[petsc-dev] PETSC_VERSION_GE
Mark Adams
mfadams at lbl.gov
Wed Apr 16 10:24:36 CDT 2014
Ed, I have to run but I found that the second argument to split_indices was
called with a PetscInt but typed as an integer.
Mark
On Wed, Apr 16, 2014 at 10:41 AM, Ed D'Azevedo <dazevedoef at ornl.gov> wrote:
> Hi Mark,
>
> I hope this back trace might be helpful.
>
> You may need to build petsc with
> ./configure \
> --with-x=0 \
> --with-debugging=0 \
> --with-log=0 \
>
>
> env003> addr2line --exe=tpetsc_madams 0x4b76e3 0x4aa3d7 0x484888 0x475798
> 0x548aa5 0x5e5df2 0x57a353 0x4a701e 0x44e9be 0x44e1f4
> /autofs/na3_home1/adams/petsc/src/sys/memory/mal.c:27
> /autofs/na3_home1/adams/petsc/src/sys/utils/str.c:188
> /autofs/na3_home1/adams/petsc/src/sys/logging/utils/eventlog.c:317
> /autofs/na3_home1/adams/petsc/src/sys/logging/plog.c:747
> /autofs/na3_home1/adams/petsc/src/mat/interface/dlregismat.c:145
> /autofs/na3_home1/adams/petsc/src/mat/utils/gcreate.c:57
> /autofs/na3_home1/adams/petsc/src/mat/impls/aij/seq/aij.c:3576
> /autofs/na3_home1/adams/petsc/src/mat/impls/aij/seq/ftn-custom/zaijf.c:14
> /autofs/na3_home1/efdazedo/test/PETSC/./tpetsc.F90:147
>
>
>
>
>
> ======= Backtrace: =========
> /lib64/libc.so.6(+0x75558)[0x2aaaba5ff558]
> /lib64/libc.so.6(cfree+0x6c)[0x2aaaba6044fc]
> ./tpetsc_madams[0x4b7759]
> /lib64/libpthread.so.0(+0xf7c0) [0x2aaaaacdb7c0]
> /lib64/libc.so.6(gsignal+0x35) [0x2aaaba5bcb55]
> /lib64/libc.so.6(abort+0x181) [0x2aaaba5be131]
> /lib64/libc.so.6(+0x7576d) [0x2aaaba5ff76d]
> /lib64/libc.so.6(+0x789f0) [0x2aaaba6029f0]
> /lib64/libc.so.6(__libc_malloc+0x77) [0x2aaaba6045e7]
> ./tpetsc_madams() [0x4b76e3]
> ./tpetsc_madams() [0x4aa3d7]
> ./tpetsc_madams() [0x484888]
> ./tpetsc_madams() [0x475798]
> ./tpetsc_madams() [0x548aa5]
> ./tpetsc_madams() [0x5e5df2]
> ./tpetsc_madams() [0x57a353]
> ./tpetsc_madams() [0x4a701e]
> ./tpetsc_madams() [0x44e9be]
> ./tpetsc_madams() [0x44e1f4]
> /lib64/libc.so.6(__libc_start_main+0xe6) [0x2aaaba5a8c36]
> ./tpetsc_madams() [0x44e0e9]
>
>
>
>
>
>
> On 04/16/2014 10:33 AM, Mark Adams wrote:
>
> cc'ing petsc-dev.
>
> I will try it.
>
> On Wed, Apr 16, 2014 at 10:21 AM, Ed D'Azevedo <dazevedoef at ornl.gov>wrote:
>
>>
>> Hi Mark,
>>
>> I got an error when I tried the simple test code (see attached) on Titan.
>>
>> Can you try to run the attached test case to see if it will work for you?
>>
>> I have also sent the simple test code to Barry.
>>
>>
>>
>> The code seems to work with 1 thread
>>
>> env003> export OMP_NUM_THREADS=1
>> env003> aprun -n 1 -d 16 ./tpetsc_madams
>> PETSC_VERSION_RELEASE 0
>> PETSC_VERSION_MAJOR 3
>> PETSC_VERSION_MINOR 4
>> PETSC_VERSION_SUBMINOR 4
>> PETSC_VERSION_PATCH 0
>> PETSC_VERSION_DATE unknown
>> petsc_version_lt(3,3,0) is false
>> nthreads = 1 NCASES = 100
>> nz = 88804
>> Warning: ieee_inexact is signaling
>> all done
>> total time is 7.268438
>> maxval(err) 6.9650285539069046E-011
>> Application 4895013 resources: utime ~8s, stime ~0s, Rss ~22300, inblocks
>> ~11428, outblocks ~35848
>>
>>
>> The code seems to have trouble using more threads
>>
>> env003> export OMP_NUM_THREADS=16
>> env003> aprun -n 1 -d 16 ./tpetsc_madams
>> *** glibc detected *** ./tpetsc_madams: double free or corruption
>> (!prev): 0x00000000015ee0b0 ***
>> PETSC_VERSION_RELEASE 0
>> PETSC_VERSION_MAJOR 3
>> PETSC_VERSION_MINOR 4
>> PETSC_VERSION_SUBMINOR 4
>> PETSC_VERSION_PATCH 0
>> PETSC_VERSION_DATE unknown
>> petsc_version_lt(3,3,0) is false
>> nthreads = 16 NCASES = 100
>> tpetsc_madams: malloc.c:3091: sYSMALLOc: Assertion `(old_top ==
>> (((mbinptr) (((char *) &((av)->bins[((1) - 1) * 2])) - __builtin_offsetof
>> (struct malloc_chunk, fd)))) && old_size == 0) || ((unsigned long)
>> (old_size) >= (unsigned long)((((__builtin_offsetof (struct malloc_chunk,
>> fd_nextsize))+((2 * (sizeof(size_t))) - 1)) & ~((2 * (sizeof(size_t))) -
>> 1))) && ((old_top)->size & 0x1) && ((unsigned long)old_end & pagemask) ==
>> 0)' failed.
>> Error: abort
>> rax 0000000000000000, rbx 0000000000000fff, rcx ffffffffffffffff
>> rdx 0000000000000006, rsp 00002aaac4554f78, rbp 00002aaad0000098
>> rsi 0000000000005200, rdi 00000000000051f1, r8 00000000ffffffff
>> r9 00002aaaba8f9e40, r10 0000000000000008, r11 0000000000000202
>> r12 0000000000000000, r13 00002aaad0008e30, r14 0000000000000020
>> r15 0000000000000000
>> ======= Backtrace: =========
>> /lib64/libc.so.6(+0x75558)[0x2aaaba5ff558]
>> /lib64/libc.so.6(cfree+0x6c)[0x2aaaba6044fc]
>> ./tpetsc_madams[0x4b7759]
>> /lib64/libpthread.so.0(+0xf7c0) [0x2aaaaacdb7c0]
>> /lib64/libc.so.6(gsignal+0x35) [0x2aaaba5bcb55]
>> /lib64/libc.so.6(abort+0x181) [0x2aaaba5be131]
>> /lib64/libc.so.6(+0x7576d) [0x2aaaba5ff76d]
>> /lib64/libc.so.6(+0x789f0) [0x2aaaba6029f0]
>> /lib64/libc.so.6(__libc_malloc+0x77) [0x2aaaba6045e7]
>> ./tpetsc_madams() [0x4b76e3]
>> ./tpetsc_madams() [0x4aa3d7]
>> ./tpetsc_madams() [0x484888]
>> ./tpetsc_madams() [0x475798]
>> ./tpetsc_madams() [0x548aa5]
>> ./tpetsc_madams() [0x5e5df2]
>> ./tpetsc_madams() [0x57a353]
>> ./tpetsc_madams() [0x4a701e]
>> ./tpetsc_madams() [0x44e9be]
>> ./tpetsc_madams() [0x44e1f4]
>> /lib64/libc.so.6(__libc_start_main+0xe6) [0x2aaaba5a8c36]
>> ./tpetsc_madams() [0x44e0e9]
>> Application 4895021 exit codes: 127
>> Application 4895021 resources: utime ~0s, stime ~0s, Rss ~12544, inblocks
>> ~11429, outblocks ~35849
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On 04/11/2014 04:34 PM, Mark Adams wrote:
>>
>> PETSc dev 'master' now has Barry's thread safe stuff so you should be
>> able to use that. I have build it in:
>>
>> PETSC_DIR=/autofs/na3_home1/adams/petsc
>> PETSC_ARCH=arch-titan-opt
>>
>> So try this version out. And revert the code to the repo version by
>> doing:
>>
>> > git checkout poisson.F90
>>
>> and any other place where #if PETSC_VERSION_GE(3,5,0) is used. I only
>> see poisson.F90.
>>
>> If this works I can install it wherever you like as Ed did.
>>
>> Mark
>>
>>
>>
>>
>>
>> On Thu, Apr 10, 2014 at 11:24 PM, Seung-Hoe Ku <sku at pppl.gov> wrote:
>>
>>> Hi Mark,
>>>
>>> I think it is not a big problem until we use petsc 3.5 other than you.
>>> Now I disabled #if #endif for other users. Sorry for the inconvenience.
>>> Could you uncomment it when you are working with 3.5, and does not commit
>>> to core_dev, please?
>>> We need Ed's thread safe petsc for performance issue, so we can find
>>> some way to resolve it when 3.5 is released and installed on titan.
>>>
>>> Thanks,
>>> Seung-Hoe
>>>
>>>
>>>
>>> On Thu, Apr 10, 2014 at 11:38 AM, Mark Adams <mfadams at lbl.gov> wrote:
>>>
>>>> We've figured out the problem (again). It will be fixed in future
>>>> versions.
>>>>
>>>> We can fix your installation. I'm guessing Ed did this installation
>>>> so it might not be worth fixing this code since you are up and running.
>>>> Let me know what you want to do.
>>>>
>>>> The problem is that is a development version of the code, which is
>>>> not as stable as the releases. This version needs to be updated to get fix
>>>> this problem. I have to tell you how to do this update so let me know if
>>>> you want to do it.
>>>>
>>>> Mark
>>>>
>>>>
>>>>
>>>> On Thu, Apr 10, 2014 at 8:58 AM, Seung-Hoe Ku <sku at pppl.gov> wrote:
>>>>
>>>>> One question is..
>>>>> If PETSC_VERSION_GE is defined with PETSC_VERSION_GT and
>>>>> PETSC_VERSION_GT is defined with something in petsc.h,
>>>>> redefinition of PETSC_VERSION_GT after petsc.h will change
>>>>> PETSC_VERSION_GE?
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Apr 10, 2014 at 10:55 AM, Seung-Hoe Ku <sku at pppl.gov> wrote:
>>>>>
>>>>>> This is the code I tried to compile.
>>>>>>
>>>>>> #if PETSC_VERSION_GE(5,5,0)
>>>>>> 214 BBBBBBBBBBBBBBBBBBB=0
>>>>>> 215 call KSPSetOperators(solver%ksp, solver%Amat, solver%Amat,
>>>>>> ierr )
>>>>>> 216 #else
>>>>>> 217 AAAAAAAAAAAA=0
>>>>>> 218 call KSPSetOperators(solver%ksp, solver%Amat, solver%Amat,
>>>>>> SAME_NONZERO_PATT ERN, ierr )
>>>>>> 219 #endif
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Thu, Apr 10, 2014 at 10:49 AM, Mark Adams <mfadams at lbl.gov>wrote:
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Apr 10, 2014 at 8:25 AM, Seung-Hoe Ku <sku at pppl.gov> wrote:
>>>>>>>
>>>>>>>> I have the same problem. I used poisson.F90 in
>>>>>>>> /lustre/atlas2/env003/scratch/shku/XGC1_3_petsc_problem/
>>>>>>>>
>>>>>>>> It seems that #undef should be after #include<finclude/petsc.h>.
>>>>>>>> Otherwise, petsc.h seems to try redefine it.
>>>>>>>>
>>>>>>>>
>>>>>>> Oh yes.
>>>>>>>
>>>>>>>
>>>>>>>> Anyway, I got the same error message:
>>>>>>>>
>>>>>>>> PGF90-S-0038-Symbol, bbbbbbbbbbbbbbbbbbb, has not been explicitly
>>>>>>>> declared (poisson.F90)
>>>>>>>> 0 inform, 0 warnings, 1 severes, 0 fatal for
>>>>>>>> init_1field_solver
>>>>>>>>
>>>>>>>>
>>>>>>> is this in the source file?
>>>>>>>
>>>>>>>
>>>>>>>> I tried 5.5.0 for the arguments of PETSC_VERSION_GE, but still
>>>>>>>> have the same problem.
>>>>>>>>
>>>>>>>> Or do you mean VERSION_GE and VERSION_LT instead of VERSION_GT and
>>>>>>>> VERSION_LE?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Seung-Hoe
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Apr 9, 2014 at 9:54 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>>>>>>>
>>>>>>>>> We might have a fix. It turns out that some fortran compilers to
>>>>>>>>> not do the #define quite right. Try this:
>>>>>>>>>
>>>>>>>>> > git checkout poisson.F90
>>>>>>>>>
>>>>>>>>> This will out the original (bad) file back. Then add to
>>>>>>>>> poisson.F90
>>>>>>>>>
>>>>>>>>> #undef PETSC_VERSION_GT
>>>>>>>>> #define PETSC_VERSION_GT(MAJOR,MINOR,SUBMINOR) \
>>>>>>>>> (0==PETSC_VERSION_LE(MAJOR,MINOR,SUBMINOR))
>>>>>>>>>
>>>>>>>>> This is the fix that Jed thinks will work. If it works we can
>>>>>>>>> propagate it.
>>>>>>>>>
>>>>>>>>> Sorry about the confusion,
>>>>>>>>> Mark
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, Apr 9, 2014 at 7:36 PM, Seung-Hoe Ku <sku at pppl.gov> wrote:
>>>>>>>>>
>>>>>>>>>> Great! Thank you.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Wed, Apr 9, 2014 at 9:35 PM, Mark Adams <mfadams at lbl.gov>wrote:
>>>>>>>>>>
>>>>>>>>>>> Good news. I'm at a meeting and Jed Brown is here and he seems
>>>>>>>>>>> to have been able to reproduce the error. Preprocessors can be a pain.
>>>>>>>>>>> I'm going to wait until Jed has a chance to look at this and come up with
>>>>>>>>>>> a solution.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Apr 9, 2014 at 7:28 PM, Seung-Hoe Ku <sku at pppl.gov>wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Now I am using iterative solver which will be replaced to
>>>>>>>>>>>> your 2 field solver later.
>>>>>>>>>>>> Sorry. The line number 3003 is wrong. It is 209 or near it.
>>>>>>>>>>>> Yes. We can take a look at this when you come. It is not
>>>>>>>>>>>> urgent problem.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Seung-Hoe
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Wed, Apr 9, 2014 at 9:25 PM, Mark Adams <mfadams at lbl.gov>wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> I noticed that your makefile was not using the new petsc
>>>>>>>>>>>>> solver. Is that intensional?
>>>>>>>>>>>>>
>>>>>>>>>>>>> The line you gave me 3003 poission.F90 seems to be the last
>>>>>>>>>>>>> line of the file.
>>>>>>>>>>>>>
>>>>>>>>>>>>> I am not getting Edison or Titan to build. We can take a
>>>>>>>>>>>>> look at this next week.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Mark
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Apr 8, 2014 at 12:38 PM, Seung-Hoe Ku <sku at pppl.gov>wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Mark,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> It seems that PETSC_VERSION_GE is not working line 3003 of
>>>>>>>>>>>>>> poisson.F90. Is there any reason of using PETSC_VERSION_GE instead of
>>>>>>>>>>>>>> PETSC_VERSION_LE? The previous code worked, I think.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>> Seung-Hoe
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>>
>
>
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