Segmentation fault when using predict on sparse csr matrix

[keanpantraw]

Environment info

Operating System: Linux CPU: Intel Python: 3.6 LightGBM version: built from 353286a8d0cd695508f6d6193468d8a8fcc8dbf7 with MPI support

lightgbm version 0.1 numpy version 1.12.1 scipy version 0.19.0

Error Message:

[LightGBM] [Info] Number of positive: 1627, number of negative: 180938
[LightGBM] [Info] Total Bins 14937
[LightGBM] [Info] Number of data: 182565, number of used features: 5242
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[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=14
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=15
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[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=14
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[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=18
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[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=22
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=20
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=15
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=19
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=16
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=19
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=15
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=14
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=15
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=16
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=13
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=13
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=17
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=16
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=14
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=15
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=14
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=15
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=18
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=17
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=21
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=15
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=15
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=24
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=24
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=23
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=19
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=27
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[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=28
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=24
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=28
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=27
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=29
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=29
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=26
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=25
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[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=27
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=25
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=24
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=27
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[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=28
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=27
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=21
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=18
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=18
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=25
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[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=19
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=24
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=16
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=25
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=16
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=17
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=21
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=23
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=20
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=22
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=14
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=21
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=18
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=23
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=18
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=17
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=15
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=19
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=23
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=16
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=22
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=16
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=19
[LightGBM] [Info] Trained a tree with leaves=31 and max_depth=23
*** Error in `/home/bfilippov/anaconda3/bin/python3.6': double free or corruption (!prev): 0x0000000004083690 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f1e5c3be7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7f1e5c3c6e0a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f1e5c3ca98c]
/home/bfilippov/anaconda3/lib/python3.6/site-packages/lightgbm-0.1-py3.6.egg/lightgbm/lib_lightgbm.so(_ZN8LightGBM7Booster7PredictEiiiSt8functionIFSt6vectorISt4pairIidESaIS4_EEiEEPdPl+0x235)[0x7f1e379aadd5]
/home/bfilippov/anaconda3/lib/python3.6/site-packages/lightgbm-0.1-py3.6.egg/lightgbm/lib_lightgbm.so(LGBM_BoosterPredictForCSR+0x98)[0x7f1e379a2fc8]
/home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_ctypes.cpython-36m-x86_64-linux-gnu.so(ffi_call_unix64+0x4c)[0x7f1e5ba70550]
/home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_ctypes.cpython-36m-x86_64-linux-gnu.so(ffi_call+0x1f5)[0x7f1e5ba6fcf5]
/home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_ctypes.cpython-36m-x86_64-linux-gnu.so(_ctypes_callproc+0x3dc)[0x7f1e5ba6783c]
/home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_ctypes.cpython-36m-x86_64-linux-gnu.so(+0x9da3)[0x7f1e5ba5fda3]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x9e)[0x7f1e5d2b092e]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(+0x147d1b)[0x7f1e5d38cd1b]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x26fd)[0x7f1e5d38fbbd]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(+0x1458d4)[0x7f1e5d38a8d4]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(+0x148048)[0x7f1e5d38d048]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x26fd)[0x7f1e5d38fbbd]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(+0x1464c0)[0x7f1e5d38b4c0]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(+0x147eea)[0x7f1e5d38ceea]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x26fd)[0x7f1e5d38fbbd]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(+0x1464c0)[0x7f1e5d38b4c0]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(+0x147eea)[0x7f1e5d38ceea]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x1e7d)[0x7f1e5d38f33d]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(+0x1464c0)[0x7f1e5d38b4c0]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(+0x147eea)[0x7f1e5d38ceea]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x26fd)[0x7f1e5d38fbbd]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(+0x1464c0)[0x7f1e5d38b4c0]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(PyEval_EvalCodeEx+0x63)[0x7f1e5d38b943]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(PyEval_EvalCode+0x3b)[0x7f1e5d38b98b]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(PyRun_FileExFlags+0x130)[0x7f1e5d3be100]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(PyRun_SimpleFileExFlags+0x173)[0x7f1e5d3bf6f3]
/home/bfilippov/anaconda3/bin/../lib/libpython3.6m.so.1.0(Py_Main+0xd41)[0x7f1e5d3daa41]
/home/bfilippov/anaconda3/bin/python3.6(main+0x16d)[0x400c1d]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f1e5c367830]
/home/bfilippov/anaconda3/bin/python3.6[0x4009e9]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:11 20448249                           /home/bfilippov/anaconda3/bin/python3.6
00601000-00602000 rw-p 00001000 08:11 20448249                           /home/bfilippov/anaconda3/bin/python3.6
00610000-042ae000 rw-p 00000000 00:00 0                                  [heap]
7f1e20000000-7f1e209ad000 rw-p 00000000 00:00 0 
7f1e209ad000-7f1e24000000 ---p 00000000 00:00 0 
7f1e24000000-7f1e24021000 rw-p 00000000 00:00 0 
7f1e24021000-7f1e28000000 ---p 00000000 00:00 0 
7f1e28000000-7f1e28a33000 rw-p 00000000 00:00 0 
7f1e28a33000-7f1e2c000000 ---p 00000000 00:00 0 
7f1e30000000-7f1e30a56000 rw-p 00000000 00:00 0 
7f1e30a56000-7f1e34000000 ---p 00000000 00:00 0 
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7f1e3435b000-7f1e3475b000 rw-p 00000000 00:00 0 
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7f1e3475c000-7f1e34b5c000 rw-p 00000000 00:00 0 
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7f1e34b5d000-7f1e364b3000 rw-p 00000000 00:00 0 
7f1e364b3000-7f1e364bc000 r-xp 00000000 08:11 20976243                   /home/bfilippov/anaconda3/lib/libltdl.so.7.3.0
7f1e364bc000-7f1e366bb000 ---p 00009000 08:11 20976243                   /home/bfilippov/anaconda3/lib/libltdl.so.7.3.0
7f1e366bb000-7f1e366bc000 rw-p 00008000 08:11 20976243                   /home/bfilippov/anaconda3/lib/libltdl.so.7.3.0
7f1e366bc000-7f1e366c6000 r-xp 00000000 08:11 1843845                    /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7f1e366c6000-7f1e368c5000 ---p 0000a000 08:11 1843845                    /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7f1e368c5000-7f1e368c6000 r--p 00009000 08:11 1843845                    /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7f1e368c6000-7f1e368c7000 rw-p 0000a000 08:11 1843845                    /usr/lib/x86_64-linux-gnu/libnuma.so.1.0.0
7f1e368c7000-7f1e36900000 r-xp 00000000 08:11 1846186                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.6.8
7f1e36900000-7f1e36aff000 ---p 00039000 08:11 1846186                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.6.8
7f1e36aff000-7f1e36b00000 r--p 00038000 08:11 1846186                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.6.8
7f1e36b00000-7f1e36b01000 rw-p 00039000 08:11 1846186                    /usr/lib/x86_64-linux-gnu/libhwloc.so.5.6.8
7f1e36b01000-7f1e36b91000 r-xp 00000000 08:11 11274973                   /usr/lib/openmpi/lib/libopen-pal.so.13.0.2
7f1e36b91000-7f1e36d91000 ---p 00090000 08:11 11274973                   /usr/lib/openmpi/lib/libopen-pal.so.13.0.2
7f1e36d91000-7f1e36d95000 r--p 00090000 08:11 11274973                   /usr/lib/openmpi/lib/libopen-pal.so.13.0.2
7f1e36d95000-7f1e36d99000 rw-p 00094000 08:11 11274973                   /usr/lib/openmpi/lib/libopen-pal.so.13.0.2
7f1e36d99000-7f1e36d9e000 rw-p 00000000 00:00 0 
7f1e36d9e000-7f1e36e13000 r-xp 00000000 08:11 11274969                   /usr/lib/openmpi/lib/libopen-rte.so.12.0.2
7f1e36e13000-7f1e37012000 ---p 00075000 08:11 11274969                   /usr/lib/openmpi/lib/libopen-rte.so.12.0.2
7f1e37012000-7f1e37013000 r--p 00074000 08:11 11274969                   /usr/lib/openmpi/lib/libopen-rte.so.12.0.2
7f1e37013000-7f1e37016000 rw-p 00075000 08:11 11274969                   /usr/lib/openmpi/lib/libopen-rte.so.12.0.2
7f1e37016000-7f1e37018000 rw-p 00000000 00:00 0 
7f1e37018000-7f1e37025000 r-xp 00000000 08:11 1846193                    /usr/lib/libibverbs.so.1.0.0
7f1e37025000-7f1e37225000 ---p 0000d000 08:11 1846193                    /usr/lib/libibverbs.so.1.0.0
7f1e37225000-7f1e37226000 r--p 0000d000 08:11 1846193                    /usr/lib/libibverbs.so.1.0.0
7f1e37226000-7f1e37227000 rw-p 0000e000 08:11 1846193                    /usr/lib/libibverbs.so.1.0.0
7f1e37227000-7f1e37247000 r-xp 00000000 08:11 20462560                   /home/bfilippov/anaconda3/lib/libgomp.so.1.0.0
7f1e37247000-7f1e37447000 ---p 00020000 08:11 20462560                   /home/bfilippov/anaconda3/lib/libgomp.so.1.0.0
7f1e37447000-7f1e3744a000 rw-p 00020000 08:11 20462560                   /home/bfilippov/anaconda3/lib/libgomp.so.1.0.0
7f1e3744a000-7f1e374fc000 r-xp 00000000 08:11 11274966                   /usr/lib/openmpi/lib/libmpi.so.12.0.2
7f1e374fc000-7f1e376fc000 ---p 000b2000 08:11 11274966                   /usr/lib/openmpi/lib/libmpi.so.12.0.2
7f1e376fc000-7f1e376fd000 r--p 000b2000 08:11 11274966                   /usr/lib/openmpi/lib/libmpi.so.12.0.2
7f1e376fd000-7f1e3770d000 rw-p 000b3000 08:11 11274966                   /usr/lib/openmpi/lib/libmpi.so.12.0.2
7f1e3770d000-7f1e37720000 rw-p 00000000 00:00 0 
7f1e37720000-7f1e37738000 r-xp 00000000 08:11 11274844                   /usr/lib/openmpi/lib/libmpi_cxx.so.1.1.3
7f1e37738000-7f1e37938000 ---p 00018000 08:11 11274844                   /usr/lib/openmpi/lib/libmpi_cxx.so.1.1.3
7f1e37938000-7f1e3793a000 r--p 00018000 08:11 11274844                   /usr/lib/openmpi/lib/libmpi_cxx.so.1.1.3
7f1e3793a000-7f1e3793b000 rw-p 0001a000 08:11 11274844                   /usr/lib/openmpi/lib/libmpi_cxx.so.1.1.3
7f1e3795d000-7f1e37a83000 r-xp 00000000 08:11 26218777                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/lightgbm-0.1-py3.6.egg/lightgbm/lib_lightgbm.so
7f1e37a83000-7f1e37c83000 ---p 00126000 08:11 26218777                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/lightgbm-0.1-py3.6.egg/lightgbm/lib_lightgbm.so
7f1e37c83000-7f1e37c88000 r--p 00126000 08:11 26218777                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/lightgbm-0.1-py3.6.egg/lightgbm/lib_lightgbm.so
7f1e37c88000-7f1e37c8a000 rw-p 0012b000 08:11 26218777                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/lightgbm-0.1-py3.6.egg/lightgbm/lib_lightgbm.so
7f1e37c8a000-7f1e37d0a000 rw-p 00000000 00:00 0 
7f1e37d0a000-7f1e37d3c000 r-xp 00000000 08:11 21372158                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/sklearn/metrics/pairwise_fast.cpython-36m-x86_64-linux-gnu.so
7f1e37d3c000-7f1e37f3b000 ---p 00032000 08:11 21372158                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/sklearn/metrics/pairwise_fast.cpython-36m-x86_64-linux-gnu.so
7f1e37f3b000-7f1e37f3f000 rw-p 00031000 08:11 21372158                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/sklearn/metrics/pairwise_fast.cpython-36m-x86_64-linux-gnu.so
7f1e37f3f000-7f1e37f42000 r-xp 00000000 08:11 21372463                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/sklearn/utils/lgamma.cpython-36m-x86_64-linux-gnu.so
7f1e37f42000-7f1e38142000 ---p 00003000 08:11 21372463                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/sklearn/utils/lgamma.cpython-36m-x86_64-linux-gnu.so
7f1e38142000-7f1e38143000 rw-p 00003000 08:11 21372463                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/sklearn/utils/lgamma.cpython-36m-x86_64-linux-gnu.so
7f1e38143000-7f1e3815c000 r-xp 00000000 08:11 21372143                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/sklearn/metrics/cluster/expected_mutual_info_fast.cpython-36m-x86_64-linux-gnu.so
7f1e3815c000-7f1e3835b000 ---p 00019000 08:11 21372143                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/sklearn/metrics/cluster/expected_mutual_info_fast.cpython-36m-x86_64-linux-gnu.so
7f1e3835b000-7f1e3835d000 rw-p 00018000 08:11 21372143                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/sklearn/metrics/cluster/expected_mutual_info_fast.cpython-36m-x86_64-linux-gnu.so
7f1e3835d000-7f1e3839d000 rw-p 00000000 00:00 0 
7f1e3839d000-7f1e383af000 r-xp 00000000 08:11 21372450                   /home/bfilippov/anaconda3/lib/python3.6/site-packages/sklearn/utils/_random.cpython-36m-x86_64-linux-gnu.so
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7f1e5aaf0000-7f1e5aaf5000 r-xp 00000000 08:11 20449761                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_hashlib.cpython-36m-x86_64-linux-gnu.so
7f1e5aaf5000-7f1e5acf5000 ---p 00005000 08:11 20449761                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_hashlib.cpython-36m-x86_64-linux-gnu.so
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7f1e5acf6000-7f1e5acff000 r-xp 00000000 08:11 20449792                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/math.cpython-36m-x86_64-linux-gnu.so
7f1e5acff000-7f1e5aefe000 ---p 00009000 08:11 20449792                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/math.cpython-36m-x86_64-linux-gnu.so
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7f1e5af00000-7f1e5af24000 r-xp 00000000 08:11 21758131                   /home/bfilippov/anaconda3/lib/liblzma.so.5.2.2
7f1e5af24000-7f1e5b124000 ---p 00024000 08:11 21758131                   /home/bfilippov/anaconda3/lib/liblzma.so.5.2.2
7f1e5b124000-7f1e5b125000 rw-p 00024000 08:11 21758131                   /home/bfilippov/anaconda3/lib/liblzma.so.5.2.2
7f1e5b125000-7f1e5b12b000 r-xp 00000000 08:11 20449765                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_lzma.cpython-36m-x86_64-linux-gnu.so
7f1e5b12b000-7f1e5b32b000 ---p 00006000 08:11 20449765                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_lzma.cpython-36m-x86_64-linux-gnu.so
7f1e5b32b000-7f1e5b32d000 rw-p 00006000 08:11 20449765                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_lzma.cpython-36m-x86_64-linux-gnu.so
7f1e5b32d000-7f1e5b33f000 r-xp 00000000 08:11 20449745                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_bz2.cpython-36m-x86_64-linux-gnu.so
7f1e5b33f000-7f1e5b53e000 ---p 00012000 08:11 20449745                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_bz2.cpython-36m-x86_64-linux-gnu.so
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7f1e5b540000-7f1e5b580000 rw-p 00000000 00:00 0 
7f1e5b580000-7f1e5b582000 r-xp 00000000 08:11 20449791                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/grp.cpython-36m-x86_64-linux-gnu.so
7f1e5b582000-7f1e5b782000 ---p 00002000 08:11 20449791                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/grp.cpython-36m-x86_64-linux-gnu.so
7f1e5b782000-7f1e5b783000 rw-p 00002000 08:11 20449791                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/grp.cpython-36m-x86_64-linux-gnu.so
7f1e5b78c000-7f1e5b84c000 rw-p 00000000 00:00 0 
7f1e5b84c000-7f1e5b854000 r-xp 00000000 08:11 20449780                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
7f1e5b854000-7f1e5ba53000 ---p 00008000 08:11 20449780                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
7f1e5ba53000-7f1e5ba56000 rw-p 00007000 08:11 20449780                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_struct.cpython-36m-x86_64-linux-gnu.so
7f1e5ba56000-7f1e5ba76000 r-xp 00000000 08:11 20449754                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_ctypes.cpython-36m-x86_64-linux-gnu.so
7f1e5ba76000-7f1e5bc75000 ---p 00020000 08:11 20449754                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_ctypes.cpython-36m-x86_64-linux-gnu.so
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7f1e5bc7a000-7f1e5bcba000 rw-p 00000000 00:00 0 
7f1e5bcba000-7f1e5bcbc000 r-xp 00000000 08:11 20449762                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
7f1e5bcbc000-7f1e5bebc000 ---p 00002000 08:11 20449762                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
7f1e5bebc000-7f1e5bebe000 rw-p 00002000 08:11 20449762                   /home/bfilippov/anaconda3/lib/python3.6/lib-dynload/_heapq.cpython-36m-x86_64-linux-gnu.so
7f1e5bebe000-7f1e5bf3e000 rw-p 00000000 00:00 0 
7f1e5bf3e000-7f1e5c347000 r--p 00000000 08:11 1836478                    /usr/lib/locale/locale-archive
7f1e5c347000-7f1e5c506000 r-xp 00000000 08:11 9961558                    /lib/x86_64-linux-gnu/libc-2.23.so
7f1e5c506000-7f1e5c706000 ---p 001bf000 08:11 9961558                    /lib/x86_64-linux-gnu/libc-2.23.so
7f1e5c706000-7f1e5c70a000 r--p 001bf000 08:11 9961558                    /lib/x86_64-linux-gnu/libc-2.23.so
7f1e5c70a000-7f1e5c70c000 rw-p 001c3000 08:11 9961558                    /lib/x86_64-linux-gnu/libc-2.23.so
7f1e5c70c000-7f1e5c710000 rw-p 00000000 00:00 0 
7f1e5c710000-7f1e5c818000 r-xp 00000000 08:11 9961556                    /lib/x86_64-linux-gnu/libm-2.23.so
7f1e5c818000-7f1e5ca17000 ---p 00108000 08:11 9961556                    /lib/x86_64-linux-gnu/libm-2.23.so
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7f1e5ca19000-7f1e5ca20000 r-xp 00000000 08:11 9961565                    /lib/x86_64-linux-gnu/librt-2.23.so
7f1e5ca20000-7f1e5cc1f000 ---p 00007000 08:11 9961565                    /lib/x86_64-linux-gnu/librt-2.23.so
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7f1e5cc21000-7f1e5cc23000 r-xp 00000000 08:11 9965992                    /lib/x86_64-linux-gnu/libutil-2.23.so
7f1e5cc23000-7f1e5ce22000 ---p 00002000 08:11 9965992                    /lib/x86_64-linux-gnu/libutil-2.23.so
7f1e5ce22000-7f1e5ce23000 r--p 00001000 08:11 9965992                    /lib/x86_64-linux-gnu/libutil-2.23.so
7f1e5ce23000-7f1e5ce24000 rw-p 00002000 08:11 9965992                    /lib/x86_64-linux-gnu/libutil-2.23.so
7f1e5ce24000-7f1e5ce27000 r-xp 00000000 08:11 9961497                    /lib/x86_64-linux-gnu/libdl-2.23.so
7f1e5ce27000-7f1e5d026000 ---p 00003000 08:11 9961497                    /lib/x86_64-linux-gnu/libdl-2.23.so
7f1e5d026000-7f1e5d027000 r--p 00002000 08:11 9961497                    /lib/x86_64-linux-gnu/libdl-2.23.so
7f1e5d027000-7f1e5d028000 rw-p 00003000 08:11 9961497                    /lib/x86_64-linux-gnu/libdl-2.23.so
7f1e5d028000-7f1e5d040000 r-xp 00000000 08:11 9961569                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7f1e5d040000-7f1e5d23f000 ---p 00018000 08:11 9961569                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7f1e5d23f000-7f1e5d240000 r--p 00017000 08:11 9961569                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7f1e5d240000-7f1e5d241000 rw-p 00018000 08:11 9961569                    /lib/x86_64-linux-gnu/libpthread-2.23.so
7f1e5d241000-7f1e5d245000 rw-p 00000000 00:00 0 
7f1e5d245000-7f1e5d4b1000 r-xp 00000000 08:11 20448557                   /home/bfilippov/anaconda3/lib/libpython3.6m.so.1.0
7f1e5d4b1000-7f1e5d6b1000 ---p 0026c000 08:11 20448557                   /home/bfilippov/anaconda3/lib/libpython3.6m.so.1.0
7f1e5d6b1000-7f1e5d71a000 rw-p 0026c000 08:11 20448557                   /home/bfilippov/anaconda3/lib/libpython3.6m.so.1.0
7f1e5d71a000-7f1e5d74a000 rw-p 00000000 00:00 0 
7f1e5d74a000-7f1e5d770000 r-xp 00000000 08:11 9961559                    /lib/x86_64-linux-gnu/ld-2.23.so
7f1e5d786000-7f1e5d94b000 rw-p 00000000 00:00 0 
7f1e5d964000-7f1e5d965000 rw-p 00000000 00:00 0 
7f1e5d965000-7f1e5d966000 rwxp 00000000 00:00 0 
7f1e5d966000-7f1e5d96d000 r--s 00000000 08:11 2099211                    /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
7f1e5d96d000-7f1e5d96f000 rw-p 00000000 00:00 0 
7f1e5d96f000-7f1e5d970000 r--p 00025000 08:11 9961559                    /lib/x86_64-linux-gnu/ld-2.23.so
7f1e5d970000-7f1e5d971000 rw-p 00026000 08:11 9961559                    /lib/x86_64-linux-gnu/ld-2.23.so
7f1e5d971000-7f1e5d972000 rw-p 00000000 00:00 0 
7ffd8d980000-7ffd8d9a2000 rw-p 00000000 00:00 0                          [stack]
7ffd8d9b7000-7ffd8d9b9000 r--p 00000000 00:00 0                          [vvar]
7ffd8d9b9000-7ffd8d9bb000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

Reproducible examples

See attached archive - it contains persisted csr matrix and script which reproduces issue.

reproducible-example.zip

Steps to reproduce

import lightgbm as lgb
import numpy as np
import scipy
from scipy.sparse import load_npz

if __name__ == "__main__":
    print("lightgbm version", lgb.__version__)
    print("numpy version", np.__version__)
    print("scipy version", scipy.__version__)

    X = load_npz('csr_matrix.npz')
    y = np.load('labels.npy')
    train_ix = np.load('train_ix.npy')
    test_ix = np.load('test_ix.npy')

    booster = lgb.LGBMClassifier(n_estimators=100, silent=False)

    booster.fit(X[train_ix, :], y[train_ix])

    booster.predict_proba(X[test_ix,:])

[guolinke]

fixed in the latest commit.

[github-actions[bot]]

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