[petsc-dev] [petsc-maint] Incident INC0122538 MKL on Cori/KNL
Mark Adams
mfadams at lbl.gov
Tue Jul 3 06:25:21 CDT 2018
Well this does work without valgrind.
On Tue, Jul 3, 2018 at 6:36 AM Mark Adams <mfadams at lbl.gov> wrote:
> I built a 32 bit integer version and now it dies in PetscInit. Ugh.
>
> ==3965== Conditional jump or move depends on uninitialised value(s)
> ==3965== at 0x27AFFD8F: _int_free (malloc.c:3945)
> ==3965== by 0x20074F48: PetscOptionsSetValue (options.c:1152)
> ==3965== by 0x20070450: PetscOptionsInsertArgs_Private (options.c:636)
> ==3965== by 0x2007189F: PetscOptionsInsert (options.c:746)
> ==3965== by 0x20093DB1: PetscInitialize (pinit.c:929)
> ==3965== by 0x2000ABCE: main (ex19.c:106)
> ==3965==
> vex amd64->IR: unhandled instruction bytes: 0x62 0xF1 0x7F 0x8 0x7B 0xC2
> 0xC5 0xFB 0x10 0xD
> vex amd64->IR: REX=0 REX.W=0 REX.R=0 REX.X=0 REX.B=0
> vex amd64->IR: VEX=0 VEX.L=0 VEX.nVVVV=0x0 ESC=NONE
> vex amd64->IR: PFX.66=0 PFX.F2=0 PFX.F3=0
> ==3965== valgrind: Unrecognised instruction at address 0x20104a53.
> ==3965== at 0x20104A53: kh_resize_HTPrinted (viewreg.c:12)
> ==3965== by 0x20104EE2: kh_put_HTPrinted (viewreg.c:12)
> ==3965== by 0x201061EF: PetscOptionsHelpPrintedCheck (viewreg.c:89)
> ==3965== by 0x2009AD61: PetscOptionsBegin_Private (aoptions.c:34)
> ==3965== by 0x2008362E: PetscOptionsSetFromOptions (options.c:2646)
> ==3965== by 0x20094689: PetscInitialize (pinit.c:967)
> ==3965== by 0x2000ABCE: main (ex19.c:106)
> ==3965== Your program just tried to execute an instruction that Valgrind
> ==3965== did not recognise. There are two possible reasons for this.
> ==3965== 1. Your program has a bug and erroneously jumped to a non-code
> ==3965== location. If you are running Memcheck and you just saw a
> ==3965== warning about a bad jump, it's probably your program's fault.
> ==3965== 2. The instruction is legitimate but Valgrind doesn't handle it,
> ==3965== i.e. it's Valgrind's fault. If you think this is the case or
> ==3965== you are not sure, please let us know and we'll try to fix it.
> ==3965== Either way, Valgrind will now raise a SIGILL signal which will
> ==3965== probably kill your program.
> [0]PETSC ERROR: ==3965== Conditional jump or move depends on uninitialised
> value(s)
> ==3965== at 0x27B18B48: strchrnul (strchr.S:106)
> ==3965== by 0x27AE30C8: __find_specmb (printf-parse.h:108)
> ==3965== by 0x27AE30C8: vfprintf (vfprintf.c:1311)
> ==3965== by 0x27AFA045: vsnprintf (vsnprintf.c:119)
> ==3965== by 0x20116802: PetscVSNPrintf (mprint.c:178)
> ==3965== by 0x20117006: PetscVFPrintfDefault (mprint.c:294)
> ==3965== by 0x20136BB2: PetscErrorPrintfDefault (errtrace.c:116)
> ==3965== by 0x2013938C: PetscSignalHandlerDefault (signal.c:131)
> ==3965== by 0x2013903B: PetscSignalHandler_Private (signal.c:43)
> ==3965== by 0x2335D07F: ??? (in
> /global/u2/m/madams/petsc_install/petsc/src/snes/examples/tutorials/ex19)
> ==3965== by 0x20104A52: kh_resize_HTPrinted (viewreg.c:12)
> ==3965== by 0x20104EE2: kh_put_HTPrinted (viewreg.c:12)
> ==3965== by 0x201061EF: PetscOptionsHelpPrintedCheck (viewreg.c:89)
> ==3965==
> ==3965== Conditional jump or move depends on uninitialised value(s)
> ==3965== at 0x27B08184: strlen (strlen.S:210)
> ==3965== by 0x200B3A48: PetscStrlen (str.c:158)
> ==3965== by 0x2011693D: PetscVSNPrintf (mprint.c:188)
> ==3965== by 0x20117006: PetscVFPrintfDefault (mprint.c:294)
> ==3965== by 0x20136BB2: PetscErrorPrintfDefault (errtrace.c:116)
> ==3965== by 0x2013938C: PetscSignalHandlerDefault (signal.c:131)
> ==3965== by 0x2013903B: PetscSignalHandler_Private (signal.c:43)
> ==3965== by 0x2335D07F: ??? (in
> /global/u2/m/madams/petsc_install/petsc/src/snes/examples/tutorials/ex19)
> ==3965== by 0x20104A52: kh_resize_HTPrinted (viewreg.c:12)
> ==3965== by 0x20104EE2: kh_put_HTPrinted (viewreg.c:12)
> ==3965== by 0x201061EF: PetscOptionsHelpPrintedCheck (viewreg.c:89)
> ==3965== by 0x2009AD61: PetscOptionsBegin_Private (aoptions.c:34)
> ==3965==
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 4 Illegal instruction: Likely due to
> memory corruption
>
>
> On Mon, Jul 2, 2018 at 8:53 PM Mark Adams <mfadams at lbl.gov> wrote:
>
>> Looping Treb and Baky back into the thread, and dropping PETSs.
>>
>> Great, thanks Barry for figuring this out.
>>
>> Treb and Baky need 64 bit indices, but in the mean time I can build a 32
>> bit version to let them test.
>>
>> I am all set up to test a 64 bit version. If you can give me a branch I
>> can test.
>>
>> Thanks,
>> Mark
>>
>>
>>
>> On Mon, Jul 2, 2018 at 7:47 PM Smith, Barry F. <bsmith at mcs.anl.gov>
>> wrote:
>>
>>>
>>> Progress has been made. These libraries do contain
>>> mkl_set_num_threads() is found so ./configure knows that it is MKL
>>> libraries (unlike before when it did not recognize that it was MKL
>>> libraries).
>>>
>>>
>>> Damn it, here is why:
>>>
>>> --with-64-bit-indices=1
>>>
>>> currently the MKL sparse stuff only works with 32 bit integers AND 32
>>> bit integer BLAS/LAPACK.
>>>
>>> It will never work with 64 bit indices and 32 bit integer BLAS/LAPACK.
>>> but maybe could be upgraded to work with 64 bit indices and 64 bit integer
>>> BLAS/LAPACK Richard?
>>>
>>>
>>> Anyways the requirement in mkl_sparse.py is
>>>
>>> self.requires32bitint = 1
>>>
>>> The problem is ./configure does not print enough information to make it
>>> immediately clear it is rejecting the package because of this
>>> incompatibility.
>>>
>>>
>>>
>>> Barry
>>>
>>>
>>>
>>>
>>> > On Jul 2, 2018, at 5:57 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>> >
>>> > Same error:
>>> >
>>> > 15:53 nid02517 master *=
>>> ~/petsc_install/petsc/src/snes/examples/tutorials$ make
>>> PETSC_DIR=/global/homes/m/madams/petsc_install/petsc-cori-knl-dbg64-intel-omp
>>> PETSC_ARCH="" ex19
>>> > cc -o ex19.o -c -g -O0 -mkl -static-intel -fopenmp
>>> -I/global/homes/m/madams/petsc_install/petsc-cori-knl-dbg64-intel-omp/include
>>> -I/global/homes/m/madams/petsc_install/petsc-cori-knl-dbg64-intel-omp/include
>>> -I/global/homes/m/madams/tmp/hypre-2.14.0/include
>>> -I/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/include
>>> -I/global/homes/m/madams/petsc_install/petsc-cori-knl-dbg64-intel-omp/include
>>> `pwd`/ex19.c
>>>
>>>
>>> > cc -g -O0 -mkl -static-intel -fopenmp -o ex19 ex19.o
>>> -L/global/homes/m/madams/petsc_install/petsc-cori-knl-dbg64-intel-omp/lib
>>> -Wl,-rpath,/global/homes/m/madams/tmp/hypre-2.14.0/lib
>>> -L/global/homes/m/madams/tmp/hypre-2.14.0/lib
>>> -Wl,-rpath,/global/homes/m/madams/petsc_install/petsc-cori-knl-dbg64-intel-omp/lib
>>> -L/global/homes/m/madams/petsc_install/petsc-cori-knl-dbg64-intel-omp/lib
>>> -L/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64
>>> -lpetsc -lHYPRE -lparmetis -lmetis -lstdc++ -ldl -lmkl_intel_ilp64
>>> -lmkl_intel_thread -lmkl_core -liomp5 -lpthread
>>> >
>>> /opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_core.a(mkl_semaphore.o):
>>> In function `mkl_serv_load_inspector':
>>>
>>> > mkl_semaphore.c:(.text+0x123): warning: Using 'dlopen' in statically
>>> linked applications requires at runtime the shared libraries from the glibc
>>> version used for linking
>>> >
>>> /global/homes/m/madams/petsc_install/petsc-cori-knl-dbg64-intel-omp/lib/libpetsc.a(send.o):
>>> In function `PetscOpenSocket':
>>>
>>> >
>>> /global/u2/m/madams/petsc_install/petsc/src/sys/classes/viewer/impls/socket/send.c:108:
>>> warning: Using 'gethostbyname' in statically linked applications requires
>>> at runtime the shared libraries from the glibc version used for linking
>>>
>>>
>>>
>>> > rm ex19.o
>>>
>>>
>>> > 15:54 nid02517 master *=
>>> ~/petsc_install/petsc/src/snes/examples/tutorials$ make
>>> PETSC_DIR=/global/homes/m/madams/petsc_install/petsc-cori-knl-dbg64-intel-omp
>>> PETSC_ARCH="" runex19_gamg
>>> > lid velocity = 0.0625, prandtl # = 1., grashof # = 1.
>>>
>>>
>>> > [0]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>>
>>> > [1]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>>
>>> > [1]PETSC ERROR: Unknown type. Check for miss-spelling or missing
>>> package:
>>> http://www.mcs.anl.gov/petsc/documentation/installation.html#external
>>>
>>> > [1]PETSC ERROR: Unknown Mat type given: aijmkl
>>> >
>>> > On Mon, Jul 2, 2018 at 6:43 PM Satish Balay <balay at mcs.anl.gov> wrote:
>>> > Hm - I suspect its an issue with mkl includes - not the libraries.
>>> >
>>> > Satish
>>> >
>>> > On Mon, 2 Jul 2018, Smith, Barry F. wrote:
>>> >
>>> > >
>>> > > Mark,
>>> > >
>>> > > This is not useful. We need the new configure log from when you
>>> list all the libraries NERSE recommends (which may work).
>>> > >
>>> > > I already said what was wrong with this configuration.
>>> > >
>>> > > Barry
>>> > >
>>> > >
>>> > > > On Jul 2, 2018, at 5:25 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>> > > >
>>> > > >
>>> > > >
>>> > > > On Mon, Jul 2, 2018 at 6:22 PM Satish Balay <balay at mcs.anl.gov>
>>> wrote:
>>> > > > I don't understand the problem here..
>>> > > >
>>> > > > > > > [0]PETSC ERROR: Unknown type. Check for miss-spelling or
>>> missing package:
>>> http://www.mcs.anl.gov/petsc/documentation/installation.html#external
>>> > > > > > > [0]PETSC ERROR: Unknown Mat type given: aijmkl
>>> > > >
>>> > > > If this is the problem - then we'll have to look at configure.log
>>> to check why PETSC_HAVE_MKL_SPARSE flag is not set.
>>> > > >
>>> > > > <configure.log>
>>> > >
>>> >
>>> > <configure.log>
>>>
>>>
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