[petsc-dev] Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI process
Antonio Trande
anto.trande at gmail.com
Sat Oct 8 03:54:24 CDT 2016
On 10/08/2016 12:42 AM, Satish Balay wrote:
> On Fri, 7 Oct 2016, Antonio Trande wrote:
>
>> On 10/07/2016 08:29 PM, Satish Balay wrote:
>>> When I build openblas from sources - I don't see this error.
>>>
>>>>>>>>>
>>> balay at asterix /home/balay/petsc/src/snes/examples/tutorials (master=)
>>> $ valgrind --tool=memcheck -q ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres
>>> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
>>> Number of SNES iterations = 2
>>> <<<<<
>>>
>>> I'm not sure why it behaves differently with a source build.. [some bugfixes since v0.2.18-5?]
>>>
>>> But there are other examples that appear to have issues.
>>>
>>> Satish
>>
>> I'm already using openblas-0.2.18-5
>
> I meant to say 'newer than version 0.2.18-5' i.e whats in the git
> repo. But I now think there are issues with openblas64 built by
> fedora.
>
> I tried the following:
>
> 1. get latest openblas
> git clone https://github.com/xianyi/OpenBLAS
>
> 2. build with 64bit int mode:
> checking - http://pkgs.fedoraproject.org/cgit/rpms/openblas.git/tree/openblas.spec - I used:
> make DEBUG=1 INTERFACE64=1 -j 4
>
> 3. Now the PETSc tests run fine.
>
> 4. Now - I attempted to replicate fedora build using info from:
> https://kojipkgs.fedoraproject.org//packages/openblas/0.2.18/5.fc25/data/logs/x86_64/build.log
> attempt a build with:
>
> make TARGET=CORE2 DYNAMIC_ARCH=1 USE_THREAD=0 USE_OPENMP=0 FC=gfortran CC=gcc 'COMMON_OPT=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fPIC' 'FCOMMON_OPT=-frecursive -fPIC' NUM_THREADS=4 LIBPREFIX=libopenfoo-blas64 INTERFACE64=1
>
> 5. Now I see errors in 'openblas' test codes - during the build. [for some reason fedora koji build doesn't run this test?]
>
>>>>>>>>>>>>>>>>>>>
> gfortran -frecursive -o sblat1 sblat1.o ../libopenfoo-blas64-r0.2.20.dev.a -lm -lgfortran -lm -lgfortran
> gfortran -frecursive -o dblat1 dblat1.o ../libopenfoo-blas64-r0.2.20.dev.a -lm -lgfortran -lm -lgfortran
> gfortran -frecursive -o cblat1 cblat1.o ../libopenfoo-blas64-r0.2.20.dev.a -lm -lgfortran -lm -lgfortran
> gfortran -frecursive -o zblat1 zblat1.o ../libopenfoo-blas64-r0.2.20.dev.a -lm -lgfortran -lm -lgfortran
> gfortran -frecursive -o sblat2 sblat2.o ../libopenfoo-blas64-r0.2.20.dev.a -lm -lgfortran -lm -lgfortran
> gfortran -frecursive -o dblat2 dblat2.o ../libopenfoo-blas64-r0.2.20.dev.a -lm -lgfortran -lm -lgfortran
> gfortran -frecursive -o cblat2 cblat2.o ../libopenfoo-blas64-r0.2.20.dev.a -lm -lgfortran -lm -lgfortran
> gfortran -frecursive -o zblat2 zblat2.o ../libopenfoo-blas64-r0.2.20.dev.a -lm -lgfortran -lm -lgfortran
> gfortran -frecursive -o sblat3 sblat3.o ../libopenfoo-blas64-r0.2.20.dev.a -lm -lgfortran -lm -lgfortran
> gfortran -frecursive -o dblat3 dblat3.o ../libopenfoo-blas64-r0.2.20.dev.a -lm -lgfortran -lm -lgfortran
> gfortran -frecursive -o cblat3 cblat3.o ../libopenfoo-blas64-r0.2.20.dev.a -lm -lgfortran -lm -lgfortran
> gfortran -frecursive -o zblat3 zblat3.o ../libopenfoo-blas64-r0.2.20.dev.a -lm -lgfortran -lm -lgfortran
> OPENBLAS_NUM_THREADS=1 OMP_NUM_THREADS=1 ./sblat1
> Real BLAS Test Program Results
>
>
> Test of subprogram number 1 SDOT
>
> Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
>
> Backtrace for this error:
> rm -f ?BLAT2.SUMM
> OPENBLAS_NUM_THREADS=1 OMP_NUM_THREADS=1 ./sblat2 < ./sblat2.dat
>
> Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
>
> Backtrace for this error:
> #0 0x7f7f62862df7 in ???
> #1 0x7f7f6286202d in ???
> #2 0x7f7f61d5699f in ???
> #3 0x16c23b0 in sdot_k_SANDYBRIDGE
> at ../kernel/x86_64/sdot.c:110
> #4 0x4094f0 in ???
> #5 0x40a594 in ???
> #6 0x40a67c in ???
> #7 0x7f7f61d41400 in ???
> #8 0x408089 in ???
> #9 0xffffffffffffffff in ???
> Makefile:8: recipe for target 'level1' failed
> make[1]: *** [level1] Segmentation fault (core dumped)
> make[1]: *** Waiting for unfinished jobs....
> #0 0x7fc591700df7 in ???
> #1 0x7fc59170002d in ???
> #2 0x7fc590bf499f in ???
> #3 0x16d38a3 in ???
> at ../kernel/x86_64/scal_sse.S:372
> /bin/sh: line 1: 14464 Segmentation fault (core dumped) OPENBLAS_NUM_THREADS=1 OMP_NUM_THREADS=1 ./sblat2 < ./sblat2.dat
> Makefile:29: recipe for target 'level2' failed
> make[1]: *** [level2] Error 139
> make[1]: Leaving directory '/home/balay/git-repo/github/foo-OpenBLAS/test'
> Makefile:111: recipe for target 'tests' failed
> make: *** [tests] Error 2
> balay at asterix /home/balay/git-repo/github/foo-OpenBLAS (develop=)
> $
> <<<<<<<<<<<<<<<<<
>
> 6. Ok - looking at both the build closely - I see:
>
> * my working build with "make DEBUG=1 INTERFACE64=1 -j 4" has stuff like:
>
> gfortran -Wall -m64 -fdefault-integer-8 -fPIC -g -c stgsen.f -o stgsen.o
> gfortran -Wall -m64 -fdefault-integer-8 -fPIC -g -c stgsja.f -o stgsja.o
> gfortran -Wall -m64 -fdefault-integer-8 -fPIC -g -c stgsna.f -o stgsna.o
> gfortran -Wall -m64 -fdefault-integer-8 -fPIC -g -c stgsy2.f -o stgsy2.o
> gfortran -Wall -m64 -fdefault-integer-8 -fPIC -g -c stgsyl.f -o stgsyl.o
> gfortran -Wall -m64 -fdefault-integer-8 -fPIC -g -c stpcon.f -o stpcon.o
>
> * broken builds - both my fedora equivalent - and
> https://kojipkgs.fedoraproject.org//packages/openblas/0.2.18/5.fc25/data/logs/x86_64/build.log
> has stuff like:
>
> gfortran -frecursive -fPIC -c stgsen.f -o stgsen.o
> gfortran -frecursive -fPIC -c stgsja.f -o stgsja.o
> gfortran -frecursive -fPIC -c stgsna.f -o stgsna.o
> gfortran -frecursive -fPIC -c stgsy2.f -o stgsy2.o
> gfortran -frecursive -fPIC -c stgsyl.f -o stgsyl.o
> gfortran -frecursive -fPIC -c stpcon.f -o stpcon.o
>
> So - 'FCOMMON_OPT=-frecursive -fPIC' option is replacing
> '-fdefault-integer-8' thats required for a correct build of 64bit int
> openblas? [tuhs creating buggy /usr/lib64/libopenblas64.so]
>
> BTW: Another issue with the fedora build - fortran sources are not
> built with '-g -O2' [similar to the c sources] - so openblas-debuginfo
> does not have any debug symbols for the fortran sources [that are part
> of libopenblas64.so].
>
> Satish
>
Okay; let me contact OpenBlas maintainer on Fedora and open a bug ticket.
Just a question, is '-fdefault-integer-8' flag required even in PETSc?
Thanks.
--
---
Antonio Trande
mailto: sagitter 'at' fedoraproject 'dot' org
http://fedoraos.wordpress.com/
https://fedoraproject.org/wiki/User:Sagitter
GPG Key: 0x6CE6D08A
Check on https://keys.fedoraproject.org/
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