Hi there,
I have encountered the same problem with HDF 1.12.0, but not with 1.10.6. I added to the minimal C program from Crash when writing parallel compressed chunks to reproduce the problem. I hope this helps:
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "hdf5.h"
#define _MPI
//#define _DSET2
//#define _COMPRESS
#define _FILTER
#define NPROC 4
#define NDIM 2
#define CHUNK0 4
// Equivalent to original gist
// Works on 1.10.5 with patch, crashes on 1.10.5 vanilla and hangs on 1.10.6
#define CHUNK1 32768
#define NCHUNK1 32
// Works on 1.10.5 with and without patch and 1.10.6
//#define CHUNK1 256
//#define NCHUNK1 8192
// Works on 1.10.5 with and without patch and 1.10.6
//#define CHUNK1 512
//#define NCHUNK1 8192
// Crashes on 1.10.5 with and without patch, 1.10.6 and 1.12.0
//#define CHUNK1 256
//#define NCHUNK1 16384
// 3 dimensional example
//#define NDIM 3
//#define CHUNK0 16
//#define NCHUNK1 28
//#define CHUNK1 256
//#define NCHUNK2 4096/128
//#define CHUNK2 128
#ifdef _FILTER
#define TEST_FILTER 305
size_t
minimal_filter(unsigned int flags, size_t cd_nelmts,
const unsigned int cd_values[], size_t nbytes,
size_t *buf_size, void **buf)
{
// memcpy the input buffer and free it
void* out_buf = malloc(*buf_size);
memcpy((char*)(*buf), out_buf, nbytes);
free(*buf);
*buf = out_buf;
out_buf = NULL;
return nbytes;
}
H5Z_class_t minimal_H5Filter[1] = {{
H5Z_CLASS_T_VERS,
(H5Z_filter_t)(TEST_FILTER),
1, 1,
"minimal test filter",
NULL,
NULL,
(H5Z_func_t)(minimal_filter)
}};
#endif
int main(int argc, char **argv) {
int mpi_size = 1, mpi_rank = 0;
hid_t fapl_id, file_id, dset_space, dcpl_id, ds, ds2, propid, mem_dspace, sel_dspace;
fapl_id = H5Pcreate(H5P_FILE_ACCESS);
#ifdef _MPI
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
MPI_Init(&argc, &argv);
MPI_Comm_size(comm, &mpi_size);
MPI_Comm_rank(comm, &mpi_rank);
H5Pset_fapl_mpio(fapl_id, comm, info);
#endif
printf("MPI rank [%i/%i]\n", mpi_rank, mpi_size);
printf("rank=%i creating file\n", mpi_rank);
file_id = H5Fcreate("test1.h5", H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id);
H5Pclose(fapl_id);
// Define total dataset size
#if NDIM==3
hsize_t dset_dims[NDIM] = {NPROC * CHUNK0, CHUNK1 * NCHUNK1, CHUNK2 * NCHUNK2};
#elif NDIM==2
hsize_t dset_dims[NDIM] = {NPROC * CHUNK0, CHUNK1 * NCHUNK1};
#else
return 0;
#endif
dset_space = H5Screate_simple (NDIM, dset_dims, NULL);
dcpl_id = H5Pcreate(H5P_DATASET_CREATE);
#ifdef _FILTER
// register and set minimal test filter
herr_t status = H5Zregister(minimal_H5Filter);
if (status < 0) {
printf("Failed to register filter. code %i\n", status);
return 1;
}
status = H5Pset_filter(dcpl_id, TEST_FILTER, 0, 0, NULL);
if (status < 0) {
printf("Failed to set filter. code %i\n", status);
return 1;
}
#endif
// Set chunking and compression params
#if NDIM==3
hsize_t chunk_dims[NDIM] = {CHUNK0, CHUNK1, CHUNK2};
#elif NDIM==2
hsize_t chunk_dims[NDIM] = {CHUNK0, CHUNK1};
#else
return 0;
#endif
H5Pset_chunk(dcpl_id, NDIM, chunk_dims);
#ifdef _COMPRESS
H5Pset_deflate(dcpl_id, 9);
#endif
// Define selection
#if NDIM==3
hsize_t sel_dims[NDIM] = {CHUNK0, CHUNK1 * NCHUNK1, CHUNK2 * NCHUNK2};
hsize_t offset[NDIM] = {mpi_rank * sel_dims[0], 0, 0};
printf("rank=%i creating selection [%llu:%llu, %llu:%llu, %llu:%llu]\n",
mpi_rank, offset[0], offset[0] + sel_dims[0], offset[1], offset[1] + sel_dims[1], offset[2], offset[2] + sel_dims[2]);
#elif NDIM==2
hsize_t sel_dims[NDIM] = {CHUNK0, CHUNK1 * NCHUNK1};
hsize_t offset[NDIM] = {mpi_rank * sel_dims[0], 0};
printf("rank=%i creating selection [%llu:%llu, %llu:%llu]\n",
mpi_rank, offset[0], offset[0] + sel_dims[0], offset[1], offset[1] + sel_dims[1]);
#else
return 0;
#endif
sel_dspace = H5Screate_simple(NDIM, dset_dims, NULL);
H5Sselect_hyperslab(sel_dspace, H5S_SELECT_SET,
offset, NULL, sel_dims, NULL);
// Set the dspace for the input data
mem_dspace = H5Screate_simple (NDIM, sel_dims, NULL);
propid = H5Pcreate(H5P_DATASET_XFER);
#ifdef _MPI
H5Pset_dxpl_mpio(propid, H5FD_MPIO_COLLECTIVE);
#endif
// Create the dataset
printf("rank=%i creating dataset1\n", mpi_rank);
ds = H5Dcreate (file_id, "dset1", H5T_NATIVE_FLOAT, dset_space, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
// Create array of data to write
// Initialise with random data.
#if NDIM==3
int totalsize = sel_dims[0] * sel_dims[1] * sel_dims[2];
#elif NDIM==2
int totalsize = sel_dims[0] * sel_dims[1];
#else
return 0;
#endif
float *data = (float *)malloc(sizeof(float) * totalsize);
for(int i = 0; i < totalsize; i++) {
data[i] = (float)drand48();
}
printf("rank=%i writing dataset1\n", mpi_rank);
H5Dwrite(ds, H5T_NATIVE_FLOAT, mem_dspace, sel_dspace, propid, data);
printf("rank=%i finished writing dataset1\n", mpi_rank);
#ifdef _DSET2
// Create the dataset
printf("rank=%i creating dataset2\n", mpi_rank);
ds2 = H5Dcreate (file_id, "dset2", H5T_NATIVE_FLOAT, dset_space, H5P_DEFAULT, dcpl_id, H5P_DEFAULT);
// Generate new data and write
printf("rank=%i writing dataset2\n", mpi_rank);
for(int i = 0; i < totalsize; i++) {
data[i] = drand48();
}
H5Dwrite(ds2, H5T_NATIVE_FLOAT, mem_dspace, sel_dspace, propid, data);
H5Dclose(ds2);
#endif
// Close down everything
printf("rank=%i closing everything\n", mpi_rank);
H5Dclose(ds);
H5Sclose(dset_space);
H5Sclose(sel_dspace);
H5Sclose(mem_dspace);
H5Pclose(dcpl_id);
H5Pclose(propid);
H5Fclose(file_id);
free(data);
MPI_Finalize();
return 0;
}
This is the output with the address sanitizer enabled:
MPI rank [0/4]
rank=0 creating file
MPI rank [1/4]
rank=1 creating file
MPI rank [2/4]
rank=2 creating file
MPI rank [3/4]
rank=3 creating file
rank=0 creating selection [0:16, 0:7168, 0:4096]
rank=0 creating dataset1
rank=1 creating selection [16:32, 0:7168, 0:4096]
rank=2 creating selection [32:48, 0:7168, 0:4096]
rank=3 creating selection [48:64, 0:7168, 0:4096]
rank=2 creating dataset1
rank=1 creating dataset1
rank=3 creating dataset1
=================================================================
==135802==ERROR: AddressSanitizer: attempting free on address which was not malloc()-ed: 0x2afbfd586830 in thread T0
=================================================================
==135803==ERROR: AddressSanitizer: attempting free on address which was not malloc()-ed: 0x2b5022fa9830 in thread T0
=================================================================
=================================================================
==135805==ERROR: AddressSanitizer: attempting free on address which was not malloc()-ed: 0x2b9116cf3830 in thread T0
==135804==ERROR: AddressSanitizer: attempting free on address which was not malloc()-ed: 0x2b2d6adf3830 in thread T0
#0 0x2afbf0f9d487 in free (/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libasan.so.5+0x106487)
#1 0x428c4e in minimal_filter /scratch/rickn/test_hdf5/test_filter.c:35
#2 0x739ef3 in H5Z_pipeline /scratch/rickn/hdf5/src/H5Z.c:1366
#0 0x2b2d5e80c487 in free (/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libasan.so.5+0x106487)
#0 0x2b910a707487 in free (/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libasan.so.5+0x106487)
#0 0x2b50169bc487 in free (/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libasan.so.5+0x106487)
#1 0x428c4e in minimal_filter /scratch/rickn/test_hdf5/test_filter.c:35
#1 0x428c4e in minimal_filter /scratch/rickn/test_hdf5/test_filter.c:35
#1 0x428c4e in minimal_filter /scratch/rickn/test_hdf5/test_filter.c:35
#2 0x739ef3 in H5Z_pipeline /scratch/rickn/hdf5/src/H5Z.c:1366
#2 0x739ef3 in H5Z_pipeline /scratch/rickn/hdf5/src/H5Z.c:1366
#2 0x739ef3 in H5Z_pipeline /scratch/rickn/hdf5/src/H5Z.c:1366
#3 0x789f89 in H5D__chunk_allocate /scratch/rickn/hdf5/src/H5Dchunk.c:4473
#3 0x789f89 in H5D__chunk_allocate /scratch/rickn/hdf5/src/H5Dchunk.c:4473
#3 0x789f89 in H5D__chunk_allocate /scratch/rickn/hdf5/src/H5Dchunk.c:4473
#3 0x789f89 in H5D__chunk_allocate /scratch/rickn/hdf5/src/H5Dchunk.c:4473
#4 0x4ae27f in H5D__init_storage /scratch/rickn/hdf5/src/H5Dint.c:2473
#5 0x4b3d31 in H5D__alloc_storage /scratch/rickn/hdf5/src/H5Dint.c:2386
#6 0x4bc06e in H5D__layout_oh_create /scratch/rickn/hdf5/src/H5Dlayout.c:507
#7 0x4ad1c4 in H5D__update_oh_info /scratch/rickn/hdf5/src/H5Dint.c:1070
#8 0x4afa39 in H5D__create /scratch/rickn/hdf5/src/H5Dint.c:1373
#9 0x79e984 in H5O__dset_create /scratch/rickn/hdf5/src/H5Doh.c:300
#4 0x4ae27f in H5D__init_storage /scratch/rickn/hdf5/src/H5Dint.c:2473
#4 0x4ae27f in H5D__init_storage /scratch/rickn/hdf5/src/H5Dint.c:2473
#4 0x4ae27f in H5D__init_storage /scratch/rickn/hdf5/src/H5Dint.c:2473
#5 0x4b3d31 in H5D__alloc_storage /scratch/rickn/hdf5/src/H5Dint.c:2386
#5 0x4b3d31 in H5D__alloc_storage /scratch/rickn/hdf5/src/H5Dint.c:2386
#5 0x4b3d31 in H5D__alloc_storage /scratch/rickn/hdf5/src/H5Dint.c:2386
#6 0x4bc06e in H5D__layout_oh_create /scratch/rickn/hdf5/src/H5Dlayout.c:507
#6 0x4bc06e in H5D__layout_oh_create /scratch/rickn/hdf5/src/H5Dlayout.c:507
#6 0x4bc06e in H5D__layout_oh_create /scratch/rickn/hdf5/src/H5Dlayout.c:507
#7 0x4ad1c4 in H5D__update_oh_info /scratch/rickn/hdf5/src/H5Dint.c:1070
#8 0x4afa39 in H5D__create /scratch/rickn/hdf5/src/H5Dint.c:1373
#7 0x4ad1c4 in H5D__update_oh_info /scratch/rickn/hdf5/src/H5Dint.c:1070
#8 0x4afa39 in H5D__create /scratch/rickn/hdf5/src/H5Dint.c:1373
#7 0x4ad1c4 in H5D__update_oh_info /scratch/rickn/hdf5/src/H5Dint.c:1070
#10 0x5b62df in H5O_obj_create /scratch/rickn/hdf5/src/H5Oint.c:2521
#8 0x4afa39 in H5D__create /scratch/rickn/hdf5/src/H5Dint.c:1373
#9 0x79e984 in H5O__dset_create /scratch/rickn/hdf5/src/H5Doh.c:300
#9 0x79e984 in H5O__dset_create /scratch/rickn/hdf5/src/H5Doh.c:300
#9 0x79e984 in H5O__dset_create /scratch/rickn/hdf5/src/H5Doh.c:300
#10 0x5b62df in H5O_obj_create /scratch/rickn/hdf5/src/H5Oint.c:2521
#11 0x57ef66 in H5L__link_cb /scratch/rickn/hdf5/src/H5L.c:1850
#10 0x5b62df in H5O_obj_create /scratch/rickn/hdf5/src/H5Oint.c:2521
#10 0x5b62df in H5O_obj_create /scratch/rickn/hdf5/src/H5Oint.c:2521
#12 0x540a49 in H5G__traverse_real /scratch/rickn/hdf5/src/H5Gtraverse.c:629
#13 0x5416c8 in H5G_traverse /scratch/rickn/hdf5/src/H5Gtraverse.c:854
#14 0x5781d7 in H5L__create_real /scratch/rickn/hdf5/src/H5L.c:2044
#15 0x580cfd in H5L_link_object /scratch/rickn/hdf5/src/H5L.c:1803
#16 0x4aed95 in H5D__create_named /scratch/rickn/hdf5/src/H5Dint.c:410
#17 0x728b3d in H5VL__native_dataset_create /scratch/rickn/hdf5/src/H5VLnative_dataset.c:74
#11 0x57ef66 in H5L__link_cb /scratch/rickn/hdf5/src/H5L.c:1850
#11 0x57ef66 in H5L__link_cb /scratch/rickn/hdf5/src/H5L.c:1850
#11 0x57ef66 in H5L__link_cb /scratch/rickn/hdf5/src/H5L.c:1850
#12 0x540a49 in H5G__traverse_real /scratch/rickn/hdf5/src/H5Gtraverse.c:629
#12 0x540a49 in H5G__traverse_real /scratch/rickn/hdf5/src/H5Gtraverse.c:629
#13 0x5416c8 in H5G_traverse /scratch/rickn/hdf5/src/H5Gtraverse.c:854
#14 0x5781d7 in H5L__create_real /scratch/rickn/hdf5/src/H5L.c:2044
#13 0x5416c8 in H5G_traverse /scratch/rickn/hdf5/src/H5Gtraverse.c:854
#12 0x540a49 in H5G__traverse_real /scratch/rickn/hdf5/src/H5Gtraverse.c:629
#15 0x580cfd in H5L_link_object /scratch/rickn/hdf5/src/H5L.c:1803
#14 0x5781d7 in H5L__create_real /scratch/rickn/hdf5/src/H5L.c:2044
#15 0x580cfd in H5L_link_object /scratch/rickn/hdf5/src/H5L.c:1803
#16 0x4aed95 in H5D__create_named /scratch/rickn/hdf5/src/H5Dint.c:410
#13 0x5416c8 in H5G_traverse /scratch/rickn/hdf5/src/H5Gtraverse.c:854
#16 0x4aed95 in H5D__create_named /scratch/rickn/hdf5/src/H5Dint.c:410
#14 0x5781d7 in H5L__create_real /scratch/rickn/hdf5/src/H5L.c:2044
#15 0x580cfd in H5L_link_object /scratch/rickn/hdf5/src/H5L.c:1803
#16 0x4aed95 in H5D__create_named /scratch/rickn/hdf5/src/H5Dint.c:410
#17 0x728b3d in H5VL__native_dataset_create /scratch/rickn/hdf5/src/H5VLnative_dataset.c:74
#17 0x728b3d in H5VL__native_dataset_create /scratch/rickn/hdf5/src/H5VLnative_dataset.c:74
#17 0x728b3d in H5VL__native_dataset_create /scratch/rickn/hdf5/src/H5VLnative_dataset.c:74
#18 0x708ac5 in H5VL__dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1834
#19 0x7115ae in H5VL_dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1868
#20 0x4a3322 in H5Dcreate2 /scratch/rickn/hdf5/src/H5D.c:150
#21 0x4295bd in main /scratch/rickn/test_hdf5/test_filter.c:122
#22 0x2afbf28ac2df in __libc_start_main (/cvmfs/soft.computecanada.ca/nix/store/63pk88rnmkzjblpxydvrmskkc8ci7cx6-glibc-2.24/lib/libc.so.6+0x202df)
#23 0x428b09 in _start (/scratch/rickn/test_hdf5/testh5+0x428b09)
0x2afbfd586830 is located 48 bytes inside of 2097208-byte region [0x2afbfd586800,0x2afbfd786838)
allocated by thread T0 here:
#0 0x2afbf0f9d838 in malloc (/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libasan.so.5+0x106838)
#18 0x708ac5 in H5VL__dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1834
#1 0x5903a1 in H5MM_malloc /scratch/rickn/hdf5/src/H5MM.c:292
#19 0x7115ae in H5VL_dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1868
#18 0x708ac5 in H5VL__dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1834
#2 0x77bc3f in H5D__chunk_mem_alloc /scratch/rickn/hdf5/src/H5Dchunk.c:1404
#19 0x7115ae in H5VL_dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1868
#18 0x708ac5 in H5VL__dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1834
#19 0x7115ae in H5VL_dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1868
#3 0x79de6d in H5D__fill_init /scratch/rickn/hdf5/src/H5Dfill.c:525
#4 0x789e9a in H5D__chunk_allocate /scratch/rickn/hdf5/src/H5Dchunk.c:4437
#5 0x4ae27f in H5D__init_storage /scratch/rickn/hdf5/src/H5Dint.c:2473
#6 0x4b3d31 in H5D__alloc_storage /scratch/rickn/hdf5/src/H5Dint.c:2386
#7 0x4bc06e in H5D__layout_oh_create /scratch/rickn/hdf5/src/H5Dlayout.c:507
#8 0x4ad1c4 in H5D__update_oh_info /scratch/rickn/hdf5/src/H5Dint.c:1070
#9 0x4afa39 in H5D__create /scratch/rickn/hdf5/src/H5Dint.c:1373
#10 0x79e984 in H5O__dset_create /scratch/rickn/hdf5/src/H5Doh.c:300
#20 0x4a3322 in H5Dcreate2 /scratch/rickn/hdf5/src/H5D.c:150
#11 0x5b62df in H5O_obj_create /scratch/rickn/hdf5/src/H5Oint.c:2521
#12 0x57ef66 in H5L__link_cb /scratch/rickn/hdf5/src/H5L.c:1850
#13 0x540a49 in H5G__traverse_real /scratch/rickn/hdf5/src/H5Gtraverse.c:629
#20 0x4a3322 in H5Dcreate2 /scratch/rickn/hdf5/src/H5D.c:150
#21 0x4295bd in main /scratch/rickn/test_hdf5/test_filter.c:122
#14 0x5416c8 in H5G_traverse /scratch/rickn/hdf5/src/H5Gtraverse.c:854
#15 0x5781d7 in H5L__create_real /scratch/rickn/hdf5/src/H5L.c:2044
#21 0x4295bd in main /scratch/rickn/test_hdf5/test_filter.c:122
#22 0x2b50182cb2df in __libc_start_main (/cvmfs/soft.computecanada.ca/nix/store/63pk88rnmkzjblpxydvrmskkc8ci7cx6-glibc-2.24/lib/libc.so.6+0x202df)
#22 0x2b2d6011b2df in __libc_start_main (/cvmfs/soft.computecanada.ca/nix/store/63pk88rnmkzjblpxydvrmskkc8ci7cx6-glibc-2.24/lib/libc.so.6+0x202df)
#23 0x428b09 in _start (/scratch/rickn/test_hdf5/testh5+0x428b09)
0x2b2d6adf3830 is located 48 bytes inside of 2097208-byte region [0x2b2d6adf3800,0x2b2d6aff3838)
#23 0x428b09 in _start (/scratch/rickn/test_hdf5/testh5+0x428b09)
#16 0x580cfd in H5L_link_object /scratch/rickn/hdf5/src/H5L.c:1803
#17 0x4aed95 in H5D__create_named /scratch/rickn/hdf5/src/H5Dint.c:410
#18 0x728b3d in H5VL__native_dataset_create /scratch/rickn/hdf5/src/H5VLnative_dataset.c:74
#20 0x4a3322 in H5Dcreate2 /scratch/rickn/hdf5/src/H5D.c:150
#21 0x4295bd in main /scratch/rickn/test_hdf5/test_filter.c:122
#22 0x2b910c0162df in __libc_start_main (/cvmfs/soft.computecanada.ca/nix/store/63pk88rnmkzjblpxydvrmskkc8ci7cx6-glibc-2.24/lib/libc.so.6+0x202df)
allocated by thread T0 here:
#0 0x2b2d5e80c838 in malloc (/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libasan.so.5+0x106838)
0x2b5022fa9830 is located 48 bytes inside of 2097208-byte region [0x2b5022fa9800,0x2b50231a9838)
allocated by thread T0 here:
#19 0x708ac5 in H5VL__dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1834
#20 0x7115ae in H5VL_dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1868
#21 0x4a3322 in H5Dcreate2 /scratch/rickn/hdf5/src/H5D.c:150
#22 0x4295bd in main /scratch/rickn/test_hdf5/test_filter.c:122
#0 0x2b50169bc838 in malloc (/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libasan.so.5+0x106838)
#23 0x428b09 in _start (/scratch/rickn/test_hdf5/testh5+0x428b09)
0x2b9116cf3830 is located 48 bytes inside of 2097208-byte region [0x2b9116cf3800,0x2b9116ef3838)
#1 0x5903a1 in H5MM_malloc /scratch/rickn/hdf5/src/H5MM.c:292
#2 0x77bc3f in H5D__chunk_mem_alloc /scratch/rickn/hdf5/src/H5Dchunk.c:1404
#23 0x2afbf28ac2df in __libc_start_main (/cvmfs/soft.computecanada.ca/nix/store/63pk88rnmkzjblpxydvrmskkc8ci7cx6-glibc-2.24/lib/libc.so.6+0x202df)
SUMMARY: AddressSanitizer: bad-free (/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libasan.so.5+0x106487) in free
allocated by thread T0 here:
#1 0x5903a1 in H5MM_malloc /scratch/rickn/hdf5/src/H5MM.c:292
#2 0x77bc3f in H5D__chunk_mem_alloc /scratch/rickn/hdf5/src/H5Dchunk.c:1404
==135802==ABORTING
#0 0x2b910a707838 in malloc (/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libasan.so.5+0x106838)
#1 0x5903a1 in H5MM_malloc /scratch/rickn/hdf5/src/H5MM.c:292
#2 0x77bc3f in H5D__chunk_mem_alloc /scratch/rickn/hdf5/src/H5Dchunk.c:1404
#3 0x79de6d in H5D__fill_init /scratch/rickn/hdf5/src/H5Dfill.c:525
#4 0x789e9a in H5D__chunk_allocate /scratch/rickn/hdf5/src/H5Dchunk.c:4437
#5 0x4ae27f in H5D__init_storage /scratch/rickn/hdf5/src/H5Dint.c:2473
#3 0x79de6d in H5D__fill_init /scratch/rickn/hdf5/src/H5Dfill.c:525
#6 0x4b3d31 in H5D__alloc_storage /scratch/rickn/hdf5/src/H5Dint.c:2386
#4 0x789e9a in H5D__chunk_allocate /scratch/rickn/hdf5/src/H5Dchunk.c:4437
#7 0x4bc06e in H5D__layout_oh_create /scratch/rickn/hdf5/src/H5Dlayout.c:507
#5 0x4ae27f in H5D__init_storage /scratch/rickn/hdf5/src/H5Dint.c:2473
#8 0x4ad1c4 in H5D__update_oh_info /scratch/rickn/hdf5/src/H5Dint.c:1070
#9 0x4afa39 in H5D__create /scratch/rickn/hdf5/src/H5Dint.c:1373
#6 0x4b3d31 in H5D__alloc_storage /scratch/rickn/hdf5/src/H5Dint.c:2386
#7 0x4bc06e in H5D__layout_oh_create /scratch/rickn/hdf5/src/H5Dlayout.c:507
#8 0x4ad1c4 in H5D__update_oh_info /scratch/rickn/hdf5/src/H5Dint.c:1070
#9 0x4afa39 in H5D__create /scratch/rickn/hdf5/src/H5Dint.c:1373
#10 0x79e984 in H5O__dset_create /scratch/rickn/hdf5/src/H5Doh.c:300
#11 0x5b62df in H5O_obj_create /scratch/rickn/hdf5/src/H5Oint.c:2521
#12 0x57ef66 in H5L__link_cb /scratch/rickn/hdf5/src/H5L.c:1850
#3 0x79de6d in H5D__fill_init /scratch/rickn/hdf5/src/H5Dfill.c:525
#4 0x789e9a in H5D__chunk_allocate /scratch/rickn/hdf5/src/H5Dchunk.c:4437
#5 0x4ae27f in H5D__init_storage /scratch/rickn/hdf5/src/H5Dint.c:2473
#10 0x79e984 in H5O__dset_create /scratch/rickn/hdf5/src/H5Doh.c:300
#11 0x5b62df in H5O_obj_create /scratch/rickn/hdf5/src/H5Oint.c:2521
#12 0x57ef66 in H5L__link_cb /scratch/rickn/hdf5/src/H5L.c:1850
#13 0x540a49 in H5G__traverse_real /scratch/rickn/hdf5/src/H5Gtraverse.c:629
#13 0x540a49 in H5G__traverse_real /scratch/rickn/hdf5/src/H5Gtraverse.c:629
#14 0x5416c8 in H5G_traverse /scratch/rickn/hdf5/src/H5Gtraverse.c:854
#15 0x5781d7 in H5L__create_real /scratch/rickn/hdf5/src/H5L.c:2044
#16 0x580cfd in H5L_link_object /scratch/rickn/hdf5/src/H5L.c:1803
#6 0x4b3d31 in H5D__alloc_storage /scratch/rickn/hdf5/src/H5Dint.c:2386
#14 0x5416c8 in H5G_traverse /scratch/rickn/hdf5/src/H5Gtraverse.c:854
#15 0x5781d7 in H5L__create_real /scratch/rickn/hdf5/src/H5L.c:2044
#16 0x580cfd in H5L_link_object /scratch/rickn/hdf5/src/H5L.c:1803
#17 0x4aed95 in H5D__create_named /scratch/rickn/hdf5/src/H5Dint.c:410
#18 0x728b3d in H5VL__native_dataset_create /scratch/rickn/hdf5/src/H5VLnative_dataset.c:74
#19 0x708ac5 in H5VL__dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1834
#17 0x4aed95 in H5D__create_named /scratch/rickn/hdf5/src/H5Dint.c:410
#18 0x728b3d in H5VL__native_dataset_create /scratch/rickn/hdf5/src/H5VLnative_dataset.c:74
#19 0x708ac5 in H5VL__dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1834
#20 0x7115ae in H5VL_dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1868
#21 0x4a3322 in H5Dcreate2 /scratch/rickn/hdf5/src/H5D.c:150
#22 0x4295bd in main /scratch/rickn/test_hdf5/test_filter.c:122
#7 0x4bc06e in H5D__layout_oh_create /scratch/rickn/hdf5/src/H5Dlayout.c:507
#8 0x4ad1c4 in H5D__update_oh_info /scratch/rickn/hdf5/src/H5Dint.c:1070
#9 0x4afa39 in H5D__create /scratch/rickn/hdf5/src/H5Dint.c:1373
#10 0x79e984 in H5O__dset_create /scratch/rickn/hdf5/src/H5Doh.c:300
#11 0x5b62df in H5O_obj_create /scratch/rickn/hdf5/src/H5Oint.c:2521
#12 0x57ef66 in H5L__link_cb /scratch/rickn/hdf5/src/H5L.c:1850
#23 0x2b2d6011b2df in __libc_start_main (/cvmfs/soft.computecanada.ca/nix/store/63pk88rnmkzjblpxydvrmskkc8ci7cx6-glibc-2.24/lib/libc.so.6+0x202df)
#20 0x7115ae in H5VL_dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1868
#13 0x540a49 in H5G__traverse_real /scratch/rickn/hdf5/src/H5Gtraverse.c:629
#14 0x5416c8 in H5G_traverse /scratch/rickn/hdf5/src/H5Gtraverse.c:854
#15 0x5781d7 in H5L__create_real /scratch/rickn/hdf5/src/H5L.c:2044
#16 0x580cfd in H5L_link_object /scratch/rickn/hdf5/src/H5L.c:1803
#17 0x4aed95 in H5D__create_named /scratch/rickn/hdf5/src/H5Dint.c:410
#18 0x728b3d in H5VL__native_dataset_create /scratch/rickn/hdf5/src/H5VLnative_dataset.c:74
#19 0x708ac5 in H5VL__dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1834
#20 0x7115ae in H5VL_dataset_create /scratch/rickn/hdf5/src/H5VLcallback.c:1868
SUMMARY: AddressSanitizer: bad-free (/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libasan.so.5+0x106487) in free
==135804==ABORTING
#21 0x4a3322 in H5Dcreate2 /scratch/rickn/hdf5/src/H5D.c:150
#22 0x4295bd in main /scratch/rickn/test_hdf5/test_filter.c:122
#23 0x2b50182cb2df in __libc_start_main (/cvmfs/soft.computecanada.ca/nix/store/63pk88rnmkzjblpxydvrmskkc8ci7cx6-glibc-2.24/lib/libc.so.6+0x202df)
SUMMARY: AddressSanitizer: bad-free (/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libasan.so.5+0x106487) in free
#21 0x4a3322 in H5Dcreate2 /scratch/rickn/hdf5/src/H5D.c:150
==135803==ABORTING
#22 0x4295bd in main /scratch/rickn/test_hdf5/test_filter.c:122
#23 0x2b910c0162df in __libc_start_main (/cvmfs/soft.computecanada.ca/nix/store/63pk88rnmkzjblpxydvrmskkc8ci7cx6-glibc-2.24/lib/libc.so.6+0x202df)
SUMMARY: AddressSanitizer: bad-free (/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib/libasan.so.5+0x106487) in free
==135805==ABORTING
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[9035,1],0]
Exit code: 1
--------------------------------------------------------------------------
Cheers,
Rick