[petsc-users] Error with SuperLU_DIST (mkl related?)

Sat Dec 31 12:35:58 CST 2016

Ah - ok. A bug in superlu_dist. Version string in CMakeLists.txt needs updating for every release..

set(VERSION_MAJOR "5")
set(VERSION_MINOR "1")
set(VERSION_BugFix "0")

cc:ing Sherry.

Satish

On Sat, 31 Dec 2016, Eric Chamberland wrote:

> Ah ok, I see!  Here look at the file name in the configure.log:
> 
> Install the project...
> /usr/bin/cmake -P cmake_install.cmake
> -- Install configuration: "DEBUG"
> -- Installing: /opt/petsc-master_debug/lib/libsuperlu_dist.so.5.1.0
> -- Installing: /opt/petsc-master_debug/lib/libsuperlu_dist.so.5
> 
> It is saying 5.1.0, but in fact you are right: it is 5.1.3 that is
> downloaded!!! :)
> 
> And FWIW, the nighlty automatic compilation of PETSc starts within a brand new
> and empty directory each night...
> 
> Thanks to both of you again! :)
> 
> Eric
> 
> 
> Le 2016-12-31 à 13:17, Satish Balay a écrit :
> >                        ===============================================================================
> >                            Trying to download
> >                        git://https://github.com/xiaoyeli/superlu_dist for
> >                        SUPERLU_DIST
> >                        ===============================================================================
> >                      
> > Executing: git clone https://github.com/xiaoyeli/superlu_dist
> > Executing: /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/arch-linux2-c-debug/externalpackages/git.superlu_dist
> > stdout: Cloning into
> > '/pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-master-debug/arch-linux2-c-debug/externalpackages/git.superlu_dist'...
> >                      Looking for SUPERLU_DIST at git.superlu_dist,
> >                      hg.superlu_dist or a directory starting with
> >                      ['superlu_dist']
> >                      Found a copy of SUPERLU_DIST in git.superlu_dist
> > Executing: ['git', 'rev-parse', '--git-dir']
> > stdout: .git
> > Executing: ['git', 'cat-file', '-e', 'v5.1.3^{commit}']
> > Executing: ['git', 'rev-parse', 'v5.1.3']
> > stdout: 7306f704c6c8d5113def649b76def3c8eb607690
> > Executing: ['git', 'stash']
> > stdout: No local changes to save
> > Executing: ['git', 'clean', '-f', '-d', '-x']
> > Executing: ['git', 'checkout', '-f',
> > Executing: '7306f704c6c8d5113def649b76def3c8eb607690']
> > <<<<<<<<
> >
> > Per log below - its using 5.1.3. Why did you think you got 5.1.0?
> >
> > Satish
> >
> > On Sat, 31 Dec 2016, Eric Chamberland wrote:
> >
> > > Hi,
> > >
> > > ok I will test with 5.1.3 with the option you gave me
> > > (--download-superlu_dit-commit=v5.1.3).
> > >
> > > But from what you and Matthew said, I should have 5.1.3 with petsc-master,
> > > but
> > > the last night log shows me library file name 5.1.0:
> > >
> > > http://www.giref.ulaval.ca/~cmpgiref/petsc-master-debug/2016.12.31.02h00m01s_configure.log
> > >
> > > So I am a bit confused: Why did I got 5.1.0 last night? (I use the
> > > petsc-master tarball, is it the reason?)
> > >
> > > Thanks,
> > >
> > > Eric
> > >
> > >
> > > Le 2016-12-31 à 11:52, Satish Balay a écrit :
> > > > On Sat, 31 Dec 2016, Eric Chamberland wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I am just starting to debug a bug encountered with and only with
> > > > > SuperLU_Dist
> > > > > combined with MKL on a 2 processes validation test.
> > > > >
> > > > > (the same test works fine with MUMPS on 2 processes).
> > > > >
> > > > > I just noticed that the SuperLU_Dist version installed by PETSc
> > > > > configure
> > > > > script is 5.1.0 and the latest SuperLU_DIST is 5.1.3.
> > > > If you use petsc-master - it will install 5.1.3 by default.
> > > > > Before going further, I just want to ask:
> > > > >
> > > > > Is there any specific reason to stick to 5.1.0?
> > > > We don't usually upgrade externalpackage version in PETSc releases
> > > > [unless its tested to work and fixes known bugs]. There could be API
> > > > changes - or build changes that can potentially conflict.
> > > >
> > > > >From what I know - 5.1.3 should work with petsc-3.7 [it fixes a couple
> > > > of
> > > > bugs].
> > > >
> > > > You might be able to do the following with petsc-3.7 [with git
> > > > externalpackage repos]
> > > >
> > > > --download-superlu_dist --download-superlu_dit-commit=v5.1.3
> > > >
> > > > Satish
> > > >
> > > > > Here is some more information:
> > > > >
> > > > > On process 2 I have this printed in stdout:
> > > > >
> > > > > Intel MKL ERROR: Parameter 6 was incorrect on entry to DTRSM .
> > > > >
> > > > > and in stderr:
> > > > >
> > > > > Test.ProblemeEFGen.opt: malloc.c:2369: sysmalloc: Assertion `(old_top
> > > > > ==
> > > > > (((mbinptr) (((char *) &((av)->bins[((1) - 1) * 2])) -
> > > > > __builtin_offsetof
> > > > > (struct malloc_chunk, fd)))) && old_size == 0) || ((unsigned long)
> > > > > (old_size)
> > > > > > = (unsigned long)((((__builtin_offsetof (struct malloc_chunk,
> > > > > fd_nextsize))+((2 *(sizeof(size_t))) - 1)) & ~((2 *(sizeof(size_t))) -
> > > > > 1))) &&
> > > > > ((old_top)->size & 0x1) && ((unsigned long) old_end & pagemask) == 0)'
> > > > > failed.
> > > > > [saruman:15771] *** Process received signal ***
> > > > >
> > > > > This is the 7th call to KSPSolve in the same execution. Here is the
> > > > > last
> > > > > KSPView:
> > > > >
> > > > > KSP Object:(o_slin) 2 MPI processes
> > > > >     type: preonly
> > > > >     maximum iterations=10000, initial guess is zero
> > > > >     tolerances:  relative=1e-05, absolute=1e-50, divergence=10000.
> > > > >     left preconditioning
> > > > >     using NONE norm type for convergence test
> > > > > PC Object:(o_slin) 2 MPI processes
> > > > >     type: lu
> > > > >       LU: out-of-place factorization
> > > > >       tolerance for zero pivot 2.22045e-14
> > > > >       matrix ordering: natural
> > > > >       factor fill ratio given 0., needed 0.
> > > > >         Factored matrix follows:
> > > > >           Mat Object:         2 MPI processes
> > > > >             type: mpiaij
> > > > >             rows=382, cols=382
> > > > >             package used to perform factorization: superlu_dist
> > > > >             total: nonzeros=0, allocated nonzeros=0
> > > > >             total number of mallocs used during MatSetValues calls =0
> > > > >               SuperLU_DIST run parameters:
> > > > >                 Process grid nprow 2 x npcol 1
> > > > >                 Equilibrate matrix TRUE
> > > > >                 Matrix input mode 1
> > > > >                 Replace tiny pivots FALSE
> > > > >                 Use iterative refinement FALSE
> > > > >                 Processors in row 2 col partition 1
> > > > >                 Row permutation LargeDiag
> > > > >                 Column permutation METIS_AT_PLUS_A
> > > > >                 Parallel symbolic factorization FALSE
> > > > >                 Repeated factorization SamePattern
> > > > >     linear system matrix = precond matrix:
> > > > >     Mat Object:  (o_slin)   2 MPI processes
> > > > >       type: mpiaij
> > > > >       rows=382, cols=382
> > > > >       total: nonzeros=4458, allocated nonzeros=4458
> > > > >       total number of mallocs used during MatSetValues calls =0
> > > > >         using I-node (on process 0) routines: found 109 nodes, limit
> > > > >         used
> > > > >         is 5
> > > > >
> > > > > I know this information is not enough to help debug, but I would like
> > > > > to
> > > > > know
> > > > > if PETSc guys will upgrade to 5.1.3 before trying to debug anything.
> > > > >
> > > > > Thanks,
> > > > > Eric
> > > > >
> > > > >
> > >
> 
> 