k-Wave User Forum » Topic: kspaceFirstOrder3DC and HD5 issue when running on a cluster

k-Wave User Forum » Topic: kspaceFirstOrder3DC and HD5 issue when running on a cluster http://www.k-wave.org/forum/topic/kspacefirstorder3dc-and-hd5-issue-when-running-on-a-cluster Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 23:41:01 +0000 http://bbpress.org/?v=1.0.2 <![CDATA[Search]]> q http://www.k-wave.org/forum/search.php ellianarv on "kspaceFirstOrder3DC and HD5 issue when running on a cluster" http://www.k-wave.org/forum/topic/kspacefirstorder3dc-and-hd5-issue-when-running-on-a-cluster#post-8462 Wed, 23 Feb 2022 22:37:56 +0000 ellianarv 8462@http://www.k-wave.org/forum/ Hi! I'm running a kspaceFirstOrder3DC simulation on a DIRAC cluster. I keep getting the following error. Does anyone have any advice? I'm new to MATLAB and k-Wave. Error using hdf5lib2 The HDF5 library encountered an error and produced the following stack trace information: H5FD_sec2_write file write failed: time = Wed Feb 23 16:28:02 2022 , filename = '/tmp/kwave_input_data23-Feb-2022-16-27-32.h5', file descriptor = 848, errno = 28, error message = 'No space left on device', buf = 0x2aaadc8cdc90, total write size = 96, bytes this sub-write = 96, bytes actually written = 18446744073709551615, offset = 0 H5FD_write driver write request failed H5F_sblock_flush unable to write superblock H5C_flush_single_entry unable to flush entry H5C_flush_cache dirty pinned entry flush failed. H5AC_flush Can't flush cache. H5F_flush unable to flush metadata cache H5F_dest unable to flush cache H5FD_sec2_write file write failed: time = Wed Feb 23 16:28:02 2022 , filename = '/tmp/kwave_input_data23-Feb-2022-16-27-32.h5', file descriptor = 848, errno = 28, error message = 'No space left on device', buf = 0x2aaadc8cdcc0, total write size = 96, bytes this sub-write = 96, bytes actually written = 18446744073709551615, offset = 0 H5FD_write driver write request failed H5F_sblock_flush unable to write superblock H5C_flush_single_entry unable to flush entry H5C_flush_invalidate_cache dirty entry flush destroy failed. H5C_dest unable to flush cache H5AC_dest can't destroy cache H5F_dest problems closing file H5F_try_close problems closing file H5F_close can't close file H5I_dec_app_ref can't decrement ID ref count H5Fclose decrementing file ID failed Error in H5ML.id/close (line 47) H5ML.hdf5lib2(obj.callback, obj.identifier); Error in H5ML.id/delete (line 36) obj.close(); Error in h5create>create_dataset (line 160) function create_dataset(options) Error in h5create (line 85) create_dataset(options); Error in writeMatrix (line 197) h5create(filename,['/' matrix_name], [Nx, Ny, Nz], ... Error in kspaceFirstOrder_saveToDisk (line 462) writeMatrix(flags.save_to_disk, eval(variable_list{cast_index}), variable_list{cast_index}, hdf_compression_level); Error in kspaceFirstOrder3D (line 673) kspaceFirstOrder_saveToDisk; Error in kspaceFirstOrder3DC (line 532) eval(run_string); Error in Simscript_EV (line 142) sensor_data = kspaceFirstOrder3DC(kgrid, medium, source, sensor, input_args{:}); > In h5create>create_dataset (line 160) In h5create (line 85) In writeMatrix (line 197) In kspaceFirstOrder_saveToDisk (line 462) In kspaceFirstOrder3D (line 673) In kspaceFirstOrder3DC (line 532) In Simscript_EV (line 142) Error using h5write (line 85) The file '/tmp/kwave_input_data23-Feb-2022-16-27-32.h5' is not an HDF5 file. Error in writeMatrix (line 204) h5write(filename, ['/' matrix_name], matrix); Error in kspaceFirstOrder_saveToDisk (line 462) writeMatrix(flags.save_to_disk, eval(variable_list{cast_index}), variable_list{cast_index}, hdf_compression_level); Error in kspaceFirstOrder3D (line 673) kspaceFirstOrder_saveToDisk; Error in kspaceFirstOrder3DC (line 532) eval(run_string); Error in Simscript_EV (line 142) sensor_data = kspaceFirstOrder3DC(kgrid, medium, source, sensor, input_args{:}); -------------------------------------------------------------------------------- Segmentation violation detected at Wed Feb 23 16:28:11 2022 -0500 -------------------------------------------------------------------------------- Configuration: Crash Decoding : Disabled - No sandbox or build area path Crash Mode : continue (default) Default Encoding : UTF-8 Deployed : false GNU C Library : 2.17 stable Graphics Driver : Unknown software Java Version : Java 1.8.0_152-b16 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode MATLAB Architecture : glnxa64 MATLAB Entitlement ID : 7561268 MATLAB Root : /opt/apps/software/MATLAB/2018b MATLAB Version : 9.5.0.944444 (R2018b) OpenGL : software Operating System : "Red Hat Enterprise Linux Server release 7.4 (Maipo)" Process ID : 215868 Processor ID : x86 Family 6 Model 85 Stepping 4, GenuineIntel Session Key : ecc18c09-d128-4e3c-950c-47a0564dd806 Static TLS mitigation : Disabled: Unable to open display Window System : No active display Fault Count: 1 Abnormal termination Register State (from fault): RAX = 0000000000000000 RBX = 00002aad41472080 RCX = 0000000000000000 RDX = 00002aad46412420 RSP = 00007fffffffbbc0 RBP = 0000000000000000 RSI = 00002aad414865d0 RDI = 00002aad41472080 R8 = 0000000000000001 R9 = 00007fffffffbc63 R10 = 0000000000000002 R11 = 0000000000000073 R12 = 0000000000000000 R13 = 0000000000000064 R14 = 00002aaae304a9f0 R15 = 00002aad41489280 RIP = 00002aad4600c30c EFL = 0000000000010206 CS = 0033 FS = 0000 GS = 0000 Stack Trace (from fault): [ 0] 0x00002aad4600c30c /opt/apps/software/MATLAB/2018b/bin/glnxa64/libhdf5.so.8+00656140 [ 1] 0x00002aad46070b27 /opt/apps/software/MATLAB/2018b/bin/glnxa64/libhdf5.so.8+01067815 H5I_clear_type+00000295 [ 2] 0x00002aad46008ab6 /opt/apps/software/MATLAB/2018b/bin/glnxa64/libhdf5.so.8+00641718 H5F_term_interface+00000086 [ 3] 0x00002aad45fa6e8e /opt/apps/software/MATLAB/2018b/bin/glnxa64/libhdf5.so.8+00241294 [ 4] 0x00002aaaac60ba69 /lib64/libc.so.6+00232041 [ 5] 0x00002aaaac60bab5 /lib64/libc.so.6+00232117 [ 6] 0x00002aaaac5f4c0c /lib64/libc.so.6+00138252 __libc_start_main+00000252 [ 7] 0x00000000004071ba /opt/apps/software/MATLAB/2018b/bin/glnxa64/MATLAB+00029114 [ 8] 0x0000000000000000 <unknown-module>+00000000 ** This crash report has been saved to disk as /home/ellianarv/matlab_crash_dump.215868-1 ** MATLAB is exiting because of fatal error /cm/local/apps/slurm/var/spool/job97698/slurm_script: line 19: 215868 Killed matlab -nodisplay -nosplash -r "Simscript_EV" -logfile /home/ellianarv/log/simscript_matlab.log