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.chamberl...@giref.ulaval.ca
<mailto:eric.chamberl...@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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