Eloi, sorry can you print out frag->hdr->tag?

Unfortunately from your last email I think it will still all have non-zero values.
If that ends up being the case then there must be something odd with the descriptor pointer to the fragment.

--td

Eloi Gaudry wrote:
Terry,

Please find enclosed the requested check outputs (using -output-filename stdout.tag.null option).

For information, Nysal In his first message referred to ompi/mca/pml/ob1/pml_ob1_hdr.h and said that hdr->tg value was wrnong on receiving side.
#define MCA_PML_OB1_HDR_TYPE_MATCH     (MCA_BTL_TAG_PML + 1)
#define MCA_PML_OB1_HDR_TYPE_RNDV      (MCA_BTL_TAG_PML + 2)
#define MCA_PML_OB1_HDR_TYPE_RGET      (MCA_BTL_TAG_PML + 3)
 #define MCA_PML_OB1_HDR_TYPE_ACK       (MCA_BTL_TAG_PML + 4)
#define MCA_PML_OB1_HDR_TYPE_NACK      (MCA_BTL_TAG_PML + 5)
#define MCA_PML_OB1_HDR_TYPE_FRAG      (MCA_BTL_TAG_PML + 6)
#define MCA_PML_OB1_HDR_TYPE_GET       (MCA_BTL_TAG_PML + 7)
 #define MCA_PML_OB1_HDR_TYPE_PUT       (MCA_BTL_TAG_PML + 8)
#define MCA_PML_OB1_HDR_TYPE_FIN       (MCA_BTL_TAG_PML + 9)
and in ompi/mca/btl/btl.h 
#define MCA_BTL_TAG_PML             0x40

Eloi

On Monday 27 September 2010 14:36:59 Terry Dontje wrote:
  
I am thinking checking the value of *frag->hdr right before the return
in the post_send function in ompi/mca/btl/openib/btl_openib_endpoint.h.
It is line 548 in the trunk
https://svn.open-mpi.org/source/xref/ompi-trunk/ompi/mca/btl/openib/btl_ope
nib_endpoint.h#548

--td

Eloi Gaudry wrote:
    
Hi Terry,

Do you have any patch that I could apply to be able to do so ? I'm
remotely working on a cluster (with a terminal) and I cannot use any
parallel debugger or sequential debugger (with a call to xterm...). I
can track frag->hdr->tag value in
ompi/mca/btl/openib/btl_openib_component.c::handle_wc in the
SEND/RDMA_WRITE case, but this is all I can think of alone.

You'll find a stacktrace (receive side) in this thread (10th or 11th
message) but it might be pointless.

Regards,
Eloi

On Monday 27 September 2010 11:43:55 Terry Dontje wrote:
      
So it sounds like coalescing is not your issue and that the problem has
something to do with the queue sizes.  It would be helpful if we could
detect the hdr->tag == 0 issue on the sending side and get at least a
stack trace.  There is something really odd going on here.

--td

Eloi Gaudry wrote:
        
Hi Terry,

I'm sorry to say that I might have missed a point here.

I've lately been relaunching all previously failing computations with
the message coalescing feature being switched off, and I saw the same
hdr->tag=0 error several times, always during a collective call
(MPI_Comm_create, MPI_Allreduce and MPI_Broadcast, so far). And as
soon as I switched to the peer queue option I was previously using
(--mca btl_openib_receive_queues P,65536,256,192,128 instead of using
--mca btl_openib_use_message_coalescing 0), all computations ran
flawlessly.

As for the reproducer, I've already tried to write something but I
haven't succeeded so far at reproducing the hdr->tag=0 issue with it.

Eloi

On 24/09/2010 18:37, Terry Dontje wrote:
          
Eloi Gaudry wrote:
            
Terry,

You were right, the error indeed seems to come from the message
coalescing feature. If I turn it off using the "--mca
btl_openib_use_message_coalescing 0", I'm not able to observe the
"hdr->tag=0" error.

There are some trac requests associated to very similar error
(https://svn.open-mpi.org/trac/ompi/search?q=coalescing) but they are
all closed (except https://svn.open-mpi.org/trac/ompi/ticket/2352
that might be related), aren't they ? What would you suggest Terry ?
              
Interesting, though it looks to me like the segv in ticket 2352 would
have happened on the send side instead of the receive side like you
have.  As to what to do next it would be really nice to have some
sort of reproducer that we can try and debug what is really going
on.  The only other thing to do without a reproducer is to inspect
the code on the send side to figure out what might make it generate
at 0 hdr->tag.  Or maybe instrument the send side to stop when it is
about ready to send a 0 hdr->tag and see if we can see how the code
got there.

I might have some cycles to look at this Monday.

--td

            
Eloi

On Friday 24 September 2010 16:00:26 Terry Dontje wrote:
              
Eloi Gaudry wrote:
                
Terry,

No, I haven't tried any other values than P,65536,256,192,128 yet.

The reason why is quite simple. I've been reading and reading again
this thread to understand the btl_openib_receive_queues meaning and
I can't figure out why the default values seem to induce the hdr-

                  
tag=0 issue
(http://www.open-mpi.org/community/lists/users/2009/01/7808.php).
                    
Yeah, the size of the fragments and number of them really should not
cause this issue.  So I too am a little perplexed about it.

                
Do you think that the default shared received queue parameters are
erroneous for this specific Mellanox card ? Any help on finding the
proper parameters would actually be much appreciated.
                  
I don't necessarily think it is the queue size for a specific card
but more so the handling of the queues by the BTL when using
certain sizes. At least that is one gut feel I have.

In my mind the tag being 0 is either something below OMPI is
polluting the data fragment or OMPI's internal protocol is some how
getting messed up.  I can imagine (no empirical data here) the
queue sizes could change how the OMPI protocol sets things up. 
Another thing may be the coalescing feature in the openib BTL which
tries to gang multiple messages into one packet when resources are
running low.   I can see where changing the queue sizes might
affect the coalescing. So, it might be interesting to turn off the
coalescing.  You can do that by setting "--mca
btl_openib_use_message_coalescing 0" in your mpirun line.

If that doesn't solve the issue then obviously there must be
something else going on :-).

Note, the reason I am interested in this is I am seeing a similar
error condition (hdr->tag == 0) on a development system.  Though my
failing case fails with np=8 using the connectivity test program
which is mainly point to point and there are not a significant
amount of data transfers going on either.

--td

                
Eloi

On Friday 24 September 2010 14:27:07 you wrote:
                  
That is interesting.  So does the number of processes affect your
runs any.  The times I've seen hdr->tag be 0 usually has been due
to protocol issues.  The tag should never be 0.  Have you tried to
do other receive_queue settings other than the default and the one
you mention.

I wonder if you did a combination of the two receive queues causes
a failure or not.  Something like

P,128,256,192,128:P,65536,256,192,128

I am wondering if it is the first queuing definition causing the
issue or possibly the SRQ defined in the default.

--td

Eloi Gaudry wrote:
                    
Hi Terry,

The messages being send/received can be of any size, but the
error seems to happen more often with small messages (as an int
being broadcasted or allreduced). The failing communication
differs from one run to another, but some spots are more likely
to be failing than another. And as far as I know, there are
always located next to a small message (an int being broadcasted
for instance) communication. Other typical messages size are

                      
10k but can be very much larger.
                        
I've been checking the hca being used, its' from mellanox (with
vendor_part_id=26428). There is no receive_queues parameters
associated to it.

 $ cat share/openmpi/mca-btl-openib-device-params.ini as well:
[...]

  # A.k.a. ConnectX
  [Mellanox Hermon]
  vendor_id = 0x2c9,0x5ad,0x66a,0x8f1,0x1708,0x03ba,0x15b3
  vendor_part_id =
  25408,25418,25428,26418,26428,25448,26438,26448,26468,26478,264
  88 use_eager_rdma = 1
  mtu = 2048
  max_inline_data = 128

[..]

$ ompi_info --param btl openib --parsable | grep receive_queues

 mca:btl:openib:param:btl_openib_receive_queues:value:P,128,256,1
 92 ,128
 
 :S ,2048,256,128,32:S,12288,256,128,32:S,65536,256,128,32
 
 mca:btl:openib:param:btl_openib_receive_queues:data_source:defau
 lt value
 mca:btl:openib:param:btl_openib_receive_queues:status:writable
 mca:btl:openib:param:btl_openib_receive_queues:help:Colon-delimi
 t ed, comma delimited list of receive queues:
 P,4096,8,6,4:P,32768,8,6,4
 mca:btl:openib:param:btl_openib_receive_queues:deprecated:no

I was wondering if these parameters (automatically computed at
openib btl init for what I understood) were not incorrect in some
way and I plugged some others values: "P,65536,256,192,128"
(someone on the list used that values when encountering a
different issue) . Since that, I haven't been able to observe the
segfault (occuring as hrd->tag = 0 in
btl_openib_component.c:2881) yet.

Eloi


/home/pp_fr/st03230/EG/Softs/openmpi-custom-1.4.2/bin/

On Thursday 23 September 2010 23:33:48 Terry Dontje wrote:
                      
Eloi, I am curious about your problem.  Can you tell me what
size of job it is?  Does it always fail on the same bcast,  or
same process?

Eloi Gaudry wrote:
                        
Hi Nysal,

Thanks for your suggestions.

I'm now able to get the checksum computed and redirected to
stdout, thanks (I forgot the  "-mca pml_base_verbose 5" option,
you were right). I haven't been able to observe the
segmentation fault (with hdr->tag=0) so far (when using pml
csum) but I 'll let you know when I am.

I've got two others question, which may be related to the error
observed:

1/ does the maximum number of MPI_Comm that can be handled by
OpenMPI somehow depends on the btl being used (i.e. if I'm
using openib, may I use the same number of MPI_Comm object as
with tcp) ? Is there something as MPI_COMM_MAX in OpenMPI ?

2/ the segfaults only appears during a mpi collective call,
with very small message (one int is being broadcast, for
instance) ; i followed the guidelines given at
http://icl.cs.utk.edu/open-
mpi/faq/?category=openfabrics#ib-small-message-rdma but the
debug-build of OpenMPI asserts if I use a different min-size
that 255. Anyway, if I deactivate eager_rdma, the segfaults
remains. Does the openib btl handle very small message
differently (even with eager_rdma
deactivated) than tcp ?
                          
Others on the list does coalescing happen with non-eager_rdma? 
If so then that would possibly be one difference between the
openib btl and tcp aside from the actual protocol used.

                        
 is there a way to make sure that large messages and small
 messages are handled the same way ?
                          
Do you mean so they all look like eager messages?  How large of
messages are we talking about here 1K, 1M or 10M?

--td

                        
Regards,
Eloi

On Friday 17 September 2010 17:57:17 Nysal Jan wrote:
                          
Hi Eloi,
Create a debug build of OpenMPI (--enable-debug) and while
running with the csum PML add "-mca pml_base_verbose 5" to the
command line. This will print the checksum details for each
fragment sent over the wire. I'm guessing it didnt catch
anything because the BTL failed. The checksum verification is
done in the PML, which the BTL calls via a callback function.
In your case the PML callback is never called because the
hdr->tag is invalid. So enabling checksum tracing also might
not be of much use. Is it the first Bcast that fails or the
nth Bcast and what is the message size? I'm not sure what
could be the problem at this moment. I'm afraid you will have
to debug the BTL to find out more.

--Nysal

On Fri, Sep 17, 2010 at 4:39 PM, Eloi Gaudry <eg@fft.be> wrote:
                            
Hi Nysal,

thanks for your response.

I've been unable so far to write a test case that could
illustrate the hdr->tag=0 error.
Actually, I'm only observing this issue when running an
internode computation involving infiniband hardware from
Mellanox (MT25418, ConnectX IB DDR, PCIe 2.0
2.5GT/s, rev a0) with our time-domain software.

I checked, double-checked, and rechecked again every MPI use
performed during a parallel computation and I couldn't find
any error so far. The fact that the very
same parallel computation run flawlessly when using tcp (and
disabling openib support) might seem to indicate that the
issue is somewhere located inside the
openib btl or at the hardware/driver level.

I've just used the "-mca pml csum" option and I haven't seen
any related messages (when hdr->tag=0 and the segfaults
occurs). Any suggestion ?

Regards,
Eloi

On Friday 17 September 2010 16:03:34 Nysal Jan wrote:
                              
Hi Eloi,
Sorry for the delay in response. I haven't read the entire
email thread, but do you have a test case which can
reproduce this error? Without that it will be difficult to
nail down the cause. Just to clarify, I do not work for an
iwarp vendor. I can certainly try to reproduce it on an IB
system. There is also a PML called csum, you can use it via
"-mca pml csum", which will checksum the MPI messages and
verify it at the receiver side for any data
corruption. You can try using it to see if it is able
                                
to

                              
catch anything.

Regards
--Nysal

On Thu, Sep 16, 2010 at 3:48 PM, Eloi Gaudry <eg@fft.be> wrote:
                                
Hi Nysal,

I'm sorry to intrrupt, but I was wondering if you had a
chance to look
                                  
at

                              
this error.

Regards,
Eloi



--


Eloi Gaudry

Free Field Technologies
Company Website: http://www.fft.be
Company Phone:   +32 10 487 959


---------- Forwarded message ----------
From: Eloi Gaudry <eg@fft.be>
To: Open MPI Users <users@open-mpi.org>
Date: Wed, 15 Sep 2010 16:27:43 +0200
Subject: Re: [OMPI users] [openib] segfault when using
openib btl Hi,

I was wondering if anybody got a chance to have a look at
this issue.

Regards,
Eloi

On Wednesday 18 August 2010 09:16:26 Eloi Gaudry wrote:
                                  
Hi Jeff,

Please find enclosed the output (valgrind.out.gz) from
/opt/openmpi-debug-1.4.2/bin/orterun -np 2 --host
pbn11,pbn10 --mca
                                    
btl

                              
openib,self --display-map --verbose --mca mpi_warn_on_fork
0 --mca btl_openib_want_fork_support 0 -tag-output
/opt/valgrind-3.5.0/bin/valgrind --tool=memcheck
--suppressions=/opt/openmpi-debug-1.4.2/share/openmpi/open
mp i- valgrind.supp
--suppressions=./suppressions.python.supp
/opt/actran/bin/actranpy_mp ...

Thanks,
Eloi

On Tuesday 17 August 2010 09:32:53 Eloi Gaudry wrote:
                                    
On Monday 16 August 2010 19:14:47 Jeff Squyres wrote:
                                      
On Aug 16, 2010, at 10:05 AM, Eloi Gaudry wrote:
                                        
I did run our application through valgrind but it
couldn't find any "Invalid write": there is a bunch of
"Invalid read" (I'm using
                                          
1.4.2

                                  
with the suppression file), "Use of uninitialized
bytes" and "Conditional jump depending on
uninitialized bytes" in
                                          
different

                              
ompi

                                  
routines. Some of them are located in
btl_openib_component.c. I'll send you an output of
valgrind shortly.
                                          
A lot of them in btl_openib_* are to be expected --
OpenFabrics uses OS-bypass methods for some of its
memory, and therefore valgrind is unaware of them (and
therefore incorrectly marks them as
uninitialized).
                                        
would it  help if i use the upcoming 1.5 version of
openmpi ? i
                                      
read

                              
that

                                  
a huge effort has been done to clean-up the valgrind
output ? but maybe that this doesn't concern this btl
(for the reasons you mentionned).

                                      
Another question, you said that the callback function
pointer
                                          
should

                                  
never be 0. But can the tag be null (hdr->tag) ?
                                          
The tag is not a pointer -- it's just an integer.
                                        
I was worrying that its value could not be null.

I'll send a valgrind output soon (i need to build
libpython without pymalloc first).

Thanks,
Eloi

                                      
Thanks for your help,
Eloi

On 16/08/2010 18:22, Jeff Squyres wrote:
                                          
Sorry for the delay in replying.

Odd; the values of the callback function pointer
should never
                                            
be

                              
0.

                                  
This seems to suggest some kind of memory corruption
is occurring.

I don't know if it's possible, because the stack trace
looks like you're calling through python, but can you
run this application through valgrind, or some other
memory-checking debugger?

On Aug 10, 2010, at 7:15 AM, Eloi Gaudry wrote:
                                            
Hi,

sorry, i just forgot to add the values of the
function
                                              
parameters:
                                  
(gdb) print reg->cbdata
$1 = (void *) 0x0
(gdb) print openib_btl->super
$2 = {btl_component = 0x2b341edd7380, btl_eager_limit
=
                                              
12288,

                              
btl_rndv_eager_limit = 12288, btl_max_send_size =
65536, btl_rdma_pipeline_send_length = 1048576,

  btl_rdma_pipeline_frag_size = 1048576,
                                              
btl_min_rdma_pipeline_size

                                  
  = 1060864, btl_exclusivity = 1024, btl_latency =
  10, btl_bandwidth = 800, btl_flags = 310,
  btl_add_procs =
  0x2b341eb8ee47<mca_btl_openib_add_procs>,
  btl_del_procs =
  0x2b341eb90156<mca_btl_openib_del_procs>,
  btl_register = 0, btl_finalize =
  0x2b341eb93186<mca_btl_openib_finalize>,
                                              
btl_alloc

                                  
  = 0x2b341eb90a3e<mca_btl_openib_alloc>, btl_free =
  0x2b341eb91400<mca_btl_openib_free>,
  btl_prepare_src =
  0x2b341eb91813<mca_btl_openib_prepare_src>,
  btl_prepare_dst
                                              
=

                              
  0x2b341eb91f2e<mca_btl_openib_prepare_dst>,
  btl_send = 0x2b341eb94517<mca_btl_openib_send>,
  btl_sendi = 0x2b341eb9340d<mca_btl_openib_sendi>,
  btl_put = 0x2b341eb94660<mca_btl_openib_put>,
  btl_get = 0x2b341eb94c4e<mca_btl_openib_get>,
  btl_dump = 0x2b341acd45cb<mca_btl_base_dump>,
  btl_mpool = 0xf3f4110, btl_register_error =
  0x2b341eb90565<mca_btl_openib_register_error_cb>,
  btl_ft_event
                                              
=

                                  
  0x2b341eb952e7<mca_btl_openib_ft_event>}

(gdb) print hdr->tag
$3 = 0 '\0'
(gdb) print des
$4 = (mca_btl_base_descriptor_t *) 0xf4a6700
(gdb) print reg->cbfunc
$5 = (mca_btl_base_module_recv_cb_fn_t) 0

Eloi

On Tuesday 10 August 2010 16:04:08 Eloi Gaudry wrote:
                                              
Hi,

Here is the output of a core file generated during a
                                                
segmentation

                                  
fault observed during a collective call (using
openib):

#0  0x0000000000000000 in ?? ()
(gdb) where
#0  0x0000000000000000 in ?? ()
#1  0x00002aedbc4e05f4 in btl_openib_handle_incoming
(openib_btl=0x1902f9b0, ep=0x1908a1c0,
frag=0x190d9700, byte_len=18) at
btl_openib_component.c:2881 #2 0x00002aedbc4e25e2 in
handle_wc (device=0x19024ac0, cq=0,
wc=0x7ffff279ce90) at
btl_openib_component.c:3178 #3  0x00002aedbc4e2e9d
in
                                                
poll_device

                                  
(device=0x19024ac0, count=2) at
btl_openib_component.c:3318
                                                
#4

                              
0x00002aedbc4e34b8 in progress_one_device
                                                
(device=0x19024ac0)

                              
at btl_openib_component.c:3426 #5 
0x00002aedbc4e3561 in btl_openib_component_progress
() at
btl_openib_component.c:3451
                                                
#6

                                  
0x00002aedb8b22ab8 in opal_progress () at
runtime/opal_progress.c:207 #7 0x00002aedb859f497 in
opal_condition_wait (c=0x2aedb888ccc0,
m=0x2aedb888cd20) at ../opal/threads/condition.h:99
#8
0x00002aedb859fa31 in ompi_request_default_wait_all
                                                
(count=2,

                              
requests=0x7ffff279d0e0, statuses=0x0) at
request/req_wait.c:262 #9 0x00002aedbd7559ad in
ompi_coll_tuned_allreduce_intra_recursivedoubling
(sbuf=0x7ffff279d444, rbuf=0x7ffff279d440, count=1,
dtype=0x6788220, op=0x6787a20,
comm=0x19d81ff0, module=0x19d82b20) at
                                                
coll_tuned_allreduce.c:223

                                  
#10 0x00002aedbd7514f7 in
ompi_coll_tuned_allreduce_intra_dec_fixed
(sbuf=0x7ffff279d444, rbuf=0x7ffff279d440, count=1,
dtype=0x6788220, op=0x6787a20, comm=0x19d81ff0,
module=0x19d82b20) at
coll_tuned_decision_fixed.c:63
#11 0x00002aedb85c7792 in PMPI_Allreduce
                                                
(sendbuf=0x7ffff279d444,

                                  
recvbuf=0x7ffff279d440, count=1, datatype=0x6788220,
                                                
op=0x6787a20,

                                  
comm=0x19d81ff0) at pallreduce.c:102 #12
0x0000000004387dbf
                                                
in

                              
FEMTown::MPI::Allreduce (sendbuf=0x7ffff279d444,
recvbuf=0x7ffff279d440, count=1, datatype=0x6788220,
                                                
op=0x6787a20,

                                  
comm=0x19d81ff0) at stubs.cpp:626 #13
0x0000000004058be8 in FEMTown::Domain::align (itf=
                                                
{<FEMTown::Boost::shared_base_ptr<FEMTown::Domain::Int

                                  
            er fa ce>>

= {_vptr.shared_base_ptr = 0x7ffff279d620, ptr_ =
{px = 0x199942a4, pn = {pi_ = 0x6}}},<No data
fields>}) at interface.cpp:371 #14
0x00000000040cb858 in
FEMTown::Field::detail::align_itfs_and_neighbhors
(dim=2,
                                                
set={px

                                  
= 0x7ffff279d780, pn = {pi_ = 0x2f279d640}},
check_info=@0x7ffff279d7f0) at check.cpp:63 #15
                                                
0x00000000040cbfa8

                                  
in FEMTown::Field::align_elements (set={px =
0x7ffff279d950, pn
                                                
=

                                  
{pi_ = 0x66e08d0}}, check_info=@0x7ffff279d7f0) at
check.cpp:159 #16 0x00000000039acdd4 in
PyField_align_elements (self=0x0,
args=0x2aaab0765050, kwds=0x19d2e950) at
check.cpp:31 #17
0x0000000001fbf76d in
FEMTown::Main::ExErrCatch<_object* (*)(_object*,
_object*, _object*)>::exec<_object>
(this=0x7ffff279dc20, s=0x0, po1=0x2aaab0765050,
po2=0x19d2e950) at
/home/qa/svntop/femtown/modules/main/py/exception.hp
p: 463
                                                
#18

                              
0x00000000039acc82 in PyField_align_elements_ewrap
                                                
(self=0x0,

                              
args=0x2aaab0765050, kwds=0x19d2e950) at
check.cpp:39 #19 0x00000000044093a0 in
PyEval_EvalFrameEx (f=0x19b52e90, throwflag=<value
optimized out>) at Python/ceval.c:3921 #20
0x000000000440aae9 in PyEval_EvalCodeEx
(co=0x2aaab754ad50, globals=<value optimized out>,
locals=<value optimized out>, args=0x3, argcount=1,
kws=0x19ace4a0, kwcount=2,
defs=0x2aaab75e4800, defcount=2, closure=0x0) at
Python/ceval.c:2968
#21 0x0000000004408f58 in PyEval_EvalFrameEx
(f=0x19ace2d0, throwflag=<value optimized out>) at
Python/ceval.c:3802 #22 0x000000000440aae9 in
PyEval_EvalCodeEx (co=0x2aaab7550120, globals=<value
optimized out>, locals=<value optimized out>,
args=0x7, argcount=1, kws=0x19acc418, kwcount=3,
defs=0x2aaab759e958, defcount=6, closure=0x0) at
Python/ceval.c:2968
#23 0x0000000004408f58 in PyEval_EvalFrameEx
(f=0x19acc1c0, throwflag=<value optimized out>) at
Python/ceval.c:3802 #24 0x000000000440aae9 in
PyEval_EvalCodeEx (co=0x2aaab8b5e738, globals=<value
optimized out>, locals=<value optimized out>,
args=0x6, argcount=1, kws=0x19abd328, kwcount=5,
defs=0x2aaab891b7e8, defcount=3, closure=0x0) at
Python/ceval.c:2968
#25 0x0000000004408f58 in PyEval_EvalFrameEx
(f=0x19abcea0, throwflag=<value optimized out>) at
Python/ceval.c:3802 #26 0x000000000440aae9 in
PyEval_EvalCodeEx (co=0x2aaab3eb4198, globals=<value
optimized out>, locals=<value optimized out>,
args=0xb, argcount=1, kws=0x19a89df0, kwcount=10,
defs=0x0, defcount=0, closure=0x0) at
Python/ceval.c:2968 #27 0x0000000004408f58 in
PyEval_EvalFrameEx
(f=0x19a89c40, throwflag=<value optimized out>) at
Python/ceval.c:3802 #28 0x000000000440aae9 in
PyEval_EvalCodeEx (co=0x2aaab3eb4288, globals=<value
optimized out>, locals=<value optimized out>,
args=0x1, argcount=0, kws=0x19a89330, kwcount=0,
defs=0x2aaab8b66668, defcount=1, closure=0x0) at
Python/ceval.c:2968
#29 0x0000000004408f58 in PyEval_EvalFrameEx
(f=0x19a891b0, throwflag=<value optimized out>) at
Python/ceval.c:3802 #30 0x000000000440aae9 in
PyEval_EvalCodeEx (co=0x2aaab8b6a738, globals=<value
optimized out>, locals=<value optimized out>,
args=0x0, argcount=0, kws=0x0, kwcount=0, defs=0x0,
defcount=0, closure=0x0) at
Python/ceval.c:2968
#31 0x000000000440ac02 in PyEval_EvalCode
(co=0x1902f9b0, globals=0x0, locals=0x190d9700) at
Python/ceval.c:522 #32 0x000000000442853c in
PyRun_StringFlags (str=0x192fd3d8
"DIRECT.Actran.main()", start=<value optimized out>,
globals=0x192213d0, locals=0x192213d0, flags=0x0) at
Python/pythonrun.c:1335 #33 0x0000000004429690 in
PyRun_SimpleStringFlags (command=0x192fd3d8
"DIRECT.Actran.main()", flags=0x0) at
Python/pythonrun.c:957 #34 0x0000000001fa1cf9 in
FEMTown::Python::FEMPy::run_application
                                                
(this=0x7ffff279f650)

                              
at fempy.cpp:873 #35 0x000000000434ce99 in
                                                
FEMTown::Main::Batch::run

                                  
(this=0x7ffff279f650) at batch.cpp:374 #36
                                                
0x0000000001f9aa25

                              
in main (argc=8, argv=0x7ffff279fa48) at main.cpp:10
(gdb) f 1 #1  0x00002aedbc4e05f4 in
btl_openib_handle_incoming (openib_btl=0x1902f9b0,
ep=0x1908a1c0, frag=0x190d9700, byte_len=18) at
btl_openib_component.c:2881 2881 reg->cbfunc(
&openib_btl->super, hdr->tag, des, reg->cbdata
                                                
);

                              
Current language: auto; currently c
(gdb)
#1  0x00002aedbc4e05f4 in btl_openib_handle_incoming
(openib_btl=0x1902f9b0, ep=0x1908a1c0,
frag=0x190d9700, byte_len=18) at
btl_openib_component.c:2881 2881 reg->cbfunc(
&openib_btl->super, hdr->tag, des, reg->cbdata
                                                
);

                              
(gdb) l 2876
2877        if(OPAL_LIKELY(!(is_credit_msg =
is_credit_message(frag)))) { 2878            /* call
registered callback */
2879            mca_btl_active_message_callback_t*
reg; 2880            reg =
mca_btl_base_active_message_trigger + hdr->tag; 2881
reg->cbfunc(&openib_btl->super, hdr->tag, des,
reg->cbdata ); 2882
if(MCA_BTL_OPENIB_RDMA_FRAG(frag)) { 2883
cqp
                                                
=

                              
(hdr->credits>>  11)&  0x0f;
2884                hdr->credits&= 0x87ff;
2885            } else {

Regards,
Eloi

On Friday 16 July 2010 16:01:02 Eloi Gaudry wrote:
                                                
Hi Edgar,

The only difference I could observed was that the
segmentation fault appeared sometimes later during
the parallel computation.

I'm running out of idea here. I wish I could use
the "--mca
                                                  
coll

                                  
tuned" with "--mca self,sm,tcp" so that I could
check that the issue is not somehow limited to the
tuned collective routines.

Thanks,
Eloi

On Thursday 15 July 2010 17:24:24 Edgar Gabriel wrote:
                                                  
On 7/15/2010 10:18 AM, Eloi Gaudry wrote:
                                                    
hi edgar,

thanks for the tips, I'm gonna try this option as
well.
                                                      
the

                              
segmentation fault i'm observing always happened
during a collective communication indeed... does
it basically
                                                      
switch

                              
all

                                  
collective communication to basic mode, right ?

sorry for my ignorance, but what's a NCA ?
                                                      
sorry, I meant to type HCA (InifinBand networking
card)

Thanks
Edgar

                                                    
thanks,
éloi

On Thursday 15 July 2010 16:20:54 Edgar Gabriel wrote:
                                                      
you could try first to use the algorithms in the
basic
                                                        
module,

                                  
e.g.

mpirun -np x --mca coll basic ./mytest

and see whether this makes a difference. I used
to
                                                        
observe

                              
sometimes a (similar ?) problem in the openib
btl triggered from the tuned collective
component, in cases where the ofed libraries
were installed but no NCA was found on a node.
It used to work however with the basic
component.

Thanks
Edgar

On 7/15/2010 3:08 AM, Eloi Gaudry wrote:
                                                        
hi Rolf,

unfortunately, i couldn't get rid of that
annoying segmentation fault when selecting
another bcast algorithm. i'm now going to
replace MPI_Bcast with a naive
implementation (using MPI_Send and MPI_Recv)
and see if
                                                          
that

                                  
helps.

regards,
éloi

On Wednesday 14 July 2010 10:59:53 Eloi Gaudry wrote:
                                                          
Hi Rolf,

thanks for your input. You're right, I miss
the coll_tuned_use_dynamic_rules option.

I'll check if I the segmentation fault
disappears when
                                                            
using

                                  
the basic bcast linear algorithm using the
proper command line you provided.

Regards,
Eloi

On Tuesday 13 July 2010 20:39:59 Rolf
vandeVaart
                                                            
wrote:
                              
Hi Eloi:
To select the different bcast algorithms, you
need to add an extra mca parameter that tells
the library to use dynamic selection. --mca
coll_tuned_use_dynamic_rules 1

One way to make sure you are typing this in
correctly is
                                                              
to

                                  
use it with ompi_info.  Do the following:
ompi_info -mca coll_tuned_use_dynamic_rules 1
--param
                                                              
coll

                                  
You should see lots of output with all the
different algorithms that can be selected for
the various collectives. Therefore, you need
this:

--mca coll_tuned_use_dynamic_rules 1 --mca
coll_tuned_bcast_algorithm 1

Rolf

On 07/13/10 11:28, Eloi Gaudry wrote:
                                                              
Hi,

I've found that "--mca
coll_tuned_bcast_algorithm 1" allowed to
switch to the basic linear algorithm. Anyway
whatever the algorithm used, the
segmentation fault remains.

Does anyone could give some advice on ways
to
                                                                
diagnose

                              
the

                                  
issue I'm facing ?

Regards,
Eloi

On Monday 12 July 2010 10:53:58 Eloi Gaudry wrote:
                                                                
Hi,

I'm focusing on the MPI_Bcast routine that
seems to randomly segfault when using the
openib btl. I'd
                                                                  
like

                              
to

                                  
know if there is any way to make OpenMPI
switch to
                                                                  
a

                              
different algorithm than the default one
being selected for MPI_Bcast.

Thanks for your help,
Eloi

On Friday 02 July 2010 11:06:52 Eloi Gaudry wrote:
                                                                  
Hi,

I'm observing a random segmentation fault
during
                                                                    
an

                              
internode parallel computation involving
the
                                                                    
openib

                              
btl

                                  
and OpenMPI-1.4.2 (the same issue can be
observed with OpenMPI-1.3.3).

   mpirun (Open MPI) 1.4.2
   Report bugs to
   http://www.open-mpi.org/community/help/
   [pbn08:02624] *** Process received
   signal *** [pbn08:02624] Signal:
   Segmentation fault (11) [pbn08:02624]
   Signal code: Address not mapped
                                                                    
(1)

                              
   [pbn08:02624] Failing at address: (nil)
   [pbn08:02624] [ 0]
   /lib64/libpthread.so.0 [0x349540e4c0]
   [pbn08:02624] *** End of error
                                                                    
message

                                  
   ***
   sh: line 1:  2624 Segmentation fault
                                                                    
\/share\/hpc3\/actran_suite\/Actran_11\.0\.rc2\.41872\/R

                                  
ed Ha tE L\ -5 \/ x 86 _6 4\
/bin\/actranpy_mp
                                                                    
'--apl=/share/hpc3/actran_suite/Actran_11.0.rc2.41872/Re

                                  
dH at EL -5 /x 86 _ 64 /A c
tran_11.0.rc2.41872'
                                                                    
'--inputfile=/work/st25652/LSF_130073_0_47696_0/Case1_3D

                                  
re al _m 4_ n2 .d a t'
                                                                    
'--scratch=/scratch/st25652/LSF_130073_0_47696_0/scratch

                                  
' '--mem=3200' '--threads=1'
'--errorlevel=FATAL' '--t_max=0.1'
'--parallel=domain'

If I choose not to use the openib btl (by
using --mca btl self,sm,tcp on the command
line, for instance), I don't encounter any
problem and the parallel computation runs
flawlessly.

I would like to get some help to be able:
- to diagnose the issue I'm facing with
the openib btl - understand why this
issue is observed only when
                                                                    
using

                                  
the openib btl and not when using
self,sm,tcp

Any help would be very much appreciated.

The outputs of ompi_info and the configure
scripts of OpenMPI are enclosed to this
email, and some
                                                                    
information

                                  
on the infiniband drivers as well.

Here is the command line used when
launching a
                                                                    
parallel

                                  
computation

using infiniband:
   path_to_openmpi/bin/mpirun -np
   $NPROCESS --hostfile host.list --mca

btl openib,sm,self,tcp  --display-map
--verbose --version --mca mpi_warn_on_fork
0 --mca btl_openib_want_fork_support 0
[...]

and the command line used if not using infiniband:
   path_to_openmpi/bin/mpirun -np
   $NPROCESS --hostfile host.list --mca

btl self,sm,tcp  --display-map --verbose
--version
                                                                    
--mca

                                  
mpi_warn_on_fork 0 --mca
btl_openib_want_fork_support
                                                                    
0

                                  
[...]

Thanks,
Eloi
                                                                    
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