[Dune] UG grid code: Segfault on large core counts
Eike Mueller
e.mueller at bath.ac.uk
Tue Dec 4 17:05:10 CET 2012
Dear dune-list,
now my code runs on 6, 24, 96 and 384 processors. However, on 1536 cores it crashes with a (different) segmentation faullt, when I inspect the core dump with
gdb <executable> --core=<core>
I get this backtrace:
Core was generated by `/work/n02/n02/eike/Code/DUNEGeometricMultigrid/geometricmultigrid_nz128_r130_DE'.
Program terminated with signal 11, Segmentation fault.
#0 0x0000000000898d7a in PPIF::RecvASync (v=0x100000001, data=0x13b80a0,
size=4, error=0x7fffffff41f0) at ppif.c:656
656 ((MPIVChannel*)v)->p, ((MPIVChannel*)v)->chanid, COMM, req) )
(gdb) backtrace
#0 0x0000000000898d7a in PPIF::RecvASync (v=0x100000001, data=0x13b80a0,
size=4, error=0x7fffffff41f0) at ppif.c:656
#1 0x000000000081ce2b in NumberOfDesc () at wop.c:21095
#2 0x000000000082b2db in UG::D2::InitWOP () at wop.c:24677
#3 0x00000000007fbb1d in UG::D2::InitUGGraph () at initgraph.c:90
#4 0x00000000007fbac5 in UG::D2::InitGraphics () at graphics.c:133
#5 0x0000000000715e4c in UG::D2::InitUg (argcp=0x7fffffff465c,
argvp=0x7fffffff4648) at ../initug.c:293
#6 0x000000000051bb8c in Dune::UG_NS<2>::InitUg (argcp=0x7fffffff465c,
argvp=0x7fffffff4648) at ../../../dune/grid/uggrid/ugwrapper.hh:910
#7 0x000000000052062a in Dune::UGGrid<3>::UGGrid (this=0x1603360)
at uggrid.cc:74
#8 0x000000000059332f in Dune::GridFactory<Dune::UGGrid<3> >::GridFactory (
this=0x7fffffff9cd8) at uggridfactory.cc:74
#9 0x000000000040faa2 in SphericalGridGenerator::SphericalGridGenerator (
this=0x7fffffff9cd0, filename=..., refcount=5)
at sphericalgridgenerator.hh:37
#10 0x00000000004010c8 in main (argc=2, argv=0x7fffffffb778)
at geometricmultigrid.cc:167
I'm setting up a grid with one element on each core, and then refine it 5 times, so the total grid size is 49152. I don't know whether this has any influence, but I set the default heap size to 8000.
Any ideas what might be going on here, or just suggestions on how to proceed with debugging a code with this large number of cores would be much appreciated. I'm now trying to get a better trace with the Cray ATP tool.
Thank you very much,
Eike
On 30 Nov 2012, at 18:47, Eike Mueller wrote:
> Hi Oliver,
>
> I just did some detective work and I think I know why it crashes and how it can be fixed.
>
> The problem is that in parallel/ddd/include/ddd.h the type DDD_PROC is defined as 'unsigned short', so can only store up to 2^16 different processor IDs. In the subroutine IFCreateFromScratch(), where the segfault occurs, the variable lastproc, which is initialised to PROC_INVALID is of this type. According to parallel/ddd/dddi.h, PROC_INVALID=(MAX_PROCS+1) and MAX_PROCS=(1<<MAX_PROCBITS_IN_GID). Investigating the core dump with gdb, lastproc is indeed 1, at least for MAX_PROCBITS_IN_GID=16 and then on processor 1 the pointer ifHead never gets initialised, so dereferencing it with ifHead->nItems++; causes the segfault.
>
> I now changed DDD_PROC to 'unsigned int' in parallel/ddd/include/ddd.h and then the test program I sent you works fine if I run on 6 processors (I can also look at the .vtu files if I write them out in ascii format).
> I can run with up to 6 refinement steps, and if I go to 7 it runs out of memory with
>
> testsphericalgridgenerator: xfer/xfer.c:942: void UG::D3::ddd_XferRegisterDelete(UG::D3::DDD_HDR): Assertion `0' failed.
> DDD [000] FATAL 06060: out of memory during XferEnd()
> _pmiu_daemon(SIGCHLD): [NID 01842] [c11-0c1s6n0] [Fri Nov 30 18:35:27 2012] PE RANK 0 exit signal Aborted
> DDD [001] WARNING 02514: increased coupling table, now 131072 entries
> DDD [001] WARNING 02224: increased object table, now 131072 entries
> [NID 01842] 2012-11-30 18:35:27 Apid 3144197: initiated application termination
> Application 3144197 exit codes: 134
> Application 3144197 resources: utime ~24s, stime ~1s
>
> but I think this is another problem, and in my case 6 should actually be enough.
>
> Do you think the change I made makes sense and doesn't break anything else? If that is the case, what's the best way of setting up a patch? To be on the safe side, maybe something like this:
>
> #if (DDD_MAX_PROCBITS_IN_GID < 16)
> typedef unsigned short DDD_PROC;
> #else
> typedef unsigned int DDD_PROC;
> #endif // (DDD_MAX_PROCBITS_IN_GID < 16)
>
> I need to do some more testing to check that it all works for my full code, and I will keep you updated on any progress.
>
> Thanks,
>
> Eike
>
> Oliver Sander wrote:
>> Okay, with maxprocbits = 16 I do see a crash. 2 processors and 1 level is enough.
>> I'm in a bit of a hurry right now, but I'll have a look at it later.
>> best,
>> Oliver
>> Am 29.11.2012 19:36, schrieb Eike Mueller:
>>> Hi Oliver,
>>>
>>> thank you very much for trying this out and for the patch. I now rebuilt UG with the latest patch file you sent me this morning and I still get the segfault. However, this only occurs if I specify the with_ddd_maxprocbits flag, if I do not set this (i.e. only use DDD_GID=long, as you do), then it runs fine (I have only done a small run so far, and haven't tried 7 refinement steps, so can not say anything about that other error you get).
>>> I tried both with_ddd_maxprocbits=20 and 16, but it does not work in any of these cases. The default is 2^9=512, and unfortunately that's not enough for me, I would need at least 2^16=65536.
>>> As for the error message you get when reading the .vtu files, could that be because they are written out in Dune::VTK::appendedbase64 format? I also get an error message when I open them in paraview
>>>
>>> ERROR: In /home/kitware/ParaView3/Utilities/BuildScripts/ParaView-3.6/ParaView3/VTK/IO/vtkXMLUnstructuredDataReader.cxx, line 522
>>> vtkXMLUnstructuredGridReader (0xa16c918): Cannot read points array from Points in piece 0. The data array in the element may be too short.
>>>
>>> When I opened .vtu files produced by my main solver code on HECToR, paraview actually crashed, and this was before I modified any of the UG settings. I could fix this by writing data out in Dune::VTK::ascii format instead. Could this be a big/little endian issue? HECToR is 64bit, but my local desktop, where I run paraview to look at the output is 32bit, not sure if that has any impact.
>>>
>>> Eike
>>>
>>> Oliver Sander wrote:
>>>> Hi Eike,
>>>> I tried your example with DDD_GID==long, on my laptop where sizeof(long)==8 and sizeof(uint)==4.
>>>> I started the program with
>>>>
>>>> mpirun -np 6 ./testsphericalgridgenerator sphericalshell_cube_6.dgf 6
>>>>
>>>> Besides a few DDD warnings that I have never seen before, it works like a charm.
>>>>
>>>> What version of UG are you using? I'll send you the very latest patch file just
>>>> to be sure.
>>>>
>>>> The programs runs, but paraview gives me an error message when trying to open
>>>> the output file. Does that happen to you, too?
>>>>
>>>> I didn't try the with_ddd_maxprocbits setting. Does your program crash if you
>>>> do _not_ set this?
>>>>
>>>> For the worst case: is it possible to get a temporary account on your hector computer?
>>>>
>>>> best,
>>>> Oliver
>>>>
>>>> Am 28.11.2012 10:28, schrieb Eike Mueller:
>>>>> Hi Oliver,
>>>>>
>>>>> thanks a lot, that would be great. My desktop is a 32bit machine, where sizeof(long) = sizeof(int) = 4, so I'm not sure if recompiling everything with GID=long there will make a difference.
>>>>>
>>>>> Eike
>>>>>
>>>>> Oliver Sander wrote:
>>>>>> Thanks for the backtrace. I'll try and see whether I can reproduce the crash
>>>>>> on my machine. If that's not possible things will be a bit difficult :-)
>>>>>> --
>>>>>> Oliver
>>>>>>
>>>>>> Am 26.11.2012 18:39, schrieb Eike Mueller:
>>>>>>> Hi Markus and Oliver,
>>>>>>>
>>>>>>> to get to the bottom of this I recompiled everything (UG+Dune+my code) with -O0 -g, and that way I was able to get some more information out of the core dump. On 1 processor it runs fine now, but when running on 6, this is what I get, looks like it crashes in loadBalance(), but I can't make sense of what's happening inside UG. It always seems to crash inside ifcreate.c, either in line 482 or 489:
>>>>>>>
>>>>>>> Program terminated with signal 11, Segmentation fault.
>>>>>>> #0 0x0000000000a438b0 in UG::D3::IFCreateFromScratch (tmpcpl=0x1462ad0,
>>>>>>> ifId=1) at if/ifcreate.c:489
>>>>>>> 489 ifHead->nItems++;
>>>>>>> (gdb) backtrace
>>>>>>> #0 0x0000000000a438b0 in UG::D3::IFCreateFromScratch (tmpcpl=0x1462ad0,
>>>>>>> ifId=1) at if/ifcreate.c:489
>>>>>>> #1 0x0000000000a44dae in UG::D3::IFRebuildAll () at if/ifcreate.c:1059
>>>>>>> #2 0x0000000000a44e71 in UG::D3::IFAllFromScratch () at if/ifcreate.c:1097
>>>>>>> #3 0x0000000000a4bd89 in UG::D3::DDD_XferEnd () at xfer/cmds.c:869
>>>>>>> #4 0x0000000000a65b5c in UG::D3::TransferGridFromLevel (theMG=0x1441880,
>>>>>>> level=0) at trans.c:835
>>>>>>> #5 0x0000000000a5df4b in UG::D3::lbs (argv=0x7fffffffa390 "0",
>>>>>>> theMG=0x1441880) at lb.c:659
>>>>>>> #6 0x0000000000a0bd83 in UG::D3::LBCommand (argc=4, argv=0x7fffffffab90)
>>>>>>> at commands.c:10658
>>>>>>> #7 0x00000000004a1e2d in Dune::UG_NS<3>::LBCommand (argc=4,
>>>>>>> argv=0x7fffffffab90) at ../../../dune/grid/uggrid/ugwrapper.hh:979
>>>>>>> #8 0x00000000004a8df9 in Dune::UGGrid<3>::loadBalance (this=0x134e490,
>>>>>>> strategy=0, minlevel=0, depth=2, maxLevel=32, minelement=1)
>>>>>>> at uggrid.cc:556
>>>>>>> #9 0x00000000004077bf in Dune::UGGrid<3>::loadBalance (this=0x134e490)
>>>>>>> at /home/n02/n02/eike/work/Library/Dune2.2/include/dune/grid/uggrid.hh:738
>>>>>>> #10 0x0000000000400928 in main (argc=3, argv=0x7fffffffb5a8)
>>>>>>> at testsphericalgridgenerator.cc:65
>>>>>>>
>>>>>>> but I sometimes also get:
>>>>>>>
>>>>>>> Core was generated by `./testsphericalgridgenerator sphericalshell_cube_6.dgf 4'.
>>>>>>> Program terminated with signal 11, Segmentation fault.
>>>>>>> #0 0x0000000000a438b0 in UG::D3::IFCreateFromScratch (tmpcpl=0x1462ad0,
>>>>>>> ifId=1) at if/ifcreate.c:482
>>>>>>> 482 ifAttr->nAB = ifAttr->nBA = ifAttr->nABA = 0;
>>>>>>> (gdb) backtrace
>>>>>>> #0 0x0000000000a438b0 in UG::D3::IFCreateFromScratch (tmpcpl=0x1462ad0,
>>>>>>> ifId=1) at if/ifcreate.c:482
>>>>>>> #1 0x0000000000a44dae in UG::D3::IFRebuildAll () at if/ifcreate.c:1049
>>>>>>> #2 0x0000000000a44e71 in UG::D3::IFRebuildAll () at if/ifcreate.c:1057
>>>>>>> #3 0x0000000000a4bd89 in UG::D3::DDD_XferEnd () at xfer/cmds.c:850
>>>>>>> #4 0x0000000000a65b5c in UG::D3::TransferGridFromLevel (theMG=0x1441880,
>>>>>>> level=0) at trans.c:824
>>>>>>> #5 0x0000000000a5df4b in UG::D3::lbs (argv=0x7fffffffa390 "0",
>>>>>>> theMG=0x1441880) at lb.c:644
>>>>>>> #6 0x0000000000a0bd83 in UG::D3::LBCommand (argc=4, argv=0x7fffffffab90)
>>>>>>> at commands.c:10644
>>>>>>> #7 0x00000000004a1e2d in Dune::UG_NS<3>::LBCommand (argc=0,
>>>>>>> argv=0x7fffffffa420) at ../../../dune/grid/uggrid/ugwrapper.hh:977
>>>>>>> #8 0x00000000004a8df9 in Dune::UGGrid<3>::loadBalance (this=0x134e490,
>>>>>>> strategy=0, minlevel=0, depth=2, maxLevel=32, minelement=1)
>>>>>>> at uggrid.cc:554
>>>>>>> #9 0x00000000004077bf in std::__shared_count<(__gnu_cxx::_Lock_policy)2>::~__shared_count (this=0x134e490, __in_chrg=<optimized out>)
>>>>>>> at /opt/gcc/4.6.3/snos/include/g++/bits/shared_ptr_base.h:550
>>>>>>> #10 0x0000000000400928 in main (argc=0, argv=0x520)
>>>>>>> at testsphericalgridgenerator.cc:66
>>>>>>>
>>>>>>> I've tried different load balancing strategies, but for all I get a segfault.
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> Eike
>>>>>>>
>>>>>>>
>>>>>>> Markus Blatt wrote:
>>>>>>>> On Mon, Nov 26, 2012 at 01:57:15PM +0000, Eike Mueller wrote:
>>>>>>>>> thanks a lot for the patch, unfortunately I still get a segfault when I run on HECToR.
>>>>>>>>>
>>>>>>>>
>>>>>>>> I feared that, but it was still worth a shot. The change probably
>>>>>>>> interferes with the memory allocation in ddd.
>>>>>>>>
>>>>>>>> Markus
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>
>
> --
> Dr Eike Mueller
> Research Officer
>
> Department of Mathematical Sciences
> University of Bath
> Bath BA2 7AY, United Kingdom
>
> +44 1225 38 5633
> e.mueller at bath.ac.uk
> http://people.bath.ac.uk/em459/
>
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