June 2015 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] hdf5 viewer question
by Matthew Knepley 23 Jun '15

23 Jun '15

On Tue, Jun 23, 2015 at 9:38 AM, Dominic Meiser <dmeiser(a)txcorp.com> wrote: > Hi, > > I'm running into an issue with the Hdf5 viewer. For parallel vectors of > length larger than 2^16 I get the error message below. The vector is > created from a 1D DMDA with 2 dofs. Serial vectors work fine as do vectors > of length <= 2^16. The error message is reproduced below. The issue can be > reproduced with the attached example with 'mpirun -np 2 ./testcase > -da_grid_x 65537'. > > Do I need to configure the viewer in some way before using it? > You may have to configure with --with-64-bit-indices Thanks, Matt > Thanks, > Dominic > > > > HDF5-DIAG: Error detected in HDF5 (1.8.12) MPI-process 0: > #000: H5D.c line 170 in H5Dcreate2(): unable to create dataset > major: Dataset > minor: Unable to initialize object > #001: H5Dint.c line 439 in H5D__create_named(): unable to create and > link to dataset > major: Dataset > minor: Unable to initialize object > #002: H5L.c line 1638 in H5L_link_object(): unable to create new link to > object > major: Links > minor: Unable to initialize object > #003: H5L.c line 1882 in H5L_create_real(): can't insert link > major: Symbol table > minor: Unable to insert object > #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal > failed > major: Symbol table > minor: Object not found > #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator > failed > major: Symbol table > minor: Callback failed > #006: H5L.c line 1685 in H5L_link_cb(): unable to create object > major: Object header > minor: Unable to initialize object > #007: H5O.c line 3015 in H5O_obj_create(): unable to open object > major: Object header > HDF5-DIAG: Error detected in HDF5 (1.8.12) MPI-process 1: > #000: H5D.c line 170 in H5Dcreate2(): unable to create dataset > major: Dataset > minor: Unable to initialize object > #001: H5Dint.c line 439 in H5D__create_named(): unable to create and > link to dataset > major: Dataset > minor: Unable to initialize object > #002: H5L.c line 1638 in H5L_link_object(): unable to create new link to > object > major: Links > minor: Unable to initialize object > #003: H5L.c line 1882 in H5L_create_real(): can't insert link > major: Symbol table > minor: Unable to insert object > #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal > failed > major: Symbol table > minor: Object not found > #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator > failed > major: Symbol table > minor: Callback failed > #006: H5L.c line 1685 in H5L_link_cb(): unable to create object > major: Object header > minor: Unable to initialize object > #007: H5O.c line 3015 in H5O_obj_create(): unable to open object > major: Object header > minor: Can't open object > #008: H5Doh.c line 293 in H5O__dset_create(): unable to create dataset > major: Dataset > minor: Unable to initialize object > #009: H5Dint.c line 1044 in H5D__create(): unable to construct layout > information > major: Dataset > minor: Unable to initialize object > #010: H5Dchunk.c line 539 in H5D__chunk_construct(): chunk size must be > <= maximum dimension size for fixed-sized dimensions > major: Dataset > minor: Unable to initialize object > minor: Can't open object > #008: H5Doh.c line 293 in H5O__dset_create(): unable to create dataset > major: Dataset > minor: Unable to initialize object > #009: H5Dint.c line 1044 in H5D__create(): unable to construct layout > information > major: Dataset > minor: Unable to initialize object > #010: H5Dchunk.c line 539 in H5D__chunk_construct(): chunk size must be > <= maximum dimension size for fixed-sized dimensions > major: Dataset > minor: Unable to initialize object > [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: [1]PETSC ERROR: Error in external library > Error in external library > [0]PETSC ERROR: Error in HDF5 call H5Dcreate2() Status -1 > [0]PETSC ERROR: [1]PETSC ERROR: Error in HDF5 call H5Dcreate2() Status -1 > [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > shooting. > [0]PETSC ERROR: Petsc Release Version 3.6.0, unknown > [0]PETSC ERROR: [1]PETSC ERROR: Petsc Release Version 3.6.0, unknown > [1]PETSC ERROR: ./testcase on a fftw_test named longspeak.txcorp.com by > dmeiser Mon Jun 22 16:59:21 2015 > ./testcase on a fftw_test named longspeak.txcorp.com by dmeiser Mon Jun > 22 16:59:21 2015 > [0]PETSC ERROR: Configure options --download-hdf5=1 --download-fftw=1 > --with-mpi=1 PETSC_ARCH=fftw_test > [0]PETSC ERROR: [1]PETSC ERROR: Configure options --download-hdf5=1 > --download-fftw=1 --with-mpi=1 PETSC_ARCH=fftw_test > [1]PETSC ERROR: #1 VecView_MPI_HDF5_DA() line 535 in > /home/scratch/petsc/src/dm/impls/da/gr2.c > #1 VecView_MPI_HDF5_DA() line 535 in > /home/scratch/petsc/src/dm/impls/da/gr2.c > [0]PETSC ERROR: #2 VecView_MPI_DA() line 713 in > /home/scratch/petsc/src/dm/impls/da/gr2.c > [1]PETSC ERROR: #2 VecView_MPI_DA() line 713 in > /home/scratch/petsc/src/dm/impls/da/gr2.c > [0]PETSC ERROR: #3 VecView() line 618 in > /home/scratch/petsc/src/vec/vec/interface/vector.c > [1]PETSC ERROR: #3 VecView() line 618 in > /home/scratch/petsc/src/vec/vec/interface/vector.c > [0]PETSC ERROR: [1]PETSC ERROR: #4 dump() line 75 in testcase.c > #4 dump() line 75 in testcase.c > [0]PETSC ERROR: #5 main() line 31 in testcase.c > [1]PETSC ERROR: #5 main() line 31 in testcase.c > [0]PETSC ERROR: [1]PETSC ERROR: PETSc Option Table entries: > [1]PETSC ERROR: PETSc Option Table entries: > [0]PETSC ERROR: -da_grid_x 65537 > [0]PETSC ERROR: -da_grid_x 65537 > [1]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-maint(a)mcs.anl.gov---------- > ----------------End of Error Message -------send entire error message to > petsc-maint(a)mcs.anl.gov---------- > [cli_0]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 76) - process 0 > [cli_1]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 76) - process 1 > > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = PID 15847 RUNNING AT longspeak.txcorp.com > = EXIT CODE: 76 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > =================================================================================== > > -- > Dominic Meiser > Tech-X Corporation > 5621 Arapahoe Avenue > Boulder, CO 80303 > USA > Telephone: 303-996-2036 > Fax: 303-448-7756 > www.txcorp.com > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener

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hdf5 viewer question
by Dominic Meiser 23 Jun '15

23 Jun '15

Hi, I'm running into an issue with the Hdf5 viewer. For parallel vectors of length larger than 2^16 I get the error message below. The vector is created from a 1D DMDA with 2 dofs. Serial vectors work fine as do vectors of length <= 2^16. The error message is reproduced below. The issue can be reproduced with the attached example with 'mpirun -np 2 ./testcase -da_grid_x 65537'. Do I need to configure the viewer in some way before using it? Thanks, Dominic HDF5-DIAG: Error detected in HDF5 (1.8.12) MPI-process 0: #000: H5D.c line 170 in H5Dcreate2(): unable to create dataset major: Dataset minor: Unable to initialize object #001: H5Dint.c line 439 in H5D__create_named(): unable to create and link to dataset major: Dataset minor: Unable to initialize object #002: H5L.c line 1638 in H5L_link_object(): unable to create new link to object major: Links minor: Unable to initialize object #003: H5L.c line 1882 in H5L_create_real(): can't insert link major: Symbol table minor: Unable to insert object #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed major: Symbol table minor: Object not found #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed major: Symbol table minor: Callback failed #006: H5L.c line 1685 in H5L_link_cb(): unable to create object major: Object header minor: Unable to initialize object #007: H5O.c line 3015 in H5O_obj_create(): unable to open object major: Object header HDF5-DIAG: Error detected in HDF5 (1.8.12) MPI-process 1: #000: H5D.c line 170 in H5Dcreate2(): unable to create dataset major: Dataset minor: Unable to initialize object #001: H5Dint.c line 439 in H5D__create_named(): unable to create and link to dataset major: Dataset minor: Unable to initialize object #002: H5L.c line 1638 in H5L_link_object(): unable to create new link to object major: Links minor: Unable to initialize object #003: H5L.c line 1882 in H5L_create_real(): can't insert link major: Symbol table minor: Unable to insert object #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed major: Symbol table minor: Object not found #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed major: Symbol table minor: Callback failed #006: H5L.c line 1685 in H5L_link_cb(): unable to create object major: Object header minor: Unable to initialize object #007: H5O.c line 3015 in H5O_obj_create(): unable to open object major: Object header minor: Can't open object #008: H5Doh.c line 293 in H5O__dset_create(): unable to create dataset major: Dataset minor: Unable to initialize object #009: H5Dint.c line 1044 in H5D__create(): unable to construct layout information major: Dataset minor: Unable to initialize object #010: H5Dchunk.c line 539 in H5D__chunk_construct(): chunk size must be <= maximum dimension size for fixed-sized dimensions major: Dataset minor: Unable to initialize object minor: Can't open object #008: H5Doh.c line 293 in H5O__dset_create(): unable to create dataset major: Dataset minor: Unable to initialize object #009: H5Dint.c line 1044 in H5D__create(): unable to construct layout information major: Dataset minor: Unable to initialize object #010: H5Dchunk.c line 539 in H5D__chunk_construct(): chunk size must be <= maximum dimension size for fixed-sized dimensions major: Dataset minor: Unable to initialize object [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: [1]PETSC ERROR: Error in external library Error in external library [0]PETSC ERROR: Error in HDF5 call H5Dcreate2() Status -1 [0]PETSC ERROR: [1]PETSC ERROR: Error in HDF5 call H5Dcreate2() Status -1 [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.6.0, unknown [0]PETSC ERROR: [1]PETSC ERROR: Petsc Release Version 3.6.0, unknown [1]PETSC ERROR: ./testcase on a fftw_test named longspeak.txcorp.com by dmeiser Mon Jun 22 16:59:21 2015 ./testcase on a fftw_test named longspeak.txcorp.com by dmeiser Mon Jun 22 16:59:21 2015 [0]PETSC ERROR: Configure options --download-hdf5=1 --download-fftw=1 --with-mpi=1 PETSC_ARCH=fftw_test [0]PETSC ERROR: [1]PETSC ERROR: Configure options --download-hdf5=1 --download-fftw=1 --with-mpi=1 PETSC_ARCH=fftw_test [1]PETSC ERROR: #1 VecView_MPI_HDF5_DA() line 535 in /home/scratch/petsc/src/dm/impls/da/gr2.c #1 VecView_MPI_HDF5_DA() line 535 in /home/scratch/petsc/src/dm/impls/da/gr2.c [0]PETSC ERROR: #2 VecView_MPI_DA() line 713 in /home/scratch/petsc/src/dm/impls/da/gr2.c [1]PETSC ERROR: #2 VecView_MPI_DA() line 713 in /home/scratch/petsc/src/dm/impls/da/gr2.c [0]PETSC ERROR: #3 VecView() line 618 in /home/scratch/petsc/src/vec/vec/interface/vector.c [1]PETSC ERROR: #3 VecView() line 618 in /home/scratch/petsc/src/vec/vec/interface/vector.c [0]PETSC ERROR: [1]PETSC ERROR: #4 dump() line 75 in testcase.c #4 dump() line 75 in testcase.c [0]PETSC ERROR: #5 main() line 31 in testcase.c [1]PETSC ERROR: #5 main() line 31 in testcase.c [0]PETSC ERROR: [1]PETSC ERROR: PETSc Option Table entries: [1]PETSC ERROR: PETSc Option Table entries: [0]PETSC ERROR: -da_grid_x 65537 [0]PETSC ERROR: -da_grid_x 65537 [1]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- [cli_0]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 76) - process 0 [cli_1]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 76) - process 1 =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 15847 RUNNING AT longspeak.txcorp.com = EXIT CODE: 76 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== -- Dominic Meiser Tech-X Corporation 5621 Arapahoe Avenue Boulder, CO 80303 USA Telephone: 303-996-2036 Fax: 303-448-7756 www.txcorp.com

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Re: [petsc-dev] Missing Fortran interfaces
by John O'Sullivan 23 Jun '15

23 Jun '15

Hi guys, Attached is a very simple program in C which uses SNESSetUpdate to switch variables while solving the following nonlinear equation: In region 1 (x <= 5): x^3 - 50 = 0 In region 2 (x > 5): y = x + 3 so solve: (y - 3)^3 - 50 = 0 The variable switching stops the solution a small distance across the region boundary so: if currently in region 1 and x > 5: y -> 8 + epsilon, region -> 2 if currently in region 2 and x <= 8: x -> 5 - epsilon, region -> 1 This is very simplified but analogous to what we want to do. It seems to work ok and has similar convergence to the non-swtiching case (also included). Obviously this example doesn't change gradients when the variable is switched though. Could you guys add the fortran interfaces for SNESSetUpdate (missing), and SNESSetApplicationContext and SNESGetApplicationContext (if they're missing) and I will try it out on some more complicated examples. Thanks very much John -- Dr John O'Sullivan Lecturer Department of Engineering Science University of Auckland, New Zealand email: jp.osullivan at auckland.ac.nz<https://lists.mcs.anl.gov/mailman/listinfo/petsc-dev> tel: +64 (0)9 923 85353 ________________________________ From: Peter Lichtner [peter.lichtner(a)gmail.com] Sent: Wednesday, 17 June 2015 8:42 a.m. To: Barry Smith Cc: John O'Sullivan; petsc-dev(a)mcs.anl.gov; Richard Mills Subject: Re: [petsc-dev] Missing Fortran interfaces See comments below …Peter On Jun 16, 2015, at 13:43, Barry Smith <bsmith(a)mcs.anl.gov<mailto:[email protected]>> wrote: On Jun 12, 2015, at 10:03 PM, Peter Lichtner <peter.lichtner(a)gmail.com<mailto:[email protected]>> wrote: Barry: here is an attempt to explain how variable switching works in pflotran (we may need to iterate on this if it's not clear). I will consider as an example the 2-phase, 3-component water-supercritical CO2 system. Any grid cell (we use finite volume) can exist in one of three possible states: single-phase pure liquid water (l); single-phase pure supercritical CO2 (g); or two-phase coexistence of water and supercritical CO2 (2ph). Each of these states is described by three independent (nonunique) state variables. One possibility is: l: (p_l, T, X_CO2^l) g: (p_g, T, X_CO2^g) 2ph: (p_g, T, s_g) where p_l,g = liquid or gas pressure, T = temperature, and s_g = volume fraction of pore space occupied by supercritical CO2. Where variable switching comes into play is when a grid cell undergoes a phase change with the following possibilities: l -> 2ph g -> 2ph 2ph -> l 2ph -> g Note that we do not include directly l <-> g. As a consequence different regions of space have different primary variables the boundaries of which are changing with time along with the state variables. Line search is not feasible with the current implementation in petsc. After a completed time step or Newton iteration, the stability of the solution in each grid cell must be checked for a change of phase. For example, if the cell is in a 2 phase state, but the solution gives s_g > 1 or s_g < 1, Do you mean s_q < 0 or can s_g only be 1? This was a typo—sorry about that: I meant s_g < 0 or s_g > 1 triggers a phase change. For a two-phase system the physical values of s_g are: 0 < s_g < 1. then a phase change occurs from 2ph -> g or 2ph -> l, respectively, and a change of variables is necessary: (p_g, T, s_g) -> (p_l, T, X_CO2^l) or (p_g, T, s_g) -> (p_g, T, X_CO2^g) Agree with John here. what is the formula for these change of variables? how/when do g and l go to 2p_h ? Thanks Barry …Peter On Jun 12, 2015, at 18:14, Barry Smith <bsmith(a)mcs.anl.gov<mailto:[email protected]>> wrote: John, We can provide any Fortran stubs you need but before we do could you please outline to us (in algebraic notation; not in reference to PETSc code) how you plan to handle your "variable switching". That is, what is the problem being solved, what are the constraints, when do you need to switch variables etc? I would say everyone who has tried to do variable switching in PETSc before has failed because we (the PETSc developers) did not help them enough and understand what is needed in the Newton solver. I suspect we need to provide a bit more functionality in PETSc to make variable switching a success and I'd like to understand what that is and add it to the PETSc algorithms. Also if you know of any references that actually explain variable switching in detail, that would be great, all I've found are vague hand-wavy discussions that leave too many important details unexplained. Thanks Barry On Jun 12, 2015, at 5:54 PM, John O'Sullivan <jp.osullivan(a)auckland.ac.nz<mailto:[email protected]>> wrote: Hi, We're working on changing variables during an SNES solve so that we can handle phase changes. I'm looking into using SNESSetUpdate but there doesn't seem to be a fortran interface. I get an error: Undefined symbols for architecture x86_64: "_snessetupdate_", referenced from: _MAIN__ in phaseChange.o I've looked in the interface files and can't find it either. I tried writing one myself but things get a bit too complicated to guess... Can an interface be added please? Is this the best to do variable switching? If not where would be the right place and are there Fortran interfaces? We will be changing from Pressure, Temperature to Pressure, Saturation etc. But for now I'm just working on a simple example code. Cheers John -- Dr John O'Sullivan Lecturer Department of Engineering Science University of Auckland, New Zealand email: jp.osullivan at auckland.ac.nz<http://auckland.ac.nz> tel: +64 (0)9 923 85353

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Re: [petsc-dev] Error when calling PETSc
by Barry Smith 22 Jun '15

22 Jun '15

You are missing the ierr argument > On Jun 22, 2015, at 7:33 PM, Hector E Barrios Molano <hectorb(a)utexas.edu> wrote: > > Hi Satish, > > I run this program with petsc-master on Linux with Valgrind and idb. > > Here is how I am calling PETSc: > > call MatCreateBAIJ(MPI_COMM_WORLD,nblock/2,N_mat,N_mat, >> PETSC_DECIDE,PETSC_DECIDE,PETSC_DEFAULT_INTEGER,PNNZD, >> PETSC_DEFAULT_INTEGER,PNNZO,mat,ierr) > call MatSetup(mat,ierr) > call MatSetOption(mat, MAT_NEW_NONZERO_ALLOCATION_ERR, >> PETSC_FALSE) > > Any idea of this error?, both idb and valgrind points to matrixf.c:890 > > Thanks, > > Here is idb output: > > matsetoption_ (mat=0x36e1e48, op=0x32c2a20, flg=0x32c296c, > __ierr=0x32c296c) at > /home/hector/dwnld_prog/petsc-master/src/mat/interface/ftn-auto/matrixf.c:890 > 890 *__ierr = MatSetOption( > > > And this is the valgrind output: > > $ valgrind --track-origins=yes --leak-check=full ./prog -d 3comp.dat > ==18555== Memcheck, a memory error detector > ==18555== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al. > ==18555== Using Valgrind-3.10.1 and LibVEX; rerun with -h for copyright info > ==18555== Command: ./prog -d 3comp.dat > ==18555== > ==18555== Warning: set address range perms: large range [0x36fc000, > 0x2e2b7000) (defined) > NUMPRC: 1 > PSTD, TRSTD = 14.6960000000000 519.670000000000 in INFLUID > > TIME TIMESTEP ITERATION FLASH_RES VOLUME_RES > MASS_RES WATER_RES > going into SOLVERS > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac > OS X to find memory corruption errors > [0]PETSC ERROR: likely location of problem given in stack below > [0]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > [0]PETSC ERROR: INSTEAD the line number of the start of the function > [0]PETSC ERROR: is given. > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Signal received > [0]PETSC ERROR: See > http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > shooting. > [0]PETSC ERROR: Petsc Development GIT revision: v3.6-34-gc9ff9ea GIT > Date: 2015-06-17 23:52:21 -0500 > [0]PETSC ERROR: ./prog on a linux-intel named petros.cpge.utexas.edu > by hector Mon Jun 22 19:25:59 2015 > [0]PETSC ERROR: Configure options > --prefix=/home/hector/installed/petsc3.6-intel > --PETSC_ARCH=linux-intel > --with-mpi-dir=/home/hector/installed/openmpi-intel/ > --with-parmetis-dir=/home/hector/installed/parmetis/ > --with-metis-dir=/home/hector/installed/parmetis/ > --with-zoltan-dir=/home/hector/installed/zoltan/ --download-ptscotch > --download-hypre > --with-blas-lapack-dir=/share/apps/intel/composer_xe_2011_sp1.9.293/mkl/ > --with-valgrind=1 --with-valgrind-dir=/home/hector/installed > --with-shared-libraries=0 > [0]PETSC ERROR: #1 User provided function() line 0 in unknown file > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with errorcode 59. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > -------------------------------------------------------------------------- > ==18555== > ==18555== HEAP SUMMARY: > ==18555== in use at exit: 52,616,185 bytes in 7,935 blocks > ==18555== total heap usage: 121,248 allocs, 113,313 frees, > 69,099,609 bytes allocated > ==18555== > ==18555== 240 bytes in 6 blocks are definitely lost in loss record > 5,950 of 6,383 > ==18555== at 0x2ECBEAF0: malloc (vg_replace_malloc.c:296) > ==18555== by 0x324D4798E1: strdup (in /lib64/libc-2.5.so) > ==18555== by 0x331E1A27: opal_show_help_vstring (in > /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) > ==18555== by 0x32F30F53: orte_show_help (in > /home/hector/installed/openmpi-intel/lib/libopen-rte.so.7.0.5) > ==18555== by 0x32A5F709: PMPI_Abort (in > /home/hector/installed/openmpi-intel/lib/libmpi.so.1.6.1) > ==18555== by 0x245A9F3: PetscSignalHandlerDefault (signal.c:161) > ==18555== by 0x245A356: PetscSignalHandler_Private (signal.c:49) > ==18555== by 0x324D4302EF: ??? (in /lib64/libc-2.5.so) > ==18555== by 0x20A104E: matsetoption_ (matrixf.c:890) > ==18555== by 0x1BE0576: jpetsc3d_ (xsolver.f:382) > ==18555== by 0x1BDC9A3: xsolver_ (xsolver.f:104) > ==18555== by 0x1AB1BB3: solvers_ (xsolve.f:60) > ==18555== > ==18555== 336 bytes in 1 blocks are possibly lost in loss record 6,043 of 6,383 > ==18555== at 0x2ECC0867: calloc (vg_replace_malloc.c:623) > ==18555== by 0x324D0100A2: _dl_allocate_tls (in /lib64/ld-2.5.so) > ==18555== by 0x324E006EB8: pthread_create@@GLIBC_2.2.5 (in > /lib64/libpthread-2.5.so) > ==18555== by 0x331BABB5: opal_thread_start (in > /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) > ==18555== by 0x32F43A18: orte_ess_base_app_setup (in > /home/hector/installed/openmpi-intel/lib/libopen-rte.so.7.0.5) > ==18555== by 0x34C503DE: rte_init (in > /home/hector/installed/openmpi-intel/lib/openmpi/mca_ess_singleton.so) > ==18555== by 0x32F222F5: orte_init (in > /home/hector/installed/openmpi-intel/lib/libopen-rte.so.7.0.5) > ==18555== by 0x32A4D67E: ompi_mpi_init (in > /home/hector/installed/openmpi-intel/lib/libmpi.so.1.6.1) > ==18555== by 0x32A7052E: PMPI_Init (in > /home/hector/installed/openmpi-intel/lib/libmpi.so.1.6.1) > ==18555== by 0x3122CB27: PMPI_INIT (in > /home/hector/installed/openmpi-intel/lib/libmpi_mpifh.so.2.5.0) > ==18555== by 0x1C89281: setprcs_ (man.f:144) > ==18555== by 0x1C4CB98: MAIN__ (main.f:114) > ==18555== > ==18555== 7,550 bytes in 111 blocks are definitely lost in loss record > 6,243 of 6,383 > ==18555== at 0x2ECC0A3D: realloc (vg_replace_malloc.c:692) > ==18555== by 0x324D469725: vasprintf (in /lib64/libc-2.5.so) > ==18555== by 0x324D44D727: asprintf (in /lib64/libc-2.5.so) > ==18555== by 0x331E913D: dlopen_foreachfile (in > /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) > ==18555== by 0x331CCBC0: mca_base_component_find (in > /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) > ==18555== by 0x331D5EC0: mca_base_framework_components_register (in > /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) > ==18555== by 0x331D62DE: mca_base_framework_register (in > /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) > ==18555== by 0x331D6331: mca_base_framework_open (in > /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) > ==18555== by 0x331B71E8: opal_init (in > /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) > ==18555== by 0x32F221C4: orte_init (in > /home/hector/installed/openmpi-intel/lib/libopen-rte.so.7.0.5) > ==18555== by 0x32A4D67E: ompi_mpi_init (in > /home/hector/installed/openmpi-intel/lib/libmpi.so.1.6.1) > ==18555== by 0x32A7052E: PMPI_Init (in > /home/hector/installed/openmpi-intel/lib/libmpi.so.1.6.1) > ==18555== > ==18555== LEAK SUMMARY: > ==18555== definitely lost: 7,790 bytes in 117 blocks > ==18555== indirectly lost: 0 bytes in 0 blocks > ==18555== possibly lost: 336 bytes in 1 blocks > ==18555== still reachable: 52,608,059 bytes in 7,817 blocks > ==18555== suppressed: 0 bytes in 0 blocks > ==18555== Reachable blocks (those to which a pointer was found) are not shown. > ==18555== To see them, rerun with: --leak-check=full --show-leak-kinds=all > ==18555== > ==18555== For counts of detected and suppressed errors, rerun with: -v > ==18555== ERROR SUMMARY: 3 errors from 3 contexts (suppressed: 4 from 4) > > Hector > > On Fri, Jun 19, 2015 at 2:29 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: >>> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file >> >> PETSc thinks there is an error in user code. Its best if you run it in >> a debugger and check whats going on. [on linux one can also use >> valgrind to track down problems] >> >> There are many changes from petsc3.1 to petsc-3.6. Make sure >> you go throgh the changes files. On C - one can rely on the compiler >> prototype checks to catch most of the changes. But with fortran - you >> might have to rely on a debugger/valgrind to [and the changes docs] >> to find the changes. >> >> http://www.mcs.anl.gov/petsc/documentation/changes/index.html >> >> Satish >> >> On Fri, 19 Jun 2015, Hector E Barrios Molano wrote: >> >>> Hi Satish, >>> >>> I used MatSetOption, I'm ignoring the performance penalty for now. >>> >>> Now I have this error: >>> >>> [0]PETSC ERROR: >>> ------------------------------------------------------------------------ >>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >>> probably memory access out of range >>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >>> [0]PETSC ERROR: or see >>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac >>> OS X to find memory corruption errors >>> [0]PETSC ERROR: likely location of problem given in stack below >>> [0]PETSC ERROR: --------------------- Stack Frames >>> ------------------------------------ >>> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, >>> [0]PETSC ERROR: INSTEAD the line number of the start of the function >>> [0]PETSC ERROR: is given. >>> [0]PETSC ERROR: --------------------- Error Message >>> -------------------------------------------------------------- >>> [0]PETSC ERROR: Signal received >>> [0]PETSC ERROR: See >>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>> shooting. >>> [0]PETSC ERROR: Petsc Development GIT revision: v3.6-34-gc9ff9ea GIT >>> Date: 2015-06-17 23:52:21 -0500 >>> [0]PETSC ERROR: F:\prog_win\prog\Debug\prog.exe on a windows-intel >>> named HECTOR-PC by hector Fri Jun 19 14:06:17 2015 >>> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" >>> --with-fc="win32fe ifort" --prefix=/cygdrive/c/Installed/petsc/ >>> --PETSC_ARCH=windows-intel >>> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include >>> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib >>> --with-metis-include=/cygdrive/c/Installed/parmetis/include >>> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib >>> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]" >>> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]" >>> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]" >>> --with-scalapack-include=/cygdrive/c/Installed/mkl/include >>> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_lp64.lib]" >>> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file >>> >>> job aborted: >>> [ranks] message >>> >>> [0] application aborted >>> aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 >>> >>> On Fri, Jun 19, 2015 at 12:57 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: >>>> As the message says: >>>> >>>>> [0]PETSC ERROR: New nonzero at (0,20) caused a malloc >>>>> Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn off this check >>>> >>>> Note: mallocs make the code slow - so its up to you to do a proper >>>> preallocation of memory - or disable the check as the above message >>>> indicadtes [and ignore the performance penalty for now.]. >>>> >>>> Satish >>>> >>>> On Fri, 19 Jun 2015, Hector E Barrios Molano wrote: >>>> >>>>> Hi PETSc Experts, >>>>> >>>>> I'm compiling a Windows program using petsc-dev, this program >>>>> previously used petsc-3.1 the only change performed was: >>>>> >>>>> MatCreateMPIBAIJ --> MatCreateBAIJ >>>>> >>>>> As the PETSc documentation suggested. >>>>> >>>>> I only changed the name of the function. >>>>> >>>>> I got to a problem when the program is launched and PETSc is called by >>>>> the program: >>>>> >>>>> [0]PETSC ERROR: --------------------- Error Message >>>>> -------------------------------------------------------------- >>>>> [0]PETSC ERROR: Argument out of range >>>>> [0]PETSC ERROR: New nonzero at (0,20) caused a malloc >>>>> Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to >>>>> turn off this check >>>>> [0]PETSC ERROR: See >>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>> shooting. >>>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.6-34-gc9ff9ea GIT >>>>> Date: 2015-06-17 23:52:21 -0500 >>>>> [0]PETSC ERROR: F:\prog_win\prog\Debug\prog.exe on a windows-intel >>>>> named HECTOR-PC by hector Thu Jun 18 18:31:42 2015 >>>>> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" >>>>> --with-fc="win32fe ifort" --prefix=/cygdrive/c/Installed/petsc/ >>>>> --PETSC_ARCH=windows-intel >>>>> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include >>>>> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib >>>>> --with-metis-include=/cygdrive/c/Installed/parmetis/include >>>>> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib >>>>> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]" >>>>> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]" >>>>> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]" >>>>> --with-scalapack-include=/cygdrive/c/Installed/mkl/include >>>>> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_lp64.lib]" >>>>> [0]PETSC ERROR: #1 MatSetValues_SeqBAIJ() line 2192 in >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: #2 MatSetValues() line 1175 in >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: --------------------- Error Message >>>>> -------------------------------------------------------------- >>>>> [0]PETSC ERROR: Argument out of range >>>>> [0]PETSC ERROR: New nonzero at (1,21) caused a malloc >>>>> Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to >>>>> turn off this check >>>>> [0]PETSC ERROR: See >>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>> shooting. >>>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.6-34-gc9ff9ea GIT >>>>> Date: 2015-06-17 23:52:21 -0500 >>>>> [0]PETSC ERROR: F:\prog_win\prog\Debug\prog.exe on a windows-intel >>>>> named HECTOR-PC by hector Thu Jun 18 18:31:42 2015 >>>>> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" >>>>> --with-fc="win32fe ifort" --prefix=/cygdrive/c/Installed/petsc/ >>>>> --PETSC_ARCH=windows-intel >>>>> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include >>>>> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib >>>>> --with-metis-include=/cygdrive/c/Installed/parmetis/include >>>>> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib >>>>> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]" >>>>> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]" >>>>> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]" >>>>> --with-scalapack-include=/cygdrive/c/Installed/mkl/include >>>>> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_lp64.lib]" >>>>> [0]PETSC ERROR: #3 MatSetValues_SeqBAIJ() line 2192 in >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: #4 MatSetValues() line 1175 in >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> . >>>>> . >>>>> . >>>>> [0]PETSC ERROR: #3599 MatSetValues_SeqBAIJ() line 2192 in >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: #3600 MatSetValues() line 1175 in >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: >>>>> ------------------------------------------------------------------------ >>>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >>>>> probably memory access out of range >>>>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >>>>> [0]PETSC ERROR: or see >>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac >>>>> OS X to find memory corruption errors >>>>> [0]PETSC ERROR: likely location of problem given in stack below >>>>> [0]PETSC ERROR: --------------------- Stack Frames >>>>> ------------------------------------ >>>>> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, >>>>> [0]PETSC ERROR: INSTEAD the line number of the start of the function >>>>> [0]PETSC ERROR: is given. >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >>>>> [0]PETSC ERROR: [0] MatSetValues line 1142 >>>>> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >>>>> [0]PETSC ERROR: --------------------- Error Message >>>>> -------------------------------------------------------------- >>>>> [0]PETSC ERROR: Signal received >>>>> [0]PETSC ERROR: See >>>>> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>> shooting. >>>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.6-34-gc9ff9ea GIT >>>>> Date: 2015-06-17 23:52:21 -0500 >>>>> [0]PETSC ERROR: F:\prog_win\prog\Debug\prog.exe on a windows-intel >>>>> named HECTOR-PC by hector Fri Jun 19 12:43:06 2015 >>>>> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" >>>>> --with-fc="win32fe ifort" --prefix=/cygdrive/c/Installed/petsc/ >>>>> --PETSC_ARCH=windows-intel >>>>> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include >>>>> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib >>>>> --with-metis-include=/cygdrive/c/Installed/parmetis/include >>>>> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib >>>>> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]" >>>>> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]" >>>>> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]" >>>>> --with-scalapack-include=/cygdrive/c/Installed/mkl/include >>>>> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_lp64.lib]" >>>>> [0]PETSC ERROR: #3601 User provided function() line 0 in unknown file >>>>> >>>>> job aborted: >>>>> [ranks] message >>>>> >>>>> [0] application aborted >>>>> aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 >>>>> >>>>> >>>>> I'm compiling the program on Visual Studio, what could be the problem? >>>>> >>>>> Thanks for your help, >>>>> >>>>> Hector >>>>> >>>> >>> >>

1 0

Re: [petsc-dev] Error when calling PETSc
by Hector E Barrios Molano 22 Jun '15

22 Jun '15

Hi Satish, I run this program with petsc-master on Linux with Valgrind and idb. Here is how I am calling PETSc: call MatCreateBAIJ(MPI_COMM_WORLD,nblock/2,N_mat,N_mat, > PETSC_DECIDE,PETSC_DECIDE,PETSC_DEFAULT_INTEGER,PNNZD, > PETSC_DEFAULT_INTEGER,PNNZO,mat,ierr) call MatSetup(mat,ierr) call MatSetOption(mat, MAT_NEW_NONZERO_ALLOCATION_ERR, > PETSC_FALSE) Any idea of this error?, both idb and valgrind points to matrixf.c:890 Thanks, Here is idb output: matsetoption_ (mat=0x36e1e48, op=0x32c2a20, flg=0x32c296c, __ierr=0x32c296c) at /home/hector/dwnld_prog/petsc-master/src/mat/interface/ftn-auto/matrixf.c:890 890 *__ierr = MatSetOption( And this is the valgrind output: $ valgrind --track-origins=yes --leak-check=full ./prog -d 3comp.dat ==18555== Memcheck, a memory error detector ==18555== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al. ==18555== Using Valgrind-3.10.1 and LibVEX; rerun with -h for copyright info ==18555== Command: ./prog -d 3comp.dat ==18555== ==18555== Warning: set address range perms: large range [0x36fc000, 0x2e2b7000) (defined) NUMPRC: 1 PSTD, TRSTD = 14.6960000000000 519.670000000000 in INFLUID TIME TIMESTEP ITERATION FLASH_RES VOLUME_RES MASS_RES WATER_RES going into SOLVERS [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [0]PETSC ERROR: likely location of problem given in stack below [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, [0]PETSC ERROR: INSTEAD the line number of the start of the function [0]PETSC ERROR: is given. [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Signal received [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Development GIT revision: v3.6-34-gc9ff9ea GIT Date: 2015-06-17 23:52:21 -0500 [0]PETSC ERROR: ./prog on a linux-intel named petros.cpge.utexas.edu by hector Mon Jun 22 19:25:59 2015 [0]PETSC ERROR: Configure options --prefix=/home/hector/installed/petsc3.6-intel --PETSC_ARCH=linux-intel --with-mpi-dir=/home/hector/installed/openmpi-intel/ --with-parmetis-dir=/home/hector/installed/parmetis/ --with-metis-dir=/home/hector/installed/parmetis/ --with-zoltan-dir=/home/hector/installed/zoltan/ --download-ptscotch --download-hypre --with-blas-lapack-dir=/share/apps/intel/composer_xe_2011_sp1.9.293/mkl/ --with-valgrind=1 --with-valgrind-dir=/home/hector/installed --with-shared-libraries=0 [0]PETSC ERROR: #1 User provided function() line 0 in unknown file -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 59. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- ==18555== ==18555== HEAP SUMMARY: ==18555== in use at exit: 52,616,185 bytes in 7,935 blocks ==18555== total heap usage: 121,248 allocs, 113,313 frees, 69,099,609 bytes allocated ==18555== ==18555== 240 bytes in 6 blocks are definitely lost in loss record 5,950 of 6,383 ==18555== at 0x2ECBEAF0: malloc (vg_replace_malloc.c:296) ==18555== by 0x324D4798E1: strdup (in /lib64/libc-2.5.so) ==18555== by 0x331E1A27: opal_show_help_vstring (in /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) ==18555== by 0x32F30F53: orte_show_help (in /home/hector/installed/openmpi-intel/lib/libopen-rte.so.7.0.5) ==18555== by 0x32A5F709: PMPI_Abort (in /home/hector/installed/openmpi-intel/lib/libmpi.so.1.6.1) ==18555== by 0x245A9F3: PetscSignalHandlerDefault (signal.c:161) ==18555== by 0x245A356: PetscSignalHandler_Private (signal.c:49) ==18555== by 0x324D4302EF: ??? (in /lib64/libc-2.5.so) ==18555== by 0x20A104E: matsetoption_ (matrixf.c:890) ==18555== by 0x1BE0576: jpetsc3d_ (xsolver.f:382) ==18555== by 0x1BDC9A3: xsolver_ (xsolver.f:104) ==18555== by 0x1AB1BB3: solvers_ (xsolve.f:60) ==18555== ==18555== 336 bytes in 1 blocks are possibly lost in loss record 6,043 of 6,383 ==18555== at 0x2ECC0867: calloc (vg_replace_malloc.c:623) ==18555== by 0x324D0100A2: _dl_allocate_tls (in /lib64/ld-2.5.so) ==18555== by 0x324E006EB8: pthread_create@@GLIBC_2.2.5 (in /lib64/libpthread-2.5.so) ==18555== by 0x331BABB5: opal_thread_start (in /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) ==18555== by 0x32F43A18: orte_ess_base_app_setup (in /home/hector/installed/openmpi-intel/lib/libopen-rte.so.7.0.5) ==18555== by 0x34C503DE: rte_init (in /home/hector/installed/openmpi-intel/lib/openmpi/mca_ess_singleton.so) ==18555== by 0x32F222F5: orte_init (in /home/hector/installed/openmpi-intel/lib/libopen-rte.so.7.0.5) ==18555== by 0x32A4D67E: ompi_mpi_init (in /home/hector/installed/openmpi-intel/lib/libmpi.so.1.6.1) ==18555== by 0x32A7052E: PMPI_Init (in /home/hector/installed/openmpi-intel/lib/libmpi.so.1.6.1) ==18555== by 0x3122CB27: PMPI_INIT (in /home/hector/installed/openmpi-intel/lib/libmpi_mpifh.so.2.5.0) ==18555== by 0x1C89281: setprcs_ (man.f:144) ==18555== by 0x1C4CB98: MAIN__ (main.f:114) ==18555== ==18555== 7,550 bytes in 111 blocks are definitely lost in loss record 6,243 of 6,383 ==18555== at 0x2ECC0A3D: realloc (vg_replace_malloc.c:692) ==18555== by 0x324D469725: vasprintf (in /lib64/libc-2.5.so) ==18555== by 0x324D44D727: asprintf (in /lib64/libc-2.5.so) ==18555== by 0x331E913D: dlopen_foreachfile (in /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) ==18555== by 0x331CCBC0: mca_base_component_find (in /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) ==18555== by 0x331D5EC0: mca_base_framework_components_register (in /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) ==18555== by 0x331D62DE: mca_base_framework_register (in /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) ==18555== by 0x331D6331: mca_base_framework_open (in /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) ==18555== by 0x331B71E8: opal_init (in /home/hector/installed/openmpi-intel/lib/libopen-pal.so.6.2.1) ==18555== by 0x32F221C4: orte_init (in /home/hector/installed/openmpi-intel/lib/libopen-rte.so.7.0.5) ==18555== by 0x32A4D67E: ompi_mpi_init (in /home/hector/installed/openmpi-intel/lib/libmpi.so.1.6.1) ==18555== by 0x32A7052E: PMPI_Init (in /home/hector/installed/openmpi-intel/lib/libmpi.so.1.6.1) ==18555== ==18555== LEAK SUMMARY: ==18555== definitely lost: 7,790 bytes in 117 blocks ==18555== indirectly lost: 0 bytes in 0 blocks ==18555== possibly lost: 336 bytes in 1 blocks ==18555== still reachable: 52,608,059 bytes in 7,817 blocks ==18555== suppressed: 0 bytes in 0 blocks ==18555== Reachable blocks (those to which a pointer was found) are not shown. ==18555== To see them, rerun with: --leak-check=full --show-leak-kinds=all ==18555== ==18555== For counts of detected and suppressed errors, rerun with: -v ==18555== ERROR SUMMARY: 3 errors from 3 contexts (suppressed: 4 from 4) Hector On Fri, Jun 19, 2015 at 2:29 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: >> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file > > PETSc thinks there is an error in user code. Its best if you run it in > a debugger and check whats going on. [on linux one can also use > valgrind to track down problems] > > There are many changes from petsc3.1 to petsc-3.6. Make sure > you go throgh the changes files. On C - one can rely on the compiler > prototype checks to catch most of the changes. But with fortran - you > might have to rely on a debugger/valgrind to [and the changes docs] > to find the changes. > > http://www.mcs.anl.gov/petsc/documentation/changes/index.html > > Satish > > On Fri, 19 Jun 2015, Hector E Barrios Molano wrote: > >> Hi Satish, >> >> I used MatSetOption, I'm ignoring the performance penalty for now. >> >> Now I have this error: >> >> [0]PETSC ERROR: >> ------------------------------------------------------------------------ >> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >> probably memory access out of range >> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >> [0]PETSC ERROR: or see >> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac >> OS X to find memory corruption errors >> [0]PETSC ERROR: likely location of problem given in stack below >> [0]PETSC ERROR: --------------------- Stack Frames >> ------------------------------------ >> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, >> [0]PETSC ERROR: INSTEAD the line number of the start of the function >> [0]PETSC ERROR: is given. >> [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> [0]PETSC ERROR: Signal received >> [0]PETSC ERROR: See >> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >> shooting. >> [0]PETSC ERROR: Petsc Development GIT revision: v3.6-34-gc9ff9ea GIT >> Date: 2015-06-17 23:52:21 -0500 >> [0]PETSC ERROR: F:\prog_win\prog\Debug\prog.exe on a windows-intel >> named HECTOR-PC by hector Fri Jun 19 14:06:17 2015 >> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" >> --with-fc="win32fe ifort" --prefix=/cygdrive/c/Installed/petsc/ >> --PETSC_ARCH=windows-intel >> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include >> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib >> --with-metis-include=/cygdrive/c/Installed/parmetis/include >> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib >> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]" >> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]" >> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]" >> --with-scalapack-include=/cygdrive/c/Installed/mkl/include >> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_lp64.lib]" >> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file >> >> job aborted: >> [ranks] message >> >> [0] application aborted >> aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 >> >> On Fri, Jun 19, 2015 at 12:57 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: >> > As the message says: >> > >> >> [0]PETSC ERROR: New nonzero at (0,20) caused a malloc >> >> Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to turn off this check >> > >> > Note: mallocs make the code slow - so its up to you to do a proper >> > preallocation of memory - or disable the check as the above message >> > indicadtes [and ignore the performance penalty for now.]. >> > >> > Satish >> > >> > On Fri, 19 Jun 2015, Hector E Barrios Molano wrote: >> > >> >> Hi PETSc Experts, >> >> >> >> I'm compiling a Windows program using petsc-dev, this program >> >> previously used petsc-3.1 the only change performed was: >> >> >> >> MatCreateMPIBAIJ --> MatCreateBAIJ >> >> >> >> As the PETSc documentation suggested. >> >> >> >> I only changed the name of the function. >> >> >> >> I got to a problem when the program is launched and PETSc is called by >> >> the program: >> >> >> >> [0]PETSC ERROR: --------------------- Error Message >> >> -------------------------------------------------------------- >> >> [0]PETSC ERROR: Argument out of range >> >> [0]PETSC ERROR: New nonzero at (0,20) caused a malloc >> >> Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to >> >> turn off this check >> >> [0]PETSC ERROR: See >> >> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >> >> shooting. >> >> [0]PETSC ERROR: Petsc Development GIT revision: v3.6-34-gc9ff9ea GIT >> >> Date: 2015-06-17 23:52:21 -0500 >> >> [0]PETSC ERROR: F:\prog_win\prog\Debug\prog.exe on a windows-intel >> >> named HECTOR-PC by hector Thu Jun 18 18:31:42 2015 >> >> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" >> >> --with-fc="win32fe ifort" --prefix=/cygdrive/c/Installed/petsc/ >> >> --PETSC_ARCH=windows-intel >> >> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include >> >> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib >> >> --with-metis-include=/cygdrive/c/Installed/parmetis/include >> >> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib >> >> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]" >> >> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]" >> >> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]" >> >> --with-scalapack-include=/cygdrive/c/Installed/mkl/include >> >> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_lp64.lib]" >> >> [0]PETSC ERROR: #1 MatSetValues_SeqBAIJ() line 2192 in >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: #2 MatSetValues() line 1175 in >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: --------------------- Error Message >> >> -------------------------------------------------------------- >> >> [0]PETSC ERROR: Argument out of range >> >> [0]PETSC ERROR: New nonzero at (1,21) caused a malloc >> >> Use MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE) to >> >> turn off this check >> >> [0]PETSC ERROR: See >> >> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >> >> shooting. >> >> [0]PETSC ERROR: Petsc Development GIT revision: v3.6-34-gc9ff9ea GIT >> >> Date: 2015-06-17 23:52:21 -0500 >> >> [0]PETSC ERROR: F:\prog_win\prog\Debug\prog.exe on a windows-intel >> >> named HECTOR-PC by hector Thu Jun 18 18:31:42 2015 >> >> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" >> >> --with-fc="win32fe ifort" --prefix=/cygdrive/c/Installed/petsc/ >> >> --PETSC_ARCH=windows-intel >> >> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include >> >> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib >> >> --with-metis-include=/cygdrive/c/Installed/parmetis/include >> >> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib >> >> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]" >> >> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]" >> >> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]" >> >> --with-scalapack-include=/cygdrive/c/Installed/mkl/include >> >> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_lp64.lib]" >> >> [0]PETSC ERROR: #3 MatSetValues_SeqBAIJ() line 2192 in >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: #4 MatSetValues() line 1175 in >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> . >> >> . >> >> . >> >> [0]PETSC ERROR: #3599 MatSetValues_SeqBAIJ() line 2192 in >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: #3600 MatSetValues() line 1175 in >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: >> >> ------------------------------------------------------------------------ >> >> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >> >> probably memory access out of range >> >> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >> >> [0]PETSC ERROR: or see >> >> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >> >> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac >> >> OS X to find memory corruption errors >> >> [0]PETSC ERROR: likely location of problem given in stack below >> >> [0]PETSC ERROR: --------------------- Stack Frames >> >> ------------------------------------ >> >> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, >> >> [0]PETSC ERROR: INSTEAD the line number of the start of the function >> >> [0]PETSC ERROR: is given. >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: [0] MatSetValues_SeqBAIJ line 2148 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\impls\baij\seq\baij.c >> >> [0]PETSC ERROR: [0] MatSetValues line 1142 >> >> C:\INSTAL~1\PETSC-~1\PETSC-~1\src\mat\INTERF~1\matrix.c >> >> [0]PETSC ERROR: --------------------- Error Message >> >> -------------------------------------------------------------- >> >> [0]PETSC ERROR: Signal received >> >> [0]PETSC ERROR: See >> >> http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >> >> shooting. >> >> [0]PETSC ERROR: Petsc Development GIT revision: v3.6-34-gc9ff9ea GIT >> >> Date: 2015-06-17 23:52:21 -0500 >> >> [0]PETSC ERROR: F:\prog_win\prog\Debug\prog.exe on a windows-intel >> >> named HECTOR-PC by hector Fri Jun 19 12:43:06 2015 >> >> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" >> >> --with-fc="win32fe ifort" --prefix=/cygdrive/c/Installed/petsc/ >> >> --PETSC_ARCH=windows-intel >> >> --with-parmetis-include=/cygdrive/c/Installed/parmetis/include >> >> --with-parmetis-lib=/cygdrive/c/Installed/parmetis/lib/parmetis.lib >> >> --with-metis-include=/cygdrive/c/Installed/parmetis/include >> >> --with-metis-lib=/cygdrive/c/Installed/parmetis/lib/metis.lib >> >> --with-mpi-include="[/cygdrive/c/Installed/msmpi/Include,/cygdrive/c/Installed/msmpi/Include/x64]" >> >> --with-mpi-lib="[/cygdrive/c/Installed/msmpi/Lib/x64/msmpi.lib,/cygdrive/c/Installed/msmpi/Lib/x64/msmpifec.lib]" >> >> --with-blas-lapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_intel_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_core.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_sequential.lib]" >> >> --with-scalapack-include=/cygdrive/c/Installed/mkl/include >> >> --with-scalapack-lib="[/cygdrive/c/Installed/mkl/lib/intel64/mkl_scalapack_lp64.lib,/cygdrive/c/Installed/mkl/lib/intel64/mkl_blacs_msmpi_lp64.lib]" >> >> [0]PETSC ERROR: #3601 User provided function() line 0 in unknown file >> >> >> >> job aborted: >> >> [ranks] message >> >> >> >> [0] application aborted >> >> aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 >> >> >> >> >> >> I'm compiling the program on Visual Studio, what could be the problem? >> >> >> >> Thanks for your help, >> >> >> >> Hector >> >> >> > >> >

1 0

Re: [petsc-dev] Behaviour of PetscLogEventGetId() and PetscLogStageGetId()
by Barry Smith 21 Jun '15

21 Jun '15

> On Jun 21, 2015, at 9:33 AM, Dave May <dave.mayhem23(a)gmail.com> wrote: > > Hi Barry, > > > Likely Matt had a few more beers between writing the first one and the second one. > > Heh - thanks for providing the patch to make both functions behave in the same manner. > > > > > > My use case is that within one of my custom preconditioners, I wanted > > to call PetscLogStageRegister() during the creation phase, but obviously > > I can only register the stage once. To enable multiple instances of the > > preconditioner to exist, I need to ensure that the stage is only registered once. > > Hence I would like to check for the existence of the stage prior to calling > > the register function. > > > > Is there currently a way to check for the existence of a registered stage? > > No, we don't recommend doing it this way. The way we do it in PETSc is to have a static global variable that contains the stage ID and simply check the value of that id to determine if it has been set (set it to -1 at compile time) so your test can then just be that it is not -1. The stage register stuff goes through string comparisons so it should not be called a bunch of times. > > > Okay, thanks for the advice on how best to do this. > I did notice that typical usage in petsc was via a static global variable, > but as a general rule, I try to not introduce global variables into my code base. Good policy > > Is the string comparison for an event/stage name really that bad a thing to do? > I mean, can it be worse than processing the enormous list of command line arguments > every time XXXSetFromOptions() is called? The intention is that XXXSetFromOptions() should never be within the inner iterations, so for example, once TSSetFromOptions() is called the intention is that TSSolve() -> SNESSolve() -> KSPSolve() -> PCApply() should not pass through any XXXSetFromOptions(). Yes this is violated in places but over time we hope to organize our libraries so they remain simple but do not violate this rule. Barry > > > Cheers, > Dave > > > Barry > > > > > > > > Cheers > > Dave > > > > > > >

1 0

Re: [petsc-dev] Behaviour of PetscLogEventGetId() and PetscLogStageGetId()
by Matthew Knepley 21 Jun '15

21 Jun '15

On Sun, Jun 21, 2015 at 9:33 AM, Dave May <dave.mayhem23(a)gmail.com> wrote: > Hi Barry, > > > Likely Matt had a few more beers between writing the first one and the >> second one. >> > > Heh - thanks for providing the patch to make both functions behave in the > same manner. > > >> >> > >> > My use case is that within one of my custom preconditioners, I wanted >> > to call PetscLogStageRegister() during the creation phase, but obviously >> > I can only register the stage once. To enable multiple instances of the >> > preconditioner to exist, I need to ensure that the stage is only >> registered once. >> > Hence I would like to check for the existence of the stage prior to >> calling >> > the register function. >> > >> > Is there currently a way to check for the existence of a registered >> stage? >> >> No, we don't recommend doing it this way. The way we do it in PETSc is >> to have a static global variable that contains the stage ID and simply >> check the value of that id to determine if it has been set (set it to -1 at >> compile time) so your test can then just be that it is not -1. The stage >> register stuff goes through string comparisons so it should not be called a >> bunch of times. >> >> > Okay, thanks for the advice on how best to do this. > I did notice that typical usage in petsc was via a static global variable, > but as a general rule, I try to not introduce global variables into my > code base. > There is no reason it has to be global, but the pattern is to use -1 until it is initialized. > Is the string comparison for an event/stage name really that bad a thing > to do? > I mean, can it be worse than processing the enormous list of command line > arguments > every time XXXSetFromOptions() is called? > I am sanguine for a string comparison since these are only called at setup time. I did this for the C++ version you can see in the old code. Matt > Cheers, > Dave > > > >> Barry >> >> >> > >> > >> > Cheers >> > Dave >> > >> > >> >> >> > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener

1 0

Re: [petsc-dev] Behaviour of PetscLogEventGetId() and PetscLogStageGetId()
by Dave May 21 Jun '15

21 Jun '15

Hi Barry, Likely Matt had a few more beers between writing the first one and the > second one. > Heh - thanks for providing the patch to make both functions behave in the same manner. > > > > > My use case is that within one of my custom preconditioners, I wanted > > to call PetscLogStageRegister() during the creation phase, but obviously > > I can only register the stage once. To enable multiple instances of the > > preconditioner to exist, I need to ensure that the stage is only > registered once. > > Hence I would like to check for the existence of the stage prior to > calling > > the register function. > > > > Is there currently a way to check for the existence of a registered > stage? > > No, we don't recommend doing it this way. The way we do it in PETSc is > to have a static global variable that contains the stage ID and simply > check the value of that id to determine if it has been set (set it to -1 at > compile time) so your test can then just be that it is not -1. The stage > register stuff goes through string comparisons so it should not be called a > bunch of times. > > Okay, thanks for the advice on how best to do this. I did notice that typical usage in petsc was via a static global variable, but as a general rule, I try to not introduce global variables into my code base. Is the string comparison for an event/stage name really that bad a thing to do? I mean, can it be worse than processing the enormous list of command line arguments every time XXXSetFromOptions() is called? Cheers, Dave > Barry > > > > > > > > Cheers > > Dave > > > > > > >

1 0

Re: [petsc-dev] Behaviour of PetscLogEventGetId() and PetscLogStageGetId()
by Barry Smith 19 Jun '15

19 Jun '15

> On Jun 19, 2015, at 3:54 AM, Dave May <dave.mayhem23(a)gmail.com> wrote: > > I was wondering why there is different behaviour between > PetscLogEventGetId() > and > PetscLogStageGetId() > > PetscLogEventGetId() returns -1 if the event isn't found, > whilst PetscLogStageGetId() throws an error if the stage isn't found. Likely Matt had a few more beers between writing the first one and the second one. > > My use case is that within one of my custom preconditioners, I wanted > to call PetscLogStageRegister() during the creation phase, but obviously > I can only register the stage once. To enable multiple instances of the > preconditioner to exist, I need to ensure that the stage is only registered once. > Hence I would like to check for the existence of the stage prior to calling > the register function. > > Is there currently a way to check for the existence of a registered stage? No, we don't recommend doing it this way. The way we do it in PETSc is to have a static global variable that contains the stage ID and simply check the value of that id to determine if it has been set (set it to -1 at compile time) so your test can then just be that it is not -1. The stage register stuff goes through string comparisons so it should not be called a bunch of times. Barry > > > Cheers > Dave > >

1 0

sowing memory error
by Barry Smith 19 Jun '15

19 Jun '15

Satish, Thanks. I'm forwarding to Bill also so he can fix in the master copy. Barry > On Jun 19, 2015, at 3:48 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > Ok - valgrind gives the following message: > >>>>>>>>> > Testing path as file /home/balay/petsc/lib/petsc/conf > Testing file /home/balay/petsc/lib/petsc/conf/bfort-mpi.txt > Generating F90 interface for /home/balay/petsc/src/tao/unconstrained/impls/cg/f90module.f90 > Testing path as file /home/balay/petsc/lib/petsc/conf > Testing file /home/balay/petsc/lib/petsc/conf/bfort-base.txt > ==13863== Syscall param stat(file_name) points to uninitialised byte(s) > ==13863== at 0x4F25C65: _xstat (in /usr/lib64/libc-2.21.so) > ==13863== by 0x408360: SYiFileExists (in /home/balay/soft/build/sowing-1.1.17-p1/src/bfort/bfort) > ==13863== by 0x409FE4: SYReadConfigFile (in /home/balay/soft/build/sowing-1.1.17-p1/src/bfort/bfort) > ==13863== by 0x401AAA: main (in /home/balay/soft/build/sowing-1.1.17-p1/src/bfort/bfort) > ==13863== Address 0x51f68f0 is 48 bytes inside a block of size 64 alloc'd > ==13863== at 0x4C28C10: malloc (in /usr/lib64/valgrind/vgpreload_memcheck-amd64-linux.so) > ==13863== by 0x409F06: SYReadConfigFile (in /home/balay/soft/build/sowing-1.1.17-p1/src/bfort/bfort) > ==13863== by 0x401AAA: main (in /home/balay/soft/build/sowing-1.1.17-p1/src/bfort/bfort) > ==13863== > ==13863== Syscall param open(filename) points to uninitialised byte(s) > ==13863== at 0x4F260C0: __open_nocancel (in /usr/lib64/libc-2.21.so) > ==13863== by 0x4EAE264: _IO_file_fopen@@GLIBC_2.2.5 (in /usr/lib64/libc-2.21.so) > ==13863== by 0x4EA2603: __fopen_internal (in /usr/lib64/libc-2.21.so) > ==13863== by 0x409B1D: SYReadConfigFile (in /home/balay/soft/build/sowing-1.1.17-p1/src/bfort/bfort) > ==13863== by 0x40A00C: SYReadConfigFile (in /home/balay/soft/build/sowing-1.1.17-p1/src/bfort/bfort) > ==13863== by 0x401AAA: main (in /home/balay/soft/build/sowing-1.1.17-p1/src/bfort/bfort) > ==13863== Address 0x51f68f0 is 48 bytes inside a block of size 64 alloc'd > ==13863== at 0x4C28C10: malloc (in /usr/lib64/valgrind/vgpreload_memcheck-amd64-linux.so) > ==13863== by 0x409F06: SYReadConfigFile (in /home/balay/soft/build/sowing-1.1.17-p1/src/bfort/bfort) > ==13863== by 0x401AAA: main (in /home/balay/soft/build/sowing-1.1.17-p1/src/bfort/bfort) > ==13863== > Testing path as file /home/balay/petsc/lib/petsc/conf > Testing file /home/balay/petsc/lib/petsc/conf/bfort-mpi.txt > <<<<<<< > > I think the following might be the fix. [bfort is valgrind clean after this change] > >>>>>>>>>>>>>> > diff --git a/src/sys/rdconfig.c b/src/sys/rdconfig.c > index 0763c84..3606060 100644 > --- a/src/sys/rdconfig.c > +++ b/src/sys/rdconfig.c > @@ -110,6 +110,7 @@ int SYReadConfigFile(const char filename[], const char sepChar, > while (*pin) { > *pout++ = *pin++; > } > + *pout = 0; > if (SYiFileExists(fname,'r')) { > err = SYReadConfigFile(fname, sepChar, commentChar, > cmds, ncmds); > <<<<<<<<<<<<<< > > Satish > > On Fri, 19 Jun 2015, Barry Smith wrote: > >> >> Satish, >> >> Hmm, this could be a bug in sowing, could you run a full build of PETSc fortranstubs using bfort but run bfort under valgrind? >> >> Thanks >> >> Barry >> >> We had another report of the same type with a mysterious misunderstanding of a filename. >> >> >>> On Jun 19, 2015, at 10:42 AM, Satish Balay <balay(a)mcs.anl.gov> wrote: >>> >>> include config file /Users/markadams/Codes/petsc_fresh/lib/petsc/conf/bfort-petsc.txt^DP`¨^? missing >>> Unable to read configure file bfort-base.txt******* >>> >>> >>> Do you have this file? I don't know where the funny chars at the end of the filename are coming from.. >>> >>> Satish >>> >>> On Fri, 19 Jun 2015, Mark Adams wrote: >>> >>>> >>>> >>

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