[Dune] UG grid code: Segfault on large core counts
Eike Mueller
e.mueller at bath.ac.uk
Thu Dec 6 17:57:30 CET 2012
Hi Oliver,
thanks, I've now tried your patch, but I still get a segfault. I believe this is still a problem with the BTree. Here is the backtrace:
Program terminated with signal 11, Segmentation fault.
#0 0x0000000000b9a239 in UG::D3::XICopyObj_Compare (item1=0xffffffff5d4ed200,
item2=0x2aac5d4ed820) at xfer/supp.c:208
208 if (item1->dest < item2->dest) return(-1);
(gdb) backtrace
#0 0x0000000000b9a239 in UG::D3::XICopyObj_Compare (item1=0xffffffff5d4ed200,
item2=0x2aac5d4ed820) at xfer/supp.c:208
#1 0x0000000000b9865b in UG::D3::XICopyObjBTreeNode_Insert (
_oopp_this=0x2aac5d4eb920, item=0x2aac5d4ed820) at ./basic/ooppcc.h:697
#2 0x0000000000b986cf in UG::D3::XICopyObjBTreeNode_Insert (
_oopp_this=0x2aac64f04920, item=0x2aac5d4ed820) at ./basic/ooppcc.h:721
#3 0x0000000000b986cf in UG::D3::XICopyObjBTreeNode_Insert (
_oopp_this=0x2aac64423180, item=0x2aac5d4ed820) at ./basic/ooppcc.h:721
#4 0x0000000000b986cf in UG::D3::XICopyObjBTreeNode_Insert (
_oopp_this=0x2aac6eaca3b0, item=0x2aac5d4ed820) at ./basic/ooppcc.h:721
#5 0x0000000000b98b85 in UG::D3::XICopyObjBTree_Insert (_oopp_this=0x179a560,
item=0x2aac5d4ed820) at ./basic/ooppcc.h:902
#6 0x0000000000b98e2b in UG::D3::XICopyObjSet_ItemOK (_oopp_this=0x17381a0)
at ./basic/ooppcc.h:1097
#7 0x0000000000b851d9 in UG::D3::XferInitCopyInfo (hdr=0x2aab89588708,
desc=0x1483dd0, size=128, dest=487, prio=1) at xfer/cmds.c:1017
#8 0x0000000000b852dc in UG::D3::DDD_XferCopyObj (hdr=0x2aab89588708,
proc=487, prio=1) at xfer/cmds.c:1133
#9 0x0000000000cc46f3 in NodeXferCopy (
obj=0x2aab89587600 "\002\200o``\233\003", proc=487, prio=1)
at handler.c:1106
#10 0x0000000000b8525d in UG::D3::XferInitCopyInfo (hdr=0x2aab89587610,
desc=0x1484880, size=104, dest=487, prio=1) at xfer/cmds.c:1047
---Type <return> to continue, or q <return> to quit---
#11 0x0000000000b852dc in UG::D3::DDD_XferCopyObj (hdr=0x2aab89587610,
proc=487, prio=1) at xfer/cmds.c:1133
#12 0x0000000000cc4b68 in ElementXferCopy (
obj=0x2aab895887f0 "\006\223}@\224\314\001", proc=487, prio=1)
at handler.c:1373
#13 0x0000000000b8525d in UG::D3::XferInitCopyInfo (hdr=0x2aab89588808,
desc=0x1489e00, size=312, dest=487, prio=1) at xfer/cmds.c:1047
#14 0x0000000000b853cf in UG::D3::DDD_XferCopyObjX (hdr=0x2aab89588808,
proc=487, prio=1, size=312) at xfer/cmds.c:1206
#15 0x0000000000bb295c in XferGridWithOverlap (theGrid=0x2aab8023f0a8)
at trans.c:630
#16 0x0000000000bb2d0d in UG::D3::TransferGridFromLevel (theMG=0x1a3a250,
level=0) at trans.c:831
#17 0x0000000000bacb34 in UG::D3::lbs (argv=0x7fffffff3ce0 "0",
theMG=0x1a3a250) at lb.c:659
#18 0x0000000000b6db93 in UG::D3::LBCommand (argc=4, argv=0x7fffffff44e0)
at commands.c:10658
#19 0x000000000051bf07 in Dune::UG_NS<3>::LBCommand (argc=4,
argv=0x7fffffff44e0) at ../../../dune/grid/uggrid/ugwrapper.hh:979
#20 0x0000000000522b7d in Dune::UGGrid<3>::loadBalance (this=0x1652de0,
strategy=0, minlevel=0, depth=2, maxLevel=32, minelement=1)
at uggrid.cc:556
#21 0x0000000000414ed3 in Dune::UGGrid<3>::loadBalance (this=0x1652de0)
---Type <return> to continue, or q <return> to quit---
at /home/n02/n02/eike/work/Library/Dune2.2_DEBUG/include/dune/grid/uggrid.hh:738
#22 0x0000000000401110 in main (argc=2, argv=0x7fffffffb578)
at geometricmultigrid.cc:180
Eike
On 5 Dec 2012, at 15:22, Oliver Sander wrote:
> 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/
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> 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
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>>>>>>> _______________________________________________
>>>>>>> Dune mailing list
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>>>>>>> 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/
>>>>>>
>>>>> _______________________________________________
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