ERROR VIIRS AF v1.1.1 undefined symbol: H5Ovisit_by_name

[rdirienzo]

Hello everyone,
before talking about my problem I wanted to thank you for your commitment!

After following the installation provided for in the manual https://bin.ssec.wisc.edu/pub/CSPP/hidd ... v1.1.1.pdf
I got the following error:

$> cspp_active_fire_noaa.sh

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Traceback (most recent call last):
  File "/opt/CSPP/cspp-active-fire-noaa_1.1.1/scripts/cspp_active_fire_noaa.py", line 22, in <module>
    from active_fire_interface import get_afire_inputs, construct_cmd_invocations
  File "/opt/CSPP/cspp-active-fire-noaa_1.1.1/scripts/active_fire_interface.py", line 27, in <module>
    import h5py
  File "/opt/CSPP/cspp-active-fire-noaa_1.1.1/vendor/ShellB3/lib/python3.8/site-packages/h5py-2.10.0-py3.8-linux-x86_64.egg/h5py/__init__.py", line 34, in <module>
    from . import version
  File "/opt/CSPP/cspp-active-fire-noaa_1.1.1/vendor/ShellB3/lib/python3.8/site-packages/h5py-2.10.0-py3.8-linux-x86_64.egg/h5py/version.py", line 17, in <module>
    from . import h5 as _h5
  File "h5py/h5.pyx", line 1, in init h5py.h5
ImportError: /opt/CSPP/cspp-active-fire-noaa_1.1.1/vendor/ShellB3/lib/python3.8/site-packages/h5py-2.10.0-py3.8-linux-x86_64.egg/h5py/defs.cpython-38-x86_64-linux-gnu.so: undefined symbol: H5Ovisit_by_name

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$> ls -l  /opt/CSPP/cspp-active-fire-noaa_1.1.1/vendor/ShellB3/lib/python3.8/site-packages/h5py-2.10.0-py3.8-linux-x86_64.egg/h5py/defs.cpython-38-x86_64-linux-gnu.so
-rwxr-xr-x. 1 53794 700 912952 Sep 21  2020 /opt/CSPP/cspp-active-fire-noaa_1.1.1/vendor/ShellB3/lib/python3.8/site-packages/h5py-2.10.0-py3.8-linux-x86_64.egg/h5py/defs.cpython-38-x86_64-linux-gnu.so

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echo ${CSPP_ACTIVE_FIRE_HOME}
/opt/CSPP/cspp-active-fire-noaa_1.1.1

$> env

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XDG_SESSION_ID=260
HOSTNAME=toolboxes
CSPP_REV=20171024
SELINUX_ROLE_REQUESTED=
TERM=xterm-256color
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=93.41.252.46 56837 22
CSPP_VIIRS_LSR_HOME=/opt/CSPP/CSPP_VIIRS_Surface_Reflectance
SELINUX_USE_CURRENT_RANGE=
CSPP_ACSPO_BIAS=/opt/CSPP/CSPP_ACSPO_2_0/bias
SSH_TTY=/dev/pts/1
USER=root
LD_LIBRARY_PATH=:/opt/CSPP/SDR_3_3/common/local/lib/
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
JPSS_REMOTE_ANC_DIR=https://jpssdb.ssec.wisc.edu/cspp_v_2_0/ancillary
MAIL=/var/spool/mail/root
PATH=/usr/local/go/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/root/go/bin:/root/bin:/opt/CSPP/CSPP_VIIRS_Surface_Reflectance/bin:/opt/CSPP/SDR_3_3/viirs:/opt/CSPP/SDR_3_3/cris:/opt/CSPP/SDR_3_3/atms:/opt/CSPP/SDR_3_3/omps:/opt/CSPP/SDR_3_3/common:/opt/CSPP/cspp-active-fire-noaa_1.1.1/vendor/ShellB3/bin:/opt/CSPP/cspp-active-fire-noaa_1.1.1/bin:/opt/CSPP/cspp-active-fire-noaa_1.1.1/scripts
PWD=/opt/CSPP/cspp-active-fire-noaa_1.1.1/vendor/ShellB3
LANG=en_US.UTF-8
SELINUX_LEVEL_REQUESTED=
CSPP_DYNAMIC_ANCIL_DIR=/opt/CSPP/CSPP_ACSPO_2_0/dynanc
HISTCONTROL=ignoredups
CSPP_RGB_HOME=/opt/CSPP/SDR_3_3/common
CSPP_ACTIVE_FIRE_HOME=/opt/CSPP/cspp-active-fire-noaa_1.1.1
CSPP_SDR_HOME=/opt/CSPP/SDR_3_3
SHLVL=1
HOME=/root
CSPP_ACSPO_HOME=/opt/CSPP/CSPP_ACSPO_2_0
LOGNAME=root
CSPP_ACSPO_CMC_MASK=%Y%m%d120000-CMC-L4_GHRSST-SSTfnd-CMC0.1deg-GLOB-v02.0-fv03.0.nc
SSH_CONNECTION=93.41.252.46 56837 65.21.187.23 22
GOPATH=/root/go
LESSOPEN=||/usr/bin/lesspipe.sh %s
XDG_RUNTIME_DIR=/run/user/0
CSPP_ACSPO_MODIS_LEAPSEC=https://oceandata.sci.gsfc.nasa.gov/Ancillary/LUTs/modis/leapsec.dat
_=/usr/bin/env
OLDPWD=/opt

thank for your help and time.

[kathys]

Hello,

Sorry that you are having problems executing the CSPP active fire software.

From your env output, we can see that you have sourced both the CSPP ACSPO environment variables and the CSPP Active Fire variables in the same shell. Can you please try executing the software in a clean shell? It is always a good idea to run each individual script in its own environment.

If you try this and you are still seeing the same error message, can you please provide us with more information?

1). Computer hardware specifications (including memory and hard drive space);
2). Operating system name and version number.

Thank you,

Kathy

[rdirienzo]

Thanks for your invaluable help!
your suggestion worked and the tests concluded successfully.

Thanks,
Roberto