[petsc-dev] PETSC_VERSION_GE
Ed D'Azevedo
dazevedoef at ornl.gov
Wed Apr 16 09:41:18 CDT 2014
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
> <mailto: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
>> <mailto: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
>> <mailto: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 <mailto: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 <mailto: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 <mailto:mfadams at lbl.gov>> wrote:
>>
>>
>>
>>
>> On Thu, Apr 10, 2014 at 8:25 AM, Seung-Hoe Ku
>> <sku at pppl.gov <mailto: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
>> <mailto: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
>> <mailto:sku at pppl.gov>> wrote:
>>
>> Great! Thank you.
>>
>>
>>
>> On Wed, Apr 9, 2014 at 9:35 PM,
>> Mark Adams <mfadams at lbl.gov
>> <mailto: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
>> <mailto: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
>> <mailto: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
>> <mailto: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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