[petsc-users] Can't expand MemType 1: jcol 16104
Anthony Haas
aph at email.arizona.edu
Thu Jul 30 19:23:03 CDT 2015
Hi Hong, Satish,
I have been using petsc-3.6.1 with superlu_dist 4.1
(--download-superlu_dist=superlu_dist_4.1.tar.gz) for a few days now. It
seems to be working fine. However, reading Satish email below, I wonder
if there is some kind of patch I need to apply for PETSc?
Thanks
Anthony
On 07/30/2015 01:51 PM, Satish Balay wrote:
> I've updated petsc to use v4.1. The changes are in branch
> 'balay/update-superlu_dist-4.1' - and merged to 'next' for now.
>
> Satish
>
> On Wed, 29 Jul 2015, Xiaoye S. Li wrote:
>
>> Thanks for quick update. In the new tarball, I have already removed the
>> junk files, as pointed out by Satish.
>>
>> Sherry
>>
>> On Wed, Jul 29, 2015 at 8:36 AM, Hong <hzhang at mcs.anl.gov> wrote:
>>
>>> 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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