[mpich-discuss] BUG in ADIOI_NFS_WriteStrided

19 Dec 2014

      Hi Howard,

the bug is present also with MPICH-3.1.3...

So, for [email protected] 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
<[email protected]
<mailto:[email protected]>>:
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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