[Dune] UG grid code: Segfault on large core counts
Oliver Sander
sander at igpm.rwth-aachen.de
Wed Dec 5 16:22:53 CET 2012
Hi Eike,
please try the attached patch. It may fix your BTree issue.
good luck,
Oliver
Am 05.12.2012 13:32, schrieb Eike Mueller:
> Hi Oliver,
>
> thanks, it would be great if you could send me that patch for the BTree.
> This is probably an unrelated problem, but I now reran the same code and problem it with UG heap size = 16000. Now it crashes with a segfault:
>
> Program terminated with signal 11, Segmentation fault.
> #0 0x0000000000b8be5c in UG::D3::XferInitCopyInfo (hdr=0x2aab8001e6b0,
> desc=0x144b290, size=96, dest=938, prio=1) at xfer/cmds.c:1012
> 1012 xi->hdr = hdr;
> (gdb) backtrace
> #0 0x0000000000b8be5c in UG::D3::XferInitCopyInfo (hdr=0x2aab8001e6b0,
> desc=0x144b290, size=96, dest=938, prio=1) at xfer/cmds.c:1012
> #1 0x0000000000b8c088 in UG::D3::DDD_XferCopyObjX (hdr=0x2aab8001e6b0,
> proc=938, prio=1, size=96) at xfer/cmds.c:1206
> #2 0x0000000000ccee14 in ElementXferCopy (obj=0x2aab8001e088 "\006\223]@\ny",
> proc=938, prio=1) at handler.c:1442
> #3 0x0000000000b8bf16 in UG::D3::XferInitCopyInfo (hdr=0x2aab8001e0a0,
> desc=0x1452820, size=312, dest=938, prio=1) at xfer/cmds.c:1047
> #4 0x0000000000b8c088 in UG::D3::DDD_XferCopyObjX (hdr=0x2aab8001e0a0,
> proc=938, prio=1, size=312) at xfer/cmds.c:1206
> #5 0x0000000000bbb754 in XferGridWithOverlap (theGrid=0x2aab7d7e7d10)
> at trans.c:630
> #6 0x0000000000bbbb5e in UG::D3::TransferGridFromLevel (theMG=0x1a005a0,
> level=0) at trans.c:831
> #7 0x0000000000bb562f in UG::D3::lbs (argv=0x7fffffff3f00 "0",
> theMG=0x1a005a0) at lb.c:659
> #8 0x0000000000b746d1 in UG::D3::LBCommand (argc=4, argv=0x7fffffff4700)
> at commands.c:10658
> #9 0x000000000051bef7 in Dune::UG_NS<3>::LBCommand (argc=4,
> argv=0x7fffffff4700) at ../../../dune/grid/uggrid/ugwrapper.hh:979
> #10 0x0000000000522b6d in Dune::UGGrid<3>::loadBalance (this=0x1619af0,
> strategy=0, minlevel=0, depth=2, maxLevel=32, minelement=1)
> at uggrid.cc:556
> ---Type<return> to continue, or q<return> to quit---
> #11 0x0000000000414ec3 in Dune::UGGrid<3>::loadBalance (this=0x1619af0)
> at /home/n02/n02/eike/work/Library/Dune2.2_DEBUG/include/dune/grid/uggrid.hh:738
> #12 0x0000000000401100 in main (argc=2, argv=0x7fffffffb7a8)
> at geometricmultigrid.cc:180
>
> Eike
>
> On 5 Dec 2012, at 12:14, Oliver Sander wrote:
>
>> Hi,
>> that's funny. Here in Aachen people used to work with DDD, and just a few
>> days ago a guy here sent me their version of DDD. They changed very little,
>> but they did fix some bug in the BTree implementation. Seems like this may
>> be the culprit here. Unfortunately there is no revision history anymore.
>> I'll try to isolate the fix from the patch.
>> :-)
>> Oliver
>>
>> Am 05.12.2012 12:32, schrieb Eike Mueller:
>>> Dear Peter and Oliver,
>>>
>>> thanks a lot for your help. I now changed WOP_DOWN_CHANNELS_MAX to 64 (which is enough for my case), but then I get
>>>
>>> geometricmultigrid_nz128_r130_DEBUG: ./basic/ooppcc.h:724: int UG::D3::XICopyObjBTreeNode_Insert(UG::D3::XICopyObjBTreeNode*, UG::D3::XICopyObj*): Assertion `new_r!=__null' failed
>>>
>>> The gdb backtrace is this:
>>>
>>> Program terminated with signal 6, Aborted.
>>> #0 0x0000000000d97f1b in raise (sig=<optimized out>)
>>> at ../nptl/sysdeps/unix/sysv/linux/pt-raise.c:42
>>> 42 ../nptl/sysdeps/unix/sysv/linux/pt-raise.c: No such file or directory.
>>> in ../nptl/sysdeps/unix/sysv/linux/pt-raise.c
>>> (gdb) backtrace
>>> #0 0x0000000000d97f1b in raise (sig=<optimized out>)
>>> at ../nptl/sysdeps/unix/sysv/linux/pt-raise.c:42
>>> #1 0x0000000000db2f41 in abort () at abort.c:92
>>> #2 0x0000000000dadc17 in __assert_fail (assertion=0xf279ef "new_r!=__null",
>>> file=0xf27980 "./basic/ooppcc.h", line=724,
>>> function=0xf27d40 "int UG::D3::XICopyObjBTreeNode_Insert(UG::D3::XICopyObjBTreeNode*, UG::D3::XICopyObj*)") at assert.c:81
>>> #3 0x0000000000ba0637 in UG::D3::XICopyObjBTreeNode_Insert (
>>> _oopp_this=0x2aac5d4ea920, item=0x2aac5d4ec7e8) at ./basic/ooppcc.h:724
>>> #4 0x0000000000ba05e8 in UG::D3::XICopyObjBTreeNode_Insert (
>>> _oopp_this=0x2aac64f03920, item=0x2aac5d4ec7e8) at ./basic/ooppcc.h:717
>>> #5 0x0000000000ba05e8 in UG::D3::XICopyObjBTreeNode_Insert (
>>> _oopp_this=0x2aac64422180, item=0x2aac5d4ec7e8) at ./basic/ooppcc.h:717
>>> #6 0x0000000000ba05e8 in UG::D3::XICopyObjBTreeNode_Insert (
>>> _oopp_this=0x2aac6eac93b0, item=0x2aac5d4ec7e8) at ./basic/ooppcc.h:717
>>> #7 0x0000000000ba0ae3 in UG::D3::XICopyObjBTree_Insert (_oopp_this=0x17589f0,
>>> item=0x2aac5d4ec7e8) at ./basic/ooppcc.h:898
>>> #8 0x0000000000ba0e1d in UG::D3::XICopyObjSet_ItemOK (_oopp_this=0x16fed40)
>>> at ./basic/ooppcc.h:1093
>>> #9 0x0000000000b8be92 in UG::D3::XferInitCopyInfo (hdr=0x2aab89586610,
>>> desc=0x144d2a0, size=104, dest=487, prio=1) at xfer/cmds.c:1017
>>> #10 0x0000000000b8bf95 in UG::D3::DDD_XferCopyObj (hdr=0x2aab89586610,
>>> proc=487, prio=1) at xfer/cmds.c:1133
>>> ---Type<return> to continue, or q<return> to quit---
>>> #11 0x0000000000cceb58 in ElementXferCopy (
>>> obj=0x2aab895877f0 "\006\223}@\224\314\001", proc=487, prio=1)
>>> at handler.c:1373
>>> #12 0x0000000000b8bf16 in UG::D3::XferInitCopyInfo (hdr=0x2aab89587808,
>>> desc=0x1452820, size=312, dest=487, prio=1) at xfer/cmds.c:1047
>>> #13 0x0000000000b8c088 in UG::D3::DDD_XferCopyObjX (hdr=0x2aab89587808,
>>> proc=487, prio=1, size=312) at xfer/cmds.c:1206
>>> #14 0x0000000000bbb754 in XferGridWithOverlap (theGrid=0x2aab8023e0a8)
>>> at trans.c:630
>>> #15 0x0000000000bbbb5e in UG::D3::TransferGridFromLevel (theMG=0x19fe680,
>>> level=0) at trans.c:831
>>> #16 0x0000000000bb562f in UG::D3::lbs (argv=0x7fffffff3ee0 "0",
>>> theMG=0x19fe680) at lb.c:659
>>> #17 0x0000000000b746d1 in UG::D3::LBCommand (argc=4, argv=0x7fffffff46e0)
>>> at commands.c:10658
>>> #18 0x000000000051bef7 in Dune::UG_NS<3>::LBCommand (argc=4,
>>> argv=0x7fffffff46e0) at ../../../dune/grid/uggrid/ugwrapper.hh:979
>>> #19 0x0000000000522b6d in Dune::UGGrid<3>::loadBalance (this=0x1619970,
>>> strategy=0, minlevel=0, depth=2, maxLevel=32, minelement=1)
>>> at uggrid.cc:556
>>> #20 0x0000000000414ec3 in Dune::UGGrid<3>::loadBalance (this=0x1619970)
>>> at /home/n02/n02/eike/work/Library/Dune2.2_DEBUG/include/dune/grid/uggrid.hh:738
>>> ---Type<return> to continue, or q<return> to quit---
>>> #21 0x0000000000401100 in main (argc=2, argv=0x7fffffffb778)
>>> at geometricmultigrid.cc:180
>>>
>>> I have no idea what it means and it's just a wild guess, but could Set_BTreeOrder and BTreeOrder be of the wrong size? They are set to 32.
>>>
>>> Eike
>>>
>>> On 5 Dec 2012, at 10:20, Oliver Sander wrote:
>>>
>>>> Am 05.12.2012 10:48, schrieb Peter Bastian:
>>>>> Hi Oliver,
>>>>>
>>>>> you ask questions… The parallel UG graphics used some clever
>>>>> way to do depth ordering by sorting the coarse mesh in
>>>>> view direction and then "interpolating" this ordering in the
>>>>> grid hierarchy. I do not know whether it has something to
>>>>> do with that. Obviously some tree is constructed on
>>>>> the processor graph and the maximum degree is estimated
>>>>> using the strange formula. I really cannot say more as it was
>>>>> all Klaus Johannsens work.
>>>> Hi Peter,
>>>> okay, that explains why the file is 20k lines long (you guys were tough!).
>>>>
>>>> I then propose to make WOP_DOWN_CHANNELS_MAX very large(tm),
>>>> and forget about it. Since the number of channels computed in line 21023
>>>> is roughly the square root of the processor number I guess a value
>>>> of about 2000 should be okay for the nearer future.
>>>>
>>>> best,
>>>> Oliver
>>>>
>>>>> Best,
>>>>>
>>>>> Peter
>>>>>
>>>>> Am 05.12.2012 um 09:46 schrieb Oliver Sander<sander at igpm.rwth-aachen.de>:
>>>>>
>>>>>> Am 04.12.2012 20:10, schrieb Peter Bastian:
>>>>>>> Dear Eike,
>>>>>>>
>>>>>>> a quick search through the code suggests that
>>>>>>> the constant
>>>>>>> #define WOP_DOWN_CHANNELS_MAX 32
>>>>>>> in ug/graphics/uggraph/wop.h line 146 is too small.
>>>>>>>
>>>>>>> In wop.c line 21023
>>>>>>>
>>>>>>> WopDownChannels = (INT)ceil(0.5*(sqrt(4.0*(DOUBLE)procs-3.0)-1.0));
>>>>>>>
>>>>>>> evaluates to 39 which fairly close above 32. Then out of bound access in many
>>>>>>> arrays is produced. Maybe it is as simple as that.
>>>>>> Hi Peter,
>>>>>> I came to the same conclusion. Can you give us an explanation of what
>>>>>> these WopDownChannels are?
>>>>>> best,
>>>>>> Oliver
>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Peter
>>>>>>>
>>>>>>>
>>>>>>> Am 04.12.2012 um 18:39 schrieb Oliver Sander<sander at igpm.rwth-aachen.de>:
>>>>>>>
>>>>>>>> Am 04.12.2012 17:05, schrieb Eike Mueller:
>>>>>>>>> Dear dune-list,
>>>>>>>> Hi Eike,
>>>>>>>>> now my code runs on 6, 24, 96 and 384 processors. However, on 1536 cores it crashes with a (different) segmentation faullt,
>>>>>>>> is that with custom types for DDD_GID, DDD_PROC and such, or with the defaults?
>>>>>>>>
>>>>>>>> Is it possible to get a valgrind output? The crash is at program startup, so even a
>>>>>>>> slow valgrind run shouldn't take too long.
>>>>>>>>
>>>>>>>> The crash is in the ug graphics implementation, which we don't use from Dune.
>>>>>>>> So in the very worst case we could out-comment lots of stuff and make it work
>>>>>>>> that way. But I prefer a proper fix.
>>>>>>>>
>>>>>>>> best,
>>>>>>>> Oliver
>>>>>>>>
>>>>>>>>> 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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>>>>>>>> Dune mailing list
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>>>>>>> ------------------------------------------------------------
>>>>>>> Peter Bastian
>>>>>>> Interdisziplinäres Zentrum für Wissenschaftliches Rechnen
>>>>>>> Universität Heidelberg
>>>>>>> Im Neuenheimer Feld 368
>>>>>>> D-69120 Heidelberg
>>>>>>> Tel: 0049 (0) 6221 548261
>>>>>>> Fax: 0049 (0) 6221 548884
>>>>>>> email: peter.bastian at iwr.uni-heidelberg.de
>>>>>>> web: http://conan.iwr.uni-heidelberg.de/people/peter/
>>>>>>>
>>>>>>>
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>>>>>> _______________________________________________
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>>>>> ------------------------------------------------------------
>>>>> Peter Bastian
>>>>> Interdisziplinäres Zentrum für Wissenschaftliches Rechnen
>>>>> Universität Heidelberg
>>>>> Im Neuenheimer Feld 368
>>>>> D-69120 Heidelberg
>>>>> Tel: 0049 (0) 6221 548261
>>>>> Fax: 0049 (0) 6221 548884
>>>>> email: peter.bastian at iwr.uni-heidelberg.de
>>>>> web: http://conan.iwr.uni-heidelberg.de/people/peter/
>>>>>
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