+fordas@fela:~/workspace/pose_fork_depickle$ gdb
GNU gdb (Ubuntu 7.11.1-0ubuntu1~16.5) 7.11.1
  [...]

+(gdb) file python

:(gdb) run pose_serial_fork_bug.py fullsize1.pdb
Starting program: /home/fordas/workspace/pose_fork_depickle/.conda/bin/python pose_serial_fork_bug.py fullsize1.pdb
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
2018-10-20T19:04:21.935 pid: 86342 main
2018-10-20T19:04:21.935 pid: 86342 Found rosetta database at: /home/fordas/workspace/pose_fork_depickle/.conda/lib/python3.6/site-packages/pyrosetta/database; using it....
2018-10-20T19:04:21.936 pid: 86342 PyRosetta-4 2017 [Rosetta devel 2018.28.post.dev+1147.v2018.34dev60360.14e0a7acf8e14e0a7acf8eca980ba28bb1767f41fb5b7f52343 2018-08-21T11:28:04] retrieved from: ssh://git@github.com/RosettaCommons/main
(C) Copyright Rosetta Commons Member Institutions.
Created in JHU by Sergey Lyskov and PyRosetta Team.

core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: 2018.28.post.dev+1147.v2018.34dev60360.14e0a7acf8e 14e0a7acf8eca980ba28bb1767f41fb5b7f52343 ssh://git@github.com/RosettaCommons/main 2018-08-21T11:28:04
core.init: command: PyRosetta -ex1 -ex2aro -database /home/fordas/workspace/pose_fork_depickle/.conda/lib/python3.6/site-packages/pyrosetta/database
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=528287146 seed_offset=0 real_seed=528287146
core.init.random: RandomGenerator:init: Normal mode, seed=528287146 RG_type=mt19937
must make pickle in separate process for this bug to trigger
2018-10-20T19:04:21.966 pid: 86342 make_pickle_in_fork
2018-10-20T19:04:21.972 pid: 86363 make_pickle
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 1.43742 seconds.
core.import_pose.import_pose: File 'fullsize1.pdb' automatically determined to be of type PDB
loading same pose twice in fork process OK
2018-10-20T19:04:25.804 pid: 86342 load_pickle_in_fork
2018-10-20T19:04:25.813 pid: 86368 load_pickle
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 1.68418 seconds.
loaded pose with 551 residues in 86368
2018-10-20T19:04:27.958 pid: 86342 load_pickle_in_fork
2018-10-20T19:04:27.967 pid: 86373 load_pickle
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 1.69935 seconds.
loaded pose with 551 residues in 86373
loading same pose twice in main process OK
2018-10-20T19:04:30.186 pid: 86342 load_pickle
[New Thread 0x7fffceeaa700 (LWP 86378)]
[New Thread 0x7fffce528700 (LWP 86379)]
[New Thread 0x7fffcdba6700 (LWP 86380)]
[New Thread 0x7fffcd224700 (LWP 86381)]
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 617 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 1.68262 seconds.
loaded pose with 551 residues in 86342
2018-10-20T19:04:31.933 pid: 86342 load_pickle
loaded pose with 551 residues in 86342
loading same pose in fork after loading in main process hangs
2018-10-20T19:04:31.971 pid: 86342 load_pickle_in_fork
2018-10-20T19:04:31.979 pid: 86382 load_pickle

^C
Thread 1 "python" received signal SIGINT, Interrupt.
0x00007ffff7bcaf7b in __waitpid (pid=86382, stat_loc=0x7fffffffc104, options=0) at ../sysdeps/unix/sysv/linux/waitpid.c:29

+(gdb) bt
#0  0x00007ffff7bcaf7b in __waitpid (pid=86382, stat_loc=0x7fffffffc104, options=0) at ../sysdeps/unix/sysv/linux/waitpid.c:29
#1  0x000055555575e35d in os_waitpid ()
#2  0x00005555556670e1 in _PyCFunction_FastCallDict ()
#3  0x00005555556ee43c in call_function ()
  [...backtrace...]
#27 0x000055555563852e in main ()

+(gdb) attach 86382
+A program is being debugged already.  Kill it? (y or n) n
Not killed.
+(gdb) detach
Detaching from program: /home/fordas/workspace/pose_fork_depickle/.conda/bin/python, process 86342
+(gdb) attach 86382
Attaching to program: /home/fordas/workspace/pose_fork_depickle/.conda/bin/python, process 86382
done.
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
done.

  [...reading symbols...]

Program stopped.
0x00007ffff7bc8154 in futex_wait (private=0, expected=10, futex_word=0x555555f73eac) at ../sysdeps/unix/sysv/linux/futex-internal.h:61

+(gdb) bt
#0  0x00007ffff7bc8154 in futex_wait (private=0, expected=10, futex_word=0x555555f73eac) at ../sysdeps/unix/sysv/linux/futex-internal.h:61
#1  futex_wait_simple (private=0, expected=10, futex_word=0x555555f73eac) at ../sysdeps/nptl/futex-internal.h:135
#2  __pthread_barrier_wait (barrier=0x555555f73ea8) at pthread_barrier_wait.c:184
#3  0x00007fffdce408c3 in do_job () from /home/fordas/workspace/pose_fork_depickle/.conda/lib/python3.6/site-packages/blosc/../../../libblosc.so.1
#4  0x00007fffdce4221a in blosc_decompress () from /home/fordas/workspace/pose_fork_depickle/.conda/lib/python3.6/site-packages/blosc/../../../libblosc.so.1
#5  0x00007fffdd0e8afc in decompress_helper ()
   from /home/fordas/workspace/pose_fork_depickle/.conda/lib/python3.6/site-packages/blosc/blosc_extension.cpython-36m-x86_64-linux-gnu.so
#6  0x00007fffdd0e8fca in PyBlosc_decompress ()
   from /home/fordas/workspace/pose_fork_depickle/.conda/lib/python3.6/site-packages/blosc/blosc_extension.cpython-36m-x86_64-linux-gnu.so
#7  0x00005555556670e1 in _PyCFunction_FastCallDict ()
#8  0x00005555556ee43c in call_function ()
  [...backtrace...]
#58 0x00005555557706c4 in Py_Main ()
#59 0x000055555563852e in main ()