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Subject: [OMPI users] One-sided bugs
From: Jed Brown (jed_at_[hidden])
Date: 2011-12-22 16:16:19


I wrote a new communication layer that we are evaluating for use in mesh
management and PDE solvers, but it is based on MPI-2 one-sided operations
(and will eventually benefit from some of the MPI-3 one-sided proposals,
especially MPI_Fetch_and_op() and dynamic windows). All the basic
functionality works well with MPICH2, but I have run into some Open MPI
bugs regarding one-sided operations with composite data types. This email
provides a reduced test case for two such bugs. I see that there are also
some existing serious-looking bug reports regarding one-sided operations,
but they are getting pretty old now and haven't seen action in a while.

https://svn.open-mpi.org/trac/ompi/ticket/2656
https://svn.open-mpi.org/trac/ompi/ticket/1905

Is there a plan for resolving these in the near future?

Is anyone using Open MPI for serious work with one-sided operations?

Bugs I am reporting:

*1.* If an MPI_Win is used with an MPI_Datatype, even if the MPI_Win
operation has completed, I get an invalid free when MPI_Type_free() is
called before MPI_Win_free(). Since MPI_Type_free() is only supposed to
mark the datatype for deletion, the implementation should properly manage
reference counting. If you run the attached code with

$ mpiexec -n 2 ./a.out 1

(which only does part of the comm described for the second bug, below), you
can see the invalid free on rank 1 with stack still in MPI_Win_fence()

(gdb) bt
#0 0x00007ffff7288905 in raise () from /lib/libc.so.6
#1 0x00007ffff7289d7b in abort () from /lib/libc.so.6
#2 0x00007ffff72c147e in __libc_message () from /lib/libc.so.6
#3 0x00007ffff72c7396 in malloc_printerr () from /lib/libc.so.6
#4 0x00007ffff72cb26c in free () from /lib/libc.so.6
#5 0x00007ffff7a5aaa8 in ompi_datatype_release_args (pData=0x845010) at
ompi_datatype_args.c:414
#6 0x00007ffff7a5b0ea in __ompi_datatype_release (datatype=0x845010) at
ompi_datatype_create.c:47
#7 0x00007ffff218e772 in opal_obj_run_destructors (object=0x845010) at
../../../../opal/class/opal_object.h:448
#8 ompi_osc_rdma_replyreq_free (replyreq=0x680a80) at
osc_rdma_replyreq.h:136
#9 ompi_osc_rdma_replyreq_send_cb (btl=0x7ffff3680ce0, endpoint=<optimized
out>, descriptor=0x837b00, status=<optimized out>) at
osc_rdma_data_move.c:691
#10 0x00007ffff347f38f in mca_btl_sm_component_progress () at
btl_sm_component.c:645
#11 0x00007ffff7b1f80a in opal_progress () at runtime/opal_progress.c:207
#12 0x00007ffff21977c5 in opal_condition_wait (m=<optimized out>,
c=0x842ee0) at ../../../../opal/threads/condition.h:99
#13 ompi_osc_rdma_module_fence (assert=0, win=0x842270) at
osc_rdma_sync.c:207
#14 0x00007ffff7a89db5 in PMPI_Win_fence (assert=0, win=0x842270) at
pwin_fence.c:60
#15 0x00000000004010d8 in main (argc=2, argv=0x7fffffffd508) at win.c:60

meanwhile, rank 0 has already freed the datatype and is waiting in
MPI_Win_free().
(gdb) bt
#0 0x00007ffff7312107 in sched_yield () from /lib/libc.so.6
#1 0x00007ffff7b1f82b in opal_progress () at runtime/opal_progress.c:220
#2 0x00007ffff7a53fe4 in opal_condition_wait (m=<optimized out>,
c=<optimized out>) at ../opal/threads/condition.h:99
#3 ompi_request_default_wait_all (count=2, requests=0x7fffffffd210,
statuses=0x7fffffffd1e0) at request/req_wait.c:263
#4 0x00007ffff25b8d71 in ompi_coll_tuned_sendrecv_actual (sendbuf=0x0,
scount=0, sdatatype=0x7ffff7dba840, dest=1, stag=-16, recvbuf=<optimized
out>, rcount=0, rdatatype=0x7ffff7dba840, source=1, rtag=-16,
comm=0x8431a0, status=0x0) at coll_tuned_util.c:54
#5 0x00007ffff25c2de2 in ompi_coll_tuned_barrier_intra_two_procs
(comm=<optimized out>, module=<optimized out>) at coll_tuned_barrier.c:256
#6 0x00007ffff25b92ab in ompi_coll_tuned_barrier_intra_dec_fixed
(comm=0x8431a0, module=0x844980) at coll_tuned_decision_fixed.c:190
#7 0x00007ffff2186248 in ompi_osc_rdma_module_free (win=0x842170) at
osc_rdma.c:46
#8 0x00007ffff7a58a44 in ompi_win_free (win=0x842170) at win/win.c:150
#9 0x00007ffff7a8a0dd in PMPI_Win_free (win=0x7fffffffd408) at
pwin_free.c:56
#10 0x0000000000401195 in main (argc=2, argv=0x7fffffffd508) at win.c:69

*2.* This appears to be more fundamental and perhaps much harder to fix.
The attached code sets up the following graph

rank 0:
0 -> (1,0)
1 -> nothing
2 -> (1,1)

rank 1:
0 -> (0,0)
1 -> (0,2)
2 -> (0,1)

We pull over this graph using two calls to MPI_Get(), each with composite
data types defining what to pull into the first two slots, and what to put
into the third slot. It is Valgrind-clean with MPICH2, and produces the
following:

$ mpiexec.hydra -n 2 ./a.out 2
[0] provided [100,101,102] got [200, -2,201]
[1] provided [200,201,202] got [100,102,101]

With Open MPI, I see

a.out: malloc.c:3096: sYSMALLOc: Assertion `(old_top == (((mbinptr) (((char
*) &((av)->bins[((1) - 1) * 2])) - __builtin_offsetof (struct malloc_chunk,
fd)))) && old_size == 0) || ((unsigned long) (old_size) >= (unsigned
long)((((__builtin_offsetof (struct malloc_chunk, fd_nextsize))+((2 *
(sizeof(size_t))) - 1)) & ~((2 * (sizeof(size_t))) - 1))) &&
((old_top)->size & 0x1) && ((unsigned long)old_end & pagemask) == 0)'
failed.

on both ranks, with rank 0 at

(gdb) bt
#0 0x00007ffff7288905 in raise () from /lib/libc.so.6
#1 0x00007ffff7289d7b in abort () from /lib/libc.so.6
#2 0x00007ffff72c675d in __malloc_assert () from /lib/libc.so.6
#3 0x00007ffff72c96d3 in _int_malloc () from /lib/libc.so.6
#4 0x00007ffff72cad5d in malloc () from /lib/libc.so.6
#5 0x00007ffff7b46c46 in opal_free_list_grow (flist=0x7ffff239f150,
num_elements=1) at class/opal_free_list.c:93
#6 0x00007ffff2196152 in ompi_osc_rdma_replyreq_alloc
(replyreq=0x7fffffffd0f8, origin_rank=1, module=0x842d10) at
osc_rdma_replyreq.h:82
#7 ompi_osc_rdma_replyreq_alloc_init (module=0x842d10, origin=1,
origin_request=..., target_displacement=0, target_count=1,
datatype=0x8455b0, replyreq=0x7fffffffd0f8) at osc_rdma_replyreq.c:40
#8 0x00007ffff218c051 in component_fragment_cb (btl=0x7ffff3680ce0,
tag=<optimized out>, descriptor=<optimized out>, cbdata=<optimized out>) at
osc_rdma_component.c:633
#9 0x00007ffff347f25f in mca_btl_sm_component_progress () at
btl_sm_component.c:623
#10 0x00007ffff7b1f80a in opal_progress () at runtime/opal_progress.c:207
#11 0x00007ffff21977c5 in opal_condition_wait (m=<optimized out>,
c=0x842de0) at ../../../../opal/threads/condition.h:99
#12 ompi_osc_rdma_module_fence (assert=0, win=0x842170) at
osc_rdma_sync.c:207
#13 0x00007ffff7a89db5 in PMPI_Win_fence (assert=0, win=0x842170) at
pwin_fence.c:60
#14 0x00000000004010d8 in main (argc=2, argv=0x7fffffffd508) at win.c:60

and rank 1 at

(gdb) bt
#0 0x00007ffff7288905 in raise () from /lib/libc.so.6
#1 0x00007ffff7289d7b in abort () from /lib/libc.so.6
#2 0x00007ffff72c675d in __malloc_assert () from /lib/libc.so.6
#3 0x00007ffff72c96d3 in _int_malloc () from /lib/libc.so.6
#4 0x00007ffff72cad5d in malloc () from /lib/libc.so.6
#5 0x00007ffff7a5b3ce in opal_obj_new (cls=0x7ffff7db2060) at
../../opal/class/opal_object.h:469
#6 opal_obj_new_debug (line=71, file=0x7ffff7b60323
"ompi_datatype_create.c", type=0x7ffff7db2060) at
../../opal/class/opal_object.h:251
#7 ompi_datatype_create (expectedSize=3) at ompi_datatype_create.c:71
#8 0x00007ffff7a5b7e9 in ompi_datatype_create_indexed_block (count=1,
bLength=1, pDisp=0x7fffee18a834, oldType=0x7ffff7db3640,
newType=0x7fffffffd070) at ompi_datatype_create_indexed.c:124
#9 0x00007ffff7a5a349 in __ompi_datatype_create_from_args (type=9,
d=0x844f40, a=0x7fffee18a828, i=0x7fffee18a82c) at ompi_datatype_args.c:691
#10 __ompi_datatype_create_from_packed_description
(packed_buffer=0x7fffffffd108, remote_processor=0x652b90) at
ompi_datatype_args.c:626
#11 0x00007ffff7a5b045 in ompi_datatype_create_from_packed_description
(packed_buffer=<optimized out>, remote_processor=<optimized out>) at
ompi_datatype_args.c:779
#12 0x00007ffff218bf60 in ompi_osc_base_datatype_create
(payload=0x7fffffffd108, remote_proc=<optimized out>) at
../../../../ompi/mca/osc/base/osc_base_obj_convert.h:52
#13 component_fragment_cb (btl=0x7ffff3680ce0, tag=<optimized out>,
descriptor=<optimized out>, cbdata=<optimized out>) at
osc_rdma_component.c:624
#14 0x00007ffff347f25f in mca_btl_sm_component_progress () at
btl_sm_component.c:623
#15 0x00007ffff7b1f80a in opal_progress () at runtime/opal_progress.c:207
#16 0x00007ffff21977c5 in opal_condition_wait (m=<optimized out>,
c=0x842ee0) at ../../../../opal/threads/condition.h:99
#17 ompi_osc_rdma_module_fence (assert=0, win=0x842270) at
osc_rdma_sync.c:207
#18 0x00007ffff7a89db5 in PMPI_Win_fence (assert=0, win=0x842270) at
pwin_fence.c:60
#19 0x00000000004010d8 in main (argc=2, argv=0x7fffffffd508) at win.c:60

This looks like memory corruption, but Open MPI internals are too noisy
under valgrind for it to be obvious where to look. This is with Open MPI
1.5.4, but I observed the same thing with trunk. If I run with three
processes, the graph is slightly different and only ranks 1 and 2 error
(rank 0 hangs).