[petsc-dev] use of uninitialized values in PetscSF
Satish Balay
balay at mcs.anl.gov
Fri Sep 18 22:46:05 CDT 2015
I just tried a build with
http://www.mpich.org/static/downloads/3.2b4/mpich-3.2b4.tar.gz
and still see the errors.
Satish
----------
balay at es^/scratch/balay/petsc/src/vec/is/sf/examples/tutorials(master=) $ /scratch/balay/petsc/arch-linux2-c-debug/bin/mpiexec -n 2 valgrind --tool=memcheck -q ./ex2 -sf_type window
PetscSF Object: 2 MPI processes
type: window
synchronization=FENCE sort=rank-order
[0] Number of roots=1, leaves=2, remote ranks=2
[0] 0 <- (0,0)
[0] 1 <- (1,0)
[1] Number of roots=1, leaves=2, remote ranks=2
[1] 0 <- (1,0)
[1] 1 <- (0,0)
==13170== Syscall param writev(vector[...]) points to uninitialised byte(s)
==13170== at 0xA2EFD4B: writev (writev.c:51)
==13170== by 0x9C7D432: MPL_large_writev (mplsock.c:32)
==13170== by 0x9C6CD24: MPIDU_Sock_writev (sock_immed.i:610)
==13170== by 0x9C26793: MPIDI_CH3_iStartMsgv (ch3_istartmsgv.c:110)
==13170== by 0x9BB0184: issue_get_op (mpid_rma_issue.h:991)
==13170== by 0x9BB0923: issue_rma_op (mpid_rma_issue.h:1221)
==13170== by 0x9BB273F: issue_ops_target (ch3u_rma_progress.c:392)
==13170== by 0x9BB2DFB: issue_ops_win (ch3u_rma_progress.c:544)
==13170== by 0x9BB3FA4: MPIDI_CH3I_RMA_Make_progress_global (ch3u_rma_progress.c:972)
==13170== by 0x9C27A16: MPIDI_CH3i_Progress_wait (ch3_progress.c:192)
==13170== by 0x9C292B6: MPIDI_CH3I_Progress (ch3_progress.c:948)
==13170== by 0x9B34599: MPIC_Wait (helper_fns.c:225)
==13170== Address 0xc147574 is 4 bytes inside a block of size 168 alloc'd
==13170== at 0x4C2B6CD: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==13170== by 0x9BAFFD5: issue_get_op (mpid_rma_issue.h:973)
==13170== by 0x9BB0923: issue_rma_op (mpid_rma_issue.h:1221)
==13170== by 0x9BB273F: issue_ops_target (ch3u_rma_progress.c:392)
==13170== by 0x9BB2DFB: issue_ops_win (ch3u_rma_progress.c:544)
==13170== by 0x9BB3FA4: MPIDI_CH3I_RMA_Make_progress_global (ch3u_rma_progress.c:972)
==13170== by 0x9C27A16: MPIDI_CH3i_Progress_wait (ch3_progress.c:192)
==13170== by 0x9C292B6: MPIDI_CH3I_Progress (ch3_progress.c:948)
==13170== by 0x9B34599: MPIC_Wait (helper_fns.c:225)
==13170== by 0x9B3491B: MPIC_Recv (helper_fns.c:355)
==13170== by 0x99AE746: MPIR_Bcast_binomial (bcast.c:234)
==13170== by 0x99B1309: MPIR_Bcast_intra (bcast.c:1283)
==13170==
==13169== Syscall param writev(vector[...]) points to uninitialised byte(s)
==13169== at 0xA2EFD4B: writev (writev.c:51)
==13169== by 0x9C7D432: MPL_large_writev (mplsock.c:32)
==13169== by 0x9C6CD24: MPIDU_Sock_writev (sock_immed.i:610)
==13169== by 0x9C26793: MPIDI_CH3_iStartMsgv (ch3_istartmsgv.c:110)
==13169== by 0x9BB0184: issue_get_op (mpid_rma_issue.h:991)
==13169== by 0x9BB0923: issue_rma_op (mpid_rma_issue.h:1221)
==13169== by 0x9BB273F: issue_ops_target (ch3u_rma_progress.c:392)
==13169== by 0x9BB2DFB: issue_ops_win (ch3u_rma_progress.c:544)
==13169== by 0x9BB3FA4: MPIDI_CH3I_RMA_Make_progress_global (ch3u_rma_progress.c:972)
==13169== by 0x9C27A16: MPIDI_CH3i_Progress_wait (ch3_progress.c:192)
==13169== by 0x9C292B6: MPIDI_CH3I_Progress (ch3_progress.c:948)
==13169== by 0x9B34599: MPIC_Wait (helper_fns.c:225)
==13169== Address 0xbcf90e4 is 4 bytes inside a block of size 168 alloc'd
==13169== at 0x4C2B6CD: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==13169== by 0x9BAFFD5: issue_get_op (mpid_rma_issue.h:973)
==13169== by 0x9BB0923: issue_rma_op (mpid_rma_issue.h:1221)
==13169== by 0x9BB273F: issue_ops_target (ch3u_rma_progress.c:392)
==13169== by 0x9BB2DFB: issue_ops_win (ch3u_rma_progress.c:544)
==13169== by 0x9BB3FA4: MPIDI_CH3I_RMA_Make_progress_global (ch3u_rma_progress.c:972)
==13169== by 0x9C27A16: MPIDI_CH3i_Progress_wait (ch3_progress.c:192)
==13169== by 0x9C292B6: MPIDI_CH3I_Progress (ch3_progress.c:948)
==13169== by 0x9B34599: MPIC_Wait (helper_fns.c:225)
==13169== by 0x9B3491B: MPIC_Recv (helper_fns.c:355)
==13169== by 0x99B8B44: MPIR_Reduce_binomial (reduce.c:181)
==13169== by 0x99BAC95: MPIR_Reduce_intra (reduce.c:874)
==13169==
Vec Object: 2 MPI processes
type: mpi
Process [0]
0
1
Process [1]
1
0
Vec Object: 2 MPI processes
type: mpi
Process [0]
10
11
Process [1]
11
10
balay at es^/scratch/balay/petsc/src/vec/is/sf/examples/tutorials(master=) $
On Fri, 18 Sep 2015, Jed Brown wrote:
> Barry Smith <bsmith at mcs.anl.gov> writes:
>
> > Is there any way to fix this use of uninitialized values?
>
> Hmm, I don't think it's something we have any control over. I could try
> making a reduced test case to put in MPICH's test suite. Is this with
> the latest version of MPICH?
>
> > 9a10,67
> >> ==31141== Syscall param writev(vector[...]) points to uninitialised byte(s)
> >> ==31141== at 0xD164CDB: writev (writev.c:51)
> >> ==31141== by 0xCB13596: MPL_large_writev (mplsock.c:32)
> >> ==31141== by 0xCB02DC9: MPIDU_Sock_writev (sock_immed.i:610)
> >> ==31141== by 0xCAC00DD: MPIDI_CH3_iStartMsgv (ch3_istartmsgv.c:110)
> >> ==31141== by 0xCA7DC91: recv_rma_msg (ch3u_rma_sync.c:2198)
> >> ==31141== by 0xCA79CB6: MPIDI_Win_fence (ch3u_rma_sync.c:1295)
> >> ==31141== by 0xC9AD840: PMPI_Win_fence (win_fence.c:111)
> >> ==31141== by 0x51DA7E1: PetscSFRestoreWindow (sfwindow.c:348)
> >> ==31141== by 0x51DD0C9: PetscSFBcastEnd_Window (sfwindow.c:510)
> >> ==31141== by 0x51D0B66: PetscSFBcastEnd (sf.c:1001)
> >> ==31141== by 0x401EB7: main (ex2.c:81)
> >> ==31141== Address 0xe50d12c is 108 bytes inside a block of size 208 alloc'd
> >> ==31141== at 0x4C2B6CD: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
> >> ==31141== by 0xCA7328D: MPIDI_CH3I_RMA_Ops_alloc_tail (mpidrma.h:191)
> >> ==31141== by 0xCA75A49: MPIDI_Get (ch3u_rma_ops.c:290)
> >> ==31141== by 0xC99EC9C: PMPI_Get (get.c:142)
> >> ==31141== by 0x51DCC62: PetscSFBcastBegin_Window (sfwindow.c:495)
> >> ==31141== by 0x51D03C4: PetscSFBcastBegin (sf.c:968)
> >> ==31141== by 0x401DDB: main (ex2.c:79)
> >> ==31141== Uninitialised value was created by a heap allocation
> >> ==31141== at 0x4C2B6CD: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
> >> ==31141== by 0xCA7328D: MPIDI_CH3I_RMA_Ops_alloc_tail (mpidrma.h:191)
> >> ==31141== by 0xCA75A49: MPIDI_Get (ch3u_rma_ops.c:290)
> >> ==31141== by 0xC99EC9C: PMPI_Get (get.c:142)
> >> ==31141== by 0x51DCC62: PetscSFBcastBegin_Window (sfwindow.c:495)
> >> ==31141== by 0x51D03C4: PetscSFBcastBegin (sf.c:968)
> >> ==31141== by 0x401DDB: main (ex2.c:79)
> >> ==31141==
> >> ==31142== Syscall param writev(vector[...]) points to uninitialised byte(s)
> >> ==31142== at 0xD164CDB: writev (writev.c:51)
> >> ==31142== by 0xCB13596: MPL_large_writev (mplsock.c:32)
> >> ==31142== by 0xCB02DC9: MPIDU_Sock_writev (sock_immed.i:610)
> >> ==31142== by 0xCAC00DD: MPIDI_CH3_iStartMsgv (ch3_istartmsgv.c:110)
> >> ==31142== by 0xCA7DC91: recv_rma_msg (ch3u_rma_sync.c:2198)
> >> ==31142== by 0xCA79CB6: MPIDI_Win_fence (ch3u_rma_sync.c:1295)
> >> ==31142== by 0xC9AD840: PMPI_Win_fence (win_fence.c:111)
> >> ==31142== by 0x51DA7E1: PetscSFRestoreWindow (sfwindow.c:348)
> >> ==31142== by 0x51DD0C9: PetscSFBcastEnd_Window (sfwindow.c:510)
> >> ==31142== by 0x51D0B66: PetscSFBcastEnd (sf.c:1001)
> >> ==31142== by 0x401EB7: main (ex2.c:81)
> >> ==31142== Address 0xe49d88c is 108 bytes inside a block of size 208 alloc'd
> >> ==31142== at 0x4C2B6CD: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
> >> ==31142== by 0xCA7328D: MPIDI_CH3I_RMA_Ops_alloc_tail (mpidrma.h:191)
> >> ==31142== by 0xCA75A49: MPIDI_Get (ch3u_rma_ops.c:290)
> >> ==31142== by 0xC99EC9C: PMPI_Get (get.c:142)
> >> ==31142== by 0x51DCC62: PetscSFBcastBegin_Window (sfwindow.c:495)
> >> ==31142== by 0x51D03C4: PetscSFBcastBegin (sf.c:968)
> >> ==31142== by 0x401DDB: main (ex2.c:79)
> >> ==31142== Uninitialised value was created by a heap allocation
> >> ==31142== at 0x4C2B6CD: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
> >> ==31142== by 0xCA7328D: MPIDI_CH3I_RMA_Ops_alloc_tail (mpidrma.h:191)
> >> ==31142== by 0xCA75A49: MPIDI_Get (ch3u_rma_ops.c:290)
> >> ==31142== by 0xC99EC9C: PMPI_Get (get.c:142)
> >> ==31142== by 0x51DCC62: PetscSFBcastBegin_Window (sfwindow.c:495)
> >> ==31142== by 0x51D03C4: PetscSFBcastBegin (sf.c:968)
> >> ==31142== by 0x401DDB: main (ex2.c:79)
> >> ==31142==
> > /sandbox/petsc/petsc.clone/src/vec/is/sf/examples/tutorials
> > Possible problem with ex2_window, diffs above
>
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