[Dune] UG grid code: Segfault on large core counts

Eike Mueller e.mueller at bath.ac.uk
Wed Dec 5 13:32:55 CET 2012


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/
>>>>>>>>> 
>>>>>>>>> _______________________________________________
>>>>>>>>> Dune mailing list
>>>>>>>>> Dune at dune-project.org
>>>>>>>>> http://lists.dune-project.org/mailman/listinfo/dune
>>>>>>> _______________________________________________
>>>>>>> Dune mailing list
>>>>>>> Dune at dune-project.org
>>>>>>> http://lists.dune-project.org/mailman/listinfo/dune
>>>>>> ------------------------------------------------------------
>>>>>> 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/
>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
>>>>>> Dune mailing list
>>>>>> Dune at dune-project.org
>>>>>> http://lists.dune-project.org/mailman/listinfo/dune
>>>>> _______________________________________________
>>>>> Dune mailing list
>>>>> Dune at dune-project.org
>>>>> http://lists.dune-project.org/mailman/listinfo/dune
>>>> ------------------------------------------------------------
>>>> 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/
>>>> 
>>> 
>>> _______________________________________________
>>> Dune mailing list
>>> Dune at dune-project.org
>>> http://lists.dune-project.org/mailman/listinfo/dune
> 




More information about the Dune mailing list