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ocssw calibrate_viirs moudle error!
Posted: Fri May 25, 2018 2:13 am America/New_York
by xpf7622
I have downloaded file V2018077003000.LIA_SNPP.nc , when use calibrate_viirs deal with the file, there have some error as the following:
execution exception: java.io.IOException: calibrate_viirs failed with exit code 127.
Check log for more details.
calibrate_viirs: symbol lookup error: calibrate_viirs: undefined symbol: _ZN6netCDF6NcFileC1ERKSsNS0_8FileMode
when I look for the string
_ZN6netCDF6NcFileC1ERKSsNS0_8FileMode in google ?the page which url is
https://alioth-lists.debian.net/pipermail/pkg-grass-devel/2015-August/034286.html give the following message:
@@ -382,10 +501,14 @@ libnetcdf_c++4.so.1 libnetcdf-c++4-1 #MINVER#
_ZN6netCDF6NcCharD2Ev at Base 4.2.1
_ZN6netCDF6NcChareqERKS0_ at Base 4.2.1
_ZN6netCDF6NcFileC1ERKNS_7NcGroupE at Base 4.2.1
+ _ZN6netCDF6NcFileC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS0_8FileModeE at Base 4.2.1
+ _ZN6netCDF6NcFileC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS0_8FileModeENS0_10FileFormatE at Base 4.2.1
_ZN6netCDF6NcFileC1ERKSsNS0_8FileModeE at Base 4.2.1
So I try install
libnetcdf-cxx_4.2.1.orig.tar.gz and version 4.3, and I use
ldd calibrate_viirs find out the denpended lib, then I run
nm /usr/local/lib/libnetcdf_c++4.so.1 |grep _ZN6netCDF6NcFileC1ERKSsNS0_8FileMode. but However, disappointingly, the string _ZN6netCDF6NcFileC1ERKSsNS0_8FileMode can't find.
So ,who can give me some good method? (the OS is ubuntu 16.04 x64? seadas version is 7.4)
ocssw calibrate_viirs moudle error!
Posted: Fri May 25, 2018 9:15 am America/New_York
by OB SeaDAS - dshea
The name mangling for C++ changed at version g++-5, which seems to be the problem you are having. The command ldd calibrate_viirs should point to the $OCSSWROOT/opt/lib/libnetcdf_c++4.so.1 that we deliver. This assumes you have run:
$ export OCSSWROOT=<ocssw install dir>
$ source $OCSSWROOT/OCSSW_bash.env
Post the full output from ldd calibrate_viirs.
don
ocssw calibrate_viirs moudle error!
Posted: Fri May 25, 2018 11:06 am America/New_York
by xpf7622
ldd /home/xpf7622/seadas-7.4/ocssw/run/bin/linux_64/calibrate_viirs
linux-vdso.so.1 => (0x00007fff5cb3e000)
libnetcdf_c++4.so.1 => not found
libnetcdf.so.11 => not found
libhdf5.so.10.2.1 => not found
libpugixml.so.1 => not found
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f9e7101b000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f9e70d12000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f9e70990000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f9e7077a000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f9e703b0000)
/lib64/ld-linux-x86-64.so.2 (0x00007f9e71238000)
the result there can't find libnetcdf_c++4.so.1 , but I find it in directory "/home/xpf7622/seadas-7.4/ocssw/opt/lib"
by the way, I have set the enviroment variables(export OCSSWROOT=/home/pfxie/seadas-7.4/ocssw?source $OCSSWROOT/OCSSW_bash.env) in ~/.bashrc
even though I run the two commands in shell, the result of the " ldd /home/xpf7622/seadas-7.4/ocssw/run/bin/linux_64/calibrate_viirs" as the same before.
ocssw calibrate_viirs moudle error!
Posted: Fri May 25, 2018 1:38 pm America/New_York
by gnwiii
The "ldd
" output indicates a problem with the environment variables. You mention:
export OCSSWROOT=/home/pfxie/seadas-7.4/ocssw
source $OCSSWROOT/OCSSW_bash.env
, for user "pfxie", but then
ldd /home/xpf7622/seadas-7.4/ocssw/run/bin/linux_64/calibrate_viirs
for
user "xpf7622". Are you attempting to share one seadas install across multiple users?
ocssw calibrate_viirs moudle error!
Posted: Fri May 25, 2018 8:42 pm America/New_York
by xpf7622
The "ldd" output indicates a problem with the environment variables. You mention:
export OCSSWROOT=/home/pfxie/seadas-7.4/ocssw
source $OCSSWROOT/OCSSW_bash.env, for user "pfxie", but then
ldd /home/xpf7622/seadas-7.4/ocssw/run/bin/linux_64/calibrate_viirs for
user "xpf7622". Are you attempting to share one seadas install across multiple users?
above is my mistake
export OCSSWROOT=/home/xpf7622/seadas-7.4/ocssw is he original configuration?only one user xpf7622.
The main problem is why system cant't find some lib that have already exist.
Still not' working when I use add /home/xpf7622/seadas-7.4/ocssw/opt/lib in /etc/ld.so.conf and use sudo ldconfig command,
ocssw calibrate_viirs moudle error!
Posted: Fri May 25, 2018 8:42 pm America/New_York
by xpf7622
why ld.so.conf in ubuntu can't work?
ocssw calibrate_viirs moudle error!
Posted: Sat May 26, 2018 1:27 am America/New_York
by OB SeaDAS - dshea
Sorry to mislead you in my earlier post. I have been thinking SeaDAS 7.5 when you were having problems with shared objects.
In SeaDAS 7.4 all of the OCSSW executables are statically linked, so ldd does not work on the executable we provide.
I just installed 7.4 on a new install of Ubuntu 16.04 and the OCSSW binaries worked great. Including calibrate_viirs.
Did you compile from source?
The source for calibrate_viirs is not included in seadas 7.4
You may have a strange mix of 7.4 and 7.5
Not sure I can fix your current install. You may have to install a new copy in a different directory.
don
ocssw calibrate_viirs moudle error!
Posted: Sat May 26, 2018 9:14 am America/New_York
by xpf7622
you install seadas 7.5 or 7.4 and OCSSW by compliering way or binary module?
I used binary programme or module from
https://seadas.gsfc.nasa.gov/downloads/ and
https://oceandata.sci.gsfc.nasa.gov/ocssw/I have installed 7.5 and OCSSW by such command as " ./install_ocssw.py --install-dir=/home/pfxie/seadas-7.5/ocssw --git-branch=v7.5 --local=. --viirsn ", the above problem doesn't exist .
but when i deal with V2018077003000.L1A_SNPP.nc file, there produce the follwing error. (I don't understand remote sensing technology)
execution exception: java.io.IOException: calibrate_viirs failed with exit code 1.
Check log for more details.
Attempt to read Polar Wander file failed.
VcstCmnGeo::LUT initialization failure
VcstObc:: CmnGeo initialization failure
VcstViirsCal::Granule initialization failure
Main:: Calibration initialization failure
by the way when I use command: ./install_ocssw.py --install-dir=/home/pfxie/seadas-7.5/ocssw --git-branch=v7.5 --local=.
--eval, the result as follow:
Usage: install_ocssw.py [options]
install_ocssw.py: error: no such option: --eval
ocssw calibrate_viirs moudle error!
Posted: Wed Jun 06, 2018 9:14 am America/New_York
by OB SeaDAS - dshea
if you use the --local option then the LUTs are not downloaded. You need to install the LUTs for VIIRS.
yes, --eval is no longer available. It is an internal testing setup and should not be necessary to normal users.
don