Viirs Processing issue

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mshatley
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Joined: Thu Sep 30, 2010 10:27 am America/New_York
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Viirs Processing issue

by mshatley » Mon Aug 23, 2021 11:26 am America/New_York

Good Morning,

I've updated the OCSSW software on my processing system and am running into issues processing VIIRS granules now. The viirsn files were installed as part of OCSSW.

$ getanc V2021234145400.L1A_SNPP.nc -v
ancillary_data.db
Searching database: ~/seadas/ocssw/var/log/ancillary_data.db
Determining pass start and end times...
Error! dump_metadata failed.

$ l2gen ifile=V2021234145400.L1A_SNPP.nc geofile=V2021234145400.GEO-M_SNPP.nc ofile=V2021234145400.L2 l2prod1="sst qual_sst"
Loading default parameters from ~/seadas/ocssw/share/common/msl12_defaults.par
-E- /home/seadas/focs/oel_hdf4/libl1/l1_options.c Line 196: Could not find type for file V2021234145400.L1A_SNPP.nc.

I'm running Python 3.7.4 and have the requests package version 2.22 installed. I've also reinstalled OCSSW from scatch and am still seeing these messages when trying to process granules.

Any idea what could be causing the issue?

Thanks!

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OB.DAAC - amscott
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Re: Viirs Processing issue

by OB.DAAC - amscott » Mon Aug 23, 2021 1:41 pm America/New_York

Hello,

Please see this post as a possible solution to your problem: viewtopic.php?f=7&t=2524&p=8964&sid=113 ... 100b#p8964

OB SeaDAS - dshea
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Re: Viirs Processing issue

by OB SeaDAS - dshea » Tue Aug 24, 2021 9:42 pm America/New_York

Both getanc and l2gen work fine for me with that file. What OCSSW tag did you install? I would first try to download the VIIRS file again since l2gen could not figure what type the file is.

don

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Re: Viirs Processing issue

by OB SeaDAS - xuanyang02 » Wed Aug 25, 2021 10:25 am America/New_York

If you have SeaDAS 8 installed, it might be helpful to do SeaDAS-OCSSW -> SeaDAS/System Info in GUI and post the output here.

Did you install OCSSW through GUI or command line? If you have older versions of OCSSW installed with SeaDAS 7, please make sure the new OCSSW does not mixed with the older versions. You might also need to install viirsdem along with viirsn. https://seadas.gsfc.nasa.gov/downloads/

mshatley
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Re: Viirs Processing issue

by mshatley » Thu Sep 02, 2021 11:00 am America/New_York

I have SeaDas 8.1 installed on the system:
$ more ~/seadas/VERSION.txt
8.1.0

I've done the OCSSW install through the GUI(including the VIIRS DEM files) and am still seeing the same issue:
$ getanc V2021244183000.L1A_SNPP.nc -v
ancillary_data.db
Determining pass start and end times...
Error! dump_metadata failed.

$ l2gen ifile=V2021244183000.L1A_SNPP.nc geofile=V2021244183000.GEO-M_SNPP.nc ofile=V2021234145400.L2 l2prod1="sst qual_sst"
Loading default parameters from /home/1097/seadas/ocssw/share/common/msl12_defaults.par
-E- /home/seadas/focs/oel_hdf4/libl1/l1_options.c Line 196: Could not find type for file V2021244183000.L1A_SNPP.nc.

I've also tried installing from the command line as well:
./install_ocssw --tag=V2021.2 --modisa --viirsn --viirsdem --direct_broadcast --install_dir=~/seadas/ocssw/

Output from SeaDas/System info is below:
Main Application Platform:
Application Version: SeaDAS 8.1.0
Installation Directory: /home/1097/seadas
Data Directory: /home/1097/.seadas8
Configuration: /home/1097/seadas/etc/snap.properties
WARNING!! File '/home/1097/seadas/etc/snap.properties' does not exist
Configuration2: /home/1097/.seadas8/etc/snap.properties
VM Configuration: /home/1097/seadas/bin/pconvert.vmoptions
WARNING!! File '/home/1097/seadas/bin/pconvert.vmoptions' does not exist
VM Configuration (gpt): /home/1097/seadas/bin/gpt.vmoptions
WARNING!! File '/home/1097/seadas/bin/gpt.vmoptions' does not exist
Desktop Specification Version: 8.0.3
Engine Specification Version: 8.0.3
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): /home/1097/seadas/ocssw

Python3 Directory:
/opt/shared/python/3.7.4/bin/python3
NOTE: the extraneous output lines displayed were detected in your login configuration output

SeaDAS Toolbox:
SeaDAS Toolbox Specification Version: 1.1.0
Configuration: /home/1097/.seadas8/etc/seadas.properties
OCSSW Root Directory: /home/1097/seadas/ocssw
OCSSW Log Directory: /home/1097/seadas_8.1.0
OCSSW Location: local
Environment {$OCSSWROOT} (external): /home/1097/seadas/ocssw

-----------------------------------------------


NASA Science Processing (OCSSW):
Environment {$OCSSWROOT}: /home/1097/seadas/ocssw
Environment {$OCDATAROOT}: /home/1097/seadas/ocssw/share
l2gen version: msl12 9.5.1-V2021.2 (Jun 18 2021 11:22:53)
l2bin version: 7.0.1
l3bin version: 5.13
l3mapgen version: l3mapgen 2.3.0-V2021.2 (Jun 18 2021 11:24:42)
Installed Missions: ['aqua', 'viirsn']

General System and Software:
NOTE: the extraneous output lines displayed were detected in your login configuration output

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Re: Viirs Processing issue

by OB SeaDAS - xuanyang02 » Wed Sep 15, 2021 3:53 pm America/New_York

Are there anything else below
"General System and Software:
NOTE: the extraneous output lines displayed were detected in your login configuration output"
in the output of SeaDAS/System Info?

Do you have two copies of OCSSW?
/home/1097/seadas/ocssw
/home/seadas/ocssw

mshatley
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Re: Viirs Processing issue

by mshatley » Thu Sep 16, 2021 2:23 pm America/New_York

Are there anything else below
"General System and Software:
NOTE: the extraneous output lines displayed were detected in your login configuration output"
in the output of SeaDAS/System Info?

No, I'm running SeaDas on an HPC, so I think this is getting logged from output on starting the shell.

Do you have two copies of OCSSW?
/home/1097/seadas/ocssw
/home/seadas/ocssw

No, just a single copy of OCSSW is installed. I think the /home/seadas/... message is from the error handling code inside SeaDas.

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Re: Viirs Processing issue

by OB SeaDAS - xuanyang02 » Thu Sep 16, 2021 3:03 pm America/New_York

I have the following under "General System and Software:"
Operating system: MacOS 10.15.7
Java version: 1.8.0_241
Python3 version: 3.8.5
Python3 Path: /usr/local/bin/python3
Env: ASAP_PARMS=/Users/bingyang/seadas-8.1.0/ocssw/share/common/nav
CC=gcc
CXX=g++
ELEMENTS=/Users/bingyang/seadas-8.1.0/ocssw/var/seawifs
EOS_LIB_PREFIX=macintel64
FC=gfortran
GCC_TUNE=
HDFEOS_LIB=/Users/bingyang/seadas-8.1.0/ocssw/opt/EOS/lib/macintel64
HOME=/Users/bingyang
HRPT_STATION_IDENTIFICATION_FILE=/Users/bingyang/seadas-8.1.0/ocssw/share/seawifs/station/station_id.dat
J2D_PIXMAPS=shared
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk/Contents/Home
JAVA_MAIN_CLASS_17752=org.netbeans.Main
JDK_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk/Contents/Home
L2GEN_ANC=/Users/bingyang/seadas-8.1.0/ocssw/var/anc
LANG=en_US.UTF-8
LC_CTYPE=UTF-8
LIB3_BIN=/Users/bingyang/seadas-8.1.0/ocssw/opt/bin
LIB3_CHECK=0
LIB3_DIR=/Users/bingyang/seadas-8.1.0/ocssw/opt
LIB3_INC=/Users/bingyang/seadas-8.1.0/ocssw/opt/include
LIB3_LIB=/Users/bingyang/seadas-8.1.0/ocssw/opt/lib
LOGNAME=bingyang
LaunchInstanceID=2ADD84A5-0AE8-4F26-B659-71BF204C72E3
M2=/Users/bingyang/apache-maven-3.6.3/bin
M2_HOME=/Users/bingyang/apache-maven-3.6.3
NAVCTL=/Users/bingyang/seadas-8.1.0/ocssw/share/seawifs/nav
NAVQC=/Users/bingyang/seadas-8.1.0/ocssw/share/seawifs/nav
OCDATAROOT=/Users/bingyang/seadas-8.1.0/ocssw/share
OCSSWROOT=/Users/bingyang/seadas-8.1.0/ocssw
OCSSW_ARCH=macosx_intel
OCSSW_BIN=/Users/bingyang/seadas-8.1.0/ocssw/bin
OCSSW_DEBUG=1
OCSSW_SVN=localhost
OCTS_REGISTRATION_TABLES=/Users/bingyang/seadas-8.1.0/ocssw/share/octs/nav
OCVARROOT=/Users/bingyang/seadas-8.1.0/ocssw/var
ORBCTL=/Users/bingyang/seadas-8.1.0/ocssw/share/seawifs/nav
PATH=/Users/bingyang/apache-maven-3.6.3/bin:/Users/bingyang/bin:/Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk/Contents/Home/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/bingyang/apache-maven-3.6.3/bin:/Users/bingyang/bin:/Users/bingyang/seadas-8.1.0/ocssw/opt/bin:/Users/bingyang/seadas-8.1.0/ocssw/bin:/Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk/Contents/Home/bin
PGSINC=/Users/bingyang/seadas-8.1.0/ocssw/opt/EOS/include
PGSLIB=/Users/bingyang/seadas-8.1.0/ocssw/opt/EOS/lib/macintel64
PROJ_LIB=/Users/bingyang/seadas-8.1.0/ocssw/opt/share/proj
PWD=/Users/bingyang
SEADASROOT=/Applications/seadas-7.5.3
SECURITYSESSIONID=186a7
SHELL=/bin/bash
SHLVL=4
SNAPROOT=/Applications/snap
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.Lh71QuWvq3/Listeners
SWFTBL=/Users/bingyang/seadas-8.1.0/ocssw/share/seawifs/qc
SWTBL=/Users/bingyang/seadas-8.1.0/ocssw/share/seawifs
TERM=xterm-256color
TERM_PROGRAM=Apple_Terminal
TERM_PROGRAM_VERSION=433
TERM_SESSION_ID=75C6E586-A908-4118-B006-B5185FA43238
TMPDIR=/var/folders/k0/27vgxm6d5gd3q_p5s3p941p80000gp/T/
USER=bingyang
XPC_FLAGS=0x0
XPC_SERVICE_NAME=0
_=/usr/bin/env
__CF_USER_TEXT_ENCODING=0x1F6:0x0:0x0

It seems "SeaDAS/System Info" broke when it tried to get your OS information. Can you do

Code: Select all

uname
java -version
python3 --version
which python3
env | sort
and post the output here?

mshatley
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Joined: Thu Sep 30, 2010 10:27 am America/New_York
Answers: 0

Re: Viirs Processing issue

by mshatley » Fri Sep 17, 2021 9:16 am America/New_York

uname
$ uname
Linux

java -version
$ java -version
openjdk version "1.8.0_161"

python3 --version
$ python3 --version
Python 3.7.4

which python3
$ which python3
/opt/shared/python/3.7.4/bin/python3

env | sort
$ env | sort
ASAP_PARMS=/home/1097/seadas/ocssw/share/common/nav
BASH_FUNC___valetcompl_pkgs()=() { cur=${COMP_WORDS[COMP_CWORD]};
BASH_FUNC___valetcompl_vers()=() { cur=${COMP_WORDS[COMP_CWORD]};
BASH_FUNC_vpkg_devrequire()=() { local vpkg_conf_quiet=0;
BASH_FUNC_vpkg_help()=() { man valet
BASH_FUNC_vpkg_history()=() { echo $VALET_HISTORY | /bin/sed -r -e 's/\|/\n/g' -e 's/\]/]\n /g' -e 's/;/\n /g'
BASH_FUNC_vpkg_replicate_parent()=() { local vpkg_my_uniqpid=`${VALET_PREFIX}/bin/valet_uniqpid $$`;
BASH_FUNC_vpkg_require()=() { local vpkg_conf_quiet=0;
BASH_FUNC_vpkg_rollback()=() { local vpkg_rollback_all=0;
CC=gcc
-c | --context)
chmod 600 "$vpkg_rollback_cmds";
chmod 600 "$vpkg_rollback_cmds";
colonprefixes=${cur%"${cur##*:}"};
COMPREPLY=($( compgen -W "$packages" -- $cur ));
COMPREPLY=($(compgen -W "$packages" -- $cur));
COMPREPLY=($( compgen -W "$versions" -- $cur ));
COMPREPLY[$i]=${COMPREPLY[$i]#"$colonprefixes"};
cp "${TMPDIR:-/tmp}/VALET-${vpkg_parent_uniqpid}/"* "${TMPDIR:-/tmp}/VALET-${vpkg_my_uniqpid}";
CXX=g++
DISPLAY=localhost:12.0
ELEMENTS=/home/1097/seadas/ocssw/var/seawifs
EOS_LIB_PREFIX=linux64
FC=gfortran
GCC_TUNE=
GQUEUE_PREFIX=/opt/shared/gqueue
GQUEUE_SCHEDULER=Slurm
hasSlash=`echo "$cur" | grep / | wc -l`;
HDFEOS_LIB=/home/1097/seadas/ocssw/opt/EOS/lib/linux64
HISTCONTROL=ignoredups
HISTSIZE=1000
HOME=/home/1097
HOSTNAME=login00
HRPT_STATION_IDENTIFICATION_FILE=/home/1097/seadas/ocssw/share/seawifs/station/station_id.dat
INFOPATH=/opt/shared/netcdf/4.1.3/share/info
KDEDIRS=/usr
L2GEN_ANC=/home/1097/seadas/ocssw/var/anc
LANG=en_US.UTF-8
LD_LIBRARY_PATH=/opt/shared/python/3.7.4/lib:/opt/shared/netcdf/4.1.3/lib:/opt/shared/hdf5/1.8.20/lib:/opt/shared/hdf4/4.2.13/lib:/opt/shared/szip/2.1.1/lib:/opt/shared/slurm/lib
LESSOPEN=||/usr/bin/lesspipe.sh %s
LIB3_BIN=/home/1097/seadas/ocssw/opt/bin
LIB3_CHECK=0
LIB3_DIR=/home/1097/seadas/ocssw/opt
LIB3_INC=/home/1097/seadas/ocssw/opt/include
LIB3_LIB=/home/1097/seadas/ocssw/opt/lib
local i=${#COMPREPLY[*]};
local vpkg_args=();
local vpkg_args=();
local vpkg_conf_cmd='';
local vpkg_conf_cmd='';
local vpkg_conf_rc=0;
local vpkg_conf_rc=0;
local vpkg_conf_verbose=0;
local vpkg_conf_verbose=0;
local vpkg_parent_index=1;
local vpkg_parent_uniqpid=`${VALET_PREFIX}/bin/valet_uniqpid -p $$`;
local vpkg_rollback_cmds;
local vpkg_rollback_count=0;
LOGNAME=mshatley
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:
MAIL=/var/spool/mail/mshatley
MANPATH=/opt/shared/python/3.7.4/share/man:/opt/shared/python/3.7.4/man:/opt/shared/netcdf/4.1.3/share/man:/opt/shared/hdf4/4.2.13/share/man::/opt/shared/valet/2.1/man:/opt/shared/slurm/share/man:
NAVCTL=/home/1097/seadas/ocssw/share/seawifs/nav
NAVQC=/home/1097/seadas/ocssw/share/seawifs/nav
OCDATAROOT=/home/1097/seadas/ocssw/share
OCSSW_ARCH=linux_64
OCSSW_BIN=/home/1097/seadas/ocssw/bin
OCSSW_DEBUG=0
OCSSWROOT=/home/1097/seadas/ocssw
OCSSW_SVN=localhost
OCTS_REGISTRATION_TABLES=/home/1097/seadas/ocssw/share/octs/nav
OCVARROOT=/home/1097/seadas/ocssw/var
ORBCTL=/home/1097/seadas/ocssw/share/seawifs/nav
PATH=/opt/shared/python/3.7.4/bin:/opt/shared/netcdf/4.1.3/bin:/opt/shared/hdf5/1.8.20/bin:/opt/shared/hdf4/4.2.13/bin:/home/1097/seadas/ocssw/opt/bin:/home/1097/seadas/ocssw/bin:/opt/shared/valet/2.1/bin/bash:/opt/shared/valet/2.1/bin:/opt/shared/slurm/add-ons/bin:/opt/shared/slurm/bin:/usr/lib64/qt-3.3/bin:/opt/shared/gqueue/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/1097/.local/bin:/home/1097/bin
PGSINC=/home/1097/seadas/ocssw/opt/EOS/include
PGSLIB=/home/1097/seadas/ocssw/opt/EOS/lib/linux64
PKG_CONFIG_PATH=/opt/shared/python/3.7.4/lib/pkgconfig:/opt/shared/netcdf/4.1.3/lib/pkgconfig
PROJ_LIB=/home/1097/seadas/ocssw/opt/share/proj
PROMPT_COMMAND=printf "\033]0;%s@%s:%s\007" "${USER}" "" "${PWD/#$HOME/~}"
PS1=[(orb:\u)@login00 \W]\$
PWD=/home/1097
PYTHONPATH=/opt/shared/gqueue/lib/python2.7/site-packages
PYTHON=python3
PYTHON_SITE_PACKAGES=lib/python3.7/site-packages
PYTHON_VERSION_LONG=3.7.4
PYTHON_VERSION_SHORT=3.7
QTDIR=/usr/lib64/qt-3.3
QT_GRAPHICSSYSTEM_CHECKED=1
QTINC=/usr/lib64/qt-3.3/include
QTLIB=/usr/lib64/qt-3.3/lib
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
SHLVL=2
SSH_TTY=/dev/pts/46
SWFTBL=/home/1097/seadas/ocssw/share/seawifs/qc
SWTBL=/home/1097/seadas/ocssw/share/seawifs
TERM=xterm
USER=mshatley
_=/usr/bin/env
VALET_HISTORY=[standard]szip/2.1.1;hdf4/4.2.13;hdf5/1.8.20;netcdf/4.1.3|[standard]python/3.7.4
VALET_PREFIX=/opt/shared/valet/2.1
VALET_SESSION_ID=a14aed0b-7953-48ff-9ad9-0e82936b674e
versions=`vpkg_versions_completionHelper "$cur"`;
vpkg_args+=("$1")
vpkg_args+=("$1")
vpkg_conf_cmd=$(vpkg_emitconf --context=development "${vpkg_args[@]}");
vpkg_conf_cmd=$(vpkg_emitconf --verbose --context=development "${vpkg_args[@]}");
vpkg_conf_cmd=$(vpkg_emitconf --verbose "${vpkg_args[@]}");
vpkg_conf_cmd=$(vpkg_emitconf "${vpkg_args[@]}");
vpkg_conf_quiet=0;
vpkg_conf_quiet=0;
vpkg_conf_quiet=1;
vpkg_conf_quiet=1;
vpkg_conf_rc=$?;
vpkg_conf_rc=$?;
vpkg_conf_rc=$?;
vpkg_conf_rc=$?;
vpkg_conf_rc=0;
vpkg_conf_rc=0;
vpkg_conf_verbose=0
vpkg_conf_verbose=0
vpkg_conf_verbose=1
vpkg_conf_verbose=1
__vpkg_emitrollback_driver "$vpkg_rollback_cmds";
__vpkg_emitrollback_driver "$vpkg_rollback_cmds";
vpkg_parent_index=$((vpkg_parent_index+1));
vpkg_parent_uniqpid=`${VALET_PREFIX}/bin/valet_uniqpid -p=${vpkg_parent_index} $$`;
vpkg_rollback_cmds="${TMPDIR:-/tmp}/VALET-`${VALET_PREFIX}/bin/valet_uniqpid $$`-${VALET_SESSION_ID}.rollback";
vpkg_rollback_count=$1;
vpkg_rollback_count=1;
vpkg_rollback_count=$((vpkg_rollback_count - 1));
WORKDIR=/work/orb
WORKGROUP=orb
XDG_DATA_DIRS=/home/1097/.local/share/flatpak/exports/share/:/var/lib/flatpak/exports/share/:/usr/local/share/:/usr/share/
XDG_RUNTIME_DIR=/run/user/1097
XDG_SESSION_ID=196674

gnwiii
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Re: Viirs Processing issue

by gnwiii » Mon Sep 20, 2021 9:03 pm America/New_York

I noticed "/home/1097". Few if any linux distros support usernames that start with a number. "man useradd" should give the rules for usernames on your distro, but even if they are allowed, you may encounter 3rd party software that breaks when it encounters a username that starts with a number.

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