[petsc-dev] [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed
Matthew Knepley
knepley at gmail.com
Sun Mar 3 17:03:30 CST 2019
Another good example of C++ saving time and making things easier.
Matt
On Sun, Mar 3, 2019 at 5:33 PM Jed Brown <jed at jedbrown.org> wrote:
> The compiler doesn't know anything special about PetscFinalize.
> Destructors are called after all executable statements in their scope.
> So you need the extra scoping if the destructor should be called
> earlier.
>
> Yuyun Yang <yyang85 at stanford.edu> writes:
>
> > Oh interesting, so I need to add those extra brackets around my class
> object and function calls. I thought the destructor is automatically at
> Finalize.
> >
> > Thanks!
> > Yuyun
> >
> > -----Original Message-----
> > From: Jed Brown <jed at jedbrown.org>
> > Sent: Sunday, March 3, 2019 2:19 PM
> > To: Yuyun Yang <yyang85 at stanford.edu>; Matthew Knepley <
> knepley at gmail.com>
> > Cc: petsc-users at mcs.anl.gov
> > Subject: Re: [petsc-users] AddressSanitizer: attempting free on address
> which was not malloc()-ed
> >
> > If you run this with MPICH, it prints
> >
> > Attempting to use an MPI routine after finalizing MPICH
> >
> > You need to ensure that the C++ class destructor is called before
> PetscFinalize. For example, like this:
> >
> > diff --git i/test_domain.cpp w/test_domain.cpp index 0cfe22f..23545f2
> 100644
> > --- i/test_domain.cpp
> > +++ w/test_domain.cpp
> > @@ -8,11 +8,12 @@ int main(int argc, char **argv) {
> > PetscErrorCode ierr = 0;
> > PetscInitialize(&argc, &argv, NULL, NULL);
> >
> > - Domain d;
> > + {
> > + Domain d;
> >
> > - ierr = d.setFields(); CHKERRQ(ierr);
> > - ierr = d.setScatters(); CHKERRQ(ierr);
> > -
> > + ierr = d.setFields(); CHKERRQ(ierr);
> > + ierr = d.setScatters(); CHKERRQ(ierr); }
> > PetscFinalize();
> > return ierr;
> > }
> >
> >
> > Yuyun Yang via petsc-users <petsc-users at mcs.anl.gov> writes:
> >
> >> Yes, please see the attached files for a minimal example. Thanks a lot!
> >>
> >> Best regards,
> >> Yuyun
> >>
> >> From: Matthew Knepley <knepley at gmail.com>
> >> Sent: Sunday, March 3, 2019 12:46 PM
> >> To: Yuyun Yang <yyang85 at stanford.edu>
> >> Cc: Zhang, Junchao <jczhang at mcs.anl.gov>; petsc-users at mcs.anl.gov
> >> Subject: Re: [petsc-users] AddressSanitizer: attempting free on
> >> address which was not malloc()-ed
> >>
> >> On Sun, Mar 3, 2019 at 3:05 PM Yuyun Yang <yyang85 at stanford.edu<mailto:
> yyang85 at stanford.edu>> wrote:
> >> Actually, I tried just creating a domain object (since the address
> sanitizer was complaining about that code to start with). Simply creating
> that object gave me a core dump, so I suppose the issue must be there. I
> got the following message when running the code with -objects_dump flag on
> the command line, but couldn’t find a problem with the code (I’ve attached
> it here with only the relevant functions).
> >>
> >> I think what we are going to need from you is a minimal example that
> >> has the error. I am guessing you have a logic bug in the C++, which we
> cannot debug by looking.
> >>
> >> Thanks,
> >>
> >> Matt
> >>
> >> Thanks a lot for your help!
> >>
> >> The following objects were never freed
> >> -----------------------------------------
> >> [0] Vec seq y
> >> [0] VecCreate() in
> >> /home/yyy910805/petsc/src/vec/vec/interface/veccreate.c
> >> [0] Vec seq Vec_0x84000000_0
> >> [0] VecCreate() in
> >> /home/yyy910805/petsc/src/vec/vec/interface/veccreate.c
> >> [0] Vec seq Vec_0x84000000_1
> >> [0] VecCreate() in
> >> /home/yyy910805/petsc/src/vec/vec/interface/veccreate.c
> >> [0] VecScatter seq VecScatter_0x84000000_2
> >> [0] VecScatterCreate() in
> >> /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c
> >> [0] VecScatter seq VecScatter_0x84000000_3
> >> [0] VecScatterCreate() in
> >> /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c
> >> [0] VecScatter seq VecScatter_0x84000000_4
> >> [0] VecScatterCreate() in
> >> /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c
> >> [0] VecScatter seq VecScatter_0x84000000_5
> >> [0] VecScatterCreate() in
> >> /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c
> >> Attempting to use an MPI routine after finalizing MPICH
> >>
> >> ----------------------------------------------------------------------
> >> ----------------------------------------------------------------------
> >> -----
> >> From: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>
> >> Sent: Sunday, March 3, 2019 11:28 AM
> >> To: Yuyun Yang <yyang85 at stanford.edu<mailto:yyang85 at stanford.edu>>
> >> Cc: Zhang, Junchao <jczhang at mcs.anl.gov<mailto:jczhang at mcs.anl.gov>>;
> >> petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>
> >> Subject: Re: [petsc-users] AddressSanitizer: attempting free on
> >> address which was not malloc()-ed
> >>
> >> On Sun, Mar 3, 2019 at 1:03 PM Yuyun Yang via petsc-users <
> petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
> >> I tried compiling without the sanitizer and running on valgrind. Got a
> bunch of errors “Uninitialised value was created by a stack allocation at
> 0x41B280: ComputeVel_qd::computeVel(double*, double, int&, int)”.
> >>
> >> There is no memory management code here, so other parts of the code
> must be relevant.
> >>
> >> Thanks,
> >>
> >> Matt
> >>
> >>
> >> HEAP SUMMARY:
> >> ==74== in use at exit: 96,637 bytes in 91 blocks
> >> ==74== total heap usage: 47,774 allocs, 47,522 frees, 308,253,653
> bytes allocated
> >> LEAK SUMMARY:
> >> ==74== definitely lost: 0 bytes in 0 blocks
> >> ==74== indirectly lost: 0 bytes in 0 blocks
> >> ==74== possibly lost: 0 bytes in 0 blocks
> >> ==74== still reachable: 96,637 bytes in 91 blocks
> >> ==74== suppressed: 0 bytes in 0 blocks
> >>
> >> The error is located in the attached code (I’ve extracted only the
> relevant functions), but I couldn’t figure out what is wrong. Is this
> causing the memory corruption/double free error that happens when I execute
> the code?
> >>
> >> Thanks a lot for your help.
> >>
> >> Best regards,
> >> Yuyun
> >>
> >> From: Zhang, Junchao <jczhang at mcs.anl.gov<mailto:jczhang at mcs.anl.gov>>
> >> Sent: Friday, March 1, 2019 7:36 AM
> >> To: Yuyun Yang <yyang85 at stanford.edu<mailto:yyang85 at stanford.edu>>
> >> Subject: Re: [petsc-users] AddressSanitizer: attempting free on
> >> address which was not malloc()-ed
> >>
> >>
> >> On Fri, Mar 1, 2019 at 1:02 AM Yuyun Yang <yyang85 at stanford.edu<mailto:
> yyang85 at stanford.edu>> wrote:
> >> Actually, I also saw a line at the beginning of valgrind saying "shadow
> memory range interleaves with an existing memory mapping. ASan cannot
> proceed properly. ABORTING." I guess the code didn't really run through
> valgrind since it aborted. Should I remove the address sanitizer flag when
> compiling?
> >> From the message, it seems ASan (not valgrind) aborted. You can try to
> compile without sanitizer and then run with valgrind. If no problem, then
> it is probably a sanitizer issue.
> >>
> >>
> >> Get Outlook for iOS<https://aka.ms/o0ukef>
> >> ________________________________
> >> From: Yuyun Yang
> >> Sent: Thursday, February 28, 2019 10:54:57 PM
> >> To: Zhang, Junchao
> >> Subject: Re: [petsc-users] AddressSanitizer: attempting free on
> >> address which was not malloc()-ed
> >>
> >> Hmm, still getting the same error from address sanitizer even though
> valgrind shows no errors and no leaks are possible.
> >>
> >> Should I ignore that error? My results did run alright.
> >>
> >> Best,
> >> Yuyun
> >>
> >> Get Outlook for iOS<https://aka.ms/o0ukef>
> >> ________________________________
> >> From: Zhang, Junchao <jczhang at mcs.anl.gov<mailto:jczhang at mcs.anl.gov>>
> >> Sent: Wednesday, February 27, 2019 8:27:17 PM
> >> To: Yuyun Yang
> >> Cc: Matthew Knepley;
> >> petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>
> >> Subject: Re: [petsc-users] AddressSanitizer: attempting free on
> >> address which was not malloc()-ed
> >>
> >> Try the following to see if you can catch the bug easily: 1) Get error
> >> code for each petsc function and check it with CHKERRQ; 2) Link your
> >> code with a petsc library with debugging enabled (configured with
> >> --with-debugging=1); 3) Run your code with valgrind
> >>
> >> --Junchao Zhang
> >>
> >>
> >> On Wed, Feb 27, 2019 at 9:04 PM Yuyun Yang <yyang85 at stanford.edu
> <mailto:yyang85 at stanford.edu>> wrote:
> >> Hi Junchao,
> >>
> >> This code actually involves a lot of classes and is pretty big. Might
> be an overkill for me to send everything to you. I'd like to know if I see
> this sort of error message, which points to this domain file, is it
> possible that the problem happens in another file (whose operations are
> linked to this one)? If so, I'll debug a little more and maybe send you
> more useful information later.
> >>
> >> Best regards,
> >> Yuyun
> >>
> >> Get Outlook for iOS<https://aka.ms/o0ukef>
> >> ________________________________
> >> From: Zhang, Junchao <jczhang at mcs.anl.gov<mailto:jczhang at mcs.anl.gov>>
> >> Sent: Wednesday, February 27, 2019 6:24:13 PM
> >> To: Yuyun Yang
> >> Cc: Matthew Knepley;
> >> petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>
> >> Subject: Re: [petsc-users] AddressSanitizer: attempting free on
> >> address which was not malloc()-ed
> >>
> >> Could you provide a compilable and runnable test so I can try it?
> >> --Junchao Zhang
> >>
> >>
> >> On Wed, Feb 27, 2019 at 7:34 PM Yuyun Yang <yyang85 at stanford.edu
> <mailto:yyang85 at stanford.edu>> wrote:
> >> Thanks, I fixed that, but I’m not actually calling the testScatters()
> function in my implementation (in the constructor, the only functions I
> called are setFields and setScatters). So the problem couldn’t have been
> that?
> >>
> >> Best,
> >> Yuyun
> >>
> >> From: Zhang, Junchao <jczhang at mcs.anl.gov<mailto:jczhang at mcs.anl.gov>>
> >> Sent: Wednesday, February 27, 2019 10:50 AM
> >> To: Yuyun Yang <yyang85 at stanford.edu<mailto:yyang85 at stanford.edu>>
> >> Cc: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>;
> >> petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>
> >> Subject: Re: [petsc-users] AddressSanitizer: attempting free on
> >> address which was not malloc()-ed
> >>
> >>
> >> On Wed, Feb 27, 2019 at 10:41 AM Yuyun Yang via petsc-users <
> petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
> >> I called VecDestroy() in the destructor for this object – is that not
> the right way to do it?
> >> In Domain::testScatters(), you have many VecDuplicate(,&out), You need
> >> to VecDestroy(&out) before doing new VecDuplicate(,&out); How do I
> implement CHECK ALL RETURN CODES?
> >> For each PETSc function, do ierr = ...; CHKERRQ(ierr);
> >>
> >> From: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>
> >> Sent: Wednesday, February 27, 2019 7:24 AM
> >> To: Yuyun Yang <yyang85 at stanford.edu<mailto:yyang85 at stanford.edu>>
> >> Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>
> >> Subject: Re: [petsc-users] AddressSanitizer: attempting free on
> >> address which was not malloc()-ed
> >>
> >> You call VecDuplicate() a bunch, but VecDestroy() only once in the
> bottom function. This is wrong.
> >> Also, CHECK ALL RETURN CODES. This is the fastest way to find errors.
> >>
> >> Matt
> >>
> >> On Wed, Feb 27, 2019 at 2:06 AM Yuyun Yang via petsc-users <
> petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:
> >> Hello team,
> >>
> >> I ran into the address sanitizer error that I hope you could help me
> with. I don’t really know what’s wrong with the way the code frees memory.
> The relevant code file is attached. The line number following domain.cpp
> specifically referenced to the vector _q, which seems a little odd, since
> some other vectors are constructed and freed the same way.
> >>
> >> ==1719==ERROR: AddressSanitizer: attempting free on address which was
> not malloc()-ed: 0x61f0000076c0 in thread T0
> >> #0 0x7fbf195282ca in __interceptor_free
> (/usr/lib/x86_64-linux-gnu/libasan.so.2+0x982ca)
> >> #1 0x7fbf1706f895 in PetscFreeAlign
> /home/yyy910805/petsc/src/sys/memory/mal.c:87
> >> #2 0x7fbf1731a898 in VecDestroy_Seq
> /home/yyy910805/petsc/src/vec/vec/impls/seq/bvec2.c:788
> >> #3 0x7fbf1735f795 in VecDestroy
> /home/yyy910805/petsc/src/vec/vec/interface/vector.c:408
> >> #4 0x40dd0a in Domain::~Domain()
> /home/yyy910805/scycle/source/domain.cpp:132
> >> #5 0x40b479 in main /home/yyy910805/scycle/source/main.cpp:242
> >> #6 0x7fbf14d2082f in __libc_start_main
> (/lib/x86_64-linux-gnu/libc.so.6+0x2082f)
> >> #7 0x4075d8 in _start
> >> (/home/yyy910805/scycle/source/main+0x4075d8)
> >>
> >> 0x61f0000076c0 is located 1600 bytes inside of 3220-byte region
> >> [0x61f000007080,0x61f000007d14) allocated by thread T0 here:
> >> #0 0x7fbf19528b32 in __interceptor_memalign
> (/usr/lib/x86_64-linux-gnu/libasan.so.2+0x98b32)
> >> #1 0x7fbf1706f7e0 in PetscMallocAlign
> /home/yyy910805/petsc/src/sys/memory/mal.c:41
> >> #2 0x7fbf17073022 in PetscTrMallocDefault
> /home/yyy910805/petsc/src/sys/memory/mtr.c:183
> >> #3 0x7fbf170710a1 in PetscMallocA
> /home/yyy910805/petsc/src/sys/memory/mal.c:397
> >> #4 0x7fbf17326fb0 in VecCreate_Seq
> /home/yyy910805/petsc/src/vec/vec/impls/seq/bvec3.c:35
> >> #5 0x7fbf1736f560 in VecSetType
> /home/yyy910805/petsc/src/vec/vec/interface/vecreg.c:51
> >> #6 0x7fbf1731afae in VecDuplicate_Seq
> /home/yyy910805/petsc/src/vec/vec/impls/seq/bvec2.c:807
> >> #7 0x7fbf1735eff7 in VecDuplicate
> /home/yyy910805/petsc/src/vec/vec/interface/vector.c:379
> >> #8 0x4130de in Domain::setFields()
> /home/yyy910805/scycle/source/domain.cpp:431
> >> #9 0x40c60a in Domain::Domain(char const*)
> /home/yyy910805/scycle/source/domain.cpp:57
> >> #10 0x40b433 in main /home/yyy910805/scycle/source/main.cpp:242
> >> #11 0x7fbf14d2082f in __libc_start_main
> >> (/lib/x86_64-linux-gnu/libc.so.6+0x2082f)
> >>
> >> SUMMARY: AddressSanitizer: bad-free ??:0 __interceptor_free
> >> ==1719==ABORTING
> >>
> >> Thanks very much!
> >> Yuyun
> >>
> >>
> >> --
> >> 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
> >>
> >> https://www.cse.buffalo.edu/~knepley/<http://www.cse.buffalo.edu/~knep
> >> ley/>
> >>
> >>
> >> --
> >> 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
> >>
> >> https://www.cse.buffalo.edu/~knepley/<http://www.cse.buffalo.edu/~knep
> >> ley/>
> >>
> >>
> >> --
> >> 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
> >>
> >> https://www.cse.buffalo.edu/~knepley/<http://www.cse.buffalo.edu/~knep
> >> ley/>
> >> #include "domain.hpp"
> >>
> >> using namespace std;
> >>
> >> Domain::Domain()
> >> : _sbpType("mfc_coordTrans"),_Ny(201),_Nz(1),_Ly(30),_Lz(30),
> >>
> _q(NULL),_r(NULL),_y(NULL),_z(NULL),_y0(NULL),_z0(NULL),_dq(-1),_dr(-1),
> >> _bCoordTrans(5)
> >> {
> >> if (_Ny > 1) {
> >> _dq = 1.0 / (_Ny - 1.0);
> >> }
> >> else {
> >> _dq = 1;
> >> }
> >>
> >> if (_Nz > 1) {
> >> _dr = 1.0 / (_Nz - 1.0);
> >> }
> >> else {
> >> _dr = 1;
> >> }
> >> }
> >>
> >> // destructor
> >> Domain::~Domain()
> >> {
> >> // free memory
> >> VecDestroy(&_q);
> >> VecDestroy(&_r);
> >> VecDestroy(&_y);
> >> VecDestroy(&_z);
> >> VecDestroy(&_y0);
> >> VecDestroy(&_z0);
> >>
> >> // set map iterator, free memory from VecScatter
> >> map<string,VecScatter>::iterator it;
> >> for (it = _scatters.begin(); it != _scatters.end(); it++) {
> >> VecScatterDestroy(&(it->second));
> >> }
> >> }
> >>
> >> // construct coordinate transform, setting vectors q, r, y, z
> >> PetscErrorCode Domain::setFields() {
> >> PetscErrorCode ierr = 0;
> >>
> >> // generate vector _y with size _Ny*_Nz
> >> ierr = VecCreate(PETSC_COMM_WORLD,&_y); CHKERRQ(ierr);
> >> ierr = VecSetSizes(_y,PETSC_DECIDE,_Ny*_Nz); CHKERRQ(ierr);
> >> ierr = VecSetFromOptions(_y); CHKERRQ(ierr);
> >> ierr = PetscObjectSetName((PetscObject) _y, "y"); CHKERRQ(ierr);
> >>
> >> // duplicate _y into _z, _q, _r
> >> ierr = VecDuplicate(_y,&_z); CHKERRQ(ierr);
> >> ierr = PetscObjectSetName((PetscObject) _z, "z"); CHKERRQ(ierr);
> >> ierr = VecDuplicate(_y,&_q); CHKERRQ(ierr);
> >> ierr = PetscObjectSetName((PetscObject) _q, "q"); CHKERRQ(ierr);
> >> ierr = VecDuplicate(_y,&_r); CHKERRQ(ierr);
> >> ierr = PetscObjectSetName((PetscObject) _r, "r"); CHKERRQ(ierr);
> >>
> >> // construct coordinate transform
> >> PetscInt Ii,Istart,Iend,Jj = 0;
> >> PetscScalar *y,*z,*q,*r;
> >> ierr = VecGetOwnershipRange(_q,&Istart,&Iend);CHKERRQ(ierr);
> >>
> >> // return pointers to local data arrays (the processor's portion of
> vector data)
> >> ierr = VecGetArray(_y,&y); CHKERRQ(ierr);
> >> ierr = VecGetArray(_z,&z); CHKERRQ(ierr);
> >> ierr = VecGetArray(_q,&q); CHKERRQ(ierr);
> >> ierr = VecGetArray(_r,&r); CHKERRQ(ierr);
> >>
> >> // set vector entries for q, r (coordinate transform) and y, z (no
> transform)
> >> for (Ii=Istart; Ii<Iend; Ii++) {
> >> q[Jj] = _dq*(Ii/_Nz);
> >> r[Jj] = _dr*(Ii-_Nz*(Ii/_Nz));
> >>
> >> // matrix-based, fully compatible, allows curvilinear coordinate
> transformation
> >> if (_sbpType.compare("mfc_coordTrans") ) {
> >> y[Jj] = (_dq*_Ly)*(Ii/_Nz);
> >> z[Jj] = (_dr*_Lz)*(Ii-_Nz*(Ii/_Nz));
> >> }
> >> else {
> >> // hardcoded transformation (not available for z)
> >> if (_bCoordTrans > 0) {
> >> y[Jj] = _Ly * sinh(_bCoordTrans * q[Jj]) / sinh(_bCoordTrans);
> >> }
> >> // no transformation
> >> y[Jj] = q[Jj]*_Ly;
> >> z[Jj] = r[Jj]*_Lz;
> >> }
> >> Jj++;
> >> }
> >>
> >> // restore arrays
> >> ierr = VecRestoreArray(_y,&y); CHKERRQ(ierr);
> >> ierr = VecRestoreArray(_z,&z); CHKERRQ(ierr);
> >> ierr = VecRestoreArray(_q,&q); CHKERRQ(ierr);
> >> ierr = VecRestoreArray(_r,&r); CHKERRQ(ierr);
> >>
> >> return ierr;
> >> }
> >>
> >>
> >> // scatters values from one vector to another PetscErrorCode
> >> Domain::setScatters() {
> >> PetscErrorCode ierr = 0;
> >>
> >> ierr = VecCreate(PETSC_COMM_WORLD,&_y0); CHKERRQ(ierr);
> >> ierr = VecSetSizes(_y0,PETSC_DECIDE,_Nz); CHKERRQ(ierr);
> >> ierr = VecSetFromOptions(_y0); CHKERRQ(ierr);
> >> ierr = VecSet(_y0,0.0); CHKERRQ(ierr);
> >>
> >> ierr = VecCreate(PETSC_COMM_WORLD,&_z0); CHKERRQ(ierr);
> >> ierr = VecSetSizes(_z0,PETSC_DECIDE,_Ny); CHKERRQ(ierr);
> >> ierr = VecSetFromOptions(_z0); CHKERRQ(ierr);
> >> ierr = VecSet(_z0,0.0); CHKERRQ(ierr);
> >>
> >> PetscInt *indices;
> >> IS is;
> >> ierr = PetscMalloc1(_Nz,&indices); CHKERRQ(ierr);
> >>
> >> // we want to scatter from index 0 to _Nz - 1, i.e. take the first
> _Nz components of the vector to scatter from
> >> for (PetscInt Ii = 0; Ii<_Nz; Ii++) {
> >> indices[Ii] = Ii;
> >> }
> >>
> >> ierr = ISCreateGeneral(PETSC_COMM_WORLD, _Nz, indices,
> PETSC_COPY_VALUES, &is); CHKERRQ(ierr);
> >> ierr = VecScatterCreate(_y, is, _y0, is, &_scatters["body2L"]);
> >> CHKERRQ(ierr);
> >>
> >> // free memory
> >> ierr = PetscFree(indices); CHKERRQ(ierr);
> >> ierr = ISDestroy(&is); CHKERRQ(ierr);
> >>
> >>
> //===============================================================================
> >> // set up scatter context to take values for y = Ly from body field
> and put them on a Vec of size Nz
> >> PetscInt *fi;
> >> IS isf;
> >> ierr = PetscMalloc1(_Nz,&fi); CHKERRQ(ierr);
> >>
> >> for (PetscInt Ii = 0; Ii<_Nz; Ii++) {
> >> fi[Ii] = Ii + (_Ny*_Nz-_Nz);
> >> }
> >> ierr = ISCreateGeneral(PETSC_COMM_WORLD, _Nz, fi, PETSC_COPY_VALUES,
> >> &isf); CHKERRQ(ierr);
> >>
> >> PetscInt *ti;
> >> IS ist;
> >> ierr = PetscMalloc1(_Nz,&ti); CHKERRQ(ierr);
> >> for (PetscInt Ii = 0; Ii<_Nz; Ii++) {
> >> ti[Ii] = Ii;
> >> }
> >> ierr = ISCreateGeneral(PETSC_COMM_WORLD, _Nz, ti, PETSC_COPY_VALUES,
> &ist); CHKERRQ(ierr);
> >> ierr = VecScatterCreate(_y, isf, _y0, ist, &_scatters["body2R"]);
> >> CHKERRQ(ierr);
> >>
> >> // free memory
> >> ierr = PetscFree(fi); CHKERRQ(ierr);
> >> ierr = PetscFree(ti); CHKERRQ(ierr);
> >> ierr = ISDestroy(&isf); CHKERRQ(ierr);
> >> ierr = ISDestroy(&ist); CHKERRQ(ierr);
> >>
> >>
> >>
> //==============================================================================
>
> >> IS isf2;
> >> ierr = ISCreateStride(PETSC_COMM_WORLD, _Ny, 0, _Nz, &isf2);
> >> CHKERRQ(ierr);
> >>
> >> PetscInt *ti2;
> >> IS ist2;
> >> ierr = PetscMalloc1(_Ny,&ti2); CHKERRQ(ierr);
> >>
> >> for (PetscInt Ii=0; Ii<_Ny; Ii++) {
> >> ti2[Ii] = Ii;
> >> }
> >> ierr = ISCreateGeneral(PETSC_COMM_WORLD, _Ny, ti2, PETSC_COPY_VALUES,
> &ist2); CHKERRQ(ierr);
> >> ierr = VecScatterCreate(_y, isf2, _z0, ist2, &_scatters["body2T"]);
> >> CHKERRQ(ierr);
> >>
> >> // free memory
> >> ierr = PetscFree(ti2); CHKERRQ(ierr);
> >> ierr = ISDestroy(&isf2); CHKERRQ(ierr);
> >> ierr = ISDestroy(&ist2); CHKERRQ(ierr);
> >>
> >>
> >>
> //==============================================================================
> >> IS isf3;
> >> ierr = ISCreateStride(PETSC_COMM_WORLD, _Ny, _Nz - 1, _Nz, &isf3);
> >> CHKERRQ(ierr);
> >>
> >> PetscInt *ti3;
> >> IS ist3;
> >> ierr = PetscMalloc1(_Ny,&ti3); CHKERRQ(ierr);
> >> for (PetscInt Ii = 0; Ii<_Ny; Ii++) {
> >> ti3[Ii] = Ii;
> >> }
> >> ierr = ISCreateGeneral(PETSC_COMM_WORLD, _Ny, ti3, PETSC_COPY_VALUES,
> &ist3); CHKERRQ(ierr);
> >> ierr = VecScatterCreate(_y, isf3, _z0, ist3, &_scatters["body2B"]);
> >> CHKERRQ(ierr);
> >>
> >> // free memory
> >> ierr = PetscFree(ti3); CHKERRQ(ierr);
> >> ierr = ISDestroy(&isf3); CHKERRQ(ierr);
> >> ierr = ISDestroy(&ist3); CHKERRQ(ierr);
> >>
> >> return ierr;
> >> }
> >> #include "domain.hpp"
> >>
> >> using namespace std;
> >>
> >> // creates a domain object
> >> int main(int argc, char **argv) {
> >>
> >> PetscErrorCode ierr = 0;
> >> PetscInitialize(&argc, &argv, NULL, NULL);
> >>
> >> Domain d;
> >>
> >> ierr = d.setFields(); CHKERRQ(ierr);
> >> ierr = d.setScatters(); CHKERRQ(ierr);
> >>
> >> PetscFinalize();
> >> return ierr;
> >> }
>
--
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
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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