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Seg fault with Python 3

Issue #72 resolved
Prof Garth Wells created an issue

Using master of both PETSc and petsc4py,

python2 -c "import petsc4py.PETSc"

exits as expected, but

python3 -c "import petsc4py.PETSc"

segfaults (output below). I'm using OpenMPI. Let me know if there is more info I can provide.

garth@gnw20pc:$ python3 -c "import petsc4py.PETSc"
*** Error in `python3': free(): invalid pointer: 0x00007fee571cb460 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7908b)[0x7fee5813d08b]
/lib/x86_64-linux-gnu/libc.so.6(+0x82c3a)[0x7fee58146c3a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7fee5814ad2c]
python3(PyDict_Clear+0xd6)[0x55ae8831af66]
python3(PyImport_Cleanup+0x211)[0x55ae88290371]
python3(Py_Finalize+0x61)[0x55ae88377d41]
python3(Py_Main+0x641)[0x55ae883af051]
python3(main+0xe1)[0x55ae8823ee51]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf1)[0x7fee580e43f1]
python3(_start+0x2a)[0x55ae8834548a]
======= Memory map: ========
55ae8812b000-55ae8851a000 r-xp 00000000 08:02 1187292                    /usr/bin/python3.5
55ae88719000-55ae8871c000 r--p 003ee000 08:02 1187292                    /usr/bin/python3.5
55ae8871c000-55ae887b2000 rw-p 003f1000 08:02 1187292                    /usr/bin/python3.5
55ae887b2000-55ae887e3000 rw-p 00000000 00:00 0 
55ae89317000-55ae89a0a000 rw-p 00000000 00:00 0                          [heap]
7fee34000000-7fee34021000 rw-p 00000000 00:00 0 
7fee34021000-7fee38000000 ---p 00000000 00:00 0 
7fee3895b000-7fee38979000 r-xp 00000000 08:02 1183259                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_osc_pt2pt.so
7fee38979000-7fee38b79000 ---p 0001e000 08:02 1183259                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_osc_pt2pt.so
7fee38b79000-7fee38b7a000 r--p 0001e000 08:02 1183259                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_osc_pt2pt.so
7fee38b7a000-7fee38b7b000 rw-p 0001f000 08:02 1183259                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_osc_pt2pt.so
7fee38b7b000-7fee38ba0000 r-xp 00000000 08:02 1183260                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_osc_rdma.so
7fee38ba0000-7fee38d9f000 ---p 00025000 08:02 1183260                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_osc_rdma.so
7fee38d9f000-7fee38da0000 r--p 00024000 08:02 1183260                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_osc_rdma.so
7fee38da0000-7fee38da1000 rw-p 00025000 08:02 1183260                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_osc_rdma.so
7fee38da1000-7fee38da6000 r-xp 00000000 08:02 1183261                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_osc_sm.so
7fee38da6000-7fee38fa5000 ---p 00005000 08:02 1183261                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_osc_sm.so
7fee38fa5000-7fee38fa6000 r--p 00004000 08:02 1183261                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_osc_sm.so
7fee38fa6000-7fee38fa8000 rw-p 00005000 08:02 1183261                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_osc_sm.so
7fee38fa8000-7fee38fb7000 r-xp 00000000 08:02 1183181                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_tuned.so
7fee38fb7000-7fee391b6000 ---p 0000f000 08:02 1183181                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_tuned.so
7fee391b6000-7fee391b7000 r--p 0000e000 08:02 1183181                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_tuned.so
7fee391b7000-7fee391b8000 rw-p 0000f000 08:02 1183181                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_tuned.so
7fee391b8000-7fee391ba000 r-xp 00000000 08:02 1183178                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_self.so
7fee391ba000-7fee393b9000 ---p 00002000 08:02 1183178                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_self.so
7fee393b9000-7fee393ba000 r--p 00001000 08:02 1183178                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_self.so
7fee393ba000-7fee393bb000 rw-p 00002000 08:02 1183178                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_self.so
7fee393bb000-7fee393be000 r-xp 00000000 08:02 1183174                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_inter.so
7fee393be000-7fee395be000 ---p 00003000 08:02 1183174                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_inter.so
7fee395be000-7fee395bf000 r--p 00003000 08:02 1183174                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_inter.so
7fee395bf000-7fee395c0000 rw-p 00004000 08:02 1183174                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_inter.so
7fee395c0000-7fee395cc000 r-xp 00000000 08:02 1183173                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_basic.so
7fee395cc000-7fee397cc000 ---p 0000c000 08:02 1183173                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_basic.so
7fee397cc000-7fee397cd000 r--p 0000c000 08:02 1183173                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_basic.so
7fee397cd000-7fee397ce000 rw-p 0000d000 08:02 1183173                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_basic.so
7fee397ce000-7fee397ea000 r-xp 00000000 08:02 1183175                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_libnbc.so
7fee397ea000-7fee399ea000 ---p 0001c000 08:02 1183175                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_libnbc.so
7fee399ea000-7fee399eb000 r--p 0001c000 08:02 1183175                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_libnbc.so
7fee399eb000-7fee399ec000 rw-p 0001d000 08:02 1183175                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_libnbc.so
7fee399ec000-7fee399ef000 r-xp 00000000 08:02 1183180                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_sync.so
7fee399ef000-7fee39bee000 ---p 00003000 08:02 1183180                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_sync.so
7fee39bee000-7fee39bef000 r--p 00002000 08:02 1183180                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_sync.so
7fee39bef000-7fee39bf0000 rw-p 00003000 08:02 1183180                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_sync.so
7fee3a908000-7fee3a911000 r-xp 00000000 08:02 1183405                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_vprotocol_pessimist.so
7fee3a911000-7fee3ab10000 ---p 00009000 08:02 1183405                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_vprotocol_pessimist.so
7fee3ab10000-7fee3ab11000 r--p 00008000 08:02 1183405                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_vprotocol_pessimist.so
7fee3ab11000-7fee3ab12000 rw-p 00009000 08:02 1183405                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_vprotocol_pessimist.so
7fee3ab12000-7fee3ab20000 r-xp 00000000 08:02 1183171                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_btl_tcp.so
7fee3ab20000-7fee3ad20000 ---p 0000e000 08:02 1183171                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_btl_tcp.so
7fee3ad20000-7fee3ad21000 r--p 0000e000 08:02 1183171                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_btl_tcp.so
7fee3ad21000-7fee3ad22000 rw-p 0000f000 08:02 1183171                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_btl_tcp.so
7fee3ad22000-7fee3ada3000 rw-p 00000000 00:00 0 
7fee3adae000-7fee3add3000 r-xp 00000000 08:02 1183268                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_pml_ob1.so
7fee3add3000-7fee3afd2000 ---p 00025000 08:02 1183268                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_pml_ob1.so
7fee3afd2000-7fee3afd3000 r--p 00024000 08:02 1183268                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_pml_ob1.so
7fee3afd3000-7fee3afd4000 rw-p 00025000 08:02 1183268                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_pml_ob1.so
7fee3b1de000-7fee3b1e1000 r-xp 00000000 08:02 1183169                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_btl_self.so
7fee3b1e1000-7fee3b3e0000 ---p 00003000 08:02 1183169                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_btl_self.so
7fee3b3e0000-7fee3b3e1000 r--p 00002000 08:02 1183169                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_btl_self.so
7fee3b3e1000-7fee3b3e2000 rw-p 00003000 08:02 1183169                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_btl_self.so
7fee3b3e4000-7fee3b3ea000 r-xp 00000000 08:02 1183179                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_sm.so
7fee3b3ea000-7fee3b5e9000 ---p 00006000 08:02 1183179                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_sm.so
7fee3b5e9000-7fee3b5ea000 r--p 00005000 08:02 1183179                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_sm.so
7fee3b5ea000-7fee3b5eb000 rw-p 00006000 08:02 1183179                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_coll_sm.so
7fee3b5eb000-7fee3b5ef000 r-xp 00000000 08:02 1183088                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_bml_r2.so
7fee3b5ef000-7fee3b7ee000 ---p 00004000 08:02 1183088                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_bml_r2.so
7fee3b7ee000-7fee3b7ef000 r--p 00003000 08:02 1183088                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_bml_r2.so
7fee3b7ef000-7fee3b7f0000 rw-p 00004000 08:02 1183088                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_bml_r2.so
7fee3b7f0000-7fee3b7f3000 r-xp 00000000 08:02 1183250                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_mpool_grdma.so
7fee3b7f3000-7fee3b9f3000 ---p 00003000 08:02 1183250                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_mpool_grdma.so
7fee3b9f3000-7fee3b9f4000 r--p 00003000 08:02 1183250                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_mpool_grdma.so
7fee3b9f4000-7fee3b9f5000 rw-p 00004000 08:02 1183250                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_mpool_grdma.so
7fee3b9f5000-7fee3b9f7000 r-xp 00000000 08:02 1182701                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmca_common_sm.so.20.0.0
7fee3b9f7000-7fee3bbf6000 ---p 00002000 08:02 1182701                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmca_common_sm.so.20.0.0
7fee3bbf6000-7fee3bbf7000 r--p 00001000 08:02 1182701                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmca_common_sm.so.20.0.0
7fee3bbf7000-7fee3bbf8000 rw-p 00002000 08:02 1182701                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmca_common_sm.so.20.0.0
7fee3bbf8000-7fee3bbfa000 r-xp 00000000 08:02 1183251                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_mpool_sm.so
7fee3bbfa000-7fee3bdf9000 ---p 00002000 08:02 1183251                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_mpool_sm.so
7fee3bdf9000-7fee3bdfa000 r--p 00001000 08:02 1183251                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_mpool_sm.so
7fee3bdfa000-7fee3bdfb000 rw-p 00002000 08:02 1183251                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_mpool_sm.so
7fee3bdfb000-7fee3bdff000 r-xp 00000000 08:02 1183274                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_rcache_vma.so
7fee3bdff000-7fee3bffe000 ---p 00004000 08:02 1183274                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_rcache_vma.so
7fee3bffe000-7fee3bfff000 r--p 00003000 08:02 1183274                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_rcache_vma.so
7fee3bfff000-7fee3c000000 rw-p 00004000 08:02 1183274                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_rcache_vma.so
7fee3c000000-7fee3c021000 rw-p 00000000 00:00 0 
7fee3c021000-7fee40000000 ---p 00000000 00:00 0 
7fee40155000-7fee40157000 r-xp 00000000 08:02 1183084                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_allocator_bucket.so
7fee40157000-7fee40356000 ---p 00002000 08:02 1183084                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_allocator_bucket.so
7fee40356000-7fee40357000 r--p 00001000 08:02 1183084                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_allocator_bucket.so
7fee40357000-7fee40358000 rw-p 00002000 08:02 1183084                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_allocator_bucket.so
7fee40358000-7fee4035b000 r-xp 00000000 08:02 1183285                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_rml_oob.so
7fee4035b000-7fee4055b000 ---p 00003000 08:02 1183285                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_rml_oob.so
7fee4055b000-7fee4055c000 r--p 00003000 08:02 1183285                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_rml_oob.so
7fee4055c000-7fee4055d000 rw-p 00004000 08:02 1183285                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_rml_oob.so
7fee4055d000-7fee40570000 r-xp 00000000 08:02 1183256                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_oob_tcp.so
7fee40570000-7fee40770000 ---p 00013000 08:02 1183256                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_oob_tcp.so
7fee40770000-7fee40771000 r--p 00013000 08:02 1183256                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_oob_tcp.so
7fee40771000-7fee40772000 rw-p 00014000 08:02 1183256                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_oob_tcp.so
7fee40772000-7fee4077e000 r-xp 00000000 08:02 1183258                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_oob_usock.so
7fee4077e000-7fee4097e000 ---p 0000c000 08:02 1183258                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_oob_usock.so
7fee4097e000-7fee4097f000 r--p 0000c000 08:02 1183258                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_oob_usock.so
7fee4097f000-7fee40980000 rw-p 0000d000 08:02 1183258                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_oob_usock.so
7fee40980000-7fee4099e000 r-xp 00000000 08:02 12320981                   /lib/x86_64-linux-gnu/libnl-3.so.200.24.0
7fee4099e000-7fee40b9d000 ---p 0001e000 08:02 12320981                   /lib/x86_64-linux-gnu/libnl-3.so.200.24.0
7fee40b9d000-7fee40b9f000 r--p 0001d000 08:02 12320981                   /lib/x86_64-linux-gnu/libnl-3.so.200.24.0
7fee40b9f000-7fee40ba0000 rw-p 0001f000 08:02 12320981                   /lib/x86_64-linux-gnu/libnl-3.so.200.24.0
7fee40ba0000-7fee40c0b000 r-xp 00000000 08:02 1181562                    /usr/lib/x86_64-linux-gnu/libnl-route-3.so.200.24.0
7fee40c0b000-7fee40e0b000 ---p 0006b000 08:02 1181562                    /usr/lib/x86_64-linux-gnu/libnl-route-3.so.200.24.0
7fee40e0b000-7fee40e0e000 r--p 0006b000 08:02 1181562                    /usr/lib/x86_64-linux-gnu/libnl-route-3.so.200.24.0
7fee40e0e000-7fee40e12000 rw-p 0006e000 08:02 1181562                    /usr/lib/x86_64-linux-gnu/libnl-route-3.so.200.24.0
7fee40e12000-7fee40e15000 rw-p 00000000 00:00 0 
7fee40e15000-7fee40e19000 r-xp 00000000 08:02 1182702                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmca_common_verbs.so.20.0.0
7fee40e19000-7fee41018000 ---p 00004000 08:02 1182702                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmca_common_verbs.so.20.0.0
7fee41018000-7fee41019000 r--p 00003000 08:02 1182702                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmca_common_verbs.so.20.0.0
7fee41019000-7fee4101a000 rw-p 00004000 08:02 1182702                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmca_common_verbs.so.20.0.0
7fee4101a000-7fee4102b000 r-xp 00000000 08:02 1181565                    /usr/lib/x86_64-linux-gnu/libibverbs.so.1.0.0
7fee4102b000-7fee4122a000 ---p 00011000 08:02 1181565                    /usr/lib/x86_64-linux-gnu/libibverbs.so.1.0.0
7fee4122a000-7fee4122b000 r--p 00010000 08:02 1181565                    /usr/lib/x86_64-linux-gnu/libibverbs.so.1.0.0
7fee4122b000-7fee4122c000 rw-p 00011000 08:02 1181565                    /usr/lib/x86_64-linux-gnu/libibverbs.so.1.0.0
7fee4122c000-7fee4123c000 r-xp 00000000 08:02 1183257                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_oob_ud.so
7fee4123c000-7fee4143c000 ---p 00010000 08:02 1183257                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_oob_ud.so
7fee4143c000-7fee4143d000 r--p 00010000 08:02 1183257                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_oob_ud.so
7fee4143d000-7fee4143e000 rw-p 00011000 08:02 1183257                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_oob_ud.so
7fee4143e000-7fee41440000 r-xp 00000000 08:02 1183396                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_state_app.so
7fee41440000-7fee4163f000 ---p 00002000 08:02 1183396                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_state_app.so
7fee4163f000-7fee41640000 r--p 00001000 08:02 1183396                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_state_app.so
7fee41640000-7fee41641000 rw-p 00002000 08:02 1183396                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_state_app.so
7fee41641000-7fee41645000 r-xp 00000000 08:02 1183318                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_routed_radix.so
7fee41645000-7fee41844000 ---p 00004000 08:02 1183318                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_routed_radix.so
7fee41844000-7fee41845000 r--p 00003000 08:02 1183318                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_routed_radix.so
7fee41845000-7fee41846000 rw-p 00004000 08:02 1183318                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_routed_radix.so
7fee41847000-7fee41849000 r-xp 00000000 08:02 1183082                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_allocator_basic.so
7fee41849000-7fee41a49000 ---p 00002000 08:02 1183082                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_allocator_basic.so
7fee41a49000-7fee41a4a000 r--p 00002000 08:02 1183082                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_allocator_basic.so
7fee41a4a000-7fee41a4b000 rw-p 00003000 08:02 1183082                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_allocator_basic.so
7fee41a4b000-7fee41a4d000 r-xp 00000000 08:02 1183190                    /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_errmgr_default_app.so
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7fee4ff0c000-7fee4ff0d000 rw-p 00003000 08:02 1187843                    /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7fee4ff0d000-7fee4ff16000 r-xp 00000000 08:02 1188647                    /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.1
7fee4ff16000-7fee50115000 ---p 00009000 08:02 1188647                    /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.1
7fee50115000-7fee50116000 r--p 00008000 08:02 1188647                    /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.1
7fee50116000-7fee50117000 rw-p 00009000 08:02 1188647                    /usr/lib/x86_64-linux-gnu/libltdl.so.7.3.1
7fee50117000-7fee50121000 r-xp 00000000 08:02 1188831                    /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7fee50121000-7fee50320000 ---p 0000a000 08:02 1188831                    /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7fee50320000-7fee50321000 r--p 00009000 08:02 1188831                    /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7fee50321000-7fee50322000 rw-p 0000a000 08:02 1188831                    /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7fee50322000-7fee50361000 r-xp 00000000 08:02 1188949                    /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7fee50361000-7fee50560000 ---p 0003f000 08:02 1188949                    /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7fee50560000-7fee50561000 r--p 0003e000 08:02 1188949                    /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7fee50561000-7fee50562000 rw-p 0003f000 08:02 1188949                    /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7fee50562000-7fee50583000 r-xp 00000000 08:02 1189270                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fee50583000-7fee50782000 ---p 00021000 08:02 1189270                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fee50782000-7fee50783000 r--p 00020000 08:02 1189270                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fee50783000-7fee50784000 rw-p 00021000 08:02 1189270                    /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7fee50784000-7fee5269b000 r-xp 00000000 08:02 1192281                    /usr/lib/libopenblasp-r0.2.19.so
7fee5269b000-7fee5289a000 ---p 01f17000 08:02 1192281                    /usr/lib/libopenblasp-r0.2.19.so
7fee5289a000-7fee528a0000 r--p 01f16000 08:02 1192281                    /usr/lib/libopenblasp-r0.2.19.so
7fee528a0000-7fee528b2000 rw-p 01f1c000 08:02 1192281                    /usr/lib/libopenblasp-r0.2.19.so
7fee528b2000-7fee528cb000 rw-p 00000000 00:00 0 
7fee528cb000-7fee52905000 r-xp 00000000 08:02 1190231                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.7.2
7fee52905000-7fee52b04000 ---p 0003a000 08:02 1190231                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.7.2
7fee52b04000-7fee52b05000 r--p 00039000 08:02 1190231                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.7.2
7fee52b05000-7fee52b06000 rw-p 0003a000 08:02 1190231                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.7.2
7fee52b06000-7fee52ba4000 r-xp 00000000 08:02 1183073                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.20.2.0
7fee52ba4000-7fee52da4000 ---p 0009e000 08:02 1183073                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.20.2.0
7fee52da4000-7fee52da8000 r--p 0009e000 08:02 1183073                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.20.2.0
7fee52da8000-7fee52dac000 rw-p 000a2000 08:02 1183073                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so.20.2.0
7fee52dac000-7fee52db3000 rw-p 00000000 00:00 0 
7fee52db3000-7fee52e37000 r-xp 00000000 08:02 1183074                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-rte.so.20.1.0
7fee52e37000-7fee53036000 ---p 00084000 08:02 1183074                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-rte.so.20.1.0
7fee53036000-7fee53037000 r--p 00083000 08:02 1183074                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-rte.so.20.1.0
7fee53037000-7fee5303a000 rw-p 00084000 08:02 1183074                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-rte.so.20.1.0
7fee5303a000-7fee5303c000 rw-p 00000000 00:00 0 
7fee5303c000-7fee53052000 r-xp 00000000 08:02 12325382                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fee53052000-7fee53251000 ---p 00016000 08:02 12325382                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fee53251000-7fee53252000 r--p 00015000 08:02 12325382                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fee53252000-7fee53253000 rw-p 00016000 08:02 12325382                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7fee53253000-7fee5325a000 r-xp 00000000 08:02 12324269                   /lib/x86_64-linux-gnu/librt-2.24.so
7fee5325a000-7fee53459000 ---p 00007000 08:02 12324269                   /lib/x86_64-linux-gnu/librt-2.24.so
7fee53459000-7fee5345a000 r--p 00006000 08:02 12324269                   /lib/x86_64-linux-gnu/librt-2.24.so
7fee5345a000-7fee5345b000 rw-p 00007000 08:02 12324269                   /lib/x86_64-linux-gnu/librt-2.24.so
7fee5345b000-7fee53589000 r-xp 00000000 08:02 1188347                    /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fee53589000-7fee53789000 ---p 0012e000 08:02 1188347                    /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fee53789000-7fee5378a000 r--p 0012e000 08:02 1188347                    /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fee5378a000-7fee5378c000 rw-p 0012f000 08:02 1188347                    /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fee5378c000-7fee537e2000 r-xp 00000000 08:02 1182709                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_mpifh.so.20.1.0
7fee537e2000-7fee539e1000 ---p 00056000 08:02 1182709                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_mpifh.so.20.1.0
7fee539e1000-7fee539e2000 r--p 00055000 08:02 1182709                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_mpifh.so.20.1.0
7fee539e2000-7fee539e3000 rw-p 00056000 08:02 1182709                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_mpifh.so.20.1.0
7fee539e3000-7fee53b17000 r-xp 00000000 08:02 1187839                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fee53b17000-7fee53d17000 ---p 00134000 08:02 1187839                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fee53d17000-7fee53d18000 r--p 00134000 08:02 1187839                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fee53d18000-7fee53d1c000 rw-p 00135000 08:02 1187839                    /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7fee53d1c000-7fee53d8b000 r-xp 00000000 08:02 12198717                   /home/garth/local/packages/petsc-dev/lib/libmetis.so
7fee53d8b000-7fee53f8a000 ---p 0006f000 08:02 12198717                   /home/garth/local/packages/petsc-dev/lib/libmetis.so
7fee53f8a000-7fee53f8b000 r--p 0006e000 08:02 12198717                   /home/garth/local/packages/petsc-dev/lib/libmetis.so
7fee53f8b000-7fee53f8c000 rw-p 0006f000 08:02 12198717                   /home/garth/local/packages/petsc-dev/lib/libmetis.so
7fee53f8c000-7fee53f94000 rw-p 00000000 00:00 0 
7fee53f94000-7fee53fdd000 r-xp 00000000 08:02 12198718                   /home/garth/local/packages/petsc-dev/lib/libparmetis.so
7fee53fdd000-7fee541dc000 ---p 00049000 08:02 12198718                   /home/garth/local/packages/petsc-dev/lib/libparmetis.so
7fee541dc000-7fee541dd000 r--p 00048000 08:02 12198718                   /home/garth/local/packages/petsc-dev/lib/libparmetis.so
7fee541dd000-7fee541de000 rw-p 00049000 08:02 12198718                   /home/garth/local/packages/petsc-dev/lib/libparmetis.so
7fee541de000-7fee54236000 r-xp 00000000 08:02 1192283                    /usr/lib/openblas-base/libblas.so.3
7fee54236000-7fee54436000 ---p 00058000 08:02 1192283                    /usr/lib/openblas-base/libblas.so.3
7fee54436000-7fee5443b000 r--p 00058000 08:02 1192283                    /usr/lib/openblas-base/libblas.so.3
7fee5443b000-7fee5443c000 rw-p 0005d000 08:02 1192283                    /usr/lib/openblas-base/libblas.so.3
7fee5443c000-7fee54ac7000 r-xp 00000000 08:02 1192284                    /usr/lib/openblas-base/liblapack.so.3
7fee54ac7000-7fee54cc6000 ---p 0068b000 08:02 1192284                    /usr/lib/openblas-base/liblapack.so.3
7fee54cc6000-7fee54cc7000 r--p 0068a000 08:02 1192284                    /usr/lib/openblas-base/liblapack.so.3
7fee54cc7000-7fee54cc9000 rw-p 0068b000 08:02 1192284                    /usr/lib/openblas-base/liblapack.so.3
7fee54cc9000-7fee54d6a000 r-xp 00000000 08:02 12199662                   /home/garth/local/packages/petsc-dev/lib/libsuperlu_dist.so.5.1.3
7fee54d6a000-7fee54f69000 ---p 000a1000 08:02 12199662                   /home/garth/local/packages/petsc-dev/lib/libsuperlu_dist.so.5.1.3
7fee54f69000-7fee54f6a000 r--p 000a0000 08:02 12199662                   /home/garth/local/packages/petsc-dev/lib/libsuperlu_dist.so.5.1.3
7fee54f6a000-7fee54f6b000 rw-p 000a1000 08:02 12199662                   /home/garth/local/packages/petsc-dev/lib/libsuperlu_dist.so.5.1.3
7fee54f6b000-7fee54ff5000 r-xp 00000000 08:02 12199665                   /home/garth/local/packages/petsc-dev/lib/libsuperlu.so.5.2.1
7fee54ff5000-7fee551f4000 ---p 0008a000 08:02 12199665                   /home/garth/local/packages/petsc-dev/lib/libsuperlu.so.5.2.1
7fee551f4000-7fee551f5000 r--p 00089000 08:02 12199665                   /home/garth/local/packages/petsc-dev/lib/libsuperlu.so.5.2.1
7fee551f5000-7fee551f6000 rw-p 0008a000 08:02 12199665                   /home/garth/local/packages/petsc-dev/lib/libsuperlu.so.5.2.1
7fee551f6000-7fee552c3000 r-xp 00000000 08:02 1182704                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.20.0.2
7fee552c3000-7fee554c3000 ---p 000cd000 08:02 1182704                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.20.0.2
7fee554c3000-7fee554c4000 r--p 000cd000 08:02 1182704                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.20.0.2
7fee554c4000-7fee554d3000 rw-p 000ce000 08:02 1182704                    /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so.20.0.2
7fee554d3000-7fee554e5000 rw-p 00000000 00:00 0 
7fee554e5000-7fee5688e000 r-xp 00000000 08:02 12199809                   /home/garth/local/packages/petsc-dev/lib/libpetsc.so.3.07.6
7fee5688e000-7fee56a8d000 ---p 013a9000 08:02 12199809                   /home/garth/local/packages/petsc-dev/lib/libpetsc.so.3.07.6
7fee56a8d000-7fee56a93000 r--p 013a8000 08:02 12199809                   /home/garth/local/packages/petsc-dev/lib/libpetsc.so.3.07.6
7fee56a93000-7fee56aad000 rw-p 013ae000 08:02 12199809                   /home/garth/local/packages/petsc-dev/lib/libpetsc.so.3.07.6
7fee56aad000-7fee56cb9000 rw-p 00000000 00:00 0 
7fee56cb9000-7fee56f95000 r-xp 00000000 08:02 11671150                   /home/garth/.local/lib/python3.5/site-packages/petsc4py/lib/PETSc.cpython-35m-x86_64-linux-gnu.so
7fee56f95000-7fee57195000 ---p 002dc000 08:02 11671150                   /home/garth/.local/lib/python3.5/site-packages/petsc4py/lib/PETSc.cpython-35m-x86_64-linux-gnu.so
7fee57195000-7fee57196000 r--p 002dc000 08:02 11671150                   /home/garth/.local/lib/python3.5/site-packages/petsc4py/lib/PETSc.cpython-35m-x86_64-linux-gnu.so
7fee57196000-7fee571cd000 rw-p 002dd000 08:02 11671150                   /home/garth/.local/lib/python3.5/site-packages/petsc4py/lib/PETSc.cpython-35m-x86_64-linux-gnu.so
7fee571cd000-7fee57293000 rw-p 00000000 00:00 0 
7fee57293000-7fee5756e000 r--p 00000000 08:02 1180119                    /usr/lib/locale/locale-archive
7fee5756e000-7fee57676000 r-xp 00000000 08:02 12323263                   /lib/x86_64-linux-gnu/libm-2.24.so
7fee57676000-7fee57875000 ---p 00108000 08:02 12323263                   /lib/x86_64-linux-gnu/libm-2.24.so
7fee57875000-7fee57876000 r--p 00107000 08:02 12323263                   /lib/x86_64-linux-gnu/libm-2.24.so
7fee57876000-7fee57877000 rw-p 00108000 08:02 12323263                   /lib/x86_64-linux-gnu/libm-2.24.so
7fee57877000-7fee57892000 r-xp 00000000 08:02 12325524                   /lib/x86_64-linux-gnu/libz.so.1.2.11
7fee57892000-7fee57a91000 ---p 0001b000 08:02 12325524                   /lib/x86_64-linux-gnu/libz.so.1.2.11
7fee57a91000-7fee57a92000 r--p 0001a000 08:02 12325524                   /lib/x86_64-linux-gnu/libz.so.1.2.11
7fee57a92000-7fee57a93000 rw-p 0001b000 08:02 12325524                   /lib/x86_64-linux-gnu/libz.so.1.2.11
7fee57a93000-7fee57aba000 r-xp 00000000 08:02 12322934                   /lib/x86_64-linux-gnu/libexpat.so.1.6.2
7fee57aba000-7fee57cba000 ---p 00027000 08:02 12322934                   /lib/x86_64-linux-gnu/libexpat.so.1.6.2
7fee57cba000-7fee57cbc000 r--p 00027000 08:02 12322934                   /lib/x86_64-linux-gnu/libexpat.so.1.6.2
7fee57cbc000-7fee57cbd000 rw-p 00029000 08:02 12322934                   /lib/x86_64-linux-gnu/libexpat.so.1.6.2
7fee57cbd000-7fee57cbf000 r-xp 00000000 08:02 12324271                   /lib/x86_64-linux-gnu/libutil-2.24.so
7fee57cbf000-7fee57ebe000 ---p 00002000 08:02 12324271                   /lib/x86_64-linux-gnu/libutil-2.24.so
7fee57ebe000-7fee57ebf000 r--p 00001000 08:02 12324271                   /lib/x86_64-linux-gnu/libutil-2.24.so
7fee57ebf000-7fee57ec0000 rw-p 00002000 08:02 12324271                   /lib/x86_64-linux-gnu/libutil-2.24.so
7fee57ec0000-7fee57ec3000 r-xp 00000000 08:02 12323262                   /lib/x86_64-linux-gnu/libdl-2.24.so
7fee57ec3000-7fee580c2000 ---p 00003000 08:02 12323262                   /lib/x86_64-linux-gnu/libdl-2.24.so
7fee580c2000-7fee580c3000 r--p 00002000 08:02 12323262                   /lib/x86_64-linux-gnu/libdl-2.24.so
7fee580c3000-7fee580c4000 rw-p 00003000 08:02 12323262                   /lib/x86_64-linux-gnu/libdl-2.24.so
7fee580c4000-7fee581c2000 r-xp 00000000 08:02 12323259                   /lib/x86_64-linux-gnu/libc-2.24.so
7fee581c2000-7fee581c3000 r-xp 000fe000 08:02 12323259                   /lib/x86_64-linux-gnu/libc-2.24.so
7fee581c3000-7fee581c6000 r-xp 000ff000 08:02 12323259                   /lib/x86_64-linux-gnu/libc-2.24.so
7fee581c6000-7fee581c7000 r-xp 00102000 08:02 12323259                   /lib/x86_64-linux-gnu/libc-2.24.so
7fee581c7000-7fee581cd000 r-xp 00103000 08:02 12323259                   /lib/x86_64-linux-gnu/libc-2.24.so
7fee581cd000-7fee581cf000 r-xp 00109000 08:02 12323259                   /lib/x86_64-linux-gnu/libc-2.24.so
7fee581cf000-7fee58282000 r-xp 0010b000 08:02 12323259                   /lib/x86_64-linux-gnu/libc-2.24.so
7fee58282000-7fee58481000 ---p 001be000 08:02 12323259                   /lib/x86_64-linux-gnu/libc-2.24.so
7fee58481000-7fee58485000 r--p 001bd000 08:02 12323259                   /lib/x86_64-linux-gnu/libc-2.24.so
7fee58485000-7fee58487000 rw-p 001c1000 08:02 12323259                   /lib/x86_64-linux-gnu/libc-2.24.so
7fee58487000-7fee5848b000 rw-p 00000000 00:00 0 
7fee5848b000-7fee584a3000 r-xp 00000000 08:02 12324267                   /lib/x86_64-linux-gnu/libpthread-2.24.so
7fee584a3000-7fee586a3000 ---p 00018000 08:02 12324267                   /lib/x86_64-linux-gnu/libpthread-2.24.so
7fee586a3000-7fee586a4000 r--p 00018000 08:02 12324267                   /lib/x86_64-linux-gnu/libpthread-2.24.so
7fee586a4000-7fee586a5000 rw-p 00019000 08:02 12324267                   /lib/x86_64-linux-gnu/libpthread-2.24.so
7fee586a5000-7fee586a9000 rw-p 00000000 00:00 0 
7fee586a9000-7fee586cf000 r-xp 00000000 08:02 12320773                   /lib/x86_64-linux-gnu/ld-2.24.so
7fee586e7000-7fee588ab000 rw-p 00000000 00:00 0 
7fee588c2000-7fee588c3000 rw-p 00000000 00:00 0 
7fee588c3000-7fee588c4000 rwxp 00000000 00:00 0 
7fee588c4000-7fee588cb000 r--s 00000000 08:02 1446764                    /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
7fee588cb000-7fee588ce000 rw-p 00000000 00:00 0 
7fee588ce000-7fee588cf000 r--p 00025000 08:02 12320773                   /lib/x86_64-linux-gnu/ld-2.24.so
7fee588cf000-7fee588d0000 rw-p 00026000 08:02 12320773                   /lib/x86_64-linux-gnu/ld-2.24.so
7fee588d0000-7fee588d1000 rw-p 00000000 00:00 0 
7fff1d230000-7fff1d251000 rw-p 00000000 00:00 0                          [stack]
7fff1d2fc000-7fff1d2fe000 r--p 00000000 00:00 0                          [vvar]
7fff1d2fe000-7fff1d300000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
[gnw20pc:00555] *** Process received signal ***
[gnw20pc:00555] Signal: Aborted (6)
[gnw20pc:00555] Signal code:  (-6)
[gnw20pc:00555] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11670)[0x7fee5849c670]
[gnw20pc:00555] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x9f)[0x7fee580f977f]
[gnw20pc:00555] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)[0x7fee580fb37a]
[gnw20pc:00555] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x79090)[0x7fee5813d090]
[gnw20pc:00555] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x82c3a)[0x7fee58146c3a]
[gnw20pc:00555] [ 5] /lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7fee5814ad2c]
[gnw20pc:00555] [ 6] python3(PyDict_Clear+0xd6)[0x55ae8831af66]
[gnw20pc:00555] [ 7] python3(PyImport_Cleanup+0x211)[0x55ae88290371]
[gnw20pc:00555] [ 8] python3(Py_Finalize+0x61)[0x55ae88377d41]
[gnw20pc:00555] [ 9] python3(Py_Main+0x641)[0x55ae883af051]
[gnw20pc:00555] [10] python3(main+0xe1)[0x55ae8823ee51]
[gnw20pc:00555] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf1)[0x7fee580e43f1]
[gnw20pc:00555] [12] python3(_start+0x2a)[0x55ae8834548a]
[gnw20pc:00555] *** End of error message ***
Aborted (core dumped)

Comments (21)

  1. Lisandro Dalcin

    This is happening at Python finalization. You provided too little information to reproduce. I don't usually test with Open MPI. What version are you using? Could you run the exact same thing under valgrind?

  2. Prof Garth Wells reporter

    OpenMPI version is 2.1.1. To reproduce:

    docker run wells/petsc4py-py3-crash:latest python3 -c "import petsc4py.PETSc"

    This fails. The following exits without error:

    docker run wells/petsc4py-py3-crash:latest python2 -c "import petsc4py.PETSc"

    Here's the Dockerfile:

    FROM ubuntu:17.04

WORKDIR /tmp

RUN apt-get update && apt-get install -y \
    gcc  \
    gfortran \
    git \
    libblas-dev \
    libopenmpi-dev \
    liblapack-dev \
    openmpi-bin \
    python-minimal \
    python-pip \
    python3-minimal \
    python3-pip \
    valgrind && \
    rm -rf /var/lib/apt/lists/*

RUN git clone https://bitbucket.org/petsc/petsc.git && \
    cd petsc && \
    ./configure --prefix=/usr/local/petsc && \
    make && \
    make install && \
    rm -rf /tmp/*

RUN git clone https://bitbucket.org/petsc/petsc4py.git && \
    cd petsc4py && \
    export PETSC_DIR=/usr/local/petsc && \
    pip3 install . && \
    pip2 install . && \
    rm -rf /tmp/*
  3. Prof Garth Wells reporter

    Seeing error with MPICH too:

     docker run wells/petsc4py-py3-mpich:latest python3 -c "import petsc4py.PETSc"
  4. Lisandro Dalcin

    I'm running Fedora 26, and currently docker is not working, so I cannot try myself. On Fedora 26, system Python 3 with system MPICH seems to work just fine and valgrind runs are clean.

    Could you please run the line below?

    docker run wells/petsc4py-py3-mpich:latest valgrind -q python3 -c "import petsc4py.PETSc"
  6. Lisandro Dalcin

    Well, that was not very useful, the usual ton of false positives out of the Python memory allocator. And the final failure is most likely from the checkpoint lib at MPI initialization. Not sure what's going on. Could you try this one instead:

    docker run wells/petsc4py-py3-mpich:latest python3 -v -c "import petsc4py.PETSc;print('@@@ Import OK @@@')"
  8. Lisandro Dalcin

    Well, that confirms that the problem happens at Python shutdown. However, I believe at the failure point, PETSc is still initialized. Could you repeat the test with just python3 -c import numpy ? I'm not sure what's going on, and I cannot run docker in my desktop machine :-).

  10. Lawrence Mitchell

    We've started seeing this issue too. It looks like something broke with the release of Cython 0.27. If I pin the Cython version to 0.26, everything appears to work fine.

  11. Lawrence Mitchell

    Bisect in the cython repo blames:

    commit 9f2471dba373c8ce8f14e81da1201ace547f0b1a
Author: Stefan Behnel <stefan_ml@behnel.de>
Date:   Sat Jul 22 16:43:11 2017 +0200

    implement PEP 489 multi-phase module initialisation in Py3.5+

    Will raise a bug there.

  13. Lisandro Dalcin

    Oh! I see. I'll upgrade my Cython and give it a try ASAP. This may be related to some abuse from petsc4py side.

  14. Lisandro Dalcin

    @garth-wells Could you please try again with latest petsc4py/master? I pushed a quick fix c29fb46.

    @wence I think you should close the Cython issue. petsc4py is playing tricks with the import machinery, and the failure was not Cython's fault.

  19. Lawrence Mitchell

    Should we keep a separate issue open about long term migrating to this new import scheme?

  20. Lisandro Dalcin

    Well, not sure. This is not really about migrating to the new import scheme, but rather finding a way to refactoring some code, maybe by merging the contents of libpetsc4py.pyx with the other Cython sources.

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