Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed
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 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
> Sent: Sunday, March 3, 2019 2:19 PM
> To: Yuyun Yang ; Matthew Knepley
> Cc: petsc-users@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(, , 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 writes:
>
>> Yes, please see the attached files for a minimal example. Thanks a lot!
>>
>> Best regards,
>> Yuyun
>>
>> From: Matthew Knepley
>> Sent: Sunday, March 3, 2019 12:46 PM
>> To: Yuyun Yang
>> Cc: Zhang, Junchao ; 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 3:05 PM Yuyun Yang
>> mailto:yyan...@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_0x8400_0
>> [0] VecCreate() in
>> /home/yyy910805/petsc/src/vec/vec/interface/veccreate.c
>> [0] Vec seq Vec_0x8400_1
>> [0] VecCreate() in
>> /home/yyy910805/petsc/src/vec/vec/interface/veccreate.c
>> [0] VecScatter seq VecScatter_0x8400_2
>> [0] VecScatterCreate() in
>> /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c
>> [0] VecScatter seq VecScatter_0x8400_3
>> [0] VecScatterCreate() in
>> /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c
>> [0] VecScatter seq VecScatter_0x8400_4
>> [0] VecScatterCreate() in
>> /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c
>> [0] VecScatter seq VecScatter_0x8400_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 mailto:knep...@gmail.com>>
>> Sent: Sunday, March 3, 2019 11:28 AM
>> To: Yuyun Yang mailto:yyan...@stanford.edu>>
>> Cc: Zhang, Junchao mailto:jczh...@mcs.anl.gov>>;
>> 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 Sun, Mar 3, 2019 at 1:03 PM Yuyun Yang via petsc-users
>> 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 al
Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed
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
Sent: Sunday, March 3, 2019 2:19 PM
To: Yuyun Yang ; Matthew Knepley
Cc: petsc-users@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(, , 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 writes:
> Yes, please see the attached files for a minimal example. Thanks a lot!
>
> Best regards,
> Yuyun
>
> From: Matthew Knepley
> Sent: Sunday, March 3, 2019 12:46 PM
> To: Yuyun Yang
> Cc: Zhang, Junchao ; 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 3:05 PM Yuyun Yang
> mailto:yyan...@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_0x8400_0
> [0] VecCreate() in
> /home/yyy910805/petsc/src/vec/vec/interface/veccreate.c
> [0] Vec seq Vec_0x8400_1
> [0] VecCreate() in
> /home/yyy910805/petsc/src/vec/vec/interface/veccreate.c
> [0] VecScatter seq VecScatter_0x8400_2
> [0] VecScatterCreate() in
> /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c
> [0] VecScatter seq VecScatter_0x8400_3
> [0] VecScatterCreate() in
> /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c
> [0] VecScatter seq VecScatter_0x8400_4
> [0] VecScatterCreate() in
> /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c
> [0] VecScatter seq VecScatter_0x8400_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 mailto:knep...@gmail.com>>
> Sent: Sunday, March 3, 2019 11:28 AM
> To: Yuyun Yang mailto:yyan...@stanford.edu>>
> Cc: Zhang, Junchao mailto:jczh...@mcs.anl.gov>>;
> 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 Sun, Mar 3, 2019 at 1:03 PM Yuyun Yang via petsc-users
> 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 locate
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(, , 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 writes:
> Yes, please see the attached files for a minimal example. Thanks a lot!
>
> Best regards,
> Yuyun
>
> From: Matthew Knepley
> Sent: Sunday, March 3, 2019 12:46 PM
> To: Yuyun Yang
> Cc: Zhang, Junchao ; 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 3:05 PM Yuyun Yang
> mailto:yyan...@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_0x8400_0
> [0] VecCreate() in
> /home/yyy910805/petsc/src/vec/vec/interface/veccreate.c
> [0] Vec seq Vec_0x8400_1
> [0] VecCreate() in
> /home/yyy910805/petsc/src/vec/vec/interface/veccreate.c
> [0] VecScatter seq VecScatter_0x8400_2
> [0] VecScatterCreate() in
> /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c
> [0] VecScatter seq VecScatter_0x8400_3
> [0] VecScatterCreate() in
> /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c
> [0] VecScatter seq VecScatter_0x8400_4
> [0] VecScatterCreate() in
> /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c
> [0] VecScatter seq VecScatter_0x8400_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 mailto:knep...@gmail.com>>
> Sent: Sunday, March 3, 2019 11:28 AM
> To: Yuyun Yang mailto:yyan...@stanford.edu>>
> Cc: Zhang, Junchao mailto:jczh...@mcs.anl.gov>>;
> 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 Sun, Mar 3, 2019 at 1:03 PM Yuyun Yang via petsc-users
> 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 mailto:jczh...@mcs.anl.gov>>
> Sent: Friday, March 1, 2019 7:36 AM
> To: Yuyun Yang mailto:yyan...@
Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed
Yes, please see the attached files for a minimal example. Thanks a lot! Best regards, Yuyun From: Matthew Knepley Sent: Sunday, March 3, 2019 12:46 PM To: Yuyun Yang Cc: Zhang, Junchao ; 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 3:05 PM Yuyun Yang mailto:yyan...@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_0x8400_0 [0] VecCreate() in /home/yyy910805/petsc/src/vec/vec/interface/veccreate.c [0] Vec seq Vec_0x8400_1 [0] VecCreate() in /home/yyy910805/petsc/src/vec/vec/interface/veccreate.c [0] VecScatter seq VecScatter_0x8400_2 [0] VecScatterCreate() in /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c [0] VecScatter seq VecScatter_0x8400_3 [0] VecScatterCreate() in /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c [0] VecScatter seq VecScatter_0x8400_4 [0] VecScatterCreate() in /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c [0] VecScatter seq VecScatter_0x8400_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 mailto:knep...@gmail.com>> Sent: Sunday, March 3, 2019 11:28 AM To: Yuyun Yang mailto:yyan...@stanford.edu>> Cc: Zhang, Junchao mailto:jczh...@mcs.anl.gov>>; 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 Sun, Mar 3, 2019 at 1:03 PM Yuyun Yang via petsc-users 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 mailto:jczh...@mcs.anl.gov>> Sent: Friday, March 1, 2019 7:36 AM To: Yuyun Yang 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 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> ___
Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed
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_0x8400_0 [0] VecCreate() in /home/yyy910805/petsc/src/vec/vec/interface/veccreate.c [0] Vec seq Vec_0x8400_1 [0] VecCreate() in /home/yyy910805/petsc/src/vec/vec/interface/veccreate.c [0] VecScatter seq VecScatter_0x8400_2 [0] VecScatterCreate() in /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c [0] VecScatter seq VecScatter_0x8400_3 [0] VecScatterCreate() in /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c [0] VecScatter seq VecScatter_0x8400_4 [0] VecScatterCreate() in /home/yyy910805/petsc/src/vec/vscat/interface/vscreate.c [0] VecScatter seq VecScatter_0x8400_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 Sent: Sunday, March 3, 2019 11:28 AM To: Yuyun Yang Cc: Zhang, Junchao ; 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 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 mailto:jczh...@mcs.anl.gov>> Sent: Friday, March 1, 2019 7:36 AM To: Yuyun Yang 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 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 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 mailto:yyan...@stanford.edu>> wrote: Hi Junchao, This code actually involves a lo
Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed
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)”. 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 Sent: Friday, March 1, 2019 7:36 AM To: Yuyun Yang 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 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 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 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 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 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 mailto:jczh...@mcs.anl.gov>> Sent: Wednesday, February 27, 2019 10:50 AM To: Yuyun Yang mailto:yyan...@stanford.edu>> Cc: Matthew Knepley 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 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(,), You need to VecDestroy() before doing new VecDuplicate(,); How do I implement CHECK ALL RETURN CODES? For each PETSc function, do ierr = ...; CHKERRQ(ierr); From: Matthew Knepley mailto:knep...@gmail.com>> Sent: Wednesday, February 27, 2019 7:24 AM To: Yuyun Yang mailt
Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed
Ok, will do that. Thanks a lot! Get Outlook for iOS<https://aka.ms/o0ukef> From: Zhang, Junchao Sent: Wednesday, February 27, 2019 8:27:17 PM To: Yuyun Yang Cc: Matthew Knepley; 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 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 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 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 mailto:jczh...@mcs.anl.gov>> Sent: Wednesday, February 27, 2019 10:50 AM To: Yuyun Yang mailto:yyan...@stanford.edu>> Cc: Matthew Knepley 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 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(,), You need to VecDestroy() before doing new VecDuplicate(,); How do I implement CHECK ALL RETURN CODES? For each PETSc function, do ierr = ...; CHKERRQ(ierr); From: Matthew Knepley mailto:knep...@gmail.com>> Sent: Wednesday, February 27, 2019 7:24 AM To: Yuyun Yang 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 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: 0x61f076c0 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) 0x61f076c0 is located 1600 bytes inside of 3220-byte region [0x61f07080,0x61f07d14) 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 0x7f
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 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 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 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 mailto:jczh...@mcs.anl.gov>> Sent: Wednesday, February 27, 2019 10:50 AM To: Yuyun Yang mailto:yyan...@stanford.edu>> Cc: Matthew Knepley 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 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(,), You need to VecDestroy() before doing new VecDuplicate(,); How do I implement CHECK ALL RETURN CODES? For each PETSc function, do ierr = ...; CHKERRQ(ierr); From: Matthew Knepley mailto:knep...@gmail.com>> Sent: Wednesday, February 27, 2019 7:24 AM To: Yuyun Yang 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 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: 0x61f076c0 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) 0x61f076c0 is located 1600 bytes inside of 3220-byte region [0x61f07080,0x61f07d14) 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/i
Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed
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 Sent: Wednesday, February 27, 2019 6:24:13 PM To: Yuyun Yang Cc: Matthew Knepley; 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 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 mailto:jczh...@mcs.anl.gov>> Sent: Wednesday, February 27, 2019 10:50 AM To: Yuyun Yang mailto:yyan...@stanford.edu>> Cc: Matthew Knepley 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 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(,), You need to VecDestroy() before doing new VecDuplicate(,); How do I implement CHECK ALL RETURN CODES? For each PETSc function, do ierr = ...; CHKERRQ(ierr); From: Matthew Knepley mailto:knep...@gmail.com>> Sent: Wednesday, February 27, 2019 7:24 AM To: Yuyun Yang 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 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: 0x61f076c0 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) 0x61f076c0 is located 1600 bytes inside of 3220-byte region [0x61f07080,0x61f07d14) 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 ver
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 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 mailto:jczh...@mcs.anl.gov>> Sent: Wednesday, February 27, 2019 10:50 AM To: Yuyun Yang mailto:yyan...@stanford.edu>> Cc: Matthew Knepley 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 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(,), You need to VecDestroy() before doing new VecDuplicate(,); How do I implement CHECK ALL RETURN CODES? For each PETSc function, do ierr = ...; CHKERRQ(ierr); From: Matthew Knepley mailto:knep...@gmail.com>> Sent: Wednesday, February 27, 2019 7:24 AM To: Yuyun Yang 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 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: 0x61f076c0 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) 0x61f076c0 is located 1600 bytes inside of 3220-byte region [0x61f07080,0x61f07d14) 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/>
Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed
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 Sent: Wednesday, February 27, 2019 10:50 AM To: Yuyun Yang Cc: Matthew Knepley ; 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 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(,), You need to VecDestroy() before doing new VecDuplicate(,); How do I implement CHECK ALL RETURN CODES? For each PETSc function, do ierr = ...; CHKERRQ(ierr); From: Matthew Knepley mailto:knep...@gmail.com>> Sent: Wednesday, February 27, 2019 7:24 AM To: Yuyun Yang 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 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: 0x61f076c0 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) 0x61f076c0 is located 1600 bytes inside of 3220-byte region [0x61f07080,0x61f07d14) 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/>
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 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(,), You need to VecDestroy() before doing new VecDuplicate(,); How do I implement CHECK ALL RETURN CODES? For each PETSc function, do ierr = ...; CHKERRQ(ierr); From: Matthew Knepley mailto:knep...@gmail.com>> Sent: Wednesday, February 27, 2019 7:24 AM To: Yuyun Yang 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 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: 0x61f076c0 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) 0x61f076c0 is located 1600 bytes inside of 3220-byte region [0x61f07080,0x61f07d14) 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/>
Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed
I called VecDestroy() in the destructor for this object – is that not the right way to do it? How do I implement CHECK ALL RETURN CODES? From: Matthew Knepley Sent: Wednesday, February 27, 2019 7:24 AM To: Yuyun Yang Cc: 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 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: 0x61f076c0 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) 0x61f076c0 is located 1600 bytes inside of 3220-byte region [0x61f07080,0x61f07d14) 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/>
[petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed
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: 0x61f076c0 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)
0x61f076c0 is located 1600 bytes inside of 3220-byte region
[0x61f07080,0x61f07d14)
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
#include "domain.hpp"
#define FILENAME "sbpOps_fc.cpp"
using namespace std;
// member function definitions including constructor
// first type of constructor with 1 parameter
Domain::Domain(const char *file)
: _file(file),_delim(" = "),_outputDir("data/"),
_bulkDeformationType("linearElastic"),
_momentumBalanceType("quasidynamic"),
_sbpType("mfc_coordTrans"),_operatorType("matrix-based"),
_sbpCompatibilityType("fullyCompatible"),
_gridSpacingType("variableGridSpacing"),
_isMMS(0),_loadICs(0), _inputDir("unspecified_"),
_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)
{
#if VERBOSE > 1
std::string funcName = "Domain::Domain(const char *file)";
PetscPrintf(PETSC_COMM_WORLD,"Starting %s in
%s.\n",funcName.c_str(),FILENAME);
#endif
// 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;
}
#if VERBOSE > 2 // each processor prints loaded values to screen
PetscMPIInt rank,size;
MPI_Comm_size(PETSC_COMM_WORLD,);
MPI_Comm_rank(PETSC_COMM_WORLD,);
for (int Ii = 0; Ii < size; Ii++) {
view(Ii);
}
#endif
checkInput(); // perform some basic value checking to prevent NaNs
setFields();
setScatters();
#if VERBOSE > 1
PetscPrintf(PETSC_COMM_WORLD,"Ending %s in %s\n",funcName.c_str(),FILENAME);
#endif
}
// second type of constructor with 3 parameters
Domain::Domain(const char *file,PetscInt Ny, PetscInt Nz)
: _file(file),_delim(" = "),_outputDir("data/"),
_bulkDeformationType("linearElastic"),_momentumBalanceType("quasidynamic"),
_sbpType("mfc_coordTrans"),_operatorType("matrix-based"),_sbpCompatibilityType("fullyCompatible"),_gridSpacingType("variableGridSpacing"),
_isMMS(0),_loadICs(0),_inputDir("unspecified_"),
_order(4),_Ny(Ny),_Nz(Nz),_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)
{
#if VERBOSE > 1
std::string funcName = "Domain::Domain(const char *file,PetscInt Ny,
PetscInt Nz)";
PetscPrintf(PETSC_COMM_WORLD,"Starting %s in
%s.\n",funcName.c_str(),FILENAME);
#endif
loadData(_file);
_Ny = Ny;
_Nz = Nz;
if (_Ny > 1) {
_dq = 1.0/(_Ny-1.0);
}
else {
_dq = 1;
}
