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