Error in `python3': double free or corruption (fasttop): 0x00007f21bc00ae20

hdante commented 4 months ago

Hello, during initial tests with lephare and pz-rail-lephare, I've hit a double free error on the _lephare.so library. Crash is non-deterministic and I don't know what needs to be done to trigger the crash. The full execution output follows.

(base) [henrique.almeida@loginapl01 henrique.almeida]$ rail-train -a lephare train3.hdf5 lephare02.pkl
Start: 2024-05-16 19:01:42.646920
Estimator algorithm: lephare
Bins: 301
HDF5 group name: ""
Column template for magnitude data: "mag_{band}"
Column template for error data: "magerr_{band}"
Starting setup.
Loading all program modules...
Default work cache at /lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/work
                    is already linked. This is linked to the run directory:
                    /lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/runs/20240516T183817
Number of keywords read in the config file: 86
Number of keywords read in the config file: 86
Configuring trainer...
User defined LEPHAREDIR is set. Code runs depend on all required
                auxiliary data being present at /lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/data.
User defined LEPHAREWORK is set. All intermediate files will
                be written to /lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/runs/train.
Loading input file...
Setup done.
Starting training.
# NAME                        IDENT      Lbda_mean Lbeff(Vega)       FWHM     AB-cor    TG-cor      VEGA M_sun(AB)   CALIB      Lb_eff    Fac_corr
total_u.pb                    1             0.3664      0.3720      0.0458    0.7023   -0.2237  -20.9207    6.3126       0      0.3643      1.0000
total_g.pb                    2             0.4842      0.4744      0.1395   -0.0845   -0.2511  -20.7220    5.0903       0      0.4763      1.0000
total_r.pb                    3             0.6251      0.6162      0.1340    0.1519    0.2648  -21.5250    4.6488       0      0.6195      1.0000
total_i.pb                    4             0.7562      0.7497      0.1297    0.3697    0.5838  -22.1618    4.5362       0      0.7520      1.0000
total_z.pb                    5             0.8693      0.8670      0.1010    0.5172    0.7617  -22.6166    4.5165       0      0.8670      1.0000
total_y3.pb                   6             1.0083      1.0053      0.0577    0.5864    0.7956  -23.0094    4.5109       0      1.0065      1.0000
{'star_sed': '/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/data/sed/STAR/STAR_MOD_ALL.list'}
#######################################
# It s translating SEDs to binary library #
# with the following options :           
# Config file     : 
# Library type     : STAR
# STAR_SED    :/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/data/sed/STAR/STAR_MOD_ALL.list
# STAR_LIB    :LSST_STAR_BIN
# STAR_LIB doc:/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/runs/train/lib_bin/LSST_STAR_BIN.doc
# STAR_FSCALE :0.0000
#######################################
Number of SED in the list 254
WRONG NUMBER OF ARGUMENTS FOR OPTION MOD_EXTINC
We have 2 instead of 8
Use default value 0,0 for all filters 
 All files opened 
#######################################
# It s computing the SYNTHETIC MAGNITUDES #
# For Gal/QSO libraries with these OPTIONS #
# with the following options :           
# Config file     : 
# Filter file     : filter_lsst
# Magnitude type     : AB
# COSMOLOGY   :70.0000,0.3000,0.7000
# STAR_LIB_IN    :/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/runs/train/lib_bin/LSST_STAR_BIN(.doc & .bin)
# STAR_LIB_OUT   :/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/runs/train/lib_mag/LSST_STAR_MAG(.doc & .bin)
# LIB_ASCII   YES
# CREATION_DATE Thu May 16 19:01:46 2024
#############################################
{'gal_sed': '/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/data/examples/COSMOS_MOD.list'}
#######################################
# It s translating SEDs to binary library #
# with the following options :           
# Config file     : 
# Library type     : GAL
# GAL_SED    :/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/data/examples/COSMOS_MOD.list
# GAL_LIB    :LSST_GAL_BIN
# GAL_LIB doc:/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/runs/train/lib_bin/LSST_GAL_BIN.doc
# GAL_LIB phys:/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/runs/train/lib_bin/LSST_GAL_BIN.phys
# SEL_AGE    :none
# GAL_FSCALE :1.0000
# AGE_RANGE   0.0000 15000000000.0000
#######################################
Number of SED in the list 31
 All files opened 
#######################################
# It s computing the SYNTHETIC MAGNITUDES #
# For Gal/QSO libraries with these OPTIONS #
# with the following options :           
# Config file     : 
# Filter file     : filter_lsst
# Magnitude type     : AB
# GAL_LIB_IN    :/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/runs/train/lib_bin/LSST_GAL_BIN(.doc & .bin)
# GAL_LIB_OUT   :/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/runs/train/lib_mag/LSST_GAL_MAG(.doc & .bin)
# ZGRID_TYPE   :0
# Z_STEP   :0.0100 0.0000 7.0000
# COSMOLOGY   :70.0000,0.3000,0.7000
# EXTINC_LAW   :SMC_prevot.dat SB_calzetti.dat SB_calzetti_bump1.dat SB_calzetti_bump2.dat 
# MOD_EXTINC   :18 26 26 33 26 33 26 33 
# EB_V   :0.0000 0.0500 0.1000 0.1500 0.2000 0.2500 0.3000 0.3500 0.4000 0.5000 
# EM_LINES   EMP_UV
# EM_DISPERSION   0.5000,0.7500,1.0000,1.5000,2.0000,
# LIB_ASCII   YES
# CREATION_DATE Thu May 16 19:01:46 2024
#############################################
*** Error in `python3': double free or corruption (fasttop): 0x00007f21bc00ae20 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x7f26474f6329]
/lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/../lib/libstdc++.so.6(_ZNSs9_M_mutateEmmm+0x1b1)[0x7f21d24cf541]
/lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/../lib/libstdc++.so.6(_ZNSs12_M_leak_hardEv+0x3b)[0x7f21d24cf5bb]
/lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/lib/python3.11/site-packages/lephare/_lephare.cpython-311-x86_64-linux-gnu.so(+0x6657a)[0x7f21cce7357a]
/lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/lib/python3.11/site-packages/mkl/../../../libiomp5.so(+0xb4aac)[0x7f263f16faac]
/lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/lib/python3.11/site-packages/mkl/../../../libiomp5.so(__kmp_invoke_microtask+0x93)[0x7f263f21af13]
/lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/lib/python3.11/site-packages/mkl/../../../libiomp5.so(+0xceef3)[0x7f263f189ef3]
/lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/lib/python3.11/site-packages/mkl/../../../libiomp5.so(+0xcde32)[0x7f263f188e32]
/lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/lib/python3.11/site-packages/mkl/../../../libiomp5.so(+0x160c81)[0x7f263f21bc81]
/lib64/libpthread.so.0(+0x7ea5)[0x7f2647f53ea5]
/lib64/libc.so.6(clone+0x6d)[0x7f2647573b0d]
======= Memory map: ========
00400000-0041f000 r--p 00000000 d88:cebd0 144117923366052823             /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/python3.11
0041f000-00652000 r-xp 0001f000 d88:cebd0 144117923366052823             /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/python3.11
00652000-00770000 r--p 00252000 d88:cebd0 144117923366052823             /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/python3.11
00771000-00772000 r--p 00370000 d88:cebd0 144117923366052823             /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/python3.11
00772000-008a2000 rw-p 00371000 d88:cebd0 144117923366052823             /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/python3.11
008a2000-008e5000 rw-p 00000000 00:00 0 
00c1a000-056f8000 rw-p 00000000 00:00 0                                  [heap]
7f20d4000000-7f20d4036000 rw-p 00000000 00:00 0 
7f20d4036000-7f20d8000000 ---p 00000000 00:00 0 
7f20dc000000-7f20dc040000 rw-p 00000000 00:00 0 
7f20dc040000-7f20e0000000 ---p 00000000 00:00 0 
7f20e0000000-7f20e0040000 rw-p 00000000 00:00 0 
7f20e0040000-7f20e4000000 ---p 00000000 00:00 0 
7f20e4000000-7f20e4040000 rw-p 00000000 00:00 0 
7f20e4040000-7f20e8000000 ---p 00000000 00:00 0 
7f20e8000000-7f20e8040000 rw-p 00000000 00:00 0 
7f20e8040000-7f20ec000000 ---p 00000000 00:00 0 
7f20ec000000-7f20ec040000 rw-p 00000000 00:00 0 
7f20ec040000-7f20f0000000 ---p 00000000 00:00 0 
7f20f0000000-7f20f0040000 rw-p 00000000 00:00 0 
7f20f0040000-7f20f4000000 ---p 00000000 00:00 0 
7f20f4000000-7f20f4040000 rw-p 00000000 00:00 0 
7f20f4040000-7f20f8000000 ---p 00000000 00:00 0 
7f20fa7ee000-7f20fa7ef000 ---p 00000000 00:00 0 
7f20fa7ef000-7f20fabf1000 rw-p 00000000 00:00 0 
7f20fabf1000-7f20fabf2000 ---p 00000000 00:00 0 
7f20fabf2000-7f20faff4000 rw-p 00000000 00:00 0 
7f20faff4000-7f20faff5000 ---p 00000000 00:00 0 
7f20faff5000-7f20fb3f7000 rw-p 00000000 00:00 0 
7f20fb3f7000-7f20fb3f8000 ---p 00000000 00:00 0 
7f20fb3f8000-7f20fb7fa000 rw-p 00000000 00:00 0 
7f20fb7fa000-7f20fb7fb000 ---p 00000000 00:00 0 
7f20fb7fb000-7f20fbbfd000 rw-p 00000000 00:00 0 
7f20fbbfd000-7f20fbbfe000 ---p 00000000 00:00 0 
7f20fbbfe000-7f20fc000000 rw-p 00000000 00:00 0 
7f20fc000000-7f20fc040000 rw-p 00000000 00:00 0 
7f20fc040000-7f2100000000 ---p 00000000 00:00 0 
7f2100000000-7f2100040000 rw-p 00000000 00:00 0 
7f2100040000-7f2104000000 ---p 00000000 00:00 0 
7f2104000000-7f2104040000 rw-p 00000000 00:00 0 
7f2104040000-7f2108000000 ---p 00000000 00:00 0 
7f2108000000-7f2108040000 rw-p 00000000 00:00 0 
7f2108040000-7f210c000000 ---p 00000000 00:00 0 
7f210c000000-7f210c040000 rw-p 00000000 00:00 0 
7f210c040000-7f2110000000 ---p 00000000 00:00 0 
7f2110000000-7f2110021000 rw-p 00000000 00:00 0 
7f2110021000-7f2114000000 ---p 00000000 00:00 0 
7f2114000000-7f2114040000 rw-p 00000000 00:00 0 
7f2114040000-7f2118000000 ---p 00000000 00:00 0 
7f2118000000-7f2118040000 rw-p 00000000 00:00 0 
7f2118040000-7f211c000000 ---p 00000000 00:00 0 
7f211c000000-7f211c040000 rw-p 00000000 00:00 0 
7f211c040000-7f2120000000 ---p 00000000 00:00 0 
7f2120000000-7f2120040000 rw-p 00000000 00:00 0 
7f2120040000-7f2124000000 ---p 00000000 00:00 0 
7f2124000000-7f2124040000 rw-p 00000000 00:00 0 
7f2124040000-7f2128000000 ---p 00000000 00:00 0 
7f2128000000-7f2128040000 rw-p 00000000 00:00 0 
7f2128040000-7f212c000000 ---p 00000000 00:00 0 
7f212c000000-7f212c040000 rw-p 00000000 00:00 0 
7f212c040000-7f2130000000 ---p 00000000 00:00 0 
7f2130000000-7f2130040000 rw-p 00000000 00:00 0 
7f2130040000-7f2134000000 ---p 00000000 00:00 0 
7f2134000000-7f2134040000 rw-p 00000000 00:00 0 
7f2134040000-7f2138000000 ---p 00000000 00:00 0 
7f21383d3000-7f21383d4000 ---p 00000000 00:00 0 
7f21383d4000-7f21387d6000 rw-p 00000000 00:00 0 
7f21387d6000-7f21387d7000 ---p 00000000 00:00 0 
7f21387d7000-7f2138bd9000 rw-p 00000000 00:00 0 
7f2138bd9000-7f2138bda000 ---p 00000000 00:00 0 
7f2138bda000-7f2138fdc000 rw-p 00000000 00:00 0 
7f2138fdc000-7f2138fdd000 ---p 00000000 00:00 0 
7f2138fdd000-7f21393df000 rw-p 00000000 00:00 0 
7f21393df000-7f21393e0000 ---p 00000000 00:00 0 
7f21393e0000-7f21397e2000 rw-p 00000000 00:00 0 
7f21397e2000-7f21397e3000 ---p 00000000 00:00 0 
7f21397e3000-7f2139be5000 rw-p 00000000 00:00 0 
7f2139be5000-7f2139be6000 ---p 00000000 00:00 0 
7f2139be6000-7f2139fe8000 rw-p 00000000 00:00 0 
7f2139fe8000-7f2139fe9000 ---p 00000000 00:00 0 
7f2139fe9000-7f213a3eb000 rw-p 00000000 00:00 0 
7f213a3eb000-7f213a3ec000 ---p 00000000 00:00 0 
7f213a3ec000-7f213a7ee000 rw-p 00000000 00:00 0 
7f213a7ee000-7f213a7ef000 ---p 00000000 00:00 0 
7f213a7ef000-7f213abf1000 rw-p 00000000 00:00 0 
7f213abf1000-7f213abf2000 ---p 00000000 00:00 0 
7f213abf2000-7f213aff4000 rw-p 00000000 00:00 0 
7f213aff4000-7f213aff5000 ---p 00000000 00:00 0 
7f213aff5000-7f213b3f7000 rw-p 00000000 00:00 0 
7f213b3f7000-7f213b3f8000 ---p 00000000 00:00 0 
7f213b3f8000-7f213b7fa000 rw-p 00000000 00:00 0 
7f213b7fa000-7f213b7fb000 ---p 00000000 00:00 0 
7f213b7fb000-7f213bbfd000 rw-p 00000000 00:00 0 
7f213bbfd000-7f213bbfe000 ---p 00000000 00:00 0 
7f213bbfe000-7f213c000000 rw-p 00000000 00:00 0 
7f213c000000-7f213c040000 rw-p 00000000 00:00 0 
7f213c040000-7f2140000000 ---p 00000000 00:00 0 
7f2140000000-7f2140040000 rw-p 00000000 00:00 0 
7f2140040000-7f2144000000 ---p 00000000 00:00 0 
7f2144000000-7f2144040000 rw-p 00000000 00:00 0 
7f2144040000-7f2148000000 ---p 00000000 00:00 0 
7f2148000000-7f2148040000 rw-p 00000000 00:00 0 
7f2148040000-7f214c000000 ---p 00000000 00:00 0 
7f214c000000-7f214c040000 rw-p 00000000 00:00 0 
7f214c040000-7f2150000000 ---p 00000000 00:00 0 
7f2150000000-7f2150040000 rw-p 00000000 00:00 0 
7f2150040000-7f2154000000 ---p 00000000 00:00 0 
7f2154000000-7f2154040000 rw-p 00000000 00:00 0 
7f2154040000-7f2158000000 ---p 00000000 00:00 0 
7f2158000000-7f2158040000 rw-p 00000000 00:00 0 
7f2158040000-7f215c000000 ---p 00000000 00:00 0 
7f215c000000-7f215c040000 rw-p 00000000 00:00 0 
7f215c040000-7f2160000000 ---p 00000000 00:00 0 
7f2160000000-7f2160040000 rw-p 00000000 00:00 0 
7f2160040000-7f2164000000 ---p 00000000 00:00 0 
7f2164000000-7f2164040000 rw-p 00000000 00:00 0 
7f2164040000-7f2168000000 ---p 00000000 00:00 0 
7f2168000000-7f2168040000 rw-p 00000000 00:00 0 
7f2168040000-7f216c000000 ---p 00000000 00:00 0 
7f216c000000-7f216c040000 rw-p 00000000 00:00 0 
7f216c040000-7f2170000000 ---p 00000000 00:00 0 
7f2170000000-7f2170040000 rw-p 00000000 00:00 0 
7f2170040000-7f2174000000 ---p 00000000 00:00 0 
7f2174000000-7f2174040000 rw-p 00000000 00:00 0 
7f2174040000-7f2178000000 ---p 00000000 00:00 0 
7f21783e0000-7f21783e1000 ---p 00000000 00:00 0 
7f21783e1000-7f21787e3000 rw-p 00000000 00:00 0 
7f21787e3000-7f21787e4000 ---p 00000000 00:00 0 
7f21787e4000-7f2178be6000 rw-p 00000000 00:00 0 
7f2178be6000-7f2178be7000 ---p 00000000 00:00 0 
7f2178be7000-7f2178fe8000 rw-p 00000000 00:00 0 
7f2178fe8000-7f2178fe9000 ---p 00000000 00:00 0 
7f2178fe9000-7f21793ea000 rw-p 00000000 00:00 0 
7f21793ea000-7f21793eb000 ---p 00000000 00:00 0 
7f21793eb000-7f21797ec000 rw-p 00000000 00:00 0 
7f21797ec000-7f21797ed000 ---p 00000000 00:00 0 
7f21797ed000-7f2179bee000 rw-p 00000000 00:00 0 
7f2179bee000-7f2179bef000 ---p 00000000 00:00 0 
7f2179bef000-7f2179ff0000 rw-p 00000000 00:00 0 
7f2179ff0000-7f2179ff1000 ---p 00000000 00:00 0 
7f2179ff1000-7f217a3f2000 rw-p 00000000 00:00 0 
7f217a3f2000-7f217a3f3000 ---p 00000000 00:00 0 
7f217a3f3000-7f217a7f4000 rw-p 00000000 00:00 0 
7f217a7f4000-7f217a7f5000 ---p 00000000 00:00 0 
7f217a7f5000-7f217abf6000 rw-p 00000000 00:00 0 
7f217abf6000-7f217abf7000 ---p 00000000 00:00 0 
7f217abf7000-7f217aff8000 rw-p 00000000 00:00 0 
7f217aff8000-7f217aff9000 ---p 00000000 00:00 0 
7f217aff9000-7f217b3fa000 rw-p 00000000 00:00 0 
7f217b3fa000-7f217b3fb000 ---p 00000000 00:00 0 
7f217b3fb000-7f217b7fc000 rw-p 00000000 00:00 0 
7f217b7fc000-7f217b7fd000 ---p 00000000 00:00 0 
7f217b7fd000-7f217bbfe000 rw-p 00000000 00:00 0 
7f217bbfe000-7f217bbff000 ---p 00000000 00:00 0 
7f217bbff000-7f217c000000 rw-p 00000000 00:00 0 
7f217c000000-7f217c040000 rw-p 00000000 00:00 0 
7f217c040000-7f2180000000 ---p 00000000 00:00 0 
7f2180000000-7f2180040000 rw-p 00000000 00:00 0 
7f2180040000-7f2184000000 ---p 00000000 00:00 0 
7f2184000000-7f2184040000 rw-p 00000000 00:00 0 
7f2184040000-7f2188000000 ---p 00000000 00:00 0 ^C
^C^C^C^C
Aborted (core dumped)

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[x] I have described the situation in which the bug arose, including what code was executed, information about my environment, and any applicable data others will need to reproduce the problem.
[x] I have included available evidence of the unexpected behavior (including error messages, screenshots, and/or plots) as well as a descriprion of what I expected instead.
[x] If I have a solution in mind, I have provided an explanation and/or pseudocode and/or task list.

raphaelshirley commented 4 months ago

Hi, thanks for the report. We will try to look into what is causing this. @johannct Any ideas? Have you hit a similar issue before?

johannct commented 4 months ago

never. Can we do so that exactly the same config is run but without rail?

hdante commented 4 months ago

Hello everyone, I can't reproduce this bug. I'll need to monitor it over the time during tests.

johannct commented 2 months ago

can't reproduce, please reopen if it happens again

hdante commented 1 month ago

Hello everyone, I've got another double free error while executing the example code from the Getting Started docs. Can you reopen this issue ? Thanks,

>>> import lephare as lp
Default work cache at /lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/work
                    is already linked. This is linked to the run directory:
                    /lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/runs/20240813T173817
>>> from astropy.table import Table
>>> # The following config is highly dependent on your input data and science goals
>>> config=lp.all_types_to_keymap(lp.default_cosmos_config)
>>> lp.data_retrieval.get_auxiliary_data(keymap=config, additional_files=['examples/COSMOS.in'])
Local registry file is up to date: data_registry.txt
Checking/downloading 429 files...
429 completed.
All files downloaded successfully and are non-empty.
Checking/downloading 1 files...
1 completed.
All files downloaded successfully and are non-empty.
>>> lp.prepare(config)
# NAME                        IDENT      Lbda_mean Lbeff(Vega)       FWHM     AB-cor    TG-cor      VEGA M_sun(AB)   CALIB      Lb_eff    Fac_corr
u_cfht.lowres                 1             0.3844      0.3908      0.0538    0.3150   -0.3891  -20.6345    6.0327       0      0.3815      1.0000
u_new.pb                      2             0.3690      0.3750      0.0456    0.6195   -0.2745  -20.8527    6.3135       0      0.3668      1.0000
gHSC.pb                       3             0.4851      0.4760      0.1194   -0.0860   -0.2458  -20.7272    5.0764       0      0.4780      1.0000
rHSC.pb                       4             0.6241      0.6142      0.1539    0.1466    0.2580  -21.5143    4.6523       0      0.6178      1.0000
iHSC.pb                       5             0.7716      0.7637      0.1476    0.3942    0.6138  -22.2286    4.5323       0      0.7666      1.0000
zHSC.pb                       6             0.8915      0.8907      0.0768    0.5169    0.7625  -22.6733    4.5147       0      0.8903      1.0000
yHSC.pb                       7             0.9801      0.9771      0.0797    0.5534    0.7763  -22.9145    4.5081       0      0.9782      1.0000
Y.lowres                      8             1.0222      1.0196      0.0919    0.6043    0.8180  -23.0574    4.5130       0      1.0206      1.0000
J.lowres                      9             1.2555      1.2481      0.1712    0.9228  -99.0000  -23.8194    4.5638       0      1.2514      1.0000
H.lowres                      10            1.6497      1.6352      0.2893    1.3701  -99.0000  -24.8565    4.7045       0      1.6409      1.0000
K.lowres                      11            2.1577      2.1435      0.2926    1.8335  -99.0000  -25.9057    5.1316       0      2.1502      1.0000
IB427.lowres                  12            0.4264      0.4256      0.0207   -0.1446   -0.4942  -20.4117    5.5152       0      0.4262      1.0000
IB464.lowres                  13            0.4636      0.4633      0.0218   -0.1520   -0.3463  -20.5860    5.0658       0      0.4634      1.0000
IB484.lowres                  14            0.4851      0.4846      0.0228   -0.0241   -0.1770  -20.8122    4.9880       0      0.4849      1.0000
IB505.lowres                  15            0.5064      0.5061      0.0231   -0.0656   -0.1366  -20.8639    4.9423       0      0.5061      1.0000
IB527.lowres                  16            0.5262      0.5259      0.0242   -0.0260   -0.0464  -20.9871    4.8937       0      0.5260      1.0000
IB574.lowres                  17            0.5766      0.5762      0.0272    0.0657    0.1377  -21.2773    4.7042       0      0.5763      1.0000
IB624.lowres                  18            0.6234      0.6230      0.0301    0.1527    0.2768  -21.5339    4.6386       0      0.6232      1.0000
IB679.lowres                  19            0.6783      0.6779      0.0336    0.2542    0.4288  -21.8183    4.5709       0      0.6779      1.0000
IB709.lowres                  20            0.7075      0.7071      0.0316    0.2982    0.4968  -21.9541    4.5558       0      0.7072      1.0000
IB738.lowres                  21            0.7363      0.7358      0.0323    0.3460    0.5577  -22.0886    4.5449       0      0.7360      1.0000
IB767.lowres                  22            0.7687      0.7681      0.0364    0.3992    0.6164  -22.2351    4.5243       0      0.7683      1.0000
IB827.lowres                  23            0.8246      0.8241      0.0344    0.4891    0.7300  -22.4777    4.5161       0      0.8243      1.0000
NB711.lowres                  24            0.7120      0.7119      0.0073    0.3072    0.5084  -21.9774    4.5542       0      0.7120      1.0000
NB816.lowres                  25            0.8150      0.8149      0.0120    0.4713    0.7098  -22.4349    4.5154       0      0.8149      1.0000
NB118.lowres                  26            1.1909      1.1909      0.0112    0.8376  -99.0000  -23.6250    4.5554       0      1.1909      1.0000
irac_ch1.lowres               27            3.5763      3.5264      0.7411    2.7951  -99.0000  -27.9585    6.0679       1      3.5634      1.0036
irac_ch2.lowres               28            4.5290      4.4609      1.0105    3.2634  -99.0000  -28.9384    6.5680       1      4.5111      1.0040
irac_ch3.lowres               29            5.7873      5.6765      1.3509    3.7537  -99.0000  -29.9581    7.0472       1      5.7592      1.0050
irac_ch4.lowres               30            8.0442      7.7033      2.8394    4.3959  -99.0000  -31.2962    7.6701       1      7.9590      1.0110
{'star_sed': '/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/data/sed/STAR/STAR_MOD_ALL.list'}
#######################################
# It s translating SEDs to binary library #
# with the following options :           
# Config file     : 
# Library type     : STAR
# STAR_SED    :/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/data/sed/STAR/STAR_MOD_ALL.list
# STAR_LIB    :LIB_STAR
# STAR_LIB doc:/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/work/lib_bin/LIB_STAR.doc
# STAR_FSCALE :0.0000
#######################################
Number of SED in the list 254
WRONG NUMBER OF ARGUMENTS FOR OPTION MOD_EXTINC
We have 2 instead of 8
Use default value 0,0 for all filters 
 All files opened 
#######################################
# It s computing the SYNTHETIC MAGNITUDES #
# For Gal/QSO libraries with these OPTIONS #
# with the following options :           
# Config file     : 
# Filter file     : filter_cosmos
# Magnitude type     : AB
# COSMOLOGY   :70.0000,0.3000,0.7000
# STAR_LIB_IN    :/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/work/lib_bin/LIB_STAR(.doc & .bin)
# STAR_LIB_OUT   :/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/work/lib_mag/STAR_COSMOS(.doc & .bin)
# LIB_ASCII   NO
# CREATION_DATE Tue Aug 13 18:24:52 2024
#############################################
{'gal_sed': '/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/data/examples/COSMOS_MOD.list'}
#######################################
# It s translating SEDs to binary library #
# with the following options :           
# Config file     : 
# Library type     : GAL
# GAL_SED    :/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/data/examples/COSMOS_MOD.list
# GAL_LIB    :LIB_CE
# GAL_LIB doc:/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/work/lib_bin/LIB_CE.doc
# GAL_LIB phys:/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/work/lib_bin/LIB_CE.phys
# SEL_AGE    :none
# GAL_FSCALE :1.0000
# AGE_RANGE   0.0000 15000000000.0000
#######################################
Number of SED in the list 31
WRONG NUMBER OF ARGUMENTS FOR OPTION MOD_EXTINC
We have 2 instead of 8
Use default value 0,0 for all filters 
 All files opened 
#######################################
# It s computing the SYNTHETIC MAGNITUDES #
# For Gal/QSO libraries with these OPTIONS #
# with the following options :           
# Config file     : 
# Filter file     : filter_cosmos
# Magnitude type     : AB
# GAL_LIB_IN    :/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/work/lib_bin/LIB_CE(.doc & .bin)
# GAL_LIB_OUT   :/lustre/t1/cl/lsst/tmp/henrique.almeida/slurm-home/var/cache/lephare/work/lib_mag/CE_COSMOS(.doc & .bin)
# ZGRID_TYPE   :0
# Z_STEP   :0.0100 0.0000 7.0000
# COSMOLOGY   :70.0000,0.3000,0.7000
# EXTINC_LAW   :SMC_prevot.dat SB_calzetti.dat SB_calzetti_bump1.dat SB_calzetti_bump2.dat 
# MOD_EXTINC   :0 0 0 0 0 0 0 0 
# EB_V   :0.0000 0.0500 0.1000 0.1500 0.2000 0.2500 0.3000 0.3500 0.4000 0.5000 
# EM_LINES   EMP_UV
# EM_DISPERSION   0.5000,0.7500,1.0000,1.5000,2.0000,
# LIB_ASCII   NO
# CREATION_DATE Tue Aug 13 18:24:53 2024
#############################################
*** Error in `python': double free or corruption (fasttop): 0x00007fe55800ae00 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x7fe82bd15329]
/lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/../lib/libstdc++.so.6(_ZNSs9_M_mutateEmmm+0x1b1)[0x7fe824e88541]
/lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/../lib/libstdc++.so.6(_ZNSs12_M_leak_hardEv+0x3b)[0x7fe824e885bb]
/lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/lib/python3.11/site-packages/lephare/_lephare.cpython-311-x86_64-linux-gnu.so(+0x6657a)[0x7fe82523957a]
/lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/lib/python3.11/site-packages/lephare/../lephare.libs/libgomp-a34b3233.so.1.0.0(+0x16405)[0x7fe824fbf405]
/lib64/libpthread.so.0(+0x7ea5)[0x7fe82c772ea5]
/lib64/libc.so.6(clone+0x6d)[0x7fe82bd92b0d]
======= Memory map: ========
00400000-0041f000 r--p 00000000 d88:cebd0 144118468625624131             /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/python3.11
0041f000-00657000 r-xp 0001f000 d88:cebd0 144118468625624131             /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/python3.11
00657000-00776000 r--p 00257000 d88:cebd0 144118468625624131             /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/python3.11
00776000-00777000 r--p 00375000 d88:cebd0 144118468625624131             /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/python3.11
00777000-008a8000 rw-p 00376000 d88:cebd0 144118468625624131             /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/bin/python3.11
008a8000-008eb000 rw-p 00000000 00:00 0 
0252a000-05abb000 rw-p 00000000 00:00 0                                  [heap]
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7fe8239f6000-7fe8239f7000 r-xp 00001000 d88:cebd0 144118468625615838     /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/lib/python3.11/lib-dynload/_contextvars.cpython-311-x86_64-linux-gnu.so
7fe8239f7000-7fe8239f8000 r--p 00002000 d88:cebd0 144118468625615838     /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/lib/python3.11/lib-dynload/_contextvars.cpython-311-x86_64-linux-gnu.so
7fe8239f8000-7fe8239f9000 r--p 00002000 d88:cebd0 144118468625615838     /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/lib/python3.11/lib-dynload/_contextvars.cpython-311-x86_64-linux-gnu.so
7fe8239f9000-7fe8239fa000 rw-p 00003000 d88:cebd0 144118468625615838     /lustre/t1/cl/lsst/tmp/henrique.almeida/miniconda3/lib/python3.11/lib-dynload/_contextvars.cpython-311-x86_64-linux-gnu.soAborted (core dumped)

johannct commented 1 month ago

Do you confirm it with current main or latest release? We need to be able to reproduce it somehow. Also, can you set OMP to single core to see what happens?

hdante commented 1 month ago

Hello, I confirm it with version 0.1.9, but I don't think there was any significant change in the later versions. I'm not doing any configuration for OMP, how should I configure it ?

johannct commented 1 month ago

Yes but before you said that you could not reproduce it. Set OMP_NUM_THREADS=1 I cannot reproduce the problem with current main. And htop tells me that I am using the 12 cores of my laptop....

hdante commented 1 month ago

I still can't reproduce it, it happened once two days ago and not anymore. I can try again setting the environment variable, but same thing, I'd need to wait for some time to see if it appears again.

johannct commented 1 month ago

So there is a fragility somewhere in the code, depending on the system usage. Have you tried to immediately reproduce it, when it occurred?

johannct commented 1 month ago

double free corruption are notoriously hard to debug. Before cutting a v1 distribution we will certainly make a thorough profiling again.

hdante commented 1 month ago

Hello, Johann, I've tried to immediately reproduce the bug once after it happened, but it didn't work.

lephare-photoz / lephare

Error in `python3': double free or corruption (fasttop): 0x00007f21bc00ae20 #143