ERROR VIIRS AF v1.1.1 undefined symbol: H5Ovisit_by_name

VIIRS Environmental Data Records

ERROR VIIRS AF v1.1.1 undefined symbol: H5Ovisit_by_name

Postby rdirienzo » Mon Nov 15, 2021 5:23 am

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

Code: Select all
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



Code: Select all
$> 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

Code: Select all
echo ${CSPP_ACTIVE_FIRE_HOME}
/opt/CSPP/cspp-active-fire-noaa_1.1.1



$> env
Code: Select all
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.
rdirienzo
 
Posts: 7
Joined: Mon Nov 15, 2021 5:03 am

Re: ERROR VIIRS AF v1.1.1 undefined symbol: H5Ovisit_by_name

Postby kathys » Mon Nov 15, 2021 3:37 pm

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
kathys
 
Posts: 355
Joined: Tue Jun 22, 2010 4:51 pm

Re: ERROR VIIRS AF v1.1.1 undefined symbol: H5Ovisit_by_name

Postby rdirienzo » Tue Nov 16, 2021 3:52 am

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

Thanks,
Roberto
rdirienzo
 
Posts: 7
Joined: Mon Nov 15, 2021 5:03 am


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