to communicate with him directly. </span></span></div>
<div class="gmail_quote"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;">Let me know what we can help on this matter, </span></span></div>
<div class="gmail_quote"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;">e.g., add support for parallel implementation of <span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: small;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;">sparse </span><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: small;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;">multiple right-hand side with </span></span></span></div>
<div class="gmail_quote"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: small;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;">centralized rhs input?</span></span></span></div>
<div class="gmail_quote"> </div>
<div class="gmail_quote"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;">Hong</span></span></div>
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<h3 class="gmail-iw" style="overflow: hidden;white-space: nowrap;max-width: 92.0%;display: inline-block;font-size: inherit;font-weight: inherit;margin: inherit;"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;"><span class="gmail-gD" style="color: rgb(34,34,34);font-size: 12.8px;font-weight: bold;white-space: nowrap;display: inline;vertical-align: top;">Jean-Yves LExcellent</span><span> </span><span class="gmail-go" style="vertical-align: top;color: rgb(85,85,85);"><span><</span><a href="mailto:Jean-Yves.L.Excellent@ens-lyon.fr" onclick="parent.window.location.href='Jean-Yves.L.Excellent@ens-lyon.fr'; return false;" target="_blank">Jean-Yves.L.Excellent@ens-lyon.fr</a><span>></span></span></span></h3>
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<div class="gmail-iw gmail-ajw" style="overflow: hidden;white-space: nowrap;max-width: 92.0%;display: inline-block;"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;"><span class="gmail-hb" style="vertical-align: top;color: rgb(119,119,119);">to<span> </span><span class="gmail-g2">Hong</span>,<span> </span><span class="gmail-g2">mumps-dev</span></span></span></div>
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<div class="gmail-ii gmail-gt gmail-adP" id="gmail-:pk" style="font-size: 12.8px;direction: ltr;margin: 5.0px 15.0px 0.0px 0.0px;padding-bottom: 5.0px;">
<div class="gmail-a3s gmail-aXjCH gmail-m163bad8b399eea70" id="gmail-:pj" style="overflow: hidden;"><span style="color: rgb(34,34,34);font-family: arial , sans-serif;font-size: 12.8px;font-style: normal;font-weight: 400;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;background-color: rgb(255,255,255);float: none;display: inline;">Hello,<br/>
<br/>
We do not support distributed sparse multiple right-hand sides at<br/>
the moment. From the feedback we have from applications, the<br/>
right-hand sides are often very sparse, and having them distributed<br/>
did not seem critical.<br/>
<br/>
Since we are specifying a distributed right-hand sides feature at the<br/>
moment, could you let us know in more detail the need regarding<br/>
distributed sparse right-hand side (e.g., do all columns have the same<br/>
nonzero structure in that case) or put us in contact with the user who<br/>
needs this?<br/>
<br/>
Thanks,<br/>
Jean-Yves and Patrick</span></div>
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<blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex;border-left: 1.0px rgb(204,204,204) solid;padding-left: 1.0ex;">Thanks a lot guys, very helpful.<br/>
<span> <br/>
<br/>
<br/>
<br/>
I see MUMPS <a href="http://mumps.enseeiht.fr/" target="_blank">http://mumps.enseeiht.fr/</a></span><br/>
<br/>
Sparse multiple right-hand side, distributed solution; Exploitation of sparsity in the right-hand sidesPETSc interface computes mumps distributed solution as default (this is not new) (ICNTL(21) = 1)<br/>
<span> <br/>
I will add support for Sparse multiple right-hand side.<br/>
<br/>
Hong<br/>
</span><br/>
<span>On Thu, May 31, 2018 at 11:25 AM, Smith, Barry F. <<a href="mailto:bsmith@mcs.anl.gov" onclick="parent.window.location.href='bsmith@mcs.anl.gov'; return false;" target="_blank">bsmith@mcs.anl.gov</a>[mailto:<a href="mailto:bsmith@mcs.anl.gov" onclick="parent.window.location.href='bsmith@mcs.anl.gov'; return false;" target="_blank">bsmith@mcs.anl.gov</a>]> wrote:<br/>
Hong,<br/>
<br/>
Can you see about adding support for distributed right hand side?<br/>
<br/>
Thanks<br/>
<br/>
Barry</span><br/>
<br/>
<span>> On May 31, 2018, at 2:37 AM, Marius Buerkle <<a href="mailto:mbuerkle@web.de" onclick="parent.window.location.href='mbuerkle@web.de'; return false;" target="_blank">mbuerkle@web.de</a>[mailto:<a href="mailto:mbuerkle@web.de" onclick="parent.window.location.href='mbuerkle@web.de'; return false;" target="_blank">mbuerkle@web.de</a>]> wrote:<br/>
><br/>
> The fix for MAT_NEW_NONZERO_LOCATIONS, thanks again.<br/>
><br/>
> I have yet another question, sorry. The recent version of MUMPS supports distributed and sparse RHS is there any chance that this will be supported in PETSc in the near future?<br/>
><br/>
> <br/>
> <br/>
></span><br/>
<span>>> On May 30, 2018, at 6:55 PM, Marius Buerkle <<a href="mailto:mbuerkle@web.de" onclick="parent.window.location.href='mbuerkle@web.de'; return false;" target="_blank">mbuerkle@web.de</a>[mailto:<a href="mailto:mbuerkle@web.de" onclick="parent.window.location.href='mbuerkle@web.de'; return false;" target="_blank">mbuerkle@web.de</a>]> wrote:<br/>
>><br/>
>> Thanks for the quick fix, I will test it and report back.<br/>
>> I have another maybe related question, if MAT_NEW_NONZERO_LOCATIONS is true and let's say 1 new nonzero position is created it does not allocated 1 but several new nonzeros but only use 1.<br/>
><br/>
> Correct<br/>
><br/>
>> I think that is normal, right?<br/>
><br/>
> Yes<br/>
><br/>
>> But, at least as far as I understand the manual, a subsequent call of mat assemble with<br/>
>> MAT_FINAL_ASSEMBLY should compress out the unused allocations and release the memory, is this correct?<br/>
><br/>
> It "compresses it out" (by shifting all the nonzero entries to the beginning of the internal i, j, and a arrays), but does NOT release any memory. Since the values are stored in one big contiguous array (obtained with a single malloc) it cannot just free part of the array, so the extra locations just sit harmlessly at the end if the array unused.<br/>
><br/>
>> If so, this did not work for me, even after doing<br/>
>> MAT_FINAL_ASSEMBLY the unused nonzero allocations remain. Is this normal?<br/>
><br/>
> Yes,<br/>
><br/>
> Barry<br/>
><br/>
>><br/>
>>><br/>
>>> Fixed in the branch barry/fix-mat-new-nonzero-locations/maint<br/>
>>><br/>
>>> Once this passes testing it will go into the maint branch and then the next patch release but you can use it now in the branch barry/fix-mat-new-nonzero-locations/maint<br/>
>>><br/>
>>> Thanks for the report and reproducible example<br/>
>>><br/>
>>> Barry<br/>
>>><br/>
>>></span>
<div>
<div class="h5">>>>> On May 29, 2018, at 7:51 PM, Marius Buerkle <<a href="mailto:mbuerkle@web.de" onclick="parent.window.location.href='mbuerkle@web.de'; return false;" target="_blank">mbuerkle@web.de</a>[mailto:<a href="mailto:mbuerkle@web.de" onclick="parent.window.location.href='mbuerkle@web.de'; return false;" target="_blank">mbuerkle@web.de</a>]> wrote:<br/>
>>>><br/>
>>>> Sure, I made a small reproducer, it is Fortran though I hope that is ok. If MAT_NEW_NONZERO_LOCATIONS is set to false I get an error, if it is set to true the new nonzero element is inserted, if MAT_NEW_NONZERO_LOCATIONS is false and either MAT_NEW_NONZERO_LOCATION_ERR or MAT_NEW_NONZERO_ALLOCATION_ERR is set to false afterwards then the new nonzero is also created without an error, but if MAT_NEW_NONZERO_LOCATIONS is set to false after MAT_NEW_NONZERO_LOCATION_ERR/MAT_NEW_NONZERO_ALLOCATION_ERR have been set to false I get an error again.<br/>
>>>><br/>
>>>><br/>
>>>> program newnonzero<br/>
>>>> #include <petsc/finclude/petscmat.h><br/>
>>>> use petscmat<br/>
>>>> implicit none<br/>
>>>><br/>
>>>> Mat :: A<br/>
>>>> PetscInt :: dnnz,onnz,n,m,idxm(1),idxn(1),nl1,nl2<br/>
>>>> PetscScalar :: v(1)<br/>
>>>> PetscReal :: info(MAT_INFO_SIZE)<br/>
>>>> PetscErrorCode :: ierr<br/>
>>>><br/>
>>>> integer :: nproc,iproc,i<br/>
>>>><br/>
>>>> call PetscInitialize(PETSC_NULL_CHARACTER,ierr)<br/>
>>>><br/>
>>>> call MPI_COMM_SIZE(PETSC_COMM_WORLD, nproc,ierr)<br/>
>>>><br/>
>>>> call MPI_Comm_rank( PETSC_COMM_WORLD, iproc, ierr )<br/>
>>>><br/>
>>>> n=3<br/>
>>>> m=n<br/>
>>>> call MatCreateAIJ(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,n,m,1,PETSC_NULL_INTEGER,0,PETSC_NULL_INTEGER,A,ierr)<br/>
>>>><br/>
>>>><br/>
>>>> call MatGetOwnershipRange(A,nl1,nl2,ierr)<br/>
>>>> do i=nl1,nl2-1<br/>
>>>> idxn(1)=i<br/>
>>>> idxm(1)=i<br/>
>>>> v(1)=1d0<br/>
>>>> call MatSetValues(A,1,idxn,1,idxm, v,INSERT_VALUES,ierr)<br/>
>>>> end do<br/>
>>>> call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,ierr)<br/>
>>>> call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,ierr)<br/>
>>>><br/>
>>>> call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE,ierr)<br/>
>>>> !~ call MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE,ierr)<br/>
>>>> !~ call MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR ,PETSC_FALSE,ierr)<br/>
>>>> !~ call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE,ierr)<br/>
>>>><br/>
>>>><br/>
>>>> idxn(1)=0<br/>
>>>> idxm(1)=n-1<br/>
>>>> if ((idxn(1).ge.nl1).and.(idxn(1).le.nl2-1)) then<br/>
>>>> v(1)=2d0<br/>
>>>> call MatSetValues(A,1,idxn,1,idxm, v,INSERT_VALUES,ierr)<br/>
>>>> end if<br/>
>>>> call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,ierr)<br/>
>>>> call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,ierr)<br/>
>>>><br/>
>>>> if ((idxn(1).ge.nl1).and.(idxn(1).le.nl2-1)) then<br/>
>>>> v(1)=2d0<br/>
>>>> call MatGetValues(A,1,idxn,1,idxm, v,ierr)<br/>
>>>> write(6,*) v<br/>
>>>> end if<br/>
>>>><br/>
>>>> call PetscFinalize(ierr)<br/>
>>>><br/>
>>>> end program newnonzero<br/>
>>>><br/>
>>>><br/>
>>>><br/>
>>>> $ mpiexec.hydra -n 3 ./a.out<br/>
>>>> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------<br/>
>>>> [0]PETSC ERROR: Argument out of range<br/>
>>>> [0]PETSC ERROR: Inserting a new nonzero at global row/column (0, 2) into matrix</div>
</div>
>>>> [0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html[http://www.mcs.anl.gov/petsc/documentation/faq.html]" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html[http://www.mcs.anl.gov/petsc/documentation/faq.html]</a> for trouble shooting.<br/>
<span class="im HOEnZb">>>>> [0]PETSC ERROR: Petsc Release Version 3.9.2, May, 20, 2018<br/>
>>>> [0]PETSC ERROR: ./a.out on a named tono-hpc1 by marius Wed May 30 09:42:40 2018<br/>
>>>> [0]PETSC ERROR: Configure options --prefix=/home/marius/prog/petsc/3.9.2 --download-elemental=yes --download-metis=yes --download-parmetis=yes --download-mumps=yes --with-scalapack-lib="/home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_intel_lp64.a /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_sequential.a /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_core.a /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a -Wl,--end-group -lpthread -lm -ldl" --FC=mpiifort --CC=mpicc --CXX=mpicxx --with-scalar-type=complex --with-mpi-dir= --with-blaslapack-lib="/home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_intel_lp64.a /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_sequential.a /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_core.a /home/marius/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a -Wl,--end-group -lpthread -lm -ldl" --with-cxx-dialect=C++11 --download-superlu_dist=yes --download-ptscotch=yes --with-x --with-debugging=1 --download-superlu=yes --with-mkl_cpardiso=1 --with-mkl_pardiso=1 --with-scalapack=1<br/>
>>>> [0]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 607 in /home/marius/prog/petsc/petsc-3.9.2/src/mat/impls/aij/mpi/mpiaij.c<br/>
>>>> [0]PETSC ERROR: #2 MatSetValues() line 1312 in /home/marius/prog/petsc/petsc-3.9.2/src/mat/interface/matrix.c<br/>
>>>> (0.000000000000000E+000,0.000000000000000E+000)<br/>
>>>><br/>
>>>><br/>
>>>><br/>
>>>> Please send complete error message; type of matrix used etc. Ideally code that demonstrates the problem.<br/>
>>>><br/>
>>>> Barry<br/>
>>>><br/>
>>>></span>
<div class="HOEnZb">
<div class="h5">>>>>> On May 29, 2018, at 3:31 AM, Marius Buerkle <<a href="mailto:mbuerkle@web.de" onclick="parent.window.location.href='mbuerkle@web.de'; return false;" target="_blank">mbuerkle@web.de</a>[mailto:<a href="mailto:mbuerkle@web.de" onclick="parent.window.location.href='mbuerkle@web.de'; return false;" target="_blank">mbuerkle@web.de</a>]> wrote:<br/>
>>>>><br/>
>>>>><br/>
>>>>> Hi,<br/>
>>>>><br/>
>>>>> I tried to set MAT_NEW_NONZERO_LOCATIONS to false, as far as I understood MatSetValues should simply ignore entries which would give rise to new nonzero values not creating a new entry and not cause an error, but I get "[1]PETSC ERROR: Inserting a new nonzero at global row/column". Is this option supposed to work or not?<br/>
>>>><br/>
>>><br/>
>>><br/>
> <br/>
</div>
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