Eric,
here is a patch for the v1.8 series, it fixes a one byte overflow.
valgrind should stop complaining, and assuming this is the root cause of
the memory corruption,
that could also fix your program.
that being said, shared_fp_fname is limited to 255 characters (this is
hard coded) so even if
it gets truncated to 255 characters (instead of 256), the behavior could
be kind of random.
/* from ADIOI_Shfp_fname :
If the real file is /tmp/thakur/testfile, the shared-file-pointer
file will be /tmp/thakur/.testfile.shfp.xxxx, where xxxx is
FWIW, xxxx is a random number that takes between 1 and 10 characters
could you please give this patch a try and let us know the results ?
Cheers,
Gilles
On 2014/12/15 11:52, Eric Chamberland wrote:
> Hi again,
>
> some new hints that might help:
>
> 1- With valgrind : If I run the same test case, same data, but
> moved to a shorter path+filename, then *valgrind* does *not*
> complains!!!!!!
> 2- Without valgrind: *Sometimes*, the test case with long
> path+filename passes without "segfaulting"!
> 3- It seems to happen at the fourth file I try to open using the
> following described procedure:
>
> Also, I was wondering about this: In this 2 processes test case
> (running in the same node), I :
>
> 1- open the file collectively (which resides on the same ssd drive on
> my computer)
> 2- MPI_File_read_at_all a long int and 3 chars (11 bytes)
> 3- stop (because I detect I am not reading my MPIIO file format)
> 4- close the file
>
> A guess (FWIW): Can process rank 0, for example close the file too
> quickly, which destroys the string reserved for the filename that is
> used by process rank 1 which could be using shared memory on the same
> node?
>
> Thanks,
>
> Eric
>
> On 12/14/2014 02:06 PM, Eric Chamberland wrote:
>> Hi,
>>
>> I finally (thanks for fixing oversubscribing) tested with 1.8.4rc3 for
>> my problem with collective MPI I/O.
>>
>> A problem still there. In this 2 processes example, process rank 1
>> dies with segfault while process rank 0 wait indefinitely...
>>
>> Running with valgrind, I found these errors which may gives hints:
>>
>> *************************************************
>> Rank 1:
>> *************************************************
>> On process rank 1, without valgrind it ends with either a segmentation
>> violation or memory corruption or invalide free without valgrind).
>>
>> But running with valgrind, it tells:
>>
>> ==16715== Invalid write of size 2
>> ==16715== at 0x4C2E793: memcpy@@GLIBC_2.14 (vg_replace_strmem.c:915)
>> ==16715== by 0x1F60AA91: opal_convertor_unpack (opal_convertor.c:321)
>> ==16715== by 0x25AA8DD3: mca_pml_ob1_recv_frag_callback_match
>> (pml_ob1_recvfrag.c:225)
>> ==16715== by 0x2544110C: mca_btl_vader_check_fboxes
>> (btl_vader_fbox.h:220)
>> ==16715== by 0x25443577: mca_btl_vader_component_progress
>> (btl_vader_component.c:695)
>> ==16715== by 0x1F5F0F27: opal_progress (opal_progress.c:207)
>> ==16715== by 0x1ACB40B3: opal_condition_wait (condition.h:93)
>> ==16715== by 0x1ACB4201: ompi_request_wait_completion (request.h:381)
>> ==16715== by 0x1ACB4305: ompi_request_default_wait (req_wait.c:39)
>> ==16715== by 0x26BA2FFB: ompi_coll_tuned_bcast_intra_generic
>> (coll_tuned_bcast.c:254)
>> ==16715== by 0x26BA36F7: ompi_coll_tuned_bcast_intra_binomial
>> (coll_tuned_bcast.c:385)
>> ==16715== by 0x26B94289: ompi_coll_tuned_bcast_intra_dec_fixed
>> (coll_tuned_decision_fixed.c:258)
>> ==16715== by 0x1ACD55F2: PMPI_Bcast (pbcast.c:110)
>> ==16715== by 0x2FE1CC48: ADIOI_Shfp_fname (shfp_fname.c:67)
>> ==16715== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16715== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16715== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16715== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16715== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16715== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16715== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16715== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16715== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16715== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ==16715== Address 0x32ef3e50 is 0 bytes after a block of size 256
>> alloc'd
>> ==16715== at 0x4C2C5A4: malloc (vg_replace_malloc.c:296)
>> ==16715== by 0x2FE1C78E: ADIOI_Malloc_fn (malloc.c:50)
>> ==16715== by 0x2FE1C951: ADIOI_Shfp_fname (shfp_fname.c:25)
>> ==16715== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16715== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16715== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16715== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16715== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16715== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16715== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16715== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16715== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16715== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ...
>> ...
>> ==16715== Invalid write of size 1
>> ==16715== at 0x4C2E7BB: memcpy@@GLIBC_2.14 (vg_replace_strmem.c:915)
>> ==16715== by 0x1F60AA91: opal_convertor_unpack (opal_convertor.c:321)
>> ==16715== by 0x25AA8DD3: mca_pml_ob1_recv_frag_callback_match
>> (pml_ob1_recvfrag.c:225)
>> ==16715== by 0x2544110C: mca_btl_vader_check_fboxes
>> (btl_vader_fbox.h:220)
>> ==16715== by 0x25443577: mca_btl_vader_component_progress
>> (btl_vader_component.c:695)
>> ==16715== by 0x1F5F0F27: opal_progress (opal_progress.c:207)
>> ==16715== by 0x1ACB40B3: opal_condition_wait (condition.h:93)
>> ==16715== by 0x1ACB4201: ompi_request_wait_completion (request.h:381)
>> ==16715== by 0x1ACB4305: ompi_request_default_wait (req_wait.c:39)
>> ==16715== by 0x26BA2FFB: ompi_coll_tuned_bcast_intra_generic
>> (coll_tuned_bcast.c:254)
>> ==16715== by 0x26BA36F7: ompi_coll_tuned_bcast_intra_binomial
>> (coll_tuned_bcast.c:385)
>> ==16715== by 0x26B94289: ompi_coll_tuned_bcast_intra_dec_fixed
>> (coll_tuned_decision_fixed.c:258)
>> ==16715== by 0x1ACD55F2: PMPI_Bcast (pbcast.c:110)
>> ==16715== by 0x2FE1CC48: ADIOI_Shfp_fname (shfp_fname.c:67)
>> ==16715== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16715== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16715== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16715== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16715== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16715== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16715== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16715== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16715== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16715== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ==16715== Address 0x32ef3e60 is 16 bytes after a block of size 256
>> alloc'd
>> ==16715== at 0x4C2C5A4: malloc (vg_replace_malloc.c:296)
>> ==16715== by 0x2FE1C78E: ADIOI_Malloc_fn (malloc.c:50)
>> ==16715== by 0x2FE1C951: ADIOI_Shfp_fname (shfp_fname.c:25)
>> ==16715== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16715== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16715== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16715== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16715== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16715== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16715== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16715== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16715== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16715== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ==16715==
>>
>> *************************************************
>> Rank 0:
>> *************************************************
>>
>> ==16714== Invalid read of size 1
>> ==16714== at 0x4C2CA74: __strrchr_sse42 (vg_replace_strmem.c:194)
>> ==16714== by 0x2FE1CAB7: ADIOI_Shfp_fname (shfp_fname.c:51)
>> ==16714== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16714== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16714== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16714== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16714== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16714== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16714== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16714== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16714== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16714== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ==16714== Address 0x219377d0 is 0 bytes after a block of size 256
>> alloc'd
>> ==16714== at 0x4C2C5A4: malloc (vg_replace_malloc.c:296)
>> ==16714== by 0x2FE1C78E: ADIOI_Malloc_fn (malloc.c:50)
>> ==16714== by 0x2FE1C951: ADIOI_Shfp_fname (shfp_fname.c:25)
>> ==16714== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16714== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16714== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16714== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16714== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16714== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16714== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16714== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16714== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16714== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ==16714==
>> ...
>> ==16714== Invalid read of size 1
>> ==16714== at 0x4C2D034: strlen (vg_replace_strmem.c:412)
>> ==16714== by 0x2FE1CB81: ADIOI_Shfp_fname (shfp_fname.c:61)
>> ==16714== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16714== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16714== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16714== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16714== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16714== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16714== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16714== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16714== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16714== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ==16714== Address 0x219377d0 is 0 bytes after a block of size 256
>> alloc'd
>> ==16714== at 0x4C2C5A4: malloc (vg_replace_malloc.c:296)
>> ==16714== by 0x2FE1C78E: ADIOI_Malloc_fn (malloc.c:50)
>> ==16714== by 0x2FE1C951: ADIOI_Shfp_fname (shfp_fname.c:25)
>> ==16714== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16714== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16714== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16714== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16714== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16714== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16714== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16714== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16714== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16714== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ...
>> ==16714== Invalid read of size 2
>> ==16714== at 0x4C2E79E: memcpy@@GLIBC_2.14 (vg_replace_strmem.c:915)
>> ==16714== by 0x2543FADC: vader_prepare_src (btl_vader_module.c:590)
>> ==16714== by 0x25AB17AA: mca_bml_base_prepare_src (bml.h:341)
>> ==16714== by 0x25AB4207: mca_pml_ob1_send_request_start_prepare
>> (pml_ob1_sendreq.c:620)
>> ==16714== by 0x25AA3519: mca_pml_ob1_send_request_start_btl
>> (pml_ob1_sendreq.h:397)
>> ==16714== by 0x25AA3766: mca_pml_ob1_send_request_start_seq
>> (pml_ob1_sendreq.h:460)
>> ==16714== by 0x25AA41E1: mca_pml_ob1_isend (pml_ob1_isend.c:171)
>> ==16714== by 0x26BA2AF5: ompi_coll_tuned_bcast_intra_generic
>> (coll_tuned_bcast.c:112)
>> ==16714== by 0x26BA36F7: ompi_coll_tuned_bcast_intra_binomial
>> (coll_tuned_bcast.c:385)
>> ==16714== by 0x26B94289: ompi_coll_tuned_bcast_intra_dec_fixed
>> (coll_tuned_decision_fixed.c:258)
>> ==16714== by 0x1ACD55F2: PMPI_Bcast (pbcast.c:110)
>> ==16714== by 0x2FE1CBE5: ADIOI_Shfp_fname (shfp_fname.c:63)
>> ==16714== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16714== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16714== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16714== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16714== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16714== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16714== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16714== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16714== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16714== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ==16714== Address 0x219377d0 is 0 bytes after a block of size 256
>> alloc'd
>> ==16714== at 0x4C2C5A4: malloc (vg_replace_malloc.c:296)
>> ==16714== by 0x2FE1C78E: ADIOI_Malloc_fn (malloc.c:50)
>> ==16714== by 0x2FE1C951: ADIOI_Shfp_fname (shfp_fname.c:25)
>> ==16714== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16714== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16714== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16714== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16714== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16714== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16714== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16714== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16714== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16714== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ...
>> ==16714== Invalid read of size 2
>> ==16714== at 0x4C2E790: memcpy@@GLIBC_2.14 (vg_replace_strmem.c:915)
>> ==16714== by 0x2543FADC: vader_prepare_src (btl_vader_module.c:590)
>> ==16714== by 0x25AB17AA: mca_bml_base_prepare_src (bml.h:341)
>> ==16714== by 0x25AB4207: mca_pml_ob1_send_request_start_prepare
>> (pml_ob1_sendreq.c:620)
>> ==16714== by 0x25AA3519: mca_pml_ob1_send_request_start_btl
>> (pml_ob1_sendreq.h:397)
>> ==16714== by 0x25AA3766: mca_pml_ob1_send_request_start_seq
>> (pml_ob1_sendreq.h:460)
>> ==16714== by 0x25AA41E1: mca_pml_ob1_isend (pml_ob1_isend.c:171)
>> ==16714== by 0x26BA2AF5: ompi_coll_tuned_bcast_intra_generic
>> (coll_tuned_bcast.c:112)
>> ==16714== by 0x26BA36F7: ompi_coll_tuned_bcast_intra_binomial
>> (coll_tuned_bcast.c:385)
>> ==16714== by 0x26B94289: ompi_coll_tuned_bcast_intra_dec_fixed
>> (coll_tuned_decision_fixed.c:258)
>> ==16714== by 0x1ACD55F2: PMPI_Bcast (pbcast.c:110)
>> ==16714== by 0x2FE1CBE5: ADIOI_Shfp_fname (shfp_fname.c:63)
>> ==16714== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16714== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16714== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16714== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16714== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16714== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16714== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16714== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16714== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16714== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ==16714== Address 0x219377d2 is 2 bytes after a block of size 256
>> alloc'd
>> ==16714== at 0x4C2C5A4: malloc (vg_replace_malloc.c:296)
>> ==16714== by 0x2FE1C78E: ADIOI_Malloc_fn (malloc.c:50)
>> ==16714== by 0x2FE1C951: ADIOI_Shfp_fname (shfp_fname.c:25)
>> ==16714== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16714== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16714== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16714== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16714== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16714== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16714== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16714== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16714== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16714== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ...
>> ==16714== Invalid read of size 1
>> ==16714== at 0x4C2E7B8: memcpy@@GLIBC_2.14 (vg_replace_strmem.c:915)
>> ==16714== by 0x2543FADC: vader_prepare_src (btl_vader_module.c:590)
>> ==16714== by 0x25AB17AA: mca_bml_base_prepare_src (bml.h:341)
>> ==16714== by 0x25AB4207: mca_pml_ob1_send_request_start_prepare
>> (pml_ob1_sendreq.c:620)
>> ==16714== by 0x25AA3519: mca_pml_ob1_send_request_start_btl
>> (pml_ob1_sendreq.h:397)
>> ==16714== by 0x25AA3766: mca_pml_ob1_send_request_start_seq
>> (pml_ob1_sendreq.h:460)
>> ==16714== by 0x25AA41E1: mca_pml_ob1_isend (pml_ob1_isend.c:171)
>> ==16714== by 0x26BA2AF5: ompi_coll_tuned_bcast_intra_generic
>> (coll_tuned_bcast.c:112)
>> ==16714== by 0x26BA36F7: ompi_coll_tuned_bcast_intra_binomial
>> (coll_tuned_bcast.c:385)
>> ==16714== by 0x26B94289: ompi_coll_tuned_bcast_intra_dec_fixed
>> (coll_tuned_decision_fixed.c:258)
>> ==16714== by 0x1ACD55F2: PMPI_Bcast (pbcast.c:110)
>> ==16714== by 0x2FE1CBE5: ADIOI_Shfp_fname (shfp_fname.c:63)
>> ==16714== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16714== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16714== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16714== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16714== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16714== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16714== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16714== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16714== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16714== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ==16714== Address 0x219377e0 is 16 bytes after a block of size 256
>> alloc'd
>> ==16714== at 0x4C2C5A4: malloc (vg_replace_malloc.c:296)
>> ==16714== by 0x2FE1C78E: ADIOI_Malloc_fn (malloc.c:50)
>> ==16714== by 0x2FE1C951: ADIOI_Shfp_fname (shfp_fname.c:25)
>> ==16714== by 0x2FDEB493: mca_io_romio_dist_MPI_File_open (open.c:177)
>> ==16714== by 0x2FDE3B0D: mca_io_romio_file_open
>> (io_romio_file_open.c:40)
>> ==16714== by 0x1AD52344: module_init (io_base_file_select.c:455)
>> ==16714== by 0x1AD51DFA: mca_io_base_file_select
>> (io_base_file_select.c:238)
>> ==16714== by 0x1ACA582F: ompi_file_open (file.c:130)
>> ==16714== by 0x1AD30DA3: PMPI_File_open (pfile_open.c:94)
>> ==16714== by 0x13F9B36F:
>> PAIO::ouvreFichierMPIIO(PAGroupeProcessus&, std::string const&, int,
>> ompi_file_t*&, bool) (PAIO.cc:290)
>> ==16714== by 0xCA44252:
>> GISLectureEcriture<double>::litGISMPI(std::string,
>> GroupeInfoSur<double>&, std::string&) (GISLectureEcriture.icc:411)
>> ==16714== by 0xCA23F0D: Champ::importeParallele(std::string const&)
>> (Champ.cc:951)
>> ==16714== by 0x4D0DEE: main (Test.NormesEtProjectionChamp.cc:789)
>> ...
>>
>>
>> I have to precise that with MPICH 3.1.3, I can't reproduce the same
>> bad behavior.
>>
>> Also, the segfault is not always there: running the same code with
>> other inputs, gave me trouble-free results with or without valgrind.
>> I noticed the problem appears mors frequently with longer "paths".
>>
>> Please, help!
>>
>> Thanks,
>>
>> Eric
>>
>> ompi_info -all :
>> 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
>>
>> _______________________________________________
>> users mailing list
>> us...@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/2014/12/25983.php
>
> _______________________________________________
> users mailing list
> us...@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/2014/12/25986.php
diff --git a/ompi/mca/io/romio/romio/adio/common/shfp_fname.c
b/ompi/mca/io/romio/romio/adio/common/shfp_fname.c
index 024ced5..98ec101 100644
--- a/ompi/mca/io/romio/romio/adio/common/shfp_fname.c
+++ b/ompi/mca/io/romio/romio/adio/common/shfp_fname.c
@@ -2,6 +2,8 @@
/*
*
* Copyright (C) 1997 University of Chicago.
+ * Copyright (c) 2014 Research Organization for Information Science
+ * and Technology (RIST). All rights reserved.
* See COPYRIGHT notice in top-level directory.
*/
@@ -51,7 +53,7 @@ void ADIOI_Shfp_fname(ADIO_File fd, int rank)
slash = strrchr(fd->shared_fp_fname, '/');
#endif
ADIOI_Strncpy(slash + 1, ".", 2);
- len = 256 - (slash+2 - fd->shared_fp_fname);
+ len = 255 - (slash+2 - fd->shared_fp_fname);
ADIOI_Strncpy(slash + 2, ptr + 1, len);
}
