Need Help with Proj.db cannot find

satas12825 · September 7, 2023, 6:29am

.ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db

…10%…20%…30%…40%…50%…60%…70%…80%…90%ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db

ERROR 1: Cannot parse CRS http://www.opengis.net/def/crs/EPSG/0/5482

ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db

ERROR 1: Cannot parse CRS http://www.opengis.net/def/crs/EPSG/0/5936

ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db

ERROR 1: Cannot parse CRS http://www.opengis.net/def/crs/EPSG/0/3978

ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db

ERROR 1: Cannot parse CRS http://www.opengis.net/def/crs/EPSG/0/2193

ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db

done.

i got this Error when i run GPT via command line on Ubuntu

adraghici · September 7, 2023, 9:08am

Hi @satas12825,

In order to help you regarding the reported problem, we need more information to help us understanding your problem and provide the best solution for you.

Please let us:

the version of Operating System
the version of SNAP
the name of the product(s) used
the processing graph

Regards
Adrian

satas12825 · September 7, 2023, 9:24am

@adraghici thank you for your response:
I’m using Ubuntu 20.04.6 LTS focal
snap version 9.0.0
using Sentinel2 L2A data from Scihub
convert_mask.xml (2.1 KB)

adraghici · September 7, 2023, 10:09am

@satas12825 thank you for your quickly response.

We need one more thing to help us understanding your problem:

the SNAP log file (it can be found in ~/.snap/var/log/messages.log)

To ensure that the SNAP log file contains the information’s we need to understand you problem, please reproduce the problem and completely close the SNAP/GPT before send us the SNAP log file.

Regards
Adrian

satas12825 · September 7, 2023, 10:22am

there are not log folders in my folder:
root@e9f7e36d0261:~/.unidata/cache/root/.snap/var# cd /root/.snap

root@e9f7e36d0261:~/.snap# ls

auxdata epsg-database etc product-library var

root@e9f7e36d0261:~/.snap# cd auxdata/

root@e9f7e36d0261:~/.snap/auxdata# ls

color_palettes gdal netcdf_natives openjpeg rgb_profiles s2tbx sm_luts tool-adapters

root@e9f7e36d0261:~/.snap/auxdata# cd …

root@e9f7e36d0261:~/.snap# ls

auxdata epsg-database etc product-library var

root@e9f7e36d0261:~/.snap# cd var

root@e9f7e36d0261:~/.snap/var# ls

cache

adraghici · September 7, 2023, 11:15am

@satas12825 thank you for your reply.

I understand that the GPT not creates the LOG file.

You can send us the whole console output of GPT execution by:
./gpt [params] > ~/log_07092023.txt

Please send us the ~/log_07092023.txt after the execution finishes.

Regards
Adrian

satas12825 · September 7, 2023, 11:52am

thank you for keep repling me. It’s kind of a weird result in a log file
Anyway i got this in the terminal
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters

INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Incompatible GDAL 3.7.0 found on system. Internal GDAL 3.2.1 from distribution will be used.

INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Internal GDAL 3.2.1 set to be used by SNAP.

INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.

INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Internal GDAL 3.2.1 set to be used by SNAP.

INFO: org.esa.s2tbx.dataio.s2.ortho.S2OrthoProductReaderPlugIn: Building product reader - EPSG:32647

WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [metadata_level] does not exist

WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist

INFO: org.hsqldb.persist.Logger: dataFileCache open start

WARNING: org.esa.s2tbx.dataio.s2.ortho.metadata.S2OrthoMetadata: Warning: missing file /root/kubota-mpd/workspace/rawdata/S2A_MSIL2A_20230419T034531_N0509_R104_T47QNV_20230419T083155.zip/S2A_MSIL2A_20230419T034531_N0509_R104_T47QNV_20230419T083155.SAFE/GRANULE/L2A_T47QNV_A040856_20230419T035621/QI_DATA/L2A_T47QNV_20230419T034531_DDV_20m.jp2

WARNING: org.esa.s2tbx.dataio.s2.ortho.metadata.S2OrthoMetadata: Warning: no image files found for band quality_dense_dark_vegetation

ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db

ERROR 1: Cannot parse CRS http://www.opengis.net/def/crs/EPSG/0/5482

ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db

ERROR 1: Cannot parse CRS http://www.opengis.net/def/crs/EPSG/0/5936

ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db

ERROR 1: Cannot parse CRS http://www.opengis.net/def/crs/EPSG/0/3978

ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db

ERROR 1: Cannot parse CRS http://www.opengis.net/def/crs/EPSG/0/2193

ERROR 1: PROJ: proj_create_from_database: Cannot find proj.db

java.lang.IllegalStateException: java.lang.reflect.InvocationTargetException

at org.esa.s2tbx.dataio.gdal.drivers.GDALReflection.callGDALLibraryMethod(GDALReflection.java:58)

at org.esa.s2tbx.dataio.gdal.drivers.Driver.createCopy(Driver.java:82)

at org.esa.s2tbx.dataio.gdal.writer.GDALProductWriter.close(GDALProductWriter.java:248)

at org.esa.snap.core.gpf.common.WriteOp.dispose(WriteOp.java:465)

at org.esa.snap.core.gpf.internal.OperatorContext.dispose(OperatorContext.java:476)

at org.esa.snap.core.gpf.graph.NodeContext.dispose(NodeContext.java:178)

at org.esa.snap.core.gpf.graph.GraphContext.dispose(GraphContext.java:210)

at org.esa.snap.core.gpf.graph.GraphProcessor.executeGraph(GraphProcessor.java:129)

at org.esa.snap.core.gpf.main.DefaultCommandLineContext.executeGraph(DefaultCommandLineContext.java:86)

at org.esa.snap.core.gpf.main.CommandLineTool.executeGraph(CommandLineTool.java:547)

at org.esa.snap.core.gpf.main.CommandLineTool.runGraph(CommandLineTool.java:391)

at org.esa.snap.core.gpf.main.CommandLineTool.runGraphOrOperator(CommandLineTool.java:287)

at org.esa.snap.core.gpf.main.CommandLineTool.run(CommandLineTool.java:188)

at org.esa.snap.core.gpf.main.CommandLineTool.run(CommandLineTool.java:121)

at org.esa.snap.core.gpf.main.GPT.run(GPT.java:59)

at org.esa.snap.core.gpf.main.GPT.main(GPT.java:37)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.esa.snap.runtime.Launcher.lambda$run$0(Launcher.java:55)

at org.esa.snap.runtime.Engine.runClientCode(Engine.java:189)

at org.esa.snap.runtime.Launcher.run(Launcher.java:51)

at org.esa.snap.runtime.Launcher.main(Launcher.java:31)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:84)

at com.install4j.runtime.launcher.UnixLauncher.start(UnixLauncher.java:66)

at install4j.org.esa.snap.runtime.Launcher_gpt.main(Unknown Source)

Caused by: java.lang.reflect.InvocationTargetException

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at org.esa.s2tbx.dataio.gdal.drivers.GDALReflection.callGDALLibraryMethod(GDALReflection.java:53)

… 30 more

Caused by: java.lang.IllegalArgumentException: Received a NULL pointer.

at org.gdal.gdal.gdalJNI.Driver_CreateCopy__SWIG_0(Native Method)

at org.gdal.gdal.Driver.CreateCopy(Driver.java:117)

at org.gdal.gdal.Driver.CreateCopy(Driver.java:65)

… 35 more

Error: java.lang.reflect.InvocationTargetException

satas12825 · September 7, 2023, 11:53am

I also got this in a log file, it look like it done
log_07092023.txt (97 Bytes)

adraghici · September 7, 2023, 1:05pm

@satas12825 thank you for your replies,

We have almost understand your problem.

It seems to be related to loading the GDAL native libraries.
To confirm us this hypothesis we need some more information.

if your SNAP is updated to the latest version (9.0.6)
the contents of ~/.snap/auxdata/gdal and ~/.snap/auxdata/gdal/gdal-3-2-1

We try to reproduce your problem on our Ubuntu machine to investigate it.

Regards
Adrian

satas12825 · September 8, 2023, 2:08am

@adraghici Sorry for the late reply and thank you for helping me. I already checked my system

my snap version is up to date but I can not find /.snap/auxdata/gdal and ~/.snap/auxdata/gdal/gdal-3-2-1 in my latest system, is this effect?

For Right now I still trying to set up the program again, I will come back to update soon as possible

Best Regards

adraghici · September 8, 2023, 11:15am

@satas12825 thank you for your reply,

We have tried to reproduce your problem on our Ubuntu machine to investigate it, using the graph you provided to us, and the product you used:

, which we have downloaded from Sci-Hub.
The execution was completed successfully without any error, and the output product was successfully written:

The output of execution is:

INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.
INFO: org.esa.s2tbx.dataio.s2.ortho.S2OrthoProductReaderPlugIn: Building product reader - EPSG:32647
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [metadata_level] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
INFO: org.hsqldb.persist.Logger: dataFileCache open start
WARNING: org.esa.s2tbx.dataio.s2.ortho.metadata.S2OrthoMetadata: Warning: missing file /home/adraghici/Downloads/S2A_MSIL2A_20230419T034531_N0509_R104_T47QNV_20230419T083155.zip/S2A_MSIL2A_20230419T034531_N0509_R104_T47QNV_20230419T083155.SAFE/GRANULE/L2A_T47QNV_A040856_20230419T035621/QI_DATA/L2A_T47QNV_20230419T034531_DDV_20m.jp2

WARNING: org.esa.s2tbx.dataio.s2.ortho.metadata.S2OrthoMetadata: Warning: no image files found for band quality_dense_dark_vegetation

Warning 6: driver COG does not support creation option TILED

Next, we want to understand what’s happening on your device.

Please try to open in SNAP application, the product you’re using on the processing graph, and give us the result.

Regards
Adrian

gnwiii · September 14, 2023, 10:21am

You seem to have parts of SNAP installed in root’s home directory. For a normal single user workstation, SNAP can be installed without elevated privileges. Are you using a virtual machine with only a root user?

satas12825 · October 9, 2023, 1:59am

Sorry for the late reply and thank you for helping me. I already checked my system and I think it was a not successful install then I tried again it was was completed successfully without any error