Hi Timothy, (sorry, I had the digest mode enabled and only saw your message after replying to Mark)
Thanks for your reply. How many processes did you try to run the program with? (I'm thinking at least 5, since "process rank 4" threw the error). Did you try different numbers of processes? Did the error happen with just a particular number of mpi tasks? Strange that you get a segfault and I get a deadlock. The error traceback may indeed be helpful, but unfortunately it is not meaningful to me. Any help you could give me debugging or understanding what's going on would be much appreciated. This is not a life-and-death situation, so tomorrow would be early enough :-) Cheers, Wolf > Date: Tue, 7 Apr 2015 17:18:35 +0000 > From: Timothy Brown <[email protected]> > To: HDF Users Discussion List <[email protected]> > Subject: Re: [Hdf-forum] parallel HDF5: H5Fclose hangs when not using > a power of 2 number of processes > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > Hi Wolf, > > It doesn't hang for me. I get a seg fault with the following traceback. > By the way, I'm using > - gcc 4.9.2 > - openmpi 1.8.4 > - szip 2.1 > - hdf5 1.8.14 > On a x86_64 linux machine. > > test.hangs: test.hangs.cpp:121: void writeH5(const char*, double*) [with T = > float]: Assertion `status_h5 >= 0' failed. > HDF5-DIAG: Error detected in HDF5 (1.8.14) MPI-process 0: > #000: H5F.c line 795 in H5Fclose(): decrementing file ID failed > major: Object atom > minor: Unable to close file > #001: H5I.c line 1475 in H5I_dec_app_ref(): can't decrement ID ref count > major: Object atom > minor: Unable to decrement reference count > #002: H5Fint.c line 1259 in H5F_close(): can't close file > major: File accessibilty > minor: Unable to close file > #003: H5Fint.c line 1421 in H5F_try_close(): problems closing file > major: File accessibilty > minor: Unable to close file > #004: H5Fint.c line 861 in H5F_dest(): low level truncate failed > major: File accessibilty > minor: Write failed > #005: H5FD.c line 1908 in H5FD_truncate(): driver truncate request failed > major: Virtual File Layer > minor: Can't update object > #006: H5FDmpio.c line 1982 in H5FD_mpio_truncate(): MPI_File_set_size failed > major: Internal error (too specific to document in detail) > minor: Some MPI function failed > #007: H5FDmpio.c line 1982 in H5FD_mpio_truncate(): MPI_ERR_ARG: invalid > argument of some other kind > major: Internal error (too specific to document in detail) > minor: MPI Error String > test.hangs: test.hangs.cpp:121: void writeH5(const char*, double*) [with T = > float]: Assertion `status_h5 >= 0' failed. > -------------------------------------------------------------------------- > mpiexec noticed that process rank 4 with PID 1158 on node node1446 exited on > signal 11 (Segmentation fault). > -------------------------------------------------------------------------- > > If you want I can try and help debug it, however I am flat out today, so it'd > have to wait till tomorrow. In the mean time, hope this error helps. > > Timoth -- _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
