(Log file directory is not accessible to write) Install Seadas 8.1.0, WSL, Windows 10, OCSSW

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OB.DAAC - amscott
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Re: (Log file directory is not accessible to write) Install Seadas 8.1.0, WSL, Windows 10, OCSSW

by OB.DAAC - amscott » Tue Oct 05, 2021 7:58 am America/New_York

Dear negri,

I believe we have provided all the direction we can regarding issues with your installation. Please continue to check for errors in your commands, referencing instructions in this thread and reviewing the instructions on the SeaDAS website to verify your steps in completing installation.

Once you have successfully installed the components we will be happy to help you if you have trouble analyzing your data.
--
Alicia

Tags:

negri
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Joined: Sat Jul 10, 2021 3:42 pm America/New_York

Re: (Log file directory is not accessible to write) Install Seadas 8.1.0, WSL, Windows 10, OCSSW

by negri » Tue Oct 05, 2021 9:52 am America/New_York

Ok, yes I agree with you.
Thank you for your help!

negri
Posts: 21
Joined: Sat Jul 10, 2021 3:42 pm America/New_York

Re: (Log file directory is not accessible to write) Install Seadas 8.1.0, WSL, Windows 10, OCSSW

by negri » Wed Oct 20, 2021 5:47 pm America/New_York

I would be very grateful if I could have again your effort with this pending.
I retraced the steps carefully (Please, observe below STEPS).

OCSSW package is working using the "benchmark" package (it's OK)
$ cd $OCSSWROOT/benchmark
$ ./seadas_benchmark.bash

Now I can process landsat8 OLI images!
# PRIMARY INPUT OUTPUT FIELDS
ifile=C:\Users\negri\seadasClientServerShared\LC82160762013287LGN00_MTL.txt
ofile=C:\Users\negri\seadasClientServerShared\L2013287124741.L2_LAC_OC

But with OLCI (sentinel-3a) I still can't process...
Sentinel OLIC error
# PRIMARY INPUT OUTPUT FIELDS
ifile=C:\Users\negri\seadasClientServerShared\xfdumanifest.xml
# WARNING!!! Mission directory 'C:\home\negri\ocssw\share\olci' does not exist
I don't know why seadas is showing Mission directory with this adress 'C:\home\negri\ocssw\share\olci' because it's supposed to be in the linux environment I guess.

The directories where I install the package:
$ echo $HOME
/home/negri
$ echo $OCSSWROOT
/home/negri/ocssw

$ ls -al $OCSSWROOT/share
drwxr-xr-x 1 negri negri 512 Oct 20 15:02 .
drwxr-xr-x 1 negri negri 512 Oct 20 15:04 ..
drwxr-xr-x 1 negri negri 512 Oct 20 14:55 common
drwxr-xr-x 1 negri negri 512 Oct 20 14:56 modis
drwxr-xr-x 1 negri negri 512 Oct 20 14:58 msi
drwxr-xr-x 1 negri negri 512 Oct 20 14:59 ocrvc
drwxr-xr-x 1 negri negri 512 Oct 20 15:00 olci
drwxr-xr-x 1 negri negri 512 Oct 20 15:04 oli

$ ls -al /home/negri/ocssw
drwxr-xr-x 1 negri negri 512 Oct 20 15:04 .
drwxrwxrwx 1 negri negri 512 Oct 20 18:14 ..
-rw-rw-r-- 1 negri negri 2866 Oct 20 14:49 OCSSW.env
-rw-rw-r-- 1 negri negri 2981 Oct 20 14:49 OCSSW_bash.env
drwxr-xr-x 1 negri negri 512 Oct 20 16:31 benchmark
drwxr-xr-x 1 negri negri 512 Oct 20 14:44 bin
-rw-rw-r-- 1 negri negri 8640 Oct 20 14:49 bundleList.json
drwxr-xr-x 1 negri negri 512 Oct 20 14:45 lib
-rw-r--r-- 1 negri negri 1007 Oct 20 14:49 manifest.json
drwxr-xr-x 1 negri negri 512 Oct 20 14:46 opt
drwxr-xr-x 1 negri negri 512 Oct 20 15:02 share
drwxr-xr-x 1 negri negri 512 Oct 20 16:28 var


STEPS
1. windows subsystem WSL 1

2. Ubuntu 20.04 LTS

3. Java17 (https://www.linuxuprising.com/2021/09/h ... ts-on.html)
$ sudo apt update
$ sudo apt install oracle-java17-installer
$ sudo apt install oracle-java17-set-default

4. Python 3.8

5. Linux commands installed
$ sudo apt install git
$ sudo apt install curl

6. Put your EarthData Login credentials in a "~/.netrc" file in WSL --> (home/negri)
$ echo "machine urs.earthdata.nasa.gov login negrig@gmail.com password ABCdef123!" > .netrc

7. install OCSSW system in WSL -->(home/negri/ocssw)
I. Download the installer script and manifest script
II. ./install_ocssw --instal_dir $HOME/ocssw –tag V2021.2 --seadas --olcis3a --olcis3b --msis2a --msis2b --oli --benchmark

8. I edited the file .bashrc (-->/home/negri/) and I run "source ~/.bashrc"
export OCSSWROOT=/home/negri/ocssw
source $OCSSWROOT/OCSSW_bash.env

9. I deployed the OCSSW web services package (/home/negri/)
Server jar file
Server config file

10. Editing ocsswserver.config
ocsswrest.version=1.0
baseUriPortNumber=6400
ocsswroot=/home/negri/ocssw
serverWorkingDirectory=/mnt/c/users/negri/seadasClientServerShared
clientServerSharedDir=true
keepIntermediateFilesOnServer=false
processInputStreamPortNumber=6402
processErrorStreamPortNumber=6403

11. Editing SeaDAS Client Configuration
(--> C:\Users\negri\.seadas8\etc)
#SNAP configuration 'seadas'
#Wed Oct 13 17:38:14 BRT 2021
seadas.ocssw.location=virtualMachine
seadas.ocssw.port=6400
seadas.ocssw.sharedDir=C:\\Users\\negri\\seadasClientServerShared
seadas.client.id=negri
seadas.ocssw.keepFilesOnServer=false
seadas.ocssw.processInputStreamPort=6402
seadas.ocssw.processErrorStreamPort=6403
seadas.ocssw.tag=V2021.2
seadas.log.dir=C:\\Users\\negri\\seadasClientServerShared

OB.DAAC - amscott
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Re: (Log file directory is not accessible to write) Install Seadas 8.1.0, WSL, Windows 10, OCSSW

by OB.DAAC - amscott » Thu Oct 21, 2021 11:59 am America/New_York

One issue I see is in step 6 of your message. The .netrc file requires your login username. you have used your email address. Also if that is your real password, please change it. Never post sensitive/private information in the forum.
--
Alicia

gnwiii
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Re: (Log file directory is not accessible to write) Install Seadas 8.1.0, WSL, Windows 10, OCSSW

by gnwiii » Thu Oct 21, 2021 3:02 pm America/New_York

Step 7:

Code: Select all

II. ./install_ocssw --instal_dir $HOME/ocssw –tag V2021.2 --seadas --olcis3a --olcis3b --msis2a --msis2b --oli --benchmark 
has a small but critical typo -- "--instal_dir" should be "--install_dir" (two "ells"). I'm not sure why there is "ll." at the start of the line, but not specifying "--install_dir" might explain why system has the wrong location for the "olci" directory:

Code: Select all

# WARNING!!! Mission directory 'C:\home\negri\ocssw\share\olci' does not exist
.

This sort of problem is difficult to sort out remotely, but easy to solve once you have some basic familiarity with the bash command-line. You will find it very worthwhile to spend a bit of time with a good reference such as https://linuxcommand.org/.

negri
Posts: 21
Joined: Sat Jul 10, 2021 3:42 pm America/New_York

Re: (Log file directory is not accessible to write) Install Seadas 8.1.0, WSL, Windows 10, OCSSW

by negri » Thu Oct 21, 2021 5:37 pm America/New_York

Thank you for your attention!
Please, a little more patience.

Alice,
I didn't post my private information (fake password!). There's no problem with login name.
There seems to be nothing wrong with .netrc ---> because, as I said, I run the ./seadas_benchmark.bash and it's OK!

Gnwiii,
"./install_ocssw --instal_dir $HOME/ocssw –tag V2021.2 --seadas --olcis3a --olcis3b --msis2a --msis2b --oli --benchmark"
Sorry, I did a wrong typing in the forum page.
The command line wouldn't work if I had entered "--instal_dir" instead of "--install_dir"
"install_ocssw: error: unrecognized arguments: --instal_dir /home/negri/ocssw"


"This sort of problem is difficult to sort out remotely, but easy to solve once you have some basic familiarity with the bash command-line."

Please, can you tell me some sugestions ?

I believe I did everything that is pointed out in the SeaDAS homepage.
(maybe I should try WSL 2 configuration ?)

Below I passed the ubuntu console response while I was trying to ingest OLCI image.
Please, can you check it out to see if there is something wrong ?

argument: ocsswserver.config
-- listing properties --
java.specification.version=17
sun.jnu.encoding=UTF-8
java.class.path=seadas-ocsswserver.jar
ocsswroot=/home/negri/ocssw
java.vm.vendor=Oracle Corporation
sun.arch.data.model=64
processInputStreamPortNumber=6402
processErrorStreamPortNumber=6403
java.vendor.url=https://java.oracle.com/
java.vm.specification.version=17
os.name=Linux
sun.java.launcher=SUN_STANDARD
sun.boot.library.path=/usr/lib/jvm/java-17-oracle/lib
sun.java.command=seadas-ocsswserver.jar ocsswserver.co...
jdk.debug=release
sun.cpu.endian=little
user.home=/home/negri
user.language=en
sun.stderr.encoding=UTF-8
java.specification.vendor=Oracle Corporation
serverWorkingDirectory=/mnt/c/users/negri/seadasClientServer...
java.version.date=2021-09-14
java.home=/usr/lib/jvm/java-17-oracle
file.separator=/
java.vm.compressedOopsMode=Zero based
line.separator=

sun.stdout.encoding=UTF-8
java.vm.specification.vendor=Oracle Corporation
java.specification.name=Java Platform API Specification
sun.management.compiler=HotSpot 64-Bit Tiered Compilers
java.runtime.version=17+35-LTS-2724
user.name=negri
path.separator=:
os.version=4.4.0-22000-Microsoft
java.runtime.name=Java(TM) SE Runtime Environment
file.encoding=UTF-8
baseUriPortNumber=6400
java.vm.name=Java HotSpot(TM) 64-Bit Server VM
java.vendor.url.bug=https://bugreport.java.com/bugreport/
java.io.tmpdir=/tmp
java.version=17
user.dir=/home/negri
os.arch=amd64
java.vm.specification.name=Java Virtual Machine Specification
ocsswrest.version=1.0
native.encoding=UTF-8
java.library.path=/usr/java/packages/lib:/usr/lib64:/li...
java.vm.info=mixed mode, sharing
java.vendor=Oracle Corporation
clientServerSharedDir=true
java.vm.version=17+35-LTS-2724
sun.io.unicode.encoding=UnicodeLittle
java.class.version=61.0
keepIntermediateFilesOnServer=false
server ocssw root path: /home/negri/ocssw/bin
ORS is starting at
Oct 21, 2021 5:45:03 PM org.glassfish.jersey.internal.inject.Providers checkProviderRuntime
WARNING: A provider java.io.InputStream registered in SERVER runtime does not implement any provider interfaces applicable in the SERVER runtime. Due to constraint configuration problems the provider java.io.InputStream will be ignored.
Oct 21, 2021 5:45:03 PM org.glassfish.grizzly.http.server.NetworkListener start
INFO: Started listener bound to [0.0.0.0:6400]
Oct 21, 2021 5:45:03 PM org.glassfish.grizzly.http.server.HttpServer start
INFO: [HttpServer] Started.
Jersey new app started with WADL available at http://0.0.0.0:6400/ocsswws/application.wadl
Press 'Ctrl' + 'C' to stop it...
server ocssw root path: /home/negri/ocssw/bin
reuest for ocssw tags!
Debugging: commandArrayPrefix: /home/negri/ocssw/bin/ocssw_runner
Debugging: commandArrayPrefix: --ocsswroot
Debugging: commandArrayPrefix: /home/negri/ocssw
Debugging: command array content: /home/negri/ocssw/bin/ocssw_runner --ocsswroot /home/negri/ocssw obpg_file_type /mnt/c/users/negri/seadasClientServerShared/xfdumanifest.xml
Debugging: Running the program /home/negri/ocssw/bin/ocssw_runner --ocsswroot /home/negri/ocssw obpg_file_type /mnt/c/users/negri/seadasClientServerShared/xfdumanifest.xml
Debugging: mission suites dir: /home/negri/ocssw/share/common
Debugging: mission suite name: NPP
Debugging: mission suites dir: /home/negri/ocssw/share/common
Debugging: mission suite name: NPP

gnwiii
Posts: 640
Joined: Fri Jan 29, 2021 5:51 pm America/New_York
Answers: 2

Re: (Log file directory is not accessible to write) Install Seadas 8.1.0, WSL, Windows 10, OCSSW

by gnwiii » Fri Oct 22, 2021 12:51 pm America/New_York

I don't see anything in your post that explains:

Code: Select all

# WARNING!!! Mission directory 'C:\home\negri\ocssw\share\olci' does not exist
Normally, OLCI sensor-specific files are found in

Code: Select all

$OCDATAROOT/olci
. The value of

Code: Select all

OCDATAROOT
should be set in

Code: Select all

OCSSW_bash.env
.
Since the benchmark script works, MODIS Aqua files are found, so it is strange that OLCI files are not found. Do you have OCSSW environment variables set in Windows? Do you start the SeaDAS GUI from the start menu or using bash? What do you get for:

Code: Select all

ls $OCDATAROOT
in the bash shell?

I should mention that the client-server configuration using WSL1 is very useful for learning
with small examples or figuring out the right options for l2gen, but for running more than a few small examples it is much faster to use WSL2 and the bash command-line (similar to the benchmark script, which gives you all the steps for end-to-end processing).

negri
Posts: 21
Joined: Sat Jul 10, 2021 3:42 pm America/New_York

Re: (Log file directory is not accessible to write) Install Seadas 8.1.0, WSL, Windows 10, OCSSW

by negri » Wed Oct 27, 2021 5:42 pm America/New_York

Hi, Gnwiii, for your questions, please, see below.

1) The message below come up when I ingest the OLCI image (Seadas GUI --> l2gen)
"# WARNING!!! Mission directory 'C:\home\negri\ocssw\share\olci' does not exist"

2) "Do you start the SeaDAS GUI from the start menu or using bash? "
first I activate the Ubuntu enviroment with the command line:
$ java -Xmx4G -jar seadas-ocsswserver.jar ocsswserver.config
then I go to windows and start the SeaDAS GUI ---> l2gen

3) ls $OCDATAROOT
drwxr-xr-x 1 negri negri 512 Oct 20 14:55 common
drwxr-xr-x 1 negri negri 512 Oct 20 14:56 modis
drwxr-xr-x 1 negri negri 512 Oct 20 14:58 msi
drwxr-xr-x 1 negri negri 512 Oct 20 14:59 ocrvc
drwxr-xr-x 1 negri negri 512 Oct 20 15:00 olci
drwxr-xr-x 1 negri negri 512 Oct 20 15:04 oli

4) In the OCSSW_bash.env file (home/negri/ocsww) I can see this command line (among others):
# data tree
export OCDATAROOT=$OCSSWROOT/share


5)"Since the benchmark script works, MODIS Aqua files are found, so it is strange that OLCI files are not found. "
I agree with you. And both OLCI sensor and benchmark (MODIS) were installed with the same command line!
$./install_ocssw --install_dir $HOME/ocssw –tag V2021.2 --seadas --olcis3a --olcis3b --msis2a --msis2b --oli --benchmark

6) "Do you have OCSSW environment variables set in Windows?"
# Editing SeaDAS Client Configuration (C:\Users\negri\.seadas8\etc)
#SNAP configuration 'seadas'
#Wed Oct 13 17:38:14 BRT 2021
seadas.ocssw.location=virtualMachine
seadas.ocssw.port=6400
seadas.ocssw.sharedDir=C:\\Users\\negri\\seadasClientServerShared
seadas.client.id=negri
seadas.ocssw.keepFilesOnServer=false
seadas.ocssw.processInputStreamPort=6402
seadas.ocssw.processErrorStreamPort=6403
seadas.ocssw.tag=V2021.2
seadas.log.dir=C:\\Users\\negri\\seadasClientServerShared

gnwiii
Posts: 640
Joined: Fri Jan 29, 2021 5:51 pm America/New_York
Answers: 2

Re: (Log file directory is not accessible to write) Install Seadas 8.1.0, WSL, Windows 10, OCSSW

by gnwiii » Fri Oct 29, 2021 7:49 am America/New_York

negri wrote: Wed Oct 27, 2021 5:42 pm America/New_York Hi, Gnwiii, for your questions, please, see below.

1) The message below come up when I ingest the OLCI image (Seadas GUI --> l2gen)
"# WARNING!!! Mission directory 'C:\home\negri\ocssw\share\olci' does not exist"
This could be due to running bash from a non-WSL package (rtool40,
cygwin, Windows git, etc.). There are many possibilities, so hard to
guess remotely. Did you try to run install_ocssw in Windows?
negri wrote: Wed Oct 27, 2021 5:42 pm America/New_York 2) "Do you start the SeaDAS GUI from the start menu or using bash? "
first I activate the Ubuntu enviroment with the command line:
$ java -Xmx4G -jar seadas-ocsswserver.jar ocsswserver.config
then I go to windows and start the SeaDAS GUI ---> l2gen
Not sure what you mean by "go to Windows". You can start the SeaDAS
GUI using the Windows Start Menu or from a command line. These can give
different environments.
negri wrote: Wed Oct 27, 2021 5:42 pm America/New_York 3) ls $OCDATAROOT
drwxr-xr-x 1 negri negri 512 Oct 20 14:55 common
drwxr-xr-x 1 negri negri 512 Oct 20 14:56 modis
drwxr-xr-x 1 negri negri 512 Oct 20 14:58 msi
drwxr-xr-x 1 negri negri 512 Oct 20 14:59 ocrvc
drwxr-xr-x 1 negri negri 512 Oct 20 15:00 olci
drwxr-xr-x 1 negri negri 512 Oct 20 15:04 oli
negri wrote: Wed Oct 27, 2021 5:42 pm America/New_York 4) In the OCSSW_bash.env file (home/negri/ocsww) I can see this command line (among others):
# data tree
export OCDATAROOT=$OCSSWROOT/share
It appears that the problem is with Windows.
negri wrote: Wed Oct 27, 2021 5:42 pm America/New_York
5)"Since the benchmark script works, MODIS Aqua files are found, so it is strange that OLCI files are not found. "
I agree with you. And both OLCI sensor and benchmark (MODIS) were installed with the same command line!
$./install_ocssw --install_dir $HOME/ocssw –tag V2021.2 --seadas --olcis3a --olcis3b --msis2a --msis2b --oli --benchmark
negri wrote: Wed Oct 27, 2021 5:42 pm America/New_York 6) "Do you have OCSSW environment variables set in Windows?"

# Editing SeaDAS Client Configuration (C:\Users\negri\.seadas8\etc)
#SNAP configuration 'seadas'
#Wed Oct 13 17:38:14 BRT 2021
seadas.ocssw.location=virtualMachine
seadas.ocssw.port=6400
seadas.ocssw.sharedDir=C:\\Users\\negri\\seadasClientServerShared
seadas.client.id=negri
seadas.ocssw.keepFilesOnServer=false
seadas.ocssw.processInputStreamPort=6402
seadas.ocssw.processErrorStreamPort=6403
seadas.ocssw.tag=V2021.2
seadas.log.dir=C:\\Users\\negri\\seadasClientServerShared
These are not environment variables. If you don't understand terms in a question, you should do some research -- Microsoft has ample documentation. You need to understand the purpose of environment variables and how to examine, set, or remove them.

negri
Posts: 21
Joined: Sat Jul 10, 2021 3:42 pm America/New_York

Re: (Log file directory is not accessible to write) Install Seadas 8.1.0, WSL, Windows 10, OCSSW

by negri » Fri Oct 29, 2021 12:57 pm America/New_York

1) "Did you try to run install_ocssw in Windows?"
No, I din't.

2) "You can start the SeaDAS GUI using the Windows Start Menu or from a command line. These can give different environments."
I start the SaaDAS GUI using the Windows Start Menu

3) "You need to understand the purpose of environment variables and how to examine, set, or remove them."
Thank you for your tip.

4) "Do you have OCSSW environment variables set in Windows?"
No, I haven't.
the word OCSSW is neither in the Windows User Variables nor in the Windows System Variables.

Please, se bellow the user environment variable (path)
C:\Users\negri\AppData\Local\Microsoft\WindowsApps;C:\Program Files\snap\bin;C:\Users\negri\AppData\Local\GitHubDesktop\bin;

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