<div dir="ltr"><div><div>Nope. <br><br></div>There is a back trace:<br><br><i>* thread #1: tid = 0x3b477b4, 0x00007fffb306cd42 libsystem_kernel.dylib`__pthread_kill + 10, queue = 'com.apple.main-thread', stop reason = signal SIGABRT<br> * frame #0: 0x00007fffb306cd42 libsystem_kernel.dylib`__pthread_kill + 10<br> frame #1: 0x00007fffb315a457 libsystem_pthread.dylib`pthread_kill + 90<br> frame #2: 0x00007fffb2fd2420 libsystem_c.dylib`abort + 129<br> frame #3: 0x00000001057ff30a libpetsc.3.07.dylib`Petsc_MPI_AbortOnError(comm=<unavailable>, flag=<unavailable>) + 26 at init.c:185 [opt]<br> frame #4: 0x0000000106bd3245 libpmpi.12.dylib`MPIR_Err_return_comm + 533<br> frame #5: 0x00000001068defd4 libmpi.12.dylib`MPI_Comm_create + 3492<br> frame #6: 0x00000001061345d9 libpetsc.3.07.dylib`hypre_GenerateSubComm(comm=-1006627852, participate=<unavailable>, new_comm_ptr=<unavailable>) + 409 at gen_redcs_mat.c:531 [opt]<br> frame #7: 0x000000010618f8ba libpetsc.3.07.dylib`hypre_GaussElimSetup(amg_data=0x00007fe7ff857a00, level=<unavailable>, relax_type=9) + 74 at par_relax.c:4209 [opt]<br> frame #8: 0x0000000106140e93 libpetsc.3.07.dylib`hypre_BoomerAMGSetup(amg_vdata=<unavailable>, A=0x00007fe80842aff0, f=0x00007fe80842a980, u=0x00007fe80842a510) + 17699 at par_amg_setup.c:2108 [opt]<br> frame #9: 0x0000000105ec773c libpetsc.3.07.dylib`PCSetUp_HYPRE(pc=<unavailable>) + 2540 at hypre.c:226 [opt]<br> frame #10: 0x0000000105eea68d libpetsc.3.07.dylib`PCSetUp(pc=0x00007fe805553f50) + 797 at precon.c:968 [opt]<br> frame #11: 0x0000000105ee9fe5 libpetsc.3.07.dylib`PCApply(pc=0x00007fe805553f50, x=0x00007fe80052d420, y=0x00007fe800522c20) + 181 at precon.c:478 [opt]<br> frame #12: 0x00000001015cf218 libmesh_opt.0.dylib`libMesh::PetscPreconditioner<double>::apply(libMesh::NumericVector<double> const&, libMesh::NumericVector<double>&) + 24<br> frame #13: 0x00000001009c7998 libmoose-opt.0.dylib`PhysicsBasedPreconditioner::apply(libMesh::NumericVector<double> const&, libMesh::NumericVector<double>&) + 520<br> frame #14: 0x00000001016ad701 libmesh_opt.0.dylib`libmesh_petsc_preconditioner_apply + 129<br> frame #15: 0x0000000105e7e715 libpetsc.3.07.dylib`PCApply_Shell(pc=0x00007fe8052623f0, x=0x00007fe806805a20, y=0x00007fe806805420) + 117 at shellpc.c:123 [opt]<br> frame #16: 0x0000000105eea079 libpetsc.3.07.dylib`PCApply(pc=0x00007fe8052623f0, x=0x00007fe806805a20, y=0x00007fe806805420) + 329 at precon.c:482 [opt]<br> frame #17: 0x0000000105eeb611 libpetsc.3.07.dylib`PCApplyBAorAB(pc=0x00007fe8052623f0, side=PC_RIGHT, x=0x00007fe806805a20, y=0x00007fe806806020, work=0x00007fe806805420) + 945 at precon.c:714 [opt]<br> frame #18: 0x0000000105f31658 libpetsc.3.07.dylib`KSPGMRESCycle [inlined] KSP_PCApplyBAorAB(ksp=0x00007fe806022220, x=<unavailable>, y=0x00007fe806806020, w=<unavailable>) + 191 at kspimpl.h:295 [opt]<br> frame #19: 0x0000000105f31599 libpetsc.3.07.dylib`KSPGMRESCycle(itcount=<unavailable>, ksp=<unavailable>) + 553 at gmres.c:156 [opt]<br> frame #20: 0x0000000105f326bd libpetsc.3.07.dylib`KSPSolve_GMRES(ksp=<unavailable>) + 221 at gmres.c:240 [opt]<br> frame #21: 0x0000000105f5f671 libpetsc.3.07.dylib`KSPSolve(ksp=0x00007fe806022220, b=0x00007fe7fd946220, x=<unavailable>) + 1345 at itfunc.c:677 [opt]<br> frame #22: 0x0000000105fd0251 libpetsc.3.07.dylib`SNESSolve_NEWTONLS(snes=<unavailable>) + 1425 at ls.c:230 [opt]<br> frame #23: 0x0000000105fa10ca libpetsc.3.07.dylib`SNESSolve(snes=<unavailable>, b=<unavailable>, x=0x00007fe7fd865e20) + 858 at snes.c:4128 [opt]<br> frame #24: 0x00000001016b63c3 libmesh_opt.0.dylib`libMesh::PetscNonlinearSolver<double>::solve(libMesh::SparseMatrix<double>&, libMesh::NumericVector<double>&, libMesh::NumericVector<double>&, double, unsigned int) + 835<br> frame #25: 0x00000001016fc244 libmesh_opt.0.dylib`libMesh::NonlinearImplicitSystem::solve() + 324<br> frame #26: 0x0000000100a71dc8 libmoose-opt.0.dylib`NonlinearSystem::solve() + 472<br> frame #27: 0x00000001009fe815 libmoose-opt.0.dylib`FEProblemBase::solve() + 117<br> frame #28: 0x0000000100761fba libmoose-opt.0.dylib`Steady::execute() + 266<br> frame #29: 0x0000000100b78ac3 libmoose-opt.0.dylib`MooseApp::run() + 259<br> frame #30: 0x00000001003843aa moose_test-opt`main + 122<br> frame #31: 0x00007fffb2f3e235 libdyld.dylib`start + 1<br><br><br></i></div>Fande,<i><br></i><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Apr 2, 2018 at 4:02 PM, Stefano Zampini <span dir="ltr"><<a href="mailto:stefano.zampini@gmail.com" target="_blank">stefano.zampini@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">maybe this will fix ?<div>
<span></span>
<p class="m_5875358157558324763gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures"><b><br></b></span></p><p class="m_5875358157558324763gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures"><b>diff --git a/src/ksp/pc/impls/hypre/<wbr>hypre.c b/src/ksp/pc/impls/hypre/<wbr>hypre.c</b></span></p>
<p class="m_5875358157558324763gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures"><b>index 28addcf533..6a756d4c57 100644</b></span></p>
<p class="m_5875358157558324763gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures"><b>--- a/src/ksp/pc/impls/hypre/<wbr>hypre.c</b></span></p>
<p class="m_5875358157558324763gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures"><b>+++ b/src/ksp/pc/impls/hypre/<wbr>hypre.c</b></span></p>
<p class="m_5875358157558324763gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s2" style="font-variant-ligatures:no-common-ligatures;color:rgb(51,187,200)">@@ -142,8 +142,7 @@</span><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures"> static PetscErrorCode PCSetUp_HYPRE(PC pc)</span></p>
<p class="m_5875358157558324763gmail-p2" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255);min-height:16px"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_5875358157558324763gmail-Apple-converted-space"> </span></span></p>
<p class="m_5875358157558324763gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_5875358157558324763gmail-Apple-converted-space"> </span>ierr = PetscObjectTypeCompare((<wbr>PetscObject)pc->pmat,MATHYPRE,<wbr>&ishypre);CHKERRQ(ierr);</span></p>
<p class="m_5875358157558324763gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_5875358157558324763gmail-Apple-converted-space"> </span>if (!ishypre) {</span></p>
<p class="m_5875358157558324763gmail-p3" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(195,55,32);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures">-<span class="m_5875358157558324763gmail-Apple-converted-space"> </span>ierr = MatDestroy(&jac->hpmat);<wbr>CHKERRQ(ierr);</span></p>
<p class="m_5875358157558324763gmail-p3" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(195,55,32);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures">-<span class="m_5875358157558324763gmail-Apple-converted-space"> </span>ierr = MatConvert(pc->pmat,MATHYPRE,<wbr>MAT_INITIAL_MATRIX,&jac-><wbr>hpmat);CHKERRQ(ierr);</span></p>
<p class="m_5875358157558324763gmail-p4" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(52,188,38);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures">+<span class="m_5875358157558324763gmail-Apple-converted-space"> </span>ierr = MatConvert(pc->pmat,MATHYPRE,<wbr>jac->hpmat ? MAT_REUSE_MATRIX : MAT_INITIAL_MATRIX,&jac-><wbr>hpmat);CHKERRQ(ierr);</span></p>
<p class="m_5875358157558324763gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_5875358157558324763gmail-Apple-converted-space"> </span>} else {</span></p>
<p class="m_5875358157558324763gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_5875358157558324763gmail-Apple-converted-space"> </span>ierr = PetscObjectReference((<wbr>PetscObject)pc->pmat);CHKERRQ(<wbr>ierr);</span></p>
<p class="m_5875358157558324763gmail-p1" style="margin:0px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);background-color:rgb(255,255,255)"><span class="m_5875358157558324763gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_5875358157558324763gmail-Apple-converted-space"> </span>ierr = MatDestroy(&jac->hpmat);<wbr>CHKERRQ(ierr);</span></p>
<br><div><br></div></div></div><div class="gmail_extra"><div><div class="h5"><br><div class="gmail_quote">2018-04-02 23:46 GMT+02:00 Kong, Fande <span dir="ltr"><<a href="mailto:fande.kong@inl.gov" target="_blank">fande.kong@inl.gov</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hi All,<br><br></div>I am trying to upgrade PETSc from 3.7.6 to 3.8.3 for MOOSE and its applications. I have a error message for a standard test:<br><br><br><i>preconditioners/pbp.lots_of_va<wbr>riables: MPI had an error<br>preconditioners/pbp.lots_of_va<wbr>riables: ------------------------------<wbr>------------------<br>preconditioners/pbp.lots_of_va<wbr>riables: Other MPI error, error stack:<br>preconditioners/pbp.lots_of_va<wbr>riables: PMPI_Comm_dup(177)............<wbr>......: MPI_Comm_dup(comm=0x84000001, new_comm=0x97d1068) failed<br>preconditioners/pbp.lots_of_va<wbr>riables: PMPI_Comm_dup(162)............<wbr>......: <br>preconditioners/pbp.lots_of_va<wbr>riables: MPIR_Comm_dup_impl(57)........<wbr>......: <br>preconditioners/pbp.lots_of_va<wbr>riables: MPIR_Comm_copy(739)...........<wbr>......: <br>preconditioners/pbp.lots_of_va<wbr>riables: MPIR_Get_contextid_sparse_grou<wbr>p(614): Too many communicators (0/2048 free on this process; ignore_id=0)</i><br><br><br></div>I did "git bisect', and the following commit introduces this issue:<br><br><i>commit 49a781f5cee36db85e8d5b951eec29<wbr>f10ac13593<br>Author: Stefano Zampini <<a href="mailto:stefano.zampini@gmail.com" target="_blank">stefano.zampini@gmail.com</a>><br>Date: Sat Nov 5 20:15:19 2016 +0300<br><br> PCHYPRE: use internal Mat of type MatHYPRE<br> <br> hpmat already stores two HYPRE vectors<br></i><br> <br></div>Before I debug line-by-line, anyone has a clue on this?<span class="m_5875358157558324763HOEnZb"><font color="#888888"><br><br><br></font></span></div><span class="m_5875358157558324763HOEnZb"><font color="#888888">Fande,<br></font></span></div>
</blockquote></div><br><br clear="all"><div><br></div></div></div><span class="HOEnZb"><font color="#888888">-- <br><div class="m_5875358157558324763gmail_signature" data-smartmail="gmail_signature">Stefano</div>
</font></span></div>
</blockquote></div><br></div>