HDF5 library version mismatched error

nmatton · June 16, 2016, 11:53am

Hello there,

I was previously using sen2cor v2.0.x whitout any problem, but passing to v2.2.1 is a bit disrupted…

Installation occurs smoothly but when running L2A_Process I get a warning on HDF5 libs version mismatch:

“Warning! HDF5 library version mismatched error”
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as ‘LD_LIBRARY_PATH’.
You can, at your own risk, disable this warning by setting the environment
variable ‘HDF5_DISABLE_VERSION_CHECK’ to a value of ‘1’.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.8.16, library is 1.8.15
SUMMARY OF THE HDF5 CONFIGURATION
=================================

General Information:

       HDF5 Version: 1.8.15-patch1
      Configured on: Wed Oct 14 16:46:37 CDT 2015
      Configured by: ilan@centos5x64.corp.continuum.io
     Configure mode: production
        Host system: x86_64-unknown-linux-gnu
      Uname information: Linux centos5x64.corp.continuum.io 2.6.18-400.1.1.el5 #1 SMP Thu Dec 18 00:59:53 EST 2014 x86_64 x86_64 x86_64 GNU/Linux
           Byte sex: little-endian
          Libraries: shared
     Installation point: /home/ilan/minonda/envs/_build

Compiling Options:

           Compilation Mode: production
                 C Compiler: /usr/bin/gcc ( gcc (GCC) 4.1.2 20080704 )
                     CFLAGS: 
                  H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -O3 -fomit-frame-pointer -finline-functions
                  AM_CFLAGS: 
                   CPPFLAGS: 
                H5_CPPFLAGS: -D_DEFAULT_SOURCE -D_BSD_SOURCE -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L   -DNDEBUG -UH5_DEBUG_API
                AM_CPPFLAGS: -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE 
           Shared C Library: yes
           Static C Library: no

Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lrt -lz -ldl -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no

Languages:

                    Fortran: no

                        C++: yes
               C++ Compiler: /usr/bin/g++ ( g++ (GCC) 4.1.2 20080704 )
                  C++ Flags: 
               H5 C++ Flags:  
               AM C++ Flags: 
         Shared C++ Library: yes
         Static C++ Library: no

Features:

              Parallel HDF5: no
         High Level library: yes
               Threadsafety: no
        Default API Mapping: v18

With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
Strict File Format Checks: no
Optimization Instrumentation: no
Bye…

And then nothing more happen (still the process is not killed…)

Any clue on this ?

Thanks in advance !

Nicolas

umwilm · June 17, 2016, 10:23am

Anaconda is usually equipped with its own version of HDF5, wich fits to the pytables module. In your case it looks like as if a HDF5 library outside of Anaconda is loaded instead, which probably leads to the mismatch you observe. I assume that you LD_LIBRARY_PATH points to a HDF5 library outside of anaconda …

Guill · August 10, 2016, 2:37pm

Hello, I have exactly the same problem as mentioned by nmatton above and I can’t fix it ; does anyone have a clue on this issue ?
Thank you !
Guillaume

unnic · September 28, 2016, 3:02pm

after a complete reinstallation i encounter the same problem.
For me it’s
Headers are 1.8.15, library is 1.8.17

Is there any known solution?
What’s the correct LD_LIBRARY_PATH and how do I set it? How do I avoid the problem in a fresh installation?

Windows10
Anaconda 4.1.1.
sen2cor 2.2.1

@umwilm

umwilm · September 29, 2016, 10:18am

at first you should not set LD_LIBRARY_PATH to point to an HDF5 installation at all. Anaconda is equipped with its own HDF5 module and a pytables module which should fit together when you performed a fresh new installation of anaconda. The problems you describe look as if an incompatible version of HDF5 is searched instead, where I don’t have any explanation for at the moment. If you say that you installed a fresh new version of anaconda, everything should be right in place, including pyTables and hdf5. You can do the following test, which has nothing to do with sen2cor, but is an essential requirement for sen2cor to work:

GVA0323:~ umwilm$ python
Python 2.7.11 |Anaconda custom (x86_64)| (default, Dec 6 2015, 18:57:58)
[GCC 4.2.1 (Apple Inc. build 5577)] on darwin
Type “help”, “copyright”, “credits” or “license” for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org

from tables import *
hdf5file = openFile(‘test’)
hdf5file
File(filename=test, title=’’, mode=‘r’, root_uep=’/’, filters=Filters(complevel=0, shuffle=False, fletcher32=False, least_significant_digit=None))
/ (RootGroup) ‘’

if you get a similar result like that everything is OK, if you get errors here its an installation problem of anaconda, but not of sen2cor.

you could try a ‘conda update tables’, as I’ve seen that your version is lower than mine. As I’m currently are on a workshop I have no access to a windows machine so I cannot test your problems from here, earliest next week.

Cheers,
Uwe

unnic · September 29, 2016, 12:33pm

Thanks for your feedback.

I created a hdf5 before installing sen2cor with

import numpy as np
import h5py

m1 = np.random.random(size = (1000,20))
m2 = np.random.random(size = (1000,200))

with h5py.File('data.h5', 'w') as hf:
    hf.create_dataset('dataset_1', data=m1)
    hf.create_dataset('dataset_2', data=m2)

which can be read without error using

from tables import *
hdf5file = openFile('data.h5')

hdf5file returns an output similar to yours. no errors.

but after installing sen2cor the same script crashes on

import h5py

I pip uninstalled h5py, reinstallation resulted in an error with pip so I used conda which worked.
now running the same script above

hdf5file = openFile('data.h5')
C:\Users\User\AppData\Local\Continuum\Anaconda2\lib\site-packages\spyderlib\widgets\externalshell\start_ipython_kernel.py:2: DeprecationWarning: openFile() is pending deprecation, use open_file() instead. You may use the pt2to3 tool to update your source code.
  #

i followed the instructions

hdf5file = open_file('data.h5')

no errors.
So maybe openFile() should be replaced with open_file() in sen2cor? The former is going to be deprecated.

Further information:
‘conda update tables’ returned ‘Error: Package ‘tables’ is not installed’
‘conda install tables’ returned ‘Error: Package missing in current win-64 channels: - tables’
edit: ‘conda update pytables’ works but then ‘import h5py’ crashes with ‘Headers are 1.8.15, library is 1.8.17’

‘pip install tables’ everything ok
‘pip install tables --upgrade’ :

Collecting tables
  Using cached tables-3.3.0-cp27-cp27m-win_amd64.whl
Collecting numexpr>=2.5.2 (from tables)
Requirement already up-to-date: six in c:\users\user\appdata\local\continuum\anaconda2\lib\site-packages (from tables)
Requirement already up-to-date: numpy>=1.8.0 in c:\users\user\appdata\local\continuum\anaconda2\lib\site-packages (from tables)
Installing collected packages: numexpr, tables
  Found existing installation: numexpr 2.6.0
    DEPRECATION: Uninstalling a distutils installed project (numexpr) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project.
    Uninstalling numexpr-2.6.0:
      Successfully uninstalled numexpr-2.6.0
  Rolling back uninstall of numexpr

edit: I have no idea why but after a reinstallation of sen2cor both openFile() and open_file() work but calling ‘L2A_process’ returns an error:

  File "C:\Users\user\AppData\Local\Continuum\Anaconda2\lib\site-packages\osgeo\__init__.py", line 21, in swig_import_helper
    _mod = imp.load_module('_gdal', fp, pathname, description)
ImportError: DLL load failed: Das angegebene Modul wurde nicht gefunden.

umwilm · September 29, 2016, 3:13pm

strange … I agree that openFile should be replace by open_file in the future as it is deprecated. However at current in my version of pyTables in file.py openFile is mapped to open_file as shown below:

so that in principle this should not give an error.

module file.py, line 320:

openFile = previous_api(open_file)
I’ll create an according SPR to sen2cor to replace the deprecated commands used for pyTables like openFile with the recent ones in the upcoming version.

will go into more details during next week.

cheers,

Uwe

unnic · October 12, 2016, 7:28am

any new developments on this?

umwilm · October 12, 2016, 12:50pm

A bugfix release of sen2cor which includes also the replacement of the old command is in the test phase. The release date will be announced by ESA on their webpage after it passed the acceptance.

umwilm · October 13, 2016, 10:17am

Hi unnic,

I did a series on tests in order to reproduce the problems you described, but I’m sorry I cannot reproduce the problems you describe:

I performed following tests on a windows 64 bit machine in the order as listed:

  Started Sen2Cor 2.2.1 as it was initially installed at the state of release date – worked.

  Upgraded anaconda with ‘conda update anaconda’ receiving following info afterwards:

packages in environment at C:\Users\umuellerwilm\AppData\Local\Continuum\Anaconda2:

anaconda 4.2.0 np111py27_0

  Tested the already installed sen2Cor Version after upgrade of Anaconda - worked.

  Removed the Sen2Cor version 2.2.1 with pip uninstall, confirmed that it was uninstalled from anaconda afterwards and started a new installation from scratch using the sen2cor version as it is provided on the ESA webpage – worked.

I will now place the full trace of my final installation and a test so that you can compare with your situation:

Installed c:\users\umuellerwilm\appdata\local\continuum\anaconda2\lib\site-packages\sen2cor-2.2.1-py2.7.egg
Processing dependencies for sen2cor==2.2.1
Finished processing dependencies for sen2cor==2.2.1
Fetching package metadata …
Solving package specifications: …

Package plan for installation in environment C:\Users\umuellerwilm\AppData\Local\Continuum\Anaconda2:

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
glymur-0.8.4               |           py27_0         2.8 MB  sunpy

The following packages will be UPDATED:

glymur: 0.8.3-py27_0 sunpy --> 0.8.4-py27_0 sunpy

Fetching packages …
glymur-0.8.4-p 100% |###############################| Time: 0:00:02 1.09 MB/s
Extracting packages …
[ COMPLETE ]|##################################################| 100%
Unlinking packages …
[ COMPLETE ]|##################################################| 100%
Linking packages …
[ COMPLETE ]|##################################################| 100%
Fetching package metadata …
Solving package specifications: …
Warning: 2 possible package resolutions (only showing differing packages):

curl-7.49.0-vc9_0.tar.bz2, libnetcdf-4.3.3.1-vc9_4.tar.bz2
curl-7.45.0-vc9_1.tar.bz2, libnetcdf-4.3.3.1-vc9_5.tar.bz2

Package plan for installation in environment C:\Users\umuellerwilm\AppData\Local\Continuum\Anaconda2:

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
geos-3.5.0                 |            vc9_0         3.6 MB
proj4-4.9.2                |            vc9_0         568 KB
xerces-c-3.1.4             |            vc9_0         1.4 MB
hdf4-4.2.12                |            vc9_0        1004 KB
kealib-1.4.6               |            vc9_0         203 KB
libnetcdf-4.3.3.1          |            vc9_4         423 KB
libgdal-2.1.0              |            vc9_0         6.1 MB
                                       Total:        13.2 MB

The following packages will be UPDATED:

geos:      3.4.2-vc9_0   [vc9] --> 3.5.0-vc9_0   [vc9]
hdf4:      4.2.11-0      --> 4.2.12-vc9_0  [vc9]
kealib:    1.4.5-vc9_0   [vc9] --> 1.4.6-vc9_0   [vc9]
libgdal:   2.0.0-vc9_2   [vc9] --> 2.1.0-vc9_0   [vc9]
proj4:     4.9.1-vc9_0   [vc9] --> 4.9.2-vc9_0   [vc9]
xerces-c:  3.1.2-vc9_0   [vc9] --> 3.1.4-vc9_0   [vc9]

The following packages will be DOWNGRADED due to dependency conflicts:

libnetcdf: 4.3.3.1-vc9_5 [vc9] --> 4.3.3.1-vc9_4 [vc9]

Fetching packages …
geos-3.5.0-vc9 100% |###############################| Time: 0:00:06 578.04 kB/s
proj4-4.9.2-vc 100% |###############################| Time: 0:00:02 272.35 kB/s
xerces-c-3.1.4 100% |###############################| Time: 0:00:04 333.56 kB/s
hdf4-4.2.12-vc 100% |###############################| Time: 0:00:01 800.21 kB/s
kealib-1.4.6-v 100% |###############################| Time: 0:00:00 320.60 kB/s
libnetcdf-4.3. 100% |###############################| Time: 0:00:00 479.30 kB/s
libgdal-2.1.0- 100% |###############################| Time: 0:00:03 1.75 MB/s
Extracting packages …
[ COMPLETE ]|##################################################| 100%
Unlinking packages …
[ COMPLETE ]|##################################################| 100%
Linking packages …
[ COMPLETE ]|##################################################| 100%
Fetching package metadata …
Solving package specifications: …

Package plan for installation in environment C:\Users\umuellerwilm\AppData\Local\Continuum\Anaconda2:

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
gdal-2.1.0                 |           py27_0         501 KB

The following packages will be UPDATED:

gdal: 2.0.0-py27_1 --> 2.1.0-py27_0

Fetching packages …
gdal-2.1.0-py2 100% |###############################| Time: 0:00:00 558.18 kB/s
Extracting packages …
[ COMPLETE ]|##################################################| 100%
Unlinking packages …
[ COMPLETE ]|##################################################| 100%
Linking packages …
[ COMPLETE ]|##################################################| 100%
copying C:\Users\umuellerwilm\AppData\Local\Continuum\Anaconda2\Lib\site-packages\sen2cor-2.2.1-py2.7.egg/sen2cor\build\lib.win-amd64-2.7\openjp2.dll -> C:\User
s\umuellerwilm\AppData\Local\Continuum\Anaconda2\Scripts
copying C:\Users\umuellerwilm\AppData\Local\Continuum\Anaconda2\Lib\site-packages\sen2cor-2.2.1-py2.7.egg/sen2cor\build\lib.win-amd64-2.7\L2A_AtmCorr.pyd -> C:
Users\umuellerwilm\AppData\Local\Continuum\Anaconda2\Lib\site-packages\sen2cor-2.2.1-py2.7.egg/sen2cor

SEN2COR 2.2.1 setup script:
This will finish the configuration of the environment settings.

OK to continue? [y/n]: y

Please input a path for the sen2cor home directory:
default is: C:\Users\umuellerwilm\documents\sen2cor
Is this OK? [y/n]: y
copying C:\Users\umuellerwilm\AppData\Local\Continuum\Anaconda2\Lib\site-packages\sen2cor-2.2.1-py2.7.egg/sen2cor\cfg\L2A_GIPP.xml -> C:\Users\umuellerwilm\docu
ments\sen2cor\cfg
Setting environment for sen2cor …
Setting environment variable GDAL_DATA:
SUCCESS: Specified value was saved.
Setting environment variable SEN2COR_HOME:
SUCCESS: Specified value was saved.
Setting environment variable SEN2COR_BIN:
SUCCESS: Specified value was saved.
Congratulations, you are done!

you can call the processor from everywhere via: “L2A_Process”
you will find the default configuration called “L2A_GIPP.xml” under:
C:\Users\umuellerwilm\documents\sen2cor\cfg

Installation sucessfully performed.

tested anaconda after update:

P:\S2PMAS\Software\Testdata>conda update anaconda
Fetching package metadata …
Solving package specifications: …

All requested packages already installed.

packages in environment at C:\Users\umuellerwilm\AppData\Local\Continuum\Anaconda2:

anaconda 4.2.0 np111py27_0

cd to P:\S2PMAS\Software\Testdata and called Sen2Cor with the following commandline:

P:\S2PMAS\Software\Testdata>L2A_Process S2A_OPER_PRD_MSIL1C_PDMC_20160408T210702_R005_V20160408T055008_20160408T055008.SAFE --resolution=60

Sentinel-2 Level 2A Prototype Processor (Sen2Cor), 2.2.1, created: 2016.04.29 started …
selected resolution is 60 m.
Progress[%]: 1.60 : PID-5040, L2A_ProcessTile: processing with resolution 60 m, elapsed time[s]: 4.358
Progress[%]: 1.60 : PID-5040, L2A_ProcessTile: start of pre processing, elapsed time[s]: 0.002
Progress[%]: 1.68 : PID-5040, L2A_Tables: start import, elapsed time[s]: 0.217
Progress[%]: 2.17 : PID-5040, L2A_Tables: band B01 imported, elapsed time[s]: 1.335
Progress[%]: 14.54 : PID-5040, L2A_Tables: band B02 imported, elapsed time[s]: 33.663
Progress[%]: 27.26 : PID-5040, L2A_Tables: band B03 imported, elapsed time[s]: 34.626
Progress[%]: 40.84 : PID-5040, L2A_Tables: band B04 imported, elapsed time[s]: 36.952
Progress[%]: 44.95 : PID-5040, L2A_Tables: band B05 imported, elapsed time[s]: 11.188
Progress[%]: 48.91 : PID-5040, L2A_Tables: band B06 imported, elapsed time[s]: 10.769
Progress[%]: 52.94 : PID-5040, L2A_Tables: band B07 imported, elapsed time[s]: 10.985
Progress[%]: 57.03 : PID-5040, L2A_Tables: band B8A imported, elapsed time[s]: 11.123
Progress[%]: 57.53 : PID-5040, L2A_Tables: band B09 imported, elapsed time[s]: 1.365
Progress[%]: 57.85 : PID-5040, L2A_Tables: band B10 imported, elapsed time[s]: 0.870
Progress[%]: 61.91 : PID-5040, L2A_Tables: band B11 imported, elapsed time[s]: 11.047
Progress[%]: 66.00 : PID-5040, L2A_Tables: band B12 imported, elapsed time[s]: 11.136
Progress[%]: 66.00 : PID-5040, L2A_ProcessTile: start of Scene Classification, elapsed time[s]: 0.012
Progress[%]: 66.16 : PID-5040, Pre process , elapsed time[s]: 0.417
Progress[%]: 66.42 : PID-5040, L2A_SC init , elapsed time[s]: 0.726
Progress[%]: 66.57 : PID-5040, L2A_CSND_1_1 , elapsed time[s]: 0.387
Progress[%]: 66.69 : PID-5040, L2A_CSND_1_2 , elapsed time[s]: 0.325
Progress[%]: 66.82 : PID-5040, L2A_CSND_2_0 , elapsed time[s]: 0.378
Progress[%]: 66.90 : PID-5040, L2A_CSND_2_1 , elapsed time[s]: 0.204
Progress[%]: 66.97 : PID-5040, L2A_CSND_2_1_2, elapsed time[s]: 0.203
Progress[%]: 67.01 : PID-5040, L2A_CSND_2_2 , elapsed time[s]: 0.093
Progress[%]: 67.15 : PID-5040, L2A_CSND_2_3 , elapsed time[s]: 0.382
Progress[%]: 67.21 : PID-5040, L2A_CSND_2_4 , elapsed time[s]: 0.169
Progress[%]: 67.39 : PID-5040, L2A_CSND_2_5 , elapsed time[s]: 0.480
Progress[%]: 67.52 : PID-5040, L2A_CSND_3 , elapsed time[s]: 0.369
Progress[%]: 67.63 : PID-5040, L2A_CSND_5_1 , elapsed time[s]: 0.281
Progress[%]: 67.78 : PID-5040, L2A_CSND_5_2 , elapsed time[s]: 0.425
Progress[%]: 67.90 : PID-5040, L2A_CSND_6 , elapsed time[s]: 0.328
Progress[%]: 67.97 : PID-5040, L2A_CSND_6_2 , elapsed time[s]: 0.187
Progress[%]: 68.12 : PID-5040, L2A_CSND_7 , elapsed time[s]: 0.396
Progress[%]: 69.70 : PID-5040, L2A_SHD , elapsed time[s]: 4.301
Progress[%]: 69.78 : PID-5040, DV recovery , elapsed time[s]: 0.236
Progress[%]: 69.88 : PID-5040, WP recovery , elapsed time[s]: 0.272
Progress[%]: 69.99 : PID-5040, Snow recovery , elapsed time[s]: 0.278
Progress[%]: 70.04 : PID-5040, Soil recovery , elapsed time[s]: 0.134
Progress[%]: 70.38 : PID-5040, Post process , elapsed time[s]: 0.946
Progress[%]: 70.38 : PID-5040, L2A_ProcessTile: start of Atmospheric Correction, elapsed time[s]: 0.004
Progress[%]: 70.49 : PID-5040, L2A_AtmCorr: end of calculation terrain maps, elapsed time[s]: 0.288
Progress[%]: 70.49 : PID-5040, L2A_AtmCorr: start of AOT retrieval at 550nm, elapsed time[s]: 0.004
Progress[%]: 70.72 : PID-5040, L2A_AtmCorr: end of AOT retrieval at 550nm, elapsed time[s]: 0.616
Progress[%]: 71.62 : PID-5040, L2A_AtmCorr: end of internal classification, elapsed time[s]: 2.459
Progress[%]: 71.81 : PID-5040, L2A_AtmCorr: end of interpolation LUTs, elapsed time[s]: 0.502
Progress[%]: 71.81 : PID-5040, L2A_AtmCorr: end retrieving reference pixels for dark areas, elapsed time[s]: 0.006
Progress[%]: 72.84 : PID-5040, L2A_AtmCorr: end of check for dense bright vegetation pixels, elapsed time[s]: 2.800
Progress[%]: 73.28 : PID-5040, L2A_AtmCorr: end of receiving atmospheric functions for all altitudes and visibilities, elapsed time[s]: 1.200
Progress[%]: 73.28 : PID-5040, L2A_AtmCorr: start of WV retrieval, elapsed time[s]: 0.004
Progress[%]: 73.73 : PID-5040, L2A_AtmCorr: end of WV retrieval preparation, elapsed time[s]: 1.215
Progress[%]: 82.53 : PID-5040, L2A_AtmCorr: end of WV retrieval, elapsed time[s]: 23.957
Progress[%]: 82.53 : PID-5040, L2A_AtmCorr: start of rho retrieval, elapsed time[s]: 0.004
Progress[%]: 84.38 : PID-5040, L2A_AtmCorr: end of rho retrieval preparation, elapsed time[s]: 5.043
Progress[%]: 92.99 : PID-5040, L2A_AtmCorr: end of rho retrieval step 1, elapsed time[s]: 23.432
Progress[%]: 99.58 : PID-5040, L2A_AtmCorr: end of rho retrieval step 2, elapsed time[s]: 18.943
Progress[%]: 99.23 : PID-5040, L2A_ProcessTile: start of post processing, elapsed time[s]: 0.047
Progress[%]: 98.86 : PID-5040, L2A_Tables: start export, elapsed time[s]: 0.013
Progress[%]: 99.15 : PID-5040, L2A_Tables: band B01 exported, elapsed time[s]: 1.775
Progress[%]: 99.40 : PID-5040, L2A_Tables: band B02 exported, elapsed time[s]: 1.687
Progress[%]: 99.63 : PID-5040, L2A_Tables: band B03 exported, elapsed time[s]: 1.730
Progress[%]: 99.63 : PID-5040, L2A_Tables: band B04 exported, elapsed time[s]: 1.722
Progress[%]: 99.63 : PID-5040, L2A_Tables: band B05 exported, elapsed time[s]: 1.749
Progress[%]: 99.63 : PID-5040, L2A_Tables: band B06 exported, elapsed time[s]: 2.298
Progress[%]: 99.63 : PID-5040, L2A_Tables: band B07 exported, elapsed time[s]: 1.739
Progress[%]: 99.63 : PID-5040, L2A_Tables: band B8A exported, elapsed time[s]: 1.942
Progress[%]: 99.63 : PID-5040, L2A_Tables: band B09 exported, elapsed time[s]: 1.864
Progress[%]: 99.63 : PID-5040, L2A_Tables: band B11 exported, elapsed time[s]: 2.072
Progress[%]: 99.63 : PID-5040, L2A_Tables: band B12 exported, elapsed time[s]: 1.781
Progress[%]: 99.45 : PID-5040, L2A_Tables: band SCL exported, elapsed time[s]: 0.511
Progress[%]: 99.16 : PID-5040, L2A_Tables: band SNW exported, elapsed time[s]: 0.197
Progress[%]: 98.97 : PID-5040, L2A_Tables: band CLD exported, elapsed time[s]: 0.508
Progress[%]: 98.67 : PID-5040, L2A_Tables: band AOT exported, elapsed time[s]: 0.197
Progress[%]: 98.78 : PID-5040, L2A_Tables: band WVP exported, elapsed time[s]: 1.295
Progress[%]: 99.07 : PID-5040, L2A_Tables: preview image exported, elapsed time[s]: 1.804
Progress[%]: 98.71 : PID-5040, L2A_Tables: stop export, elapsed time[s]: 0.020
Progress[%]: 100.00 : Application terminated successfully.

unnic · October 14, 2016, 8:15am

ok, got it running again. thanks for you input.
The solution (for me) was to clean the registry (using CCleaner) after the uninstallation of sen2cor and anaconda.

Now I’m trying to get my jp2 driver back to project the resulting images…

mgeeves · December 16, 2016, 4:40pm

Installing with a newer version of Anaconda fixed it for me

I found that in my case as well as having:
/opt/anaconda/pkgs/hdf5-1.8.17-1
There was also:
/opt/anaconda/pkgs/hdf5-1.8.15-1
…but in such a way that Anaconda wasn’t “aware” of it

Somehow in the installation process (clean for Anaconda and everything else) it tried upgrading the hdf5 package but seemed to leave the files there? Attempting to install hdf5-1.8.15 then didn’t work because the available version was then going into:
/opt/anaconda/pkgs/hdf5-1.8.15-2

End fix was installing with a newer version of Anaconda, it broke when installing from scratch with:
Anaconda2-2.5.0-Linux-x86_64.sh

Worked when updating and installing instead with:
Anaconda2-4.2.0-Linux-x86_64.sh

Cheers,
Mike