December 2014 - discuss - mailman3.cels.anl.gov

Run R script via MPICH
by Riccardo Romoli 22 Dec '14

22 Dec '14

Hi my name is Riccardo, I have a linux cluster based on ubuntu with mpich2 installed. I try to run the examples: mpiexec.hydra -f hosts -n 4 /home/mpiuser/bin/cpi and all works. So I try to run a simple R script but I get an error: Syntax error: word unexpected How can I overcome this error? Regards, Riccardo _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] [OMPI devel] BUG in ADIOI_NFS_WriteStrided
by Eric Chamberland 21 Dec '14

21 Dec '14

On 12/19/2014 09:52 PM, Rob Latham wrote: > Please don't use NFS for MPI-IO. ROMIO makes a best effort but > there's no way to guarantee you won't corrupt a block of data (NFS Ok. But how can I know the type of filesystem my users will work on? For small jobs, they may have data on NFS and don't car too much for read/write speed... and I want only 1 file format that can be used on any filesystem... Do you recommend me to disable ROMIO/NFS support when configuring MPICH (how do you ask this to configure?)? What other library is recommend to use if I have to write distributed data on NFS? Does HDF5, for example, switches from MPI I/O to something else when doing collective I/O on NFS? I don't want to write a function to write to a file that depends on the final type of filesystem... I expect the library to do a good job for me... and I have chosen MPI I/O do to that job... ;-) > clients are allowed to cache... arbitrarily, it seems). There are so > many good parallel file systems with saner consistency semantics . Can't tell anything about how NFS is usable or not with MPI I/O... I Just use it because our nightly tests are writing results to NFS partitions... as our users may do... > > This looks like maybe a calloc would clean it right up. Ok, the point is: is there a bug, and can it be fixed (even if it is not recommended to use ROMIO/NFS) or at least tracked? Thanks! Eric _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] BUG in ADIOI_NFS_WriteStrided
by Rob Latham 19 Dec '14

19 Dec '14

On 12/19/2014 02:33 PM, Eric Chamberland wrote: > Hi Howard, > > the bug is present also with MPICH-3.1.3... > > So, for discuss(a)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. Please don't use NFS for MPI-IO. ROMIO makes a best effort but there's no way to guarantee you won't corrupt a block of data (NFS clients are allowed to cache... arbitrarily, it seems). There are so many good parallel file systems with saner consistency semantics . This looks like maybe a calloc would clean it right up. ==rob > > 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(a)giref.ulaval.ca >> <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 >> _________________________________________________ >> devel mailing list >> devel(a)open-mpi.org <mailto:[email protected]> >> Subscription: http://www.open-mpi.org/__mailman/listinfo.cgi/devel >> <http://www.open-mpi.org/mailman/listinfo.cgi/devel> >> 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> >> > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Rob Latham Mathematics and Computer Science Division Argonne National Lab, IL USA _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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BUG in ADIOI_NFS_WriteStrided
by Eric Chamberland 19 Dec '14

19 Dec '14

Hi Howard, the bug is present also with MPICH-3.1.3... So, for discuss(a)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(a)giref.ulaval.ca > <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 > _________________________________________________ > devel mailing list > devel(a)open-mpi.org <mailto:[email protected]> > Subscription: http://www.open-mpi.org/__mailman/listinfo.cgi/devel > <http://www.open-mpi.org/mailman/listinfo.cgi/devel> > 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> > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Fwd: Error Building MPICH
by Junchao Zhang 18 Dec '14

18 Dec '14

It is strange that the mpl library is not linked in your libmpi library. Could you make clean in your build directory and send us the output of "make V=1"? --Junchao Zhang On Thu, Dec 18, 2014 at 10:58 AM, Aaron Evans <aevans26(a)my.fau.edu> wrote: > > I tried to just configure and make in the source directory > > /users/login/ahe72/web/HarborBranch/mpif90/mpich-3.1.3 > > It gave me the same errors MPIR and MPL > > I have attached c.txt, m.txt and config.log in case you are able to help > > > On Thu, Dec 18, 2014 at 10:22 AM, Junchao Zhang <jczhang(a)mcs.anl.gov> > wrote: >> >> Hello, Aaron >> I looked at your log files as shown below. I don't know where the path >> "/users/login/ahe72/web/HarborBranch/*BuildDirectory*/mpich/src/mpl" >> comes from. >> >> <<config.log>> >> ../../mpif90/mpich-3.1.3/configure >> -prefix=/users/login/ahe72/web/HarborBranch/mpif90/install/ >> >> <<c.txt>> >> Configuring MPICH version 3.1.3 with >> '-prefix=/users/login/ahe72/web/HarborBranch/mpif90/install/' >> >> <<m.txt>> >> make[1]: Entering directory `/users12/domains/ >> tegasigns.com/web/HarborBranch/BuildDirectory/mpich' >> Making all in >> /users/login/ahe72/web/HarborBranch/BuildDirectory/mpich/src/mpl >> >> You can either try to clean up your build directory and build again, or >> try to build mpich directly in its source code directory, i.e., " >> ./configure --prefix=..." >> >> --Junchao Zhang >> >> ---------- Forwarded message ---------- >> From: Aaron Evans <aevans26(a)my.fau.edu> >> Date: Thu, Dec 18, 2014 at 8:28 AM >> Subject: Re: [mpich-discuss] Fwd: Error Building MPICH >> To: Junchao Zhang <jczhang(a)mcs.anl.gov> >> >> Mr Zhang, >> >> Thank you very much for your response. I have attached the config.log >> file. >> >> Aaron Evans >> >> On Wed, Dec 17, 2014 at 4:41 PM, Junchao Zhang <jczhang(a)mcs.anl.gov> >> wrote: >>> >>> Could you also send the config.log? >>> >>> --Junchao Zhang >>> >>> On Wed, Dec 17, 2014 at 2:33 PM, Aaron Evans <aevans26(a)my.fau.edu> >>> wrote: >>> >>>> I followed the install manual for MPICH ( >>>> http://www.mpich.org/static/downloads/3.1.3/mpich-3.1.3-installguide.pdf) >>>> and could not get it to build. It seemed to configure, but it did not build. >>>> >>>> I am attaching the c.txt and m.txt as instructed in manual. >>>> >>>> Thank you, >>>> Aaron Evans >>>> >>>> >>>> _______________________________________________ >>>> discuss mailing list discuss(a)mpich.org >>>> To manage subscription options or unsubscribe: >>>> https://lists.mpich.org/mailman/listinfo/discuss >>>> >>> _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Fwd: Error Building MPICH
by Junchao Zhang 18 Dec '14

18 Dec '14

Hello, Aaron I looked at your log files as shown below. I don't know where the path "/users/login/ahe72/web/HarborBranch/*BuildDirectory*/mpich/src/mpl" comes from. <<config.log>> ../../mpif90/mpich-3.1.3/configure -prefix=/users/login/ahe72/web/HarborBranch/mpif90/install/ <<c.txt>> Configuring MPICH version 3.1.3 with '-prefix=/users/login/ahe72/web/HarborBranch/mpif90/install/' <<m.txt>> make[1]: Entering directory `/users12/domains/ tegasigns.com/web/HarborBranch/BuildDirectory/mpich' Making all in /users/login/ahe72/web/HarborBranch/BuildDirectory/mpich/src/mpl You can either try to clean up your build directory and build again, or try to build mpich directly in its source code directory, i.e., " ./configure --prefix=..." --Junchao Zhang ---------- Forwarded message ---------- From: Aaron Evans <aevans26(a)my.fau.edu> Date: Thu, Dec 18, 2014 at 8:28 AM Subject: Re: [mpich-discuss] Fwd: Error Building MPICH To: Junchao Zhang <jczhang(a)mcs.anl.gov> Mr Zhang, Thank you very much for your response. I have attached the config.log file. Aaron Evans On Wed, Dec 17, 2014 at 4:41 PM, Junchao Zhang <jczhang(a)mcs.anl.gov> wrote: > > Could you also send the config.log? > > --Junchao Zhang > > On Wed, Dec 17, 2014 at 2:33 PM, Aaron Evans <aevans26(a)my.fau.edu> wrote: > >> I followed the install manual for MPICH ( >> http://www.mpich.org/static/downloads/3.1.3/mpich-3.1.3-installguide.pdf) >> and could not get it to build. It seemed to configure, but it did not build. >> >> I am attaching the c.txt and m.txt as instructed in manual. >> >> Thank you, >> Aaron Evans >> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] [OMPI users] OpenMPI 1.8.4rc3, 1.6.5 and 1.6.3: segmentation violation in mca_io_romio_dist_MPI_File_close
by Eric Chamberland 17 Dec '14

17 Dec '14

Hi! Here is a "poor man's fix" that works for me (the idea is not from me, thanks to Thomas H.): #1- char* lCwd = getcwd(0,0); #2- chdir(lPathToFile); #3- MPI_File_open(...,lFileNameWithoutTooLongPath,...); #4- chdir(lCwd); #5- ... I think there are some limitations but it works very well for our uses... and until a "real" fix is proposed... Thanks for helping! Eric On 12/15/2014 11:42 PM, Gilles Gouaillardet wrote: > Eric and all, > > That is clearly a limitation in romio, and this is being tracked at > https://trac.mpich.org/projects/mpich/ticket/2212 > > in the mean time, what we can do in OpenMPI is update > mca_io_romio_file_open() and fails with a user friendly error message > if strlen(filename) is larger that 225. > > Cheers, > > Gilles > > On 2014/12/16 12:43, Gilles Gouaillardet wrote: >> Eric, >> >> thanks for the simple test program. >> >> i think i see what is going wrong and i will make some changes to avoid >> the memory overflow. >> >> that being said, there is a hard coded limit of 256 characters, and your >> path is bigger than 300 characters. >> bottom line, and even if there is no more memory overflow, that cannot >> work as expected. >> >> i will report this to the mpich folks, since romio is currently imported >> from mpich. >> >> Cheers, >> >> Gilles >> >> On 2014/12/16 0:16, Eric Chamberland wrote: >>> Hi Gilles, >>> >>> just created a very simple test case! >>> >>> with this setup, you will see the bug with valgrind: >>> >>> export >>> too_long=./this/is/a_very/long/path/that/contains/a/not/so/long/filename/but/trying/to/collectively/mpi_file_open/it/you/will/have/a/memory/corruption/resulting/of/invalide/writing/or/reading/past/the/end/of/one/or/some/hidden/strings/in/mpio/Simple/user/would/like/to/have/the/parameter/checked/and/an/error/returned/or/this/limit/removed >>> >>> mpicc -o bug_MPI_File_open_path_too_long >>> bug_MPI_File_open_path_too_long.c >>> >>> mkdir -p $too_long >>> echo "header of a text file" > $too_long/toto.txt >>> >>> mpirun -np 2 valgrind ./bug_MPI_File_open_path_too_long >>> $too_long/toto.txt >>> >>> and watch the errors! >>> >>> unfortunately, the memory corruptions here doesn't seem to segfault >>> this simple test case, but in my case, it is fatal and with valgrind, >>> it is reported... >>> >>> OpenMPI 1.6.5, 1.8.3rc3 are affected >>> >>> MPICH-3.1.3 also have the error! >>> >>> thanks, >>> >>> Eric >>> >> _______________________________________________ >> users mailing list >> users(a)open-mpi.org >> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users >> Link to this post: http://www.open-mpi.org/community/lists/users/2014/12/26005.php > _______________________________________________ > users mailing list > users(a)open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: http://www.open-mpi.org/community/lists/users/2014/12/26006.php _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Fwd: Error Building MPICH
by Junchao Zhang 17 Dec '14

17 Dec '14

Could you also send the config.log? --Junchao Zhang On Wed, Dec 17, 2014 at 2:33 PM, Aaron Evans <aevans26(a)my.fau.edu> wrote: > > I followed the install manual for MPICH ( > http://www.mpich.org/static/downloads/3.1.3/mpich-3.1.3-installguide.pdf) > and could not get it to build. It seemed to configure, but it did not build. > > I am attaching the c.txt and m.txt as instructed in manual. > > Thank you, > Aaron Evans > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Problem installing and using MPE
by Fateme Hendijani 17 Dec '14

17 Dec '14

Thank you very much for all of your replies. finally, I used the version in https://wiki.mpich.org/mpich/index.php/MPE_by_example and could successfully execute both. Best, Fatemeh On Tue, Dec 16, 2014 at 2:59 PM, Balaji, Pavan <balaji(a)anl.gov> wrote: > > > Just to clarify -- MPE is a separate project than MPICH. We were > originally integrating it into the MPICH tarball as well. We now ditribute > it separately. > > -- Pavan > > > On Dec 16, 2014, at 9:07 AM, Lu, Huiwei <huiweilu(a)mcs.anl.gov> wrote: > > > > Hi, Fateme, > > > > Unfortunately MPICH has removed MPE support since 2012. > > > > If you want to log events for debugging, you can check > http://wiki.mpich.org/mpich/index.php/Debug_Event_Logging for an > alternative. > > If you want to profile MPI with event logging, you may want to take a > look at MPI Tool support ( > http://wiki.mpich.org/mpich/index.php/Tool_interfaces_(MPI-T),_MPICH_parame…) > or profiling tools like HPCToolkit and TAU that work with MPICH. > > > > Best, > > — > > Huiwei > > > >> On Dec 15, 2014, at 12:50 PM, Fateme Hendijani < > fateme.hendijani(a)gmail.com> wrote: > >> > >> Hello, > >> > >> I am a newbie in MPI. I have installed MPICH-3.0.4 on my virtual > machine, Ubuntu 14.04. It runs the cpi example and also compiles and runs > the sample Hello World example. > >> I need to create log files, using MPE. In the manuals, it is said that > the MPE is included in MPICH, however, it is not. Therefore, I have > installed the MPE2-1.3.0 with the following configuration options: > >> sudo ./configure –prefix=/path/to/install/ > --with-mpicc=/mirror/mpich2/bin/mpicc --with-mpilibs=-L/mirror/mpich2/lib/ > --with-mpiinc=-I/mirror/mpich2/include/ --disable-f77 –enable-mpe_graphics > –enable-mpedbg –enable-mpich –with-mpiio –enable-checkMPIwtime > >> > >> I had actually disabled the mpedbg, since while making, it went to a > loop that could not find it. > >> > >> While using make command, it gave me some errors and warnings like the > following. I have set the LD_LIBRARY_PATH and LIBRARY_PATH, but still > cannot create a log file. > >> > >> 1- I don't know which version of MPICH and MPE to use, and from where > to download (I have found and MPICH2 that has an MPE folder inside, > however, some libs seem to be missing) > >> > >> 2- I appreciate your help for installing. > >> > >> Thanks, > >> > >> Fatemeh > >> > >> > >> > >> In file included from log_mpi_core.c:6997:0: > >> log_mpi_io.c:1590:5: error: conflicting types for > ‘MPI_File_write_at_all_end’ > >> int MPI_File_write_at_all_end( MPI_File fh,void * buf,MPI_Status * > status ) > >> ^ > >> In file included from /mirror/mpich2/include/mpi.h:2121:0, > >> from log_mpi_core.c:10: > >> /mirror/mpich2/include/mpio.h:203:5: note: previous declaration of > ‘MPI_File_write_at_all_end’ was here > >> int MPI_File_write_at_all_end(MPI_File fh, const void *buf, MPI_Status > *status); > >> ^ > >> In file included from log_mpi_core.c:6997:0: > >> log_mpi_io.c:1689:5: error: conflicting types for > ‘MPI_File_write_all_begin’ > >> int MPI_File_write_all_begin( MPI_File fh,void * buf,int > count,MPI_Datatype datatype ) > >> ^ > >> In file included from /mirror/mpich2/include/mpi.h:2121:0, > >> from log_mpi_core.c:10: > >> /mirror/mpich2/include/mpio.h:207:5: note: previous declaration of > ‘MPI_File_write_all_begin’ was here > >> int MPI_File_write_all_begin(MPI_File fh, const void *buf, int count, > MPI_Datatype datatype) > >> ^ > >> In file included from log_mpi_core.c:6997:0: > >> log_mpi_io.c:1722:5: error: conflicting types for > ‘MPI_File_write_all_end’ > >> int MPI_File_write_all_end( MPI_File fh,void * buf,MPI_Status * > status ) > >> ^ > >> In file included from /mirror/mpich2/include/mpi.h:2121:0, > >> from log_mpi_core.c:10: > >> /mirror/mpich2/include/mpio.h:209:5: note: previous declaration of > ‘MPI_File_write_all_end’ was here > >> int MPI_File_write_all_end(MPI_File fh, const void *buf, MPI_Status > *status); > >> ^ > >> In file included from log_mpi_core.c:6997:0: > >> log_mpi_io.c:1821:5: error: conflicting types for > ‘MPI_File_write_ordered_begin’ > >> int MPI_File_write_ordered_begin( MPI_File fh,void * buf,int > count,MPI_Datatype datatype ) > >> ^ > >> In file included from /mirror/mpich2/include/mpi.h:2121:0, > >> from log_mpi_core.c:10: > >> /mirror/mpich2/include/mpio.h:213:5: note: previous declaration of > ‘MPI_File_write_ordered_begin’ was here > >> int MPI_File_write_ordered_begin(MPI_File fh, const void *buf, int > count, MPI_Datatype datatype) > >> ^ > >> In file included from log_mpi_core.c:6997:0: > >> log_mpi_io.c:1854:5: error: conflicting types for > ‘MPI_File_write_ordered_end’ > >> int MPI_File_write_ordered_end( MPI_File fh,void * buf,MPI_Status * > status ) > >> ^ > >> In file included from /mirror/mpich2/include/mpi.h:2121:0, > >> from log_mpi_core.c:10: > >> /mirror/mpich2/include/mpio.h:215:5: note: previous declaration of > ‘MPI_File_write_ordered_end’ was here > >> int MPI_File_write_ordered_end(MPI_File fh, const void *buf, MPI_Status > *status); > >> ^ > >> make[4]: *** [log_mpi_core.o] Error 1 > >> make[3]: *** [build_lib_bin] Error 2 > >> make[2]: *** [all] Error 2 > >> > >> **** Making src/graphics .... > >> make --no-print-directory build_lib_bin > >> cc -I.. -I../include -I/mirror/mpe2-1.3.0/include -I../../.. > -I../../../include -DMPE_NOMPI -o mpe_graphics.no -c mpe_graphics.c > >> cc -I.. -I../include -I/mirror/mpe2-1.3.0/include -I../../.. > -I../../../include -DMPE_NOMPI -o xcolor.no -c xcolor.c > >> cc -I.. -I../include -I/mirror/mpe2-1.3.0/include -I../../.. > -I../../../include -DMPE_NOMPI -o xframe.no -c xframe.c > >> cc -I.. -I../include -I/mirror/mpe2-1.3.0/include -I../../.. > -I../../../include -DMPE_NOMPI -o xinit.no -c xinit.c > >> cc -I.. -I../include -I/mirror/mpe2-1.3.0/include -I../../.. > -I../../../include -DMPE_NOMPI -o xwmap.no -c xwmap.c > >> cc -I.. -I../include -I/mirror/mpe2-1.3.0/include -I../../.. > -I../../../include -DMPE_NOMPI -o xmouse.no -c xmouse.c > >> cc -I.. -I../include -I/mirror/mpe2-1.3.0/include -I../../.. > -I../../../include -DMPE_NOMPI -o xkey.no -c xkey.c > >> /mirror/mpich2/bin/mpicc -I.. -I../include -I/mirror/mpe2-1.3.0/include > -I../../.. -I../../../include -I/mirror/mpich2/include/ -o > mpe_graphics.po -c mpe_graphics.c > >> /mirror/mpich2/bin/mpicc -I.. -I../include -I/mirror/mpe2-1.3.0/include > -I../../.. -I../../../include -I/mirror/mpich2/include/ -o xcolor.po -c > xcolor.c > >> /mirror/mpich2/bin/mpicc -I.. -I../include -I/mirror/mpe2-1.3.0/include > -I../../.. -I../../../include -I/mirror/mpich2/include/ -o xframe.po -c > xframe.c > >> /mirror/mpich2/bin/mpicc -I.. -I../include -I/mirror/mpe2-1.3.0/include > -I../../.. -I../../../include -I/mirror/mpich2/include/ -o xinit.po -c > xinit.c > >> /mirror/mpich2/bin/mpicc -I.. -I../include -I/mirror/mpe2-1.3.0/include > -I../../.. -I../../../include -I/mirror/mpich2/include/ -o xwmap.po -c > xwmap.c > >> /mirror/mpich2/bin/mpicc -I.. -I../include -I/mirror/mpe2-1.3.0/include > -I../../.. -I../../../include -I/mirror/mpich2/include/ -o xmouse.po -c > xmouse.c > >> /mirror/mpich2/bin/mpicc -I.. -I../include -I/mirror/mpe2-1.3.0/include > -I../../.. -I../../../include -I/mirror/mpich2/include/ -o xkey.po -c > xkey.c > >> /mirror/mpich2/bin/mpicc -I.. -I../include -I/mirror/mpe2-1.3.0/include > -I../../.. -I../../../include -I/mirror/mpich2/include/ -o > visual_mess.po -c visual_mess.c > >> visual_mess.c: In function ‘MPI_Bsend’: > >> visual_mess.c:325:8: error: argument ‘buf’ doesn’t match prototype > >> void * buf; > >> ^ > >> In file included from visual_mess.c:27:0: > >> /mirror/mpich2/include/mpi.h:847:5: error: prototype declaration > >> int MPI_Bsend(const void *buf, int count, MPI_Datatype datatype, int > dest, int tag, > >> ^ > >> visual_mess.c: In function ‘MPI_Bsend_init’: > >> visual_mess.c:349:8: error: argument ‘buf’ doesn’t match prototype > >> void * buf; > >> ^ > >> In file included from visual_mess.c:27:0: > >> /mirror/mpich2/include/mpi.h:884:5: error: prototype declaration > >> int MPI_Bsend_init(const void *buf, int count, MPI_Datatype datatype, > int dest, int tag, > >> ^ > >> visual_mess.c: In function ‘MPI_Send_init’: > >> visual_mess.c:445:8: error: argument ‘buf’ doesn’t match prototype > >> void * buf; > >> ^ > >> In file included from visual_mess.c:27:0: > >> /mirror/mpich2/include/mpi.h:882:5: error: prototype declaration > >> int MPI_Send_init(const void *buf, int count, MPI_Datatype datatype, > int dest, int tag, > >> ^ > >> visual_mess.c: In function ‘MPI_Ibsend’: > >> visual_mess.c:481:8: error: argument ‘buf’ doesn’t match prototype > >> void * buf; > >> ^ > >> In file included from visual_mess.c:27:0: > >> /mirror/mpich2/include/mpi.h:857:5: error: prototype declaration > >> int MPI_Ibsend(const void *buf, int count, MPI_Datatype datatype, int > dest, int tag, > >> ^ > >> visual_mess.c: In function ‘MPI_Irsend’: > >> visual_mess.c:546:8: error: argument ‘buf’ doesn’t match prototype > >> void * buf; > >> ^ > >> In file included from visual_mess.c:27:0: > >> /mirror/mpich2/include/mpi.h:861:5: error: prototype declaration > >> int MPI_Irsend(const void *buf, int count, MPI_Datatype datatype, int > dest, int tag, > >> ^ > >> visual_mess.c: In function ‘MPI_Isend’: > >> visual_mess.c:582:8: error: argument ‘buf’ doesn’t match prototype > >> void * buf; > >> ^ > >> In file included from visual_mess.c:27:0: > >> /mirror/mpich2/include/mpi.h:855:5: error: prototype declaration > >> int MPI_Isend(const void *buf, int count, MPI_Datatype datatype, int > dest, int tag, > >> ^ > >> visual_mess.c: In function ‘MPI_Issend’: > >> visual_mess.c:618:8: error: argument ‘buf’ doesn’t match prototype > >> void * buf; > >> ^ > >> In file included from visual_mess.c:27:0: > >> /mirror/mpich2/include/mpi.h:859:5: error: prototype declaration > >> int MPI_Issend(const void *buf, int count, MPI_Datatype datatype, int > dest, int tag, > >> ^ > >> visual_mess.c: In function ‘MPI_Rsend’: > >> visual_mess.c:679:8: error: argument ‘buf’ doesn’t match prototype > >> void * buf; > >> ^ > >> In file included from visual_mess.c:27:0: > >> /mirror/mpich2/include/mpi.h:851:5: error: prototype declaration > >> int MPI_Rsend(const void *buf, int count, MPI_Datatype datatype, int > dest, int tag, > >> ^ > >> visual_mess.c: In function ‘MPI_Rsend_init’: > >> visual_mess.c:703:8: error: argument ‘buf’ doesn’t match prototype > >> void * buf; > >> ^ > >> In file included from visual_mess.c:27:0: > >> /mirror/mpich2/include/mpi.h:888:5: error: prototype declaration > >> int MPI_Rsend_init(const void *buf, int count, MPI_Datatype datatype, > int dest, int tag, > >> ^ > >> visual_mess.c: In function ‘MPI_Send’: > >> visual_mess.c:739:8: error: argument ‘buf’ doesn’t match prototype > >> void * buf; > >> ^ > >> In file included from visual_mess.c:27:0: > >> /mirror/mpich2/include/mpi.h:842:5: error: prototype declaration > >> int MPI_Send(const void *buf, int count, MPI_Datatype datatype, int > dest, int tag, > >> ^ > >> visual_mess.c: In function ‘MPI_Sendrecv’: > >> visual_mess.c:763:8: error: argument ‘sendbuf’ doesn’t match prototype > >> void * sendbuf; > >> ^ > >> In file included from visual_mess.c:27:0: > >> /mirror/mpich2/include/mpi.h:894:5: error: prototype declaration > >> int MPI_Sendrecv(const void *sendbuf, int sendcount, MPI_Datatype > sendtype, int dest, > >> ^ > >> visual_mess.c: In function ‘MPI_Ssend’: > >> visual_mess.c:828:8: error: argument ‘buf’ doesn’t match prototype > >> void * buf; > >> ^ > >> In file included from visual_mess.c:27:0: > >> /mirror/mpich2/include/mpi.h:849:5: error: prototype declaration > >> int MPI_Ssend(const void *buf, int count, MPI_Datatype datatype, int > dest, int tag, > >> ^ > >> visual_mess.c: In function ‘MPI_Ssend_init’: > >> visual_mess.c:852:8: error: argument ‘buf’ doesn’t match prototype > >> void * buf; > >> ^ > >> In file included from visual_mess.c:27:0: > >> /mirror/mpich2/include/mpi.h:886:5: error: prototype declaration > >> int MPI_Ssend_init(const void *buf, int count, MPI_Datatype datatype, > int dest, int tag, > >> ^ > >> make[4]: *** [visual_mess.po] Error 1 > >> make[3]: *** [build_lib_bin] Error 2 > >> make[2]: *** [all] Error 2 > >> > >> **** Making src/collchk .... > >> make --no-print-directory build_lib_bin > >> make --no-print-directory /mirror/mpe2-1.3.0/lib/libmpe_collchk.a > >> /mirror/mpich2/bin/mpicc -I.. -I../include -I/mirror/mpe2-1.3.0/include > -I../../.. -I../../../include -I/mirror/mpich2/include/ -c begin.c > >> In file included from begin.c:5:0: > >> ../include/collchk.h:25:5: error: conflicting types for > ‘MPI_Add_error_string’ > >> int MPI_Add_error_string(int errorcode, char *string); > >> ^ > >> In file included from ../include/collchk.h:20:0, > >> from begin.c:5: > >> /mirror/mpich2/include/mpi.h:1157:5: note: previous declaration of > ‘MPI_Add_error_string’ was here > >> int MPI_Add_error_string(int errorcode, const char *string); > >> ^ > >> make[5]: *** [begin.o] Error 1 > >> make[4]: *** [default] Error 2 > >> make[3]: *** [build_lib_bin] Error 2 > >> make[2]: *** [all] Error 2 > >> > >> ...... > >> > >> make /mirror/mpe2-1.3.0/src/slog2sdk/trace_rlog/bin/rlog_print > >> cc -I.. -I/usr/lib/jvm/java-7-openjdk-amd64/include > -I/usr/lib/jvm/java-7-openjdk-amd64/include/linux > -I../../src/logformat/trace -g -O2 -c trace_input.c > >> cc -I.. -I/usr/lib/jvm/java-7-openjdk-amd64/include > -I/usr/lib/jvm/java-7-openjdk-amd64/include/linux > -I../../src/logformat/trace -g -O2 -c rlogutil.c > >> rlogutil.c: In function ‘RLOG_CreateInputStruct’: > >> rlogutil.c:107:7: warning: ignoring return value of ‘fread’, declared > with attribute warn_unused_result [-Wunused-result] > >> fread(&length, sizeof(int), 1, pInput->f); > >> ^ > >> rlogutil.c:159:11: warning: ignoring return value of ‘fread’, declared > with attribute warn_unused_result [-Wunused-result] > >> fread(&cur_rank, sizeof(int), 1, pInput->f); > >> ^ > >> rlogutil.c:167:11: warning: ignoring return value of ‘fread’, declared > with attribute warn_unused_result [-Wunused-result] > >> fread(&pInput->pNumEventRecursions[rank_index], sizeof(int), 1, > pInput->f); > >> > >> _______________________________________________ > >> discuss mailing list discuss(a)mpich.org > >> To manage subscription options or unsubscribe: > >> https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > -- > Pavan Balaji ✉️ > http://www.mcs.anl.gov/~balaji > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Fwd: Error Building MPICH
by Aaron Evans 17 Dec '14

17 Dec '14

I followed the install manual for MPICH ( http://www.mpich.org/static/downloads/3.1.3/mpich-3.1.3-installguide.pdf) and could not get it to build. It seemed to configure, but it did not build. I am attaching the c.txt and m.txt as instructed in manual. Thank you, Aaron Evans

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