L2gen failed with Segmentation fault

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tlin2_cuny.edu
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L2gen failed with Segmentation fault

by tlin2_cuny.edu » Tue Feb 28, 2023 3:02 pm America/New_York

Hi all,
I set up SeaDAS OCSSW but encountered some issues when running L2gen. Landsat 8 and MSI have the same problem which is:

execution exception: java.io.IOException: l2gen failed with exit code 139.
Check log for more details.
Loading default parameters from /Users/tonglin/SeaDAS/ocssw/share/common/msl12_defaults.par
Input file /Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_MTL.txt is a Landsat 8/9 OLI L1B GEOTIFF file.

Loading characteristics for OLIL8
Opening sensor information file /Users/tonglin/SeaDAS/ocssw/share/oli/msl12_sensor_info.dat
Bnd Lam Fo Tau_r k_oz k_no2 t_co2 awhite aw bbw
0 443.000 189.652 2.352e-01 2.929e-03 5.024e-19 1.000e+00 1.000e+00 7.170e-03 2.169e-03
1 482.000 200.396 1.685e-01 1.957e-02 3.213e-19 1.000e+00 1.000e+00 1.581e-02 1.529e-03
2 561.000 182.079 9.020e-02 1.038e-01 8.351e-20 1.000e+00 1.000e+00 6.998e-02 8.054e-04
3 655.000 155.038 4.793e-02 6.200e-02 1.177e-20 1.000e+00 1.000e+00 3.751e-01 4.215e-04
4 865.000 95.063 1.551e-02 2.223e-03 3.306e-23 1.000e+00 1.000e+00 4.630e+00 1.332e-04
5 1609.000 24.755 1.284e-03 0.000e+00 0.000e+00 1.000e+00 1.000e+00 7.607e+02 1.052e-05
6 2201.000 8.546 3.697e-04 0.000e+00 0.000e+00 1.000e+00 1.000e+00 2.250e+03 2.958e-06


Loading default parameters for OLIL8 from /Users/tonglin/SeaDAS/ocssw/share/oli/msl12_defaults.par
Loading default sub-sensor parameters for OLIL8 from /Users/tonglin/SeaDAS/ocssw/share/oli/l8/msl12_defaults.par
Loading parameters for suite OC from /Users/tonglin/SeaDAS/ocssw/share/oli/msl12_defaults_OC.par
Loading command line parameters

Loading user parameters for OLIL8

Internal data compression requested at compression level: 4
Reading Thuillier_F0.dat
OLI Level-1B /Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_MTL.txt
OLI Level-1B Collection 2
OLI Level-1B Band[0]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B1.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[1]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B2.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[2]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B3.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[3]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B4.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[4]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B5.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[5]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B6.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[6]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B7.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[7]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B8.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[8]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B9.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Angle File:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_ANG.txt
OLI Level-1B Band[0]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B1.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[1]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B2.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[2]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B3.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[3]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B4.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[4]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B5.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[5]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B6.TIF
OLI Level-1B Band[6]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B7.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[7]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B8.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Level-1B Band[8]:/Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/OLI_acolite_matchup_L1/LC08_L1TP_013031_20171027_20200902_02_T1/LC08_L1TP_013031_20171027_20200902_02_T1_B9.TIF
TIFFReadDirectory: Warning, Unknown field with tag 42113 (0xa481) encountered.
OLI Start Time: 2017-10-27 300 15:33:35.826468
OLI file has 7 bands, 7641 samples, 7771 lines
Allocated 7022107 bytes in L1 record.
Allocated 2659068 bytes in L2 record.

Opening: /Volumes/Tong_Lin/CUNY/Satellite_data/Landsat/LIS/Collection2/l2gen/LANDSAT8_OLI.20171027T153335.L2.OC.nc
/Users/tonglin/SeaDAS/ocssw/bin/ocssw_runner: line 23: 9497 Segmentation fault: 11 $*

I'm not sure what should I do. Can you help me with this problem?

Best,
Tong

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OB SeaDAS - xuanyang02
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Re: L2gen failed with Segmentation fault

by OB SeaDAS - xuanyang02 » Tue Feb 28, 2023 5:08 pm America/New_York

You probably are not using the latest tag of SeaDAS science processing package (OCSSW). The latest tag is V2022.3.

Can you do SeaDAS-Toolbox -> Software & System Info and post the result here if you are using SeaDAS 8.3.0?

tlin2_cuny.edu
Posts: 13
Joined: Tue Feb 28, 2023 2:16 pm America/New_York
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Re: L2gen failed with Segmentation fault

by tlin2_cuny.edu » Wed Mar 01, 2023 1:15 pm America/New_York

Hi,
Here is the SeaDAS info.

-----------------------------------------------------------
Main Application Platform:
-----------------------------------------------------------
Application Version: SeaDAS 8.3.0
SNAP Engine Version: 9.0.3* (SeaDAS Platform modified)
SNAP Desktop Version: 9.0.3* (SeaDAS Platform modified)
SNAP Engine Build Date: 202212081832
SNAP Desktop Build Date: 202212081837
Installation Directory: /Users/tonglin/SeaDAS
Data Directory: /Users/tonglin/.seadas8
Configuration: /Users/tonglin/SeaDAS/etc/snap.properties
VM Configuration: /Users/tonglin/SeaDAS/etc/seadas.conf
WARNING!! File '/Users/tonglin/SeaDAS/etc/seadas.conf' does not exist
VM Configuration: /Users/tonglin/SeaDAS/etc/snap.conf
WARNING!! File '/Users/tonglin/SeaDAS/etc/snap.conf' does not exist
VM Configuration (gpt): /Users/tonglin/SeaDAS/bin/gpt.vmoptions
VM Configuration (pconvert): /Users/tonglin/SeaDAS/bin/pconvert.vmoptions
Runtime Configuration: null
Runtime Configuration (SeaDAS Toolbox): /Users/tonglin/.seadas8/etc/seadas.properties
JRE: Java(TM) SE Runtime Environment 1.8.0_201-b09
JVM: Java HotSpot(TM) 64-Bit Server VM by Oracle Corporation
Memory: 3641 MiB
OCSSWROOT (Java Env): null
Python3 Directory: /Users/tonglin/anaconda3/bin/python3


-----------------------------------------------------------
SeaDAS Toolbox:
-----------------------------------------------------------
SeaDAS Toolbox Version: 1.3.0
SeaDAS Toolbox Build Date: 202212081844
Configuration: /Users/tonglin/.seadas8/etc/seadas.properties
OCSSW Root Directory: /Users/tonglin/SeaDAS/ocssw
OCSSW Log Directory: /
OCSSW Location: local
Environment {$OCSSWROOT} (external): null


-----------------------------------------------------------
NASA Science Processing (OCSSW):
-----------------------------------------------------------
Environment {$OCSSWROOT}: /Users/tonglin/SeaDAS/ocssw
Environment {$OCDATAROOT}: /Users/tonglin/SeaDAS/ocssw/share
l2gen version: msl12 9.6.0-V2022.2 (Nov 28 2022 12:24:20)
l2bin version: 7.0.3
l3bin version: 5.13
l3mapgen version: l3mapgen 2.3.0-V2022.2 (Nov 28 2022 12:25:33)
Installed Missions: ['msis2a', 'msis2b', 'olcis3a', 'olcis3b', 'olil8', 'olil9']


-----------------------------------------------------------
General System and Software:
-----------------------------------------------------------
Operating system: MacOS 10.16
Java version: 16
Python3 version: 3.9.13
Python3 Path: /Users/tonglin/anaconda3/bin/python3
Env: ASAP_PARMS=/Users/tonglin/SeaDAS/ocssw/share/common/nav
CC=gcc
COMMAND_MODE=unix2003
CONDA_DEFAULT_ENV=base
CONDA_EXE=/Users/tonglin/anaconda3/bin/conda
CONDA_PREFIX=/Users/tonglin/anaconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/Users/tonglin/anaconda3/bin/python
CONDA_SHLVL=1
CXX=g++
ELEMENTS=/Users/tonglin/SeaDAS/ocssw/var/seawifs
EOS_LIB_PREFIX=macintel64
FC=gfortran
GCC_TUNE=
HDFEOS_LIB=/Users/tonglin/SeaDAS/ocssw/opt/EOS/lib/macintel64
HOME=/Users/tonglin
HRPT_STATION_IDENTIFICATION_FILE=/Users/tonglin/SeaDAS/ocssw/share/seawifs/station/station_id.dat
J2D_PIXMAPS=shared
JAVA_MAIN_CLASS_14678=org.netbeans.Main
L2GEN_ANC=/Users/tonglin/SeaDAS/ocssw/var/anc
LC_CTYPE=UTF-8
LIB3_BIN=/Users/tonglin/SeaDAS/ocssw/opt/bin
LIB3_CHECK=0
LIB3_DIR=/Users/tonglin/SeaDAS/ocssw/opt
LIB3_INC=/Users/tonglin/SeaDAS/ocssw/opt/include
LIB3_LIB=/Users/tonglin/SeaDAS/ocssw/opt/lib
LOGNAME=tonglin
NAVCTL=/Users/tonglin/SeaDAS/ocssw/share/seawifs/nav
NAVQC=/Users/tonglin/SeaDAS/ocssw/share/seawifs/nav
OCDATAROOT=/Users/tonglin/SeaDAS/ocssw/share
OCSSWROOT=/Users/tonglin/SeaDAS/ocssw
OCSSW_ARCH=macosx_intel
OCSSW_BIN=/Users/tonglin/SeaDAS/ocssw/bin
OCSSW_DEBUG=0
OCTS_REGISTRATION_TABLES=/Users/tonglin/SeaDAS/ocssw/share/octs/nav
OCVARROOT=/Users/tonglin/SeaDAS/ocssw/var
ORBCTL=/Users/tonglin/SeaDAS/ocssw/share/seawifs/nav
PATH=/Users/tonglin/SeaDAS/ocssw/opt/bin:/Users/tonglin/SeaDAS/ocssw/bin:/Users/tonglin/anaconda3/bin:/Users/tonglin/anaconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
PGSINC=/Users/tonglin/SeaDAS/ocssw/opt/EOS/include
PGSLIB=/Users/tonglin/SeaDAS/ocssw/opt/EOS/lib/macintel64
PROJ_LIB=/Users/tonglin/SeaDAS/ocssw/opt/share/proj
PROJ_NETWORK=ON
PWD=/
SHELL=/bin/bash
SHLVL=3
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.gfSfnj0f67/Listeners
SWFTBL=/Users/tonglin/SeaDAS/ocssw/share/seawifs/qc
SWTBL=/Users/tonglin/SeaDAS/ocssw/share/seawifs
TMPDIR=/var/folders/bj/8yllwfhj4gl26qzwstvb8f740000gn/T/
USER=tonglin
XPC_FLAGS=0x0
XPC_SERVICE_NAME=0
_=/usr/bin/env
_CE_CONDA=
_CE_M=
__CFBundleIdentifier=gov.nasa.gsfc.seadas
__CF_USER_TEXT_ENCODING=0x1F5:0x0:0x0

OB SeaDAS - xuanyang02
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Re: L2gen failed with Segmentation fault

by OB SeaDAS - xuanyang02 » Wed Mar 01, 2023 5:41 pm America/New_York

Thanks for sharing your SeaDAS info. It says you are running on MacOS 10.16, which I doubt. Could you please find out your Mac version by "About This Mac" on the Apple menu?

I am able to run l2gen successfully on the above mentioned file with OCSSW V2022.3 on MacOS 12.6.

tlin2_cuny.edu
Posts: 13
Joined: Tue Feb 28, 2023 2:16 pm America/New_York
Answers: 0

Re: L2gen failed with Segmentation fault

by tlin2_cuny.edu » Thu Mar 02, 2023 10:47 am America/New_York

Hi,
My mac version is 11.7.4, does that mean I need to update my Mac version? Thanks.

Best,
Tong

tlin2_cuny.edu
Posts: 13
Joined: Tue Feb 28, 2023 2:16 pm America/New_York
Answers: 0

Re: L2gen failed with Segmentation fault

by tlin2_cuny.edu » Thu Mar 02, 2023 11:35 am America/New_York

Hi,

Thank you so much! I updated the Mac version to the latest and now it works!

Best,
Tong

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