Runtime segfault, below is the valgrind output.
(base) jain @ compute001 ~/F5/async_hdf5 (rajeeja/async_hdf5_io)
└─ $ ▶ valgrind --leak-check=full ./flash5
==65029== Memcheck, a memory error detector
==65029== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
==65029== Using Valgrind-3.10.1 and LibVEX; rerun with -h for copyright info
==65029== Command: ./flash5
==65029==
[Driver_initParallel]: Called MPI_Init_thread - requested level 3, given level 3
RuntimeParameters_read: ignoring unknown parameter "nriem"...
Grid_init: resolution based on runtime params:
lrefine dx dy
1 1.250 1.250
2 0.625 0.625
3 0.312 0.312
MaterialProperties initialized
attribute # 1 = 2 ->meshVar 1 1
attribute # 2 = 7 ->meshVar 8 1
pt_gcMaskForAdvance: T F F F F F F F T T F
pt_gcMaskForWrite: T F F F F F F T F F F
Particles_init: pt_velNumAttrib is 2
Particles_init: pt_velAttrib is 9 9 10 10 0 0
Source terms initialized
5.0000000000000000 1 1
flash: 2 dimensional vortex initialization
Parameters read:
gamma = 1.3999999999999999
ambient density = 1.0000000000000000
ambient pressure = 1.0000000000000000
ambient x-velocity = 1.0000000000000000
ambient y-velocity = 1.0000000000000000
vortex_strength = 5.0000000000000000
x center = 5.0000000000000000
y center = 5.0000000000000000
x subintervals = 1
y subintervals = 1
Parameters computed :
ambient temperature = 1.2027239580856474E-008
ambient int. energy = 2.5000000000000004
gas constant = 83144598.000000000
iteration, no. not moved = 0 0
Done with refinement: total blocks = 1
[amr_morton_process]: Initializing surr_blks using standard orrery implementation
INFO: Grid_fillGuardCells is ignoring masking.
iteration, no. not moved = 0 0
Done with refinement: total blocks = 5
iteration, no. not moved = 0 0
Done with refinement: total blocks = 21
Finished with Grid_initDomain, no restart
Ready to call Hydro_init
Hydro initialized
Gravity initialized
Warning: The initial timestep is too large.
initial timestep = 2.5000000000000001E-002
CFL timestep = 0.10170685742456619
Resetting dtinit to dr_tstepSlowStartFactor*dtcfl.
Initial dt verified
Particles_initPositions on processor 0 done, pt_numLocal= 100
arrays freed
==65029== Warning: client switching stacks? SP change: 0xffeffedd0 --> 0xe86c078
==65029== to suppress, use: --max-stackframe=68458982744 or greater
==65029== Warning: client switching stacks? SP change: 0xe86bfa0 --> 0xec6d078
==65029== to suppress, use: --max-stackframe=4198616 or greater
==65029== Warning: client switching stacks? SP change: 0xec6cf60 --> 0xffeffedd0
==65029== to suppress, use: --max-stackframe=68454784624 or greater
==65029== further instances of this message will not be shown.
HDF5-DIAG: Error detected in HDF5 (1.13.0) MPI-process 0:
#000: H5Pfapl.c line 5671 in H5Pget_vol_info(): not a property list
major: Invalid arguments to routine
minor: Inappropriate type
==65029== Use of uninitialised value of size 8
==65029== at 0xB62B875: H5VL_async_file_create (h5_async_vol.c:21067)
==65029== by 0x102D103: H5VL__file_create (H5VLcallback.c:3393)
==65029== by 0x102D37C: H5VL_file_create (H5VLcallback.c:3427)
==65029== by 0xC6C7E8: H5F__create_api_common (H5F.c:613)
==65029== by 0xC6D0BD: H5Fcreate_async (H5F.c:703)
==65029== by 0x8189EC: io_h5init_file_ (io_h5file_interface.c:205)
==65029== by 0x8200F3: io_initfile_ (io_initFile.F90:56)
==65029== by 0x529F0A: io_writecheckpoint_ (IO_writeCheckpoint.F90:112)
==65029== by 0x52966C: io_outputinitial_ (IO_outputInitial.F90:76)
==65029== by 0x412219: driver_initflash_ (Driver_initFlash.F90:194)
==65029== by 0x42C217: MAIN__ (Flash.F90:49)
==65029== by 0x42C284: main (Flash.F90:43)
==65029==
==65029== Invalid read of size 8
==65029== at 0xB62B875: H5VL_async_file_create (h5_async_vol.c:21067)
==65029== by 0x102D103: H5VL__file_create (H5VLcallback.c:3393)
==65029== by 0x102D37C: H5VL_file_create (H5VLcallback.c:3427)
==65029== by 0xC6C7E8: H5F__create_api_common (H5F.c:613)
==65029== by 0xC6D0BD: H5Fcreate_async (H5F.c:703)
==65029== by 0x8189EC: io_h5init_file_ (io_h5file_interface.c:205)
==65029== by 0x8200F3: io_initfile_ (io_initFile.F90:56)
==65029== by 0x529F0A: io_writecheckpoint_ (IO_writeCheckpoint.F90:112)
==65029== by 0x52966C: io_outputinitial_ (IO_outputInitial.F90:76)
==65029== by 0x412219: driver_initflash_ (Driver_initFlash.F90:194)
==65029== by 0x42C217: MAIN__ (Flash.F90:49)
==65029== by 0x42C284: main (Flash.F90:43)
==65029== Address 0x900000000000001 is not stack'd, malloc'd or (recently) free'd
==65029==
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x5272777
#1 0x5272D7E
#2 0x5F31CAF
#3 0xB62B875
#4 0x102D103 in H5VL__file_create at H5VLcallback.c:3393
#5 0x102D37C in H5VL_file_create at H5VLcallback.c:3427
#6 0xC6C7E8 in H5F__create_api_common at H5F.c:613
#7 0xC6D0BD in H5Fcreate_async at H5F.c:703
#8 0x8189EC in io_h5init_file_ at io_h5file_interface.c:205
#9 0x8200F3 in io_initfile_ at io_initFile.F90:56
#10 0x529F0A in io_writecheckpoint_ at IO_writeCheckpoint.F90:112
#11 0x52966C in io_outputinitial_ at IO_outputInitial.F90:76
#12 0x412219 in driver_initflash_ at Driver_initFlash.F90:194
#13 0x42C217 in flash at Flash.F90:49
==65029==
==65029== HEAP SUMMARY:
==65029== in use at exit: 83,157,515 bytes in 6,205 blocks
==65029== total heap usage: 32,452 allocs, 26,247 frees, 94,766,509 bytes allocated
==65029==
==65029== 8 bytes in 1 blocks are possibly lost in loss record 178 of 5,182
==65029== at 0x4C2D110: memalign (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==65029== by 0x4001149: allocate_and_init (dl-tls.c:529)
==65029== by 0x4001149: tls_get_addr_tail (dl-tls.c:742)
==65029== by 0xB840C83: local_set_xstream_internal (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB84542C: xstream_launch_root_ythread (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB854F3D: xstream_context_thread_func (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0x4E3F183: start_thread (pthread_create.c:312)
==65029== by 0x5FF903C: clone (clone.S:111)
==65029==
==65029== 336 bytes in 1 blocks are possibly lost in loss record 4,356 of 5,182
==65029== at 0x4C2CC70: calloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==65029== by 0x4012EE4: allocate_dtv (dl-tls.c:296)
==65029== by 0x4012EE4: _dl_allocate_tls (dl-tls.c:460)
==65029== by 0x4E3FD92: allocate_stack (allocatestack.c:589)
==65029== by 0x4E3FD92: pthread_create@@GLIBC_2.2.5 (pthread_create.c:500)
==65029== by 0xB855073: ABTD_xstream_context_create (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB845379: xstream_create (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB845CEC: ABT_xstream_create (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB5FA7FC: async_instance_init (h5_async_vol.c:1133)
==65029== by 0xB5FAF6D: H5VL_async_init (h5_async_vol.c:1386)
==65029== by 0x104983D: H5VL__register_connector (H5VLint.c:1237)
==65029== by 0x104A2EE: H5VL__register_connector_by_name (H5VLint.c:1379)
==65029== by 0x1046321: H5VL__set_def_conn (H5VLint.c:442)
==65029== by 0x104543D: H5VL_init_phase2 (H5VLint.c:201)
==65029==
==65029== 4,194,432 bytes in 1 blocks are possibly lost in loss record 5,175 of 5,182
==65029== at 0x4C2D110: memalign (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==65029== by 0x4C2D227: posix_memalign (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==65029== by 0xB850576: ABTI_ythread_create_root (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB845259: xstream_create (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB846F7F: ABTI_xstream_create_primary (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB83F24D: ABT_init (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB5FA1C6: async_init (h5_async_vol.c:925)
==65029== by 0xB5FA544: async_instance_init (h5_async_vol.c:1054)
==65029== by 0xB5FAF6D: H5VL_async_init (h5_async_vol.c:1386)
==65029== by 0x104983D: H5VL__register_connector (H5VLint.c:1237)
==65029== by 0x104A2EE: H5VL__register_connector_by_name (H5VLint.c:1379)
==65029== by 0x1046321: H5VL__set_def_conn (H5VLint.c:442)
==65029==
==65029== 4,194,432 bytes in 1 blocks are possibly lost in loss record 5,176 of 5,182
==65029== at 0x4C2D110: memalign (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==65029== by 0x4C2D227: posix_memalign (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==65029== by 0xB84967B: ythread_create (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB850713: ABTI_ythread_create_main_sched (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB845300: xstream_create (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB846F7F: ABTI_xstream_create_primary (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB83F24D: ABT_init (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB5FA1C6: async_init (h5_async_vol.c:925)
==65029== by 0xB5FA544: async_instance_init (h5_async_vol.c:1054)
==65029== by 0xB5FAF6D: H5VL_async_init (h5_async_vol.c:1386)
==65029== by 0x104983D: H5VL__register_connector (H5VLint.c:1237)
==65029== by 0x104A2EE: H5VL__register_connector_by_name (H5VLint.c:1379)
==65029==
==65029== 4,194,432 bytes in 1 blocks are possibly lost in loss record 5,177 of 5,182
==65029== at 0x4C2D110: memalign (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==65029== by 0x4C2D227: posix_memalign (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==65029== by 0xB84967B: ythread_create (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB850713: ABTI_ythread_create_main_sched (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB845300: xstream_create (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB845CEC: ABT_xstream_create (in /nfs/proj-flash5/argobots/install/lib/libabt.so.1.1.0)
==65029== by 0xB5FA7FC: async_instance_init (h5_async_vol.c:1133)
==65029== by 0xB5FAF6D: H5VL_async_init (h5_async_vol.c:1386)
==65029== by 0x104983D: H5VL__register_connector (H5VLint.c:1237)
==65029== by 0x104A2EE: H5VL__register_connector_by_name (H5VLint.c:1379)
==65029== by 0x1046321: H5VL__set_def_conn (H5VLint.c:442)
==65029== by 0x104543D: H5VL_init_phase2 (H5VLint.c:201)
==65029==
==65029== LEAK SUMMARY:
==65029== definitely lost: 0 bytes in 0 blocks
==65029== indirectly lost: 0 bytes in 0 blocks
==65029== possibly lost: 12,583,640 bytes in 5 blocks
==65029== still reachable: 70,573,875 bytes in 6,200 blocks
==65029== suppressed: 0 bytes in 0 blocks
==65029== Reachable blocks (those to which a pointer was found) are not shown.
==65029== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==65029==
==65029== For counts of detected and suppressed errors, rerun with: -v
==65029== Use --track-origins=yes to see where uninitialised values come from
==65029== ERROR SUMMARY: 7 errors from 7 contexts (suppressed: 0 from 0)
Killed
(base) jain @ compute001 ~/F5/async_hdf5 (rajeeja/async_hdf5_io)
└─ $ ▶ uname -a
lsLinux compute001 3.13.0-170-generic #220-Ubuntu SMP Thu May 9 12:40:49 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
(base) jain @ compute001 ~/F5/async_hdf5 (rajeeja/async_hdf5_io)
└─ $ ▶ lsb_release
Display all 2371 possibilities? (y or n)
(base) jain @ compute001 ~/F5/async_hdf5 (rajeeja/async_hdf5_io)
└─ $ ▶ lsb_release
LSB Version: core-2.0-amd64:core-2.0-noarch:core-3.0-amd64:core-3.0-noarch:core-3.1-amd64:core-3.1-noarch:core-3.2-amd64:core-3.2-noarch:core-4.0-amd64:core-4.0-noarch:core-4.1-amd64:core-4.1-noarch:security-4.0-amd64:security-4.0-noarch:security-4.1-amd64:security-4.1-noarch
(base) jain @ compute001 ~/F5/async_hdf5 (rajeeja/async_hdf5_io)
└─ $ ▶ lsb_release -a
LSB Version: core-2.0-amd64:core-2.0-noarch:core-3.0-amd64:core-3.0-noarch:core-3.1-amd64:core-3.1-noarch:core-3.2-amd64:core-3.2-noarch:core-4.0-amd64:core-4.0-noarch:core-4.1-amd64:core-4.1-noarch:security-4.0-amd64:security-4.0-noarch:security-4.1-amd64:security-4.1-noarch
Distributor ID: Ubuntu
Description: Ubuntu 14.04.6 LTS
Release: 14.04
Codename: trusty