[mpich-discuss] BUG in ADIOI_NFS_WriteStrided
Eric Chamberland
Eric.Chamberland at giref.ulaval.ca
Fri Dec 19 14:33:55 CST 2014
Hi Howard,
the bug is present also with MPICH-3.1.3...
So, for discuss at mpich.org list readers, here is the valgrind output for
a bug revealed with valgrind (sorry, I didn't compiled MPICH in debug
mode), reported to OpenMPI earlier today:
http://www.open-mpi.org/community/lists/devel/2014/12/16691.php
sorry for the "duplicated" report again.
I encountered a new bug while testing our collective MPI I/O
functionnalities over NFS. This is not a big issue for us, but I think
someone should have a look at it.
While running at 3 processes, we have this error on rank #0 and rank #2,
knowing that rank #1 have nothing to write (0 length size) on this
particular PMPI_File_write_all_begin call:
==3434== Syscall param write(buf) points to uninitialised byte(s)
==3434== at 0x108D0380: __write_nocancel (in /lib64/libpthread-2.17.so)
==3434== by 0x11DB9D46: ADIOI_NFS_WriteStrided (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x11DD264F: ADIOI_GEN_WriteStridedColl (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x11DB5F8F: MPIOI_File_write_all_begin (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x11DB60F3: PMPI_File_write_all_begin (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x4CCAE6: SYEnveloppeMessage<std::string>
PAIO::ecritureIndexeParBlocMPI<PAIOType<double>, PtrPorteurConst<Arete,
Arete>, FunctorCopieInfosSurDansVectPAType<PAIOType<double>,
std::vector<InfoSur<double, Arete>*, std::allocator<InfoSur<double,
Arete>*> > const>, FunctorAccesseurPorteurLocal<PtrPorteurConst<Arete,
Arete> > >(PAGroupeProcessus&, ADIOI_FileD*, long long,
PtrPorteurConst<Arete, Arete>, PtrPorteurConst<Arete, Arete>,
FunctorCopieInfosSurDansVectPAType<PAIOType<double>,
std::vector<InfoSur<double, Arete>*, std::allocator<InfoSur<double,
Arete>*> > const>&, FunctorAccesseurPorteurLocal<PtrPorteurConst<Arete,
Arete> >&, long, DistributionComposantes&, long, unsigned long, unsigned
long, std::string const&) (in
/home/mefpp_ericc/GIREF/bin/Test.LectureEcritureGISMPI.opt)
==3434== by 0x4DDBFE:
GISLectureEcriture<double>::visiteMaillage(Maillage const&) (in
/home/mefpp_ericc/GIREF/bin/Test.LectureEcritureGISMPI.opt)
==3434== by 0x4BCB22:
GISLectureEcriture<double>::ecritGISMPI(std::string,
GroupeInfoSur<double> const&, std::string const&) (in
/home/mefpp_ericc/GIREF/bin/Test.LectureEcritureGISMPI.opt)
==3434== by 0x48E213: main (in
/home/mefpp_ericc/GIREF/bin/Test.LectureEcritureGISMPI.opt)
==3434== Address 0x1a12cd10 is 224 bytes inside a block of size 524,448
alloc'd
==3434== at 0x4C2C27B: malloc (in
/usr/lib64/valgrind/vgpreload_memcheck-amd64-linux.so)
==3434== by 0x11DADA96: MPL_trmalloc (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x11DD9285: ADIOI_Malloc_fn (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x11DB9AC8: ADIOI_NFS_WriteStrided (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x11DD264F: ADIOI_GEN_WriteStridedColl (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x11DB5F8F: MPIOI_File_write_all_begin (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x11DB60F3: PMPI_File_write_all_begin (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x4CCAE6: SYEnveloppeMessage<std::string>
PAIO::ecritureIndexeParBlocMPI<PAIOType<double>, PtrPorteurConst<Arete,
Arete>, FunctorCopieInfosSurDansVectPAType<PAIOType<double>,
std::vector<InfoSur<double, Arete>*, std::allocator<InfoSur<double,
Arete>*> > const>, FunctorAccesseurPorteurLocal<PtrPorteurConst<Arete,
Arete> > >(PAGroupeProcessus&, ADIOI_FileD*, long long,
PtrPorteurConst<Arete, Arete>, PtrPorteurConst<Arete, Arete>,
FunctorCopieInfosSurDansVectPAType<PAIOType<double>,
std::vector<InfoSur<double, Arete>*, std::allocator<InfoSur<double,
Arete>*> > const>&, FunctorAccesseurPorteurLocal<PtrPorteurConst<Arete,
Arete> >&, long, DistributionComposantes&, long, unsigned long, unsigned
long, std::string const&) (in
/home/mefpp_ericc/GIREF/bin/Test.LectureEcritureGISMPI.opt)
==3434== by 0x4DDBFE:
GISLectureEcriture<double>::visiteMaillage(Maillage const&) (in
/home/mefpp_ericc/GIREF/bin/Test.LectureEcritureGISMPI.opt)
==3434== by 0x4BCB22:
GISLectureEcriture<double>::ecritGISMPI(std::string,
GroupeInfoSur<double> const&, std::string const&) (in
/home/mefpp_ericc/GIREF/bin/Test.LectureEcritureGISMPI.opt)
==3434== by 0x48E213: main (in
/home/mefpp_ericc/GIREF/bin/Test.LectureEcritureGISMPI.opt)
==3434== Uninitialised value was created by a client request
==3434== at 0x11DADEE5: MPL_trmalloc (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x11DD9285: ADIOI_Malloc_fn (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x11DB9AC8: ADIOI_NFS_WriteStrided (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x11DD264F: ADIOI_GEN_WriteStridedColl (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x11DB5F8F: MPIOI_File_write_all_begin (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x11DB60F3: PMPI_File_write_all_begin (in
/opt/mpich-3.1.3/lib64/libmpi.so.12.0.4)
==3434== by 0x4CCAE6: SYEnveloppeMessage<std::string>
PAIO::ecritureIndexeParBlocMPI<PAIOType<double>, PtrPorteurConst<Arete,
Arete>, FunctorCopieInfosSurDansVectPAType<PAIOType<double>,
std::vector<InfoSur<double, Arete>*, std::allocator<InfoSur<double,
Arete>*> > const>, FunctorAccesseurPorteurLocal<PtrPorteurConst<Arete,
Arete> > >(PAGroupeProcessus&, ADIOI_FileD*, long long,
PtrPorteurConst<Arete, Arete>, PtrPorteurConst<Arete, Arete>,
FunctorCopieInfosSurDansVectPAType<PAIOType<double>,
std::vector<InfoSur<double, Arete>*, std::allocator<InfoSur<double,
Arete>*> > const>&, FunctorAccesseurPorteurLocal<PtrPorteurConst<Arete,
Arete> >&, long, DistributionComposantes&, long, unsigned long, unsigned
long, std::string const&) (in
/home/mefpp_ericc/GIREF/bin/Test.LectureEcritureGISMPI.opt)
==3434== by 0x4DDBFE:
GISLectureEcriture<double>::visiteMaillage(Maillage const&) (in
/home/mefpp_ericc/GIREF/bin/Test.LectureEcritureGISMPI.opt)
==3434== by 0x4BCB22:
GISLectureEcriture<double>::ecritGISMPI(std::string,
GroupeInfoSur<double> const&, std::string const&) (in
/home/mefpp_ericc/GIREF/bin/Test.LectureEcritureGISMPI.opt)
==3434== by 0x48E213: main (in
/home/mefpp_ericc/GIREF/bin/Test.LectureEcritureGISMPI.opt)
Can't tell if it is a big issue or not, but I thought I should mention
it to the list....
We run without this valgrind error when I use my local disk partition
instead of an nfs parition or if I run with only 1 process (which
always have something to write for each PMPI_File_write_all_begin) and
write to an nfs partition.
Have you guys thinked about unifying this part of code? Making it a
sub-library? (please don't flame me... ;-) )
Anyway,
thanks,
Eric
On 12/19/2014 02:16 PM, Howard Pritchard wrote:
> HI Eric,
>
> Does your app also work with MPICH? The romio in Open MPI is getting a
> bit old, so it would be useful to know if you see the same valgrind
> error using a recent MPICH.
>
> Howard
>
>
> 2014-12-19 9:50 GMT-07:00 Eric Chamberland
> <Eric.Chamberland at giref.ulaval.ca
> <mailto:Eric.Chamberland at giref.ulaval.ca>>:
>
> Hi,
>
> I encountered a new bug while testing our collective MPI I/O
> functionnalities over NFS. This is not a big issue for us, but I
> think someone should have a look at it.
>
> While running at 3 processes, we have this error on rank #0 and rank
> #2, knowing that rank #1 have nothing to write (0 length size) on
> this particular PMPI_File_write_all_begin call:
>
>
> ==19211== Syscall param write(buf) points to uninitialised byte(s)
> ==19211== at 0x10CB739D: ??? (in /lib64/libpthread-2.17.so
> <http://libpthread-2.17.so>)
> ==19211== by 0x27438431: ADIOI_NFS_WriteStrided (ad_nfs_write.c:645)
> ==19211== by 0x27451963: ADIOI_GEN_WriteStridedColl
> (ad_write_coll.c:159)
> ==19211== by 0x274321BD: MPIOI_File_write_all_begin
> (write_allb.c:114)
> ==19211== by 0x27431DBF:
> mca_io_romio_dist_MPI_File___write_all_begin (write_allb.c:44)
> ==19211== by 0x2742A367: mca_io_romio_file_write_all___begin
> (io_romio_file_write.c:264)
> ==19211== by 0x12126520: PMPI_File_write_all_begin
> (pfile_write_all_begin.c:74)
> ==19211== by 0x4D7CFB: SYEnveloppeMessage<std::__string>
> PAIO::__ecritureIndexeParBlocMPI<__PAIOType<double>,
> PtrPorteurConst<Arete, Arete>,
> FunctorCopieInfosSurDansVectPA__Type<PAIOType<double>,
> std::vector<InfoSur<double, Arete>*, std::allocator<InfoSur<double,
> Arete>*> > const>,
> FunctorAccesseurPorteurLocal<__PtrPorteurConst<Arete, Arete> >
> >(PAGroupeProcessus&, ompi_file_t*, long long,
> PtrPorteurConst<Arete, Arete>, PtrPorteurConst<Arete, Arete>,
> FunctorCopieInfosSurDansVectPA__Type<PAIOType<double>,
> std::vector<InfoSur<double, Arete>*, std::allocator<InfoSur<double,
> Arete>*> > const>&,
> FunctorAccesseurPorteurLocal<__PtrPorteurConst<Arete, Arete> >&,
> long, DistributionComposantes&, long, unsigned long, unsigned long,
> std::string const&) (in
> /home/mefpp_ericc/GIREF/bin/__Test.LectureEcritureGISMPI.__opt)
> ==19211== by 0x4E9A67:
> GISLectureEcriture<double>::__visiteMaillage(Maillage const&) (in
> /home/mefpp_ericc/GIREF/bin/__Test.LectureEcritureGISMPI.__opt)
> ==19211== by 0x4C79A2:
> GISLectureEcriture<double>::__ecritGISMPI(std::string,
> GroupeInfoSur<double> const&, std::string const&) (in
> /home/mefpp_ericc/GIREF/bin/__Test.LectureEcritureGISMPI.__opt)
> ==19211== by 0x4961AD: main (in
> /home/mefpp_ericc/GIREF/bin/__Test.LectureEcritureGISMPI.__opt)
> ==19211== Address 0x295af060 is 144 bytes inside a block of size
> 524,288 alloc'd
> ==19211== at 0x4C2C27B: malloc (in
> /usr/lib64/valgrind/vgpreload___memcheck-amd64-linux.so)
> ==19211== by 0x2745E78E: ADIOI_Malloc_fn (malloc.c:50)
> ==19211== by 0x2743757C: ADIOI_NFS_WriteStrided (ad_nfs_write.c:497)
> ==19211== by 0x27451963: ADIOI_GEN_WriteStridedColl
> (ad_write_coll.c:159)
> ==19211== by 0x274321BD: MPIOI_File_write_all_begin
> (write_allb.c:114)
> ==19211== by 0x27431DBF:
> mca_io_romio_dist_MPI_File___write_all_begin (write_allb.c:44)
> ==19211== by 0x2742A367: mca_io_romio_file_write_all___begin
> (io_romio_file_write.c:264)
> ==19211== by 0x12126520: PMPI_File_write_all_begin
> (pfile_write_all_begin.c:74)
> ==19211== by 0x4D7CFB: SYEnveloppeMessage<std::__string>
> PAIO::__ecritureIndexeParBlocMPI<__PAIOType<double>,
> PtrPorteurConst<Arete, Arete>,
> FunctorCopieInfosSurDansVectPA__Type<PAIOType<double>,
> std::vector<InfoSur<double, Arete>*, std::allocator<InfoSur<double,
> Arete>*> > const>,
> FunctorAccesseurPorteurLocal<__PtrPorteurConst<Arete, Arete> >
> >(PAGroupeProcessus&, ompi_file_t*, long long,
> PtrPorteurConst<Arete, Arete>, PtrPorteurConst<Arete, Arete>,
> FunctorCopieInfosSurDansVectPA__Type<PAIOType<double>,
> std::vector<InfoSur<double, Arete>*, std::allocator<InfoSur<double,
> Arete>*> > const>&,
> FunctorAccesseurPorteurLocal<__PtrPorteurConst<Arete, Arete> >&,
> long, DistributionComposantes&, long, unsigned long, unsigned long,
> std::string const&) (in
> /home/mefpp_ericc/GIREF/bin/__Test.LectureEcritureGISMPI.__opt)
> ==19211== by 0x4E9A67:
> GISLectureEcriture<double>::__visiteMaillage(Maillage const&) (in
> /home/mefpp_ericc/GIREF/bin/__Test.LectureEcritureGISMPI.__opt)
> ==19211== by 0x4C79A2:
> GISLectureEcriture<double>::__ecritGISMPI(std::string,
> GroupeInfoSur<double> const&, std::string const&) (in
> /home/mefpp_ericc/GIREF/bin/__Test.LectureEcritureGISMPI.__opt)
> ==19211== by 0x4961AD: main (in
> /home/mefpp_ericc/GIREF/bin/__Test.LectureEcritureGISMPI.__opt)
> ==19211== Uninitialised value was created by a heap allocation
> ==19211== at 0x4C2C27B: malloc (in
> /usr/lib64/valgrind/vgpreload___memcheck-amd64-linux.so)
> ==19211== by 0x2745E78E: ADIOI_Malloc_fn (malloc.c:50)
> ==19211== by 0x2743757C: ADIOI_NFS_WriteStrided (ad_nfs_write.c:497)
> ==19211== by 0x27451963: ADIOI_GEN_WriteStridedColl
> (ad_write_coll.c:159)
> ==19211== by 0x274321BD: MPIOI_File_write_all_begin
> (write_allb.c:114)
> ==19211== by 0x27431DBF:
> mca_io_romio_dist_MPI_File___write_all_begin (write_allb.c:44)
> ==19211== by 0x2742A367: mca_io_romio_file_write_all___begin
> (io_romio_file_write.c:264)
> ==19211== by 0x12126520: PMPI_File_write_all_begin
> (pfile_write_all_begin.c:74)
> ==19211== by 0x4D7CFB: SYEnveloppeMessage<std::__string>
> PAIO::__ecritureIndexeParBlocMPI<__PAIOType<double>,
> PtrPorteurConst<Arete, Arete>,
> FunctorCopieInfosSurDansVectPA__Type<PAIOType<double>,
> std::vector<InfoSur<double, Arete>*, std::allocator<InfoSur<double,
> Arete>*> > const>,
> FunctorAccesseurPorteurLocal<__PtrPorteurConst<Arete, Arete> >
> >(PAGroupeProcessus&, ompi_file_t*, long long,
> PtrPorteurConst<Arete, Arete>, PtrPorteurConst<Arete, Arete>,
> FunctorCopieInfosSurDansVectPA__Type<PAIOType<double>,
> std::vector<InfoSur<double, Arete>*, std::allocator<InfoSur<double,
> Arete>*> > const>&,
> FunctorAccesseurPorteurLocal<__PtrPorteurConst<Arete, Arete> >&,
> long, DistributionComposantes&, long, unsigned long, unsigned long,
> std::string const&) (in
> /home/mefpp_ericc/GIREF/bin/__Test.LectureEcritureGISMPI.__opt)
> ==19211== by 0x4E9A67:
> GISLectureEcriture<double>::__visiteMaillage(Maillage const&) (in
> /home/mefpp_ericc/GIREF/bin/__Test.LectureEcritureGISMPI.__opt)
> ==19211== by 0x4C79A2:
> GISLectureEcriture<double>::__ecritGISMPI(std::string,
> GroupeInfoSur<double> const&, std::string const&) (in
> /home/mefpp_ericc/GIREF/bin/__Test.LectureEcritureGISMPI.__opt)
> ==19211== by 0x4961AD: main (in
> /home/mefpp_ericc/GIREF/bin/__Test.LectureEcritureGISMPI.__opt)
> ==19211==
>
> Can't tell if it is a big issue or not, but I thought I should
> mention it to the list....
>
> We run without this valgrind error when I use my local disk
> partition instead of an nfs parition or if I run with only 1
> process (which always have something to write for each
> PMPI_File_write_all_begin) and write to an nfs partition.
>
> Using openmpi-1.8.4rc3 compiled in "debug" mode:
>
> ompi_info -all :
> http://www.giref.ulaval.ca/~__ericc/ompi_bug/ompi_info.all.__184rc3.txt.gz
> <http://www.giref.ulaval.ca/~ericc/ompi_bug/ompi_info.all.184rc3.txt.gz>
> config.log:
> http://www.giref.ulaval.ca/~__ericc/ompi_bug/config.184rc3.__log.gz
> <http://www.giref.ulaval.ca/~ericc/ompi_bug/config.184rc3.log.gz>
>
> Thanks,
>
> Eric
> _________________________________________________
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> Link to this post:
> http://www.open-mpi.org/__community/lists/devel/2014/12/__16691.php
> <http://www.open-mpi.org/community/lists/devel/2014/12/16691.php>
>
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