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).
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 <knep...@gmail.com>
Sent: Sunday, March 3, 2019 11:28 AM
To: Yuyun Yang <yyan...@stanford.edu>
Cc: Zhang, Junchao <jczh...@mcs.anl.gov>; petsc-users@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@mcs.anl.gov<mailto:petsc-users@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 <jczh...@mcs.anl.gov<mailto:jczh...@mcs.anl.gov>>
Sent: Friday, March 1, 2019 7:36 AM
To: Yuyun Yang <yyan...@stanford.edu<mailto:yyan...@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
<yyan...@stanford.edu<mailto:yyan...@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 <jczh...@mcs.anl.gov<mailto:jczh...@mcs.anl.gov>>
Sent: Wednesday, February 27, 2019 8:27:17 PM
To: Yuyun Yang
Cc: Matthew Knepley; petsc-users@mcs.anl.gov<mailto:petsc-users@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
<yyan...@stanford.edu<mailto:yyan...@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 <jczh...@mcs.anl.gov<mailto:jczh...@mcs.anl.gov>>
Sent: Wednesday, February 27, 2019 6:24:13 PM
To: Yuyun Yang
Cc: Matthew Knepley; petsc-users@mcs.anl.gov<mailto:petsc-users@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
<yyan...@stanford.edu<mailto:yyan...@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 <jczh...@mcs.anl.gov<mailto:jczh...@mcs.anl.gov>>
Sent: Wednesday, February 27, 2019 10:50 AM
To: Yuyun Yang <yyan...@stanford.edu<mailto:yyan...@stanford.edu>>
Cc: Matthew Knepley <knep...@gmail.com<mailto:knep...@gmail.com>>;
petsc-users@mcs.anl.gov<mailto:petsc-users@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@mcs.anl.gov<mailto:petsc-users@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 <knep...@gmail.com<mailto:knep...@gmail.com>>
Sent: Wednesday, February 27, 2019 7:24 AM
To: Yuyun Yang <yyan...@stanford.edu<mailto:yyan...@stanford.edu>>
Cc: petsc-users@mcs.anl.gov<mailto:petsc-users@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@mcs.anl.gov<mailto:petsc-users@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/~knepley/>
--
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/>
#include "domain.hpp"
using namespace std;
Domain::Domain(const char *file)
: _file(file),_delim(" = "),_inputDir("unspecified_"),_outputDir(" "),
_bulkDeformationType("linearElastic"),
_momentumBalanceType("quasidynamic"),
_sbpType("mfc_coordTrans"),_operatorType("matrix-based"),
_sbpCompatibilityType("fullyCompatible"),
_gridSpacingType("variableGridSpacing"),
_isMMS(0),_loadICs(0),
_order(4),_Ny(-1),_Nz(-1),_Ly(-1),_Lz(-1),
_vL(1e-9),
_q(NULL),_r(NULL),_y(NULL),_z(NULL),_y0(NULL),_z0(NULL),_dq(-1),_dr(-1),
_bCoordTrans(-1)
{
// load data from file
loadData(_file);
// check domain size and set grid spacing in y direction
if (_Ny > 1) {
_dq = 1.0 / (_Ny - 1.0);
}
else {
_dq = 1;
}
// set grid spacing in z-direction
if (_Nz > 1) {
_dr = 1.0 / (_Nz - 1.0);
}
else {
_dr = 1;
}
checkInput(); // perform some basic value checking to prevent NaNs
setFields();
setScatters();
}
// 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;
#if VERBOSE > 1
string funcName = "Domain::setFields";
ierr = PetscPrintf(PETSC_COMM_WORLD,"Starting %s in
%s.\n",funcName.c_str(),FILENAME);
CHKERRQ(ierr);
#endif
// 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
// used to get slip on the fault from the displacement vector, i.e., slip =
u(1:Nz); shear stress on the fault from the stress vector sxy; surface
displacement; surface heat flux
PetscErrorCode Domain::setScatters()
{
PetscErrorCode ierr = 0;
// set _y0 to be zero vector with length _Nz
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);
// set _z0 to be zero vector with length _Ny
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);
// set up scatter context to take values for y = 0 from body field and put
them on a Vec of size Nz
PetscInt *indices;
IS is; // index set
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;
}
// creates data structure for an index set containing a list of integers
ierr = ISCreateGeneral(PETSC_COMM_WORLD, _Nz, indices, PETSC_COPY_VALUES,
&is); CHKERRQ(ierr);
// creates vector scatter context, scatters values from _y (at indices is) to
_y0 (at indices is)
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
// indices to scatter from
PetscInt *fi;
IS isf;
ierr = PetscMalloc1(_Nz,&fi); CHKERRQ(ierr);
// we want to scatter from index _Ny*_Nz - _Nz to _Ny*_Nz - 1, i.e. the last
_Nz entries of the vector to scatter from
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);
// indices to scatter to
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);
//==============================================================================
// set up scatter context to take values for z = 0 from body field and put
them on a Vec of size Ny
// indices to scatter from
IS isf2;
/* creates a data structure for an index set with a list of evenly spaced
integers
* locally owned portion of index set has length _Ny
* first element of locally owned index set is 0
* change to the next index is _Nz (the stride)
* takes indices [0, _Nz, 2*_Nz, ..., (_Ny-1)*_Nz]
*/
ierr = ISCreateStride(PETSC_COMM_WORLD, _Ny, 0, _Nz, &isf2); CHKERRQ(ierr);
// indices to scatter to
PetscInt *ti2;
IS ist2;
ierr = PetscMalloc1(_Ny,&ti2); CHKERRQ(ierr);
// length _Ny
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);
//==============================================================================
// set up scatter context to take values for z = Lz from body field and put
them on a Vec of size Ny
// indices to scatter from
IS isf3;
// takes indices [_Nz - 1, 2*_Nz - 1, ..., _Ny*_Nz - 1]
ierr = ISCreateStride(PETSC_COMM_WORLD, _Ny, _Nz - 1, _Nz, &isf3);
CHKERRQ(ierr);
// indices to scatter to
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;
}
