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). > 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. > 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::Interface>> >>>> = {_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.hpp: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\/RedHatE >>>>>>>>>>>>>> L\ -5 \/ x 86 _6 4\ /bin\/actranpy_mp >>>>>>>>>>>>>> '--apl=/share/hpc3/actran_suite/Actran_11.0.rc2.41872/RedHatEL >>>>>>>>>>>>>> -5 /x 86 _ 64 /A c tran_11.0.rc2.41872' >>>>>>>>>>>>>> '--inputfile=/work/st25652/LSF_130073_0_47696_0/Case1_3Dreal_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 >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> users mailing list >>>>>>>>>>>> us...@open-mpi.org >>>>>>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>> -- >>> >>> >>> Eloi Gaudry >>> >>> Free Field Technologies >>> Company Website: http://www.fft.be >>> Company Phone: +32 10 487 959 >>> >>> _______________________________________________ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/user > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/