[petsc-users] Can't expand MemType 1: jcol 16104
Hong
hzhang at mcs.anl.gov
Wed Jul 29 10:36:46 CDT 2015
Sherry,
With your bugfix, superlu_dist-4.1 works now:
petsc/src/ksp/ksp/examples/tutorials (master)
$ mpiexec -n 4 ./ex10 -f0 Amat_binary.m -rhs 0 -pc_type lu
-pc_factor_mat_solver_package superlu_dist -mat_superlu_dist_parsymbfact
Number of iterations = 1
Residual norm 2.11605e-11
Once you address Satish's request, we'll update petsc interface to this
version of superlu_dist.
Anthony:
Please download the latest superlu_dist-v4.1,
then configure petsc with
'--download-superlu_dist=superlu_dist_4.1.tar.gz'
Hong
On Tue, Jul 28, 2015 at 11:11 AM, Satish Balay <balay at mcs.anl.gov> wrote:
> Sherry,
>
> One minor issue with the tarball. I see the following new files in the
> v4.1 tarball
> [when comparing it with v4.0]. Some of these files are perhaps junk files
> - and can
> be removed from the tarball?
>
> EXAMPLE/dscatter.c.bak
> EXAMPLE/g10.cua
> EXAMPLE/g4.cua
> EXAMPLE/g4.postorder.eps
> EXAMPLE/g4.rua
> EXAMPLE/g4_postorder.jpg
> EXAMPLE/hostname
> EXAMPLE/pdgssvx.c
> EXAMPLE/pdgstrf2.c
> EXAMPLE/pwd
> EXAMPLE/pzgstrf2.c
> EXAMPLE/pzgstrf_v3.3.c
> EXAMPLE/pzutil.c
> EXAMPLE/test.bat
> EXAMPLE/test.cpu.bat
> EXAMPLE/test.err
> EXAMPLE/test.err.1
> EXAMPLE/zlook_ahead_update.c
> FORTRAN/make.out
> FORTRAN/zcreate_dist_matrix.c
> MAKE_INC/make.xc30
> SRC/int_t
> SRC/lnbrow
> SRC/make.out
> SRC/rnbrow
> SRC/temp
> SRC/temp1
>
>
> Thanks,
> Satish
>
>
> On Tue, 28 Jul 2015, Xiaoye S. Li wrote:
>
> > I am checking v4.1 now. I'll let you know when I fixed the problem.
> >
> > Sherry
> >
> > On Tue, Jul 28, 2015 at 8:27 AM, Hong <hzhang at mcs.anl.gov> wrote:
> >
> > > Sherry,
> > > I tested with superlu_dist v4.1. The extra printings are gone, but hang
> > > remains.
> > > It hangs at
> > >
> > > #5 0x00007fde5af1c818 in PMPI_Wait (request=0xb6e4e0,
> > > status=0x7fff9cd83d60)
> > > at src/mpi/pt2pt/wait.c:168
> > > #6 0x00007fde602dd635 in pzgstrf (options=0x9202f0, m=4900, n=4900,
> > > anorm=13.738475134194639, LUstruct=0x9203c8, grid=0x9202c8,
> > > stat=0x7fff9cd84880, info=0x7fff9cd848bc) at pzgstrf.c:1308
> > >
> > > if (recv_req[0] != MPI_REQUEST_NULL) {
> > > --> MPI_Wait (&recv_req[0], &status);
> > >
> > > We will update petsc interface to superlu_dist v4.1.
> > >
> > > Hong
> > >
> > >
> > > On Mon, Jul 27, 2015 at 11:33 PM, Xiaoye S. Li <xsli at lbl.gov> wrote:
> > >
> > >> Hong,
> > >> Thanks for trying out.
> > >> The extra printings are not properly guarded by the print level. I
> will
> > >> fix that. I will look into the hang problem soon.
> > >>
> > >> Sherry
> > >>
> > >>
> > >> On Mon, Jul 27, 2015 at 7:50 PM, Hong <hzhang at mcs.anl.gov> wrote:
> > >>
> > >>> Sherry,
> > >>>
> > >>> I can repeat hang using petsc/src/ksp/ksp/examples/tutorials/ex10.c:
> > >>> mpiexec -n 4 ./ex10 -f0 /homes/hzhang/tmp/Amat_binary.m -rhs 0
> -pc_type
> > >>> lu -pc_factor_mat_solver_package superlu_dist
> -mat_superlu_dist_parsymbfact
> > >>> ...
> > >>> .. Starting with 1 OpenMP threads
> > >>> [0] .. BIG U size 1342464
> > >>> [0] .. BIG V size 131072
> > >>> Max row size is 1311
> > >>> Using buffer_size of 5000000
> > >>> Threads per process 1
> > >>> ...
> > >>>
> > >>> using a debugger (with petsc option '-start_in_debugger'), I find
> that
> > >>> hang occurs at
> > >>> #0 0x00007f117d870998 in __GI___poll (fds=0x20da750, nfds=4,
> > >>> timeout=<optimized out>, timeout at entry=-1)
> > >>> at ../sysdeps/unix/sysv/linux/poll.c:83
> > >>> #1 0x00007f117de9f7de in MPIDU_Sock_wait (sock_set=0x20da550,
> > >>> millisecond_timeout=millisecond_timeout at entry=-1,
> > >>> eventp=eventp at entry=0x7fff654930b0)
> > >>> at src/mpid/common/sock/poll/sock_wait.i:123
> > >>> #2 0x00007f117de898b8 in MPIDI_CH3i_Progress_wait (
> > >>> progress_state=0x7fff65493120)
> > >>> at src/mpid/ch3/channels/sock/src/ch3_progress.c:218
> > >>> #3 MPIDI_CH3I_Progress (blocking=blocking at entry=1,
> > >>> state=state at entry=0x7fff65493120)
> > >>> at src/mpid/ch3/channels/sock/src/ch3_progress.c:921
> > >>> #4 0x00007f117de1a559 in MPIR_Wait_impl (request=request at entry
> > >>> =0x262df90,
> > >>> status=status at entry=0x7fff65493390) at src/mpi/pt2pt/wait.c:67
> > >>> #5 0x00007f117de1a818 in PMPI_Wait (request=0x262df90,
> > >>> status=0x7fff65493390)
> > >>> at src/mpi/pt2pt/wait.c:168
> > >>> #6 0x00007f11831da557 in pzgstrf (options=0x23dfda0, m=4900, n=4900,
> > >>> anorm=13.738475134194639, LUstruct=0x23dfe78, grid=0x23dfd78,
> > >>> stat=0x7fff65493ea0, info=0x7fff65493edc) at pzgstrf.c:1308
> > >>>
> > >>> #7 0x00007f11831bf3bd in pzgssvx (options=0x23dfda0, A=0x23dfe30,
> > >>> ScalePermstruct=0x23dfe50, B=0x0, ldb=1225, nrhs=0,
> grid=0x23dfd78,
> > >>> LUstruct=0x23dfe78, SOLVEstruct=0x23dfe98, berr=0x0,
> > >>> stat=0x7fff65493ea0,
> > >>> ---Type <return> to continue, or q <return> to quit---
> > >>> info=0x7fff65493edc) at pzgssvx.c:1063
> > >>>
> > >>> #8 0x00007f11825c2340 in MatLUFactorNumeric_SuperLU_DIST
> (F=0x23a0110,
> > >>> A=0x21bb7e0, info=0x2355068)
> > >>> at
> > >>>
> /sandbox/hzhang/petsc/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c:411
> > >>> #9 0x00007f1181c6c567 in MatLUFactorNumeric (fact=0x23a0110,
> > >>> mat=0x21bb7e0,
> > >>> info=0x2355068) at
> > >>> /sandbox/hzhang/petsc/src/mat/interface/matrix.c:2946
> > >>> #10 0x00007f1182a56489 in PCSetUp_LU (pc=0x2353a10)
> > >>> at /sandbox/hzhang/petsc/src/ksp/pc/impls/factor/lu/lu.c:152
> > >>> #11 0x00007f1182b16f24 in PCSetUp (pc=0x2353a10)
> > >>> at /sandbox/hzhang/petsc/src/ksp/pc/interface/precon.c:983
> > >>> #12 0x00007f1182be61b5 in KSPSetUp (ksp=0x232c2a0)
> > >>> at /sandbox/hzhang/petsc/src/ksp/ksp/interface/itfunc.c:332
> > >>> #13 0x0000000000405a31 in main (argc=11, args=0x7fff65499578)
> > >>> at
> /sandbox/hzhang/petsc/src/ksp/ksp/examples/tutorials/ex10.c:312
> > >>>
> > >>> You may take a look at it. Sequential symbolic factorization works
> fine.
> > >>>
> > >>> Why superlu_dist (v4.0) in complex precision displays
> > >>>
> > >>> .. Starting with 1 OpenMP threads
> > >>> [0] .. BIG U size 1342464
> > >>> [0] .. BIG V size 131072
> > >>> Max row size is 1311
> > >>> Using buffer_size of 5000000
> > >>> Threads per process 1
> > >>> ...
> > >>>
> > >>> I realize that I use superlu_dist v4.0. Would v4.1 works? I'll give
> it a
> > >>> try tomorrow.
> > >>>
> > >>> Hong
> > >>>
> > >>> On Mon, Jul 27, 2015 at 1:25 PM, Anthony Paul Haas <
> > >>> aph at email.arizona.edu> wrote:
> > >>>
> > >>>> Hi Hong,
> > >>>>
> > >>>> No that is not the correct matrix. Note that I forgot to mention
> that
> > >>>> it is a complex matrix. I tried loading the matrix I sent you this
> morning
> > >>>> with:
> > >>>>
> > >>>> !...Load a Matrix in Binary Format
> > >>>> call
> > >>>>
> PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Amat_binary.m",FILE_MODE_READ,viewer,ierr)
> > >>>> call MatCreate(PETSC_COMM_WORLD,DLOAD,ierr)
> > >>>> call MatSetType(DLOAD,MATAIJ,ierr)
> > >>>> call MatLoad(DLOAD,viewer,ierr)
> > >>>> call PetscViewerDestroy(viewer,ierr)
> > >>>>
> > >>>> call MatView(DLOAD,PETSC_VIEWER_STDOUT_WORLD,ierr)
> > >>>>
> > >>>> The first 37 rows should look like this:
> > >>>>
> > >>>> Mat Object: 2 MPI processes
> > >>>> type: mpiaij
> > >>>> row 0: (0, 1)
> > >>>> row 1: (1, 1)
> > >>>> row 2: (2, 1)
> > >>>> row 3: (3, 1)
> > >>>> row 4: (4, 1)
> > >>>> row 5: (5, 1)
> > >>>> row 6: (6, 1)
> > >>>> row 7: (7, 1)
> > >>>> row 8: (8, 1)
> > >>>> row 9: (9, 1)
> > >>>> row 10: (10, 1)
> > >>>> row 11: (11, 1)
> > >>>> row 12: (12, 1)
> > >>>> row 13: (13, 1)
> > >>>> row 14: (14, 1)
> > >>>> row 15: (15, 1)
> > >>>> row 16: (16, 1)
> > >>>> row 17: (17, 1)
> > >>>> row 18: (18, 1)
> > >>>> row 19: (19, 1)
> > >>>> row 20: (20, 1)
> > >>>> row 21: (21, 1)
> > >>>> row 22: (22, 1)
> > >>>> row 23: (23, 1)
> > >>>> row 24: (24, 1)
> > >>>> row 25: (25, 1)
> > >>>> row 26: (26, 1)
> > >>>> row 27: (27, 1)
> > >>>> row 28: (28, 1)
> > >>>> row 29: (29, 1)
> > >>>> row 30: (30, 1)
> > >>>> row 31: (31, 1)
> > >>>> row 32: (32, 1)
> > >>>> row 33: (33, 1)
> > >>>> row 34: (34, 1)
> > >>>> row 35: (35, 1)
> > >>>> row 36: (1, -41.2444) (35, -41.2444) (36, 118.049 - 0.999271 i)
> (37,
> > >>>> -21.447) (38, 5.18873) (39, -2.34856) (40, 1.3607) (41,
> -0.898206)
> > >>>> (42, 0.642715) (43, -0.48593) (44, 0.382471) (45, -0.310476)
> (46,
> > >>>> 0.258302) (47, -0.219268) (48, 0.189304) (49, -0.165815) (50,
> > >>>> 0.147076) (51, -0.131907) (52, 0.119478) (53, -0.109189) (54,
> 0.1006)
> > >>>> (55, -0.0933795) (56, 0.0872779) (57, -0.0821019) (58,
> 0.0777011) (59,
> > >>>> -0.0739575) (60, 0.0707775) (61, -0.0680868) (62, 0.0658258)
> (63,
> > >>>> -0.0639473) (64, 0.0624137) (65, -0.0611954) (66, 0.0602698)
> (67,
> > >>>> -0.0596202) (68, 0.0592349) (69, -0.0295536) (71, -21.447) (106,
> > >>>> 5.18873) (141, -2.34856) (176, 1.3607) (211, -0.898206) (246,
> > >>>> 0.642715) (281, -0.48593) (316, 0.382471) (351, -0.310476) (386,
> > >>>> 0.258302) (421, -0.219268) (456, 0.189304) (491, -0.165815)
> (526,
> > >>>> 0.147076) (561, -0.131907) (596, 0.119478) (631, -0.109189)
> (666,
> > >>>> 0.1006) (701, -0.0933795) (736, 0.0872779) (771, -0.0821019)
> (806,
> > >>>> 0.0777011) (841, -0.0739575) (876, 0.0707775) (911, -0.0680868)
> (946,
> > >>>> 0.0658258) (981, -0.0639473) (1016, 0.0624137) (1051, -0.0611954)
> > >>>> (1086, 0.0602698) (1121, -0.0596202) (1156, 0.0592349) (1191,
> > >>>> -0.0295536) (1261, 0) (3676, 117.211) (3711, -58.4801) (3746,
> > >>>> -78.3633) (3781, 29.4911) (3816, -15.8073) (3851, 9.94324)
> (3886,
> > >>>> -6.87205) (3921, 5.05774) (3956, -3.89521) (3991, 3.10522)
> (4026,
> > >>>> -2.54388) (4061, 2.13082) (4096, -1.8182) (4131, 1.57606) (4166,
> > >>>> -1.38491) (4201, 1.23155) (4236, -1.10685) (4271, 1.00428)
> (4306,
> > >>>> -0.919116) (4341, 0.847829) (4376, -0.787776) (4411, 0.736933)
> (4446,
> > >>>> -0.693735) (4481, 0.656958) (4516, -0.625638) (4551, 0.599007)
> (4586,
> > >>>> -0.576454) (4621, 0.557491) (4656, -0.541726) (4691, 0.528849)
> (4726,
> > >>>> -0.518617) (4761, 0.51084) (4796, -0.50538) (4831, 0.502142)
> (4866,
> > >>>> -0.250534)
> > >>>>
> > >>>>
> > >>>> Thanks,
> > >>>>
> > >>>> Anthony
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>> On Fri, Jul 24, 2015 at 7:56 PM, Hong <hzhang at mcs.anl.gov> wrote:
> > >>>>
> > >>>>> Anthony:
> > >>>>> I test your Amat_binary.m
> > >>>>> using petsc/src/ksp/ksp/examples/tutorials/ex10.c.
> > >>>>> Your matrix has many zero rows:
> > >>>>> ./ex10 -f0 ~/tmp/Amat_binary.m -rhs 0 -mat_view |more
> > >>>>> Mat Object: 1 MPI processes
> > >>>>> type: seqaij
> > >>>>> row 0: (0, 1)
> > >>>>> row 1: (1, 0)
> > >>>>> row 2: (2, 1)
> > >>>>> row 3: (3, 0)
> > >>>>> row 4: (4, 1)
> > >>>>> row 5: (5, 0)
> > >>>>> row 6: (6, 1)
> > >>>>> row 7: (7, 0)
> > >>>>> row 8: (8, 1)
> > >>>>> row 9: (9, 0)
> > >>>>> ...
> > >>>>> row 36: (1, 1) (35, 0) (36, 1) (37, 0) (38, 1) (39, 0) (40,
> 1)
> > >>>>> (41, 0) (42, 1) (43, 0) (44, 1) (45,
> > >>>>> 0) (46, 1) (47, 0) (48, 1) (49, 0) (50, 1) (51, 0) (52, 1)
> > >>>>> (53, 0) (54, 1) (55, 0) (56, 1) (57, 0)
> > >>>>> (58, 1) (59, 0) (60, 1) ...
> > >>>>>
> > >>>>> Do you send us correct matrix?
> > >>>>>
> > >>>>>>
> > >>>>>> I ran my code through valgrind and gdb as suggested by Barry. I am
> > >>>>>> now coming back to some problem I have had while running with
> parallel
> > >>>>>> symbolic factorization. I am attaching a test matrix (petsc
> binary format)
> > >>>>>> that I LU decompose and then use to solve a linear system (see
> code below).
> > >>>>>> I can run on 2 processors with parsymbfact or with 4 processors
> without
> > >>>>>> parsymbfact. However, if I run on 4 procs with parsymbfact, the
> code is
> > >>>>>> just hanging. Below is the simplified test case that I have used
> to test.
> > >>>>>> The matrix A and B are built somewhere else in my program. The
> matrix I am
> > >>>>>> attaching is A-sigma*B (see below).
> > >>>>>>
> > >>>>>> One thing is that I don't know for sparse matrices what is the
> > >>>>>> optimum number of processors to use for a LU decomposition? Does
> it depend
> > >>>>>> on the total number of nonzero? Do you have an easy way to
> compute it?
> > >>>>>>
> > >>>>>
> > >>>>> You have to experiment your matrix on a target machine to find out.
> > >>>>>
> > >>>>> Hong
> > >>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>> Subroutine HowBigLUCanBe(rank)
> > >>>>>>
> > >>>>>> IMPLICIT NONE
> > >>>>>>
> > >>>>>> integer(i4b),intent(in) :: rank
> > >>>>>> integer(i4b) :: i,ct
> > >>>>>> real(dp) :: begin,endd
> > >>>>>> complex(dpc) :: sigma
> > >>>>>>
> > >>>>>> PetscErrorCode ierr
> > >>>>>>
> > >>>>>>
> > >>>>>> if (rank==0) call cpu_time(begin)
> > >>>>>>
> > >>>>>> if (rank==0) then
> > >>>>>> write(*,*)
> > >>>>>> write(*,*)'Testing How Big LU Can Be...'
> > >>>>>> write(*,*)'============================'
> > >>>>>> write(*,*)
> > >>>>>> endif
> > >>>>>>
> > >>>>>> sigma = (1.0d0,0.0d0)
> > >>>>>> call MatAXPY(A,-sigma,B,DIFFERENT_NONZERO_PATTERN,ierr) ! on
> > >>>>>> exit A = A-sigma*B
> > >>>>>>
> > >>>>>> !.....Write Matrix to ASCII and Binary Format
> > >>>>>> !call
> > >>>>>> PetscViewerASCIIOpen(PETSC_COMM_WORLD,"Amat.m",viewer,ierr)
> > >>>>>> !call MatView(DXX,viewer,ierr)
> > >>>>>> !call PetscViewerDestroy(viewer,ierr)
> > >>>>>>
> > >>>>>> call
> > >>>>>>
> PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Amat_binary.m",FILE_MODE_WRITE,viewer,ierr)
> > >>>>>> call MatView(A,viewer,ierr)
> > >>>>>> call PetscViewerDestroy(viewer,ierr)
> > >>>>>>
> > >>>>>> !.....Create Linear Solver Context
> > >>>>>> call KSPCreate(PETSC_COMM_WORLD,ksp,ierr)
> > >>>>>>
> > >>>>>> !.....Set operators. Here the matrix that defines the linear
> system
> > >>>>>> also serves as the preconditioning matrix.
> > >>>>>> !call
> KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN,ierr)
> > >>>>>> !aha commented and replaced by next line
> > >>>>>> call KSPSetOperators(ksp,A,A,ierr) ! remember: here A =
> > >>>>>> A-sigma*B
> > >>>>>>
> > >>>>>> !.....Set Relative and Absolute Tolerances and Uses Default for
> > >>>>>> Divergence Tol
> > >>>>>> tol = 1.e-10
> > >>>>>> call
> > >>>>>>
> KSPSetTolerances(ksp,tol,tol,PETSC_DEFAULT_REAL,PETSC_DEFAULT_INTEGER,ierr)
> > >>>>>>
> > >>>>>> !.....Set the Direct (LU) Solver
> > >>>>>> call KSPSetType(ksp,KSPPREONLY,ierr)
> > >>>>>> call KSPGetPC(ksp,pc,ierr)
> > >>>>>> call PCSetType(pc,PCLU,ierr)
> > >>>>>> call
> PCFactorSetMatSolverPackage(pc,MATSOLVERSUPERLU_DIST,ierr)
> > >>>>>> ! MATSOLVERSUPERLU_DIST MATSOLVERMUMPS
> > >>>>>>
> > >>>>>> !.....Create Right-Hand-Side Vector
> > >>>>>> call MatCreateVecs(A,frhs,PETSC_NULL_OBJECT,ierr)
> > >>>>>> call MatCreateVecs(A,sol,PETSC_NULL_OBJECT,ierr)
> > >>>>>>
> > >>>>>> allocate(xwork1(IendA-IstartA))
> > >>>>>> allocate(loc(IendA-IstartA))
> > >>>>>>
> > >>>>>> ct=0
> > >>>>>> do i=IstartA,IendA-1
> > >>>>>> ct=ct+1
> > >>>>>> loc(ct)=i
> > >>>>>> xwork1(ct)=(1.0d0,0.0d0)
> > >>>>>> enddo
> > >>>>>>
> > >>>>>> call
> > >>>>>> VecSetValues(frhs,IendA-IstartA,loc,xwork1,INSERT_VALUES,ierr)
> > >>>>>> call VecZeroEntries(sol,ierr)
> > >>>>>>
> > >>>>>> deallocate(xwork1,loc)
> > >>>>>>
> > >>>>>> !.....Assemble Vectors
> > >>>>>> call VecAssemblyBegin(frhs,ierr)
> > >>>>>> call VecAssemblyEnd(frhs,ierr)
> > >>>>>>
> > >>>>>> !.....Solve the Linear System
> > >>>>>> call KSPSolve(ksp,frhs,sol,ierr)
> > >>>>>>
> > >>>>>> !call VecView(sol,PETSC_VIEWER_STDOUT_WORLD,ierr)
> > >>>>>>
> > >>>>>> if (rank==0) then
> > >>>>>> call cpu_time(endd)
> > >>>>>> write(*,*)
> > >>>>>> print '("Total time for HowBigLUCanBe = ",f21.3,"
> > >>>>>> seconds.")',endd-begin
> > >>>>>> endif
> > >>>>>>
> > >>>>>> call SlepcFinalize(ierr)
> > >>>>>>
> > >>>>>> STOP
> > >>>>>>
> > >>>>>>
> > >>>>>> end Subroutine HowBigLUCanBe
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>> On 07/08/2015 11:23 AM, Xiaoye S. Li wrote:
> > >>>>>>
> > >>>>>> Indeed, the parallel symbolic factorization routine needs power
> of
> > >>>>>> 2 processes, however, you can use however many processes you need;
> > >>>>>> internally, we redistribute matrix to nearest power of 2
> processes, do
> > >>>>>> symbolic, then redistribute back to all the processes to do
> factorization,
> > >>>>>> triangular solve etc. So, there is no restriction from the users
> > >>>>>> viewpoint.
> > >>>>>>
> > >>>>>> It's difficult to tell what the problem is. Do you think you can
> > >>>>>> print your matrix, then, I can do some debugging by running
> superlu_dist
> > >>>>>> standalone?
> > >>>>>>
> > >>>>>> Sherry
> > >>>>>>
> > >>>>>>
> > >>>>>> On Wed, Jul 8, 2015 at 10:34 AM, Anthony Paul Haas <
> > >>>>>> aph at email.arizona.edu> wrote:
> > >>>>>>
> > >>>>>>> Hi,
> > >>>>>>>
> > >>>>>>> I have used the switch -mat_superlu_dist_parsymbfact in my pbs
> > >>>>>>> script. However, although my program worked fine with sequential
> symbolic
> > >>>>>>> factorization, I get one of the following 2 behaviors when I run
> with
> > >>>>>>> parallel symbolic factorization (depending on the number of
> processors that
> > >>>>>>> I use):
> > >>>>>>>
> > >>>>>>> 1) the program just hangs (it seems stuck in some subroutine ==>
> > >>>>>>> see test.out-hangs)
> > >>>>>>> 2) I get a floating point exception ==> see
> > >>>>>>> test.out-floating-point-exception
> > >>>>>>>
> > >>>>>>> Note that as suggested in the Superlu manual, I use a power of 2
> > >>>>>>> number of procs. Are there any tunable parameters for the
> parallel symbolic
> > >>>>>>> factorization? Note that when I build my sparse matrix, most
> elements I add
> > >>>>>>> are nonzero of course but to simplify the programming, I also
> add a few
> > >>>>>>> zero elements in the sparse matrix. I was thinking that maybe if
> the
> > >>>>>>> parallel symbolic factorization proceed by block, there could be
> some
> > >>>>>>> blocks where the pivot would be zero, hence creating the FPE??
> > >>>>>>>
> > >>>>>>> Thanks,
> > >>>>>>>
> > >>>>>>> Anthony
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>
> > >>>>>>> On Wed, Jul 8, 2015 at 6:46 AM, Xiaoye S. Li <xsli at lbl.gov>
> wrote:
> > >>>>>>>
> > >>>>>>>> Did you find out how to change option to use parallel symbolic
> > >>>>>>>> factorization? Perhaps PETSc team can help.
> > >>>>>>>>
> > >>>>>>>> Sherry
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>> On Tue, Jul 7, 2015 at 3:58 PM, Xiaoye S. Li <xsli at lbl.gov>
> wrote:
> > >>>>>>>>
> > >>>>>>>>> Is there an inquiry function that tells you all the available
> > >>>>>>>>> options?
> > >>>>>>>>>
> > >>>>>>>>> Sherry
> > >>>>>>>>>
> > >>>>>>>>> On Tue, Jul 7, 2015 at 3:25 PM, Anthony Paul Haas <
> > >>>>>>>>> aph at email.arizona.edu> wrote:
> > >>>>>>>>>
> > >>>>>>>>>> Hi Sherry,
> > >>>>>>>>>>
> > >>>>>>>>>> Thanks for your message. I have used superlu_dist default
> > >>>>>>>>>> options. I did not realize that I was doing serial symbolic
> factorization.
> > >>>>>>>>>> That is probably the cause of my problem.
> > >>>>>>>>>> Each node on Garnet has 60GB usable memory and I can run with
> > >>>>>>>>>> 1,2,4,8,16 or 32 core per node.
> > >>>>>>>>>>
> > >>>>>>>>>> So I should use:
> > >>>>>>>>>>
> > >>>>>>>>>> -mat_superlu_dist_r 20
> > >>>>>>>>>> -mat_superlu_dist_c 32
> > >>>>>>>>>>
> > >>>>>>>>>> How do you specify the parallel symbolic factorization
> option?
> > >>>>>>>>>> is it -mat_superlu_dist_matinput 1
> > >>>>>>>>>>
> > >>>>>>>>>> Thanks,
> > >>>>>>>>>>
> > >>>>>>>>>> Anthony
> > >>>>>>>>>>
> > >>>>>>>>>>
> > >>>>>>>>>> On Tue, Jul 7, 2015 at 3:08 PM, Xiaoye S. Li <xsli at lbl.gov>
> > >>>>>>>>>> wrote:
> > >>>>>>>>>>
> > >>>>>>>>>>> For superlu_dist failure, this occurs during symbolic
> > >>>>>>>>>>> factorization. Since you are using serial symbolic
> factorization, it
> > >>>>>>>>>>> requires the entire graph of A to be available in the memory
> of one MPI
> > >>>>>>>>>>> task. How much memory do you have for each MPI task?
> > >>>>>>>>>>>
> > >>>>>>>>>>> It won't help even if you use more processes. You should
> try
> > >>>>>>>>>>> to use parallel symbolic factorization option.
> > >>>>>>>>>>>
> > >>>>>>>>>>> Another point. You set up process grid as:
> > >>>>>>>>>>> Process grid nprow 32 x npcol 20
> > >>>>>>>>>>> For better performance, you show swap the grid dimension.
> That
> > >>>>>>>>>>> is, it's better to use 20 x 32, never gives nprow larger
> than npcol.
> > >>>>>>>>>>>
> > >>>>>>>>>>>
> > >>>>>>>>>>> Sherry
> > >>>>>>>>>>>
> > >>>>>>>>>>>
> > >>>>>>>>>>> On Tue, Jul 7, 2015 at 1:27 PM, Barry Smith <
> bsmith at mcs.anl.gov>
> > >>>>>>>>>>> wrote:
> > >>>>>>>>>>>
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> I would suggest running a sequence of problems, 101 by
> 101
> > >>>>>>>>>>>> 111 by 111 etc and get the memory usage in each case (when
> you run out of
> > >>>>>>>>>>>> memory you can get NO useful information out about memory
> needs). You can
> > >>>>>>>>>>>> then plot memory usage as a function of problem size to get
> a handle on how
> > >>>>>>>>>>>> much memory it is using. You can also run on more and more
> processes
> > >>>>>>>>>>>> (which have a total of more memory) to see how large a
> problem you may be
> > >>>>>>>>>>>> able to reach.
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> MUMPS also has an "out of core" version (which we have
> never
> > >>>>>>>>>>>> used) that could in theory anyways let you get to large
> problems if you
> > >>>>>>>>>>>> have lots of disk space, but you are on your own figuring
> out how to use it.
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> Barry
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> > On Jul 7, 2015, at 2:37 PM, Anthony Paul Haas <
> > >>>>>>>>>>>> aph at email.arizona.edu> wrote:
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > Hi Jose,
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > In my code, I use once PETSc to solve a linear system to
> get
> > >>>>>>>>>>>> the baseflow (without using SLEPc) and then I use SLEPc to
> do the stability
> > >>>>>>>>>>>> analysis of that baseflow. This is why, there are some
> SLEPc options that
> > >>>>>>>>>>>> are not used in test.out-superlu_dist-151x151 (when I am
> solving for the
> > >>>>>>>>>>>> baseflow with PETSc only). I have attached a 101x101 case
> for which I get
> > >>>>>>>>>>>> the eigenvalues. That case works fine. However If i
> increase to 151x151, I
> > >>>>>>>>>>>> get the error that you can see in
> test.out-superlu_dist-151x151 (similar
> > >>>>>>>>>>>> error with mumps: see test.out-mumps-151x151 line 2918 ).
> If you look a the
> > >>>>>>>>>>>> very end of the files test.out-superlu_dist-151x151 and
> > >>>>>>>>>>>> test.out-mumps-151x151, you will see that the last info
> message printed is:
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > On Processor (after EPSSetFromOptions) 0 memory:
> > >>>>>>>>>>>> 0.65073152000E+08 =====> (see line 807 of
> module_petsc.F90)
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > This means that the memory error probably occurs in the
> call
> > >>>>>>>>>>>> to EPSSolve (see module_petsc.F90 line 810). I would like
> to evaluate how
> > >>>>>>>>>>>> much memory is required by the most memory intensive
> operation within
> > >>>>>>>>>>>> EPSSolve. Since I am solving a generalized EVP, I would
> imagine that it
> > >>>>>>>>>>>> would be the LU decomposition. But is there an accurate way
> of doing it?
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > Before starting with iterative solvers, I would like to
> > >>>>>>>>>>>> exploit as much as I can direct solvers. I tried GMRES with
> default
> > >>>>>>>>>>>> preconditioner at some point but I had convergence problem.
> What
> > >>>>>>>>>>>> solver/preconditioner would you recommend for a generalized
> non-Hermitian
> > >>>>>>>>>>>> (EPS_GNHEP) EVP?
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > Thanks,
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > Anthony
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > On Tue, Jul 7, 2015 at 12:17 AM, Jose E. Roman <
> > >>>>>>>>>>>> jroman at dsic.upv.es> wrote:
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > El 07/07/2015, a las 02:33, Anthony Haas escribió:
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > > Hi,
> > >>>>>>>>>>>> > >
> > >>>>>>>>>>>> > > I am computing eigenvalues using PETSc/SLEPc and
> > >>>>>>>>>>>> superlu_dist for the LU decomposition (my problem is a
> generalized
> > >>>>>>>>>>>> eigenvalue problem). The code runs fine for a grid with
> 101x101 but when I
> > >>>>>>>>>>>> increase to 151x151, I get the following error:
> > >>>>>>>>>>>> > >
> > >>>>>>>>>>>> > > Can't expand MemType 1: jcol 16104 (and then [NID
> 00037]
> > >>>>>>>>>>>> 2015-07-06 19:19:17 Apid 31025976: OOM killer terminated
> this process.)
> > >>>>>>>>>>>> > >
> > >>>>>>>>>>>> > > It seems to be a memory problem. I monitor the memory
> usage
> > >>>>>>>>>>>> as far as I can and it seems that memory usage is pretty
> low. The most
> > >>>>>>>>>>>> memory intensive part of the program is probably the LU
> decomposition in
> > >>>>>>>>>>>> the context of the generalized EVP. Is there a way to
> evaluate how much
> > >>>>>>>>>>>> memory will be required for that step? I am currently
> running the debug
> > >>>>>>>>>>>> version of the code which I would assume would use more
> memory?
> > >>>>>>>>>>>> > >
> > >>>>>>>>>>>> > > I have attached the output of the job. Note that the
> > >>>>>>>>>>>> program uses twice PETSc: 1) to solve a linear system for
> which no problem
> > >>>>>>>>>>>> occurs, and, 2) to solve the Generalized EVP with SLEPc,
> where I get the
> > >>>>>>>>>>>> error.
> > >>>>>>>>>>>> > >
> > >>>>>>>>>>>> > > Thanks
> > >>>>>>>>>>>> > >
> > >>>>>>>>>>>> > > Anthony
> > >>>>>>>>>>>> > > <test.out-superlu_dist-151x151>
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > In the output you are attaching there are no SLEPc
> objects in
> > >>>>>>>>>>>> the report and SLEPc options are not used. It seems that
> SLEPc calls are
> > >>>>>>>>>>>> skipped?
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > Do you get the same error with MUMPS? Have you tried to
> solve
> > >>>>>>>>>>>> linear systems with a preconditioned iterative solver?
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> > Jose
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>> >
> > >>>>>>>>>>>>
> <module_petsc.F90><test.out-mumps-151x151><test.out_superlu_dist-101x101><test.out-superlu_dist-151x151>
> > >>>>>>>>>>>>
> > >>>>>>>>>>>>
> > >>>>>>>>>>>
> > >>>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>
> > >>>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>
> > >>>>
> > >>>
> > >>
> > >
> >
>
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