BESCatalogDirectory - root directory /usr/share/hyrax does not exist

[albertotb]

When I run:

docker run --volume /home/user:/usr/share/hyrax opendap/hyrax

I get the following error:

############################## HYRAX ##################################
Greetings, I am root.
SERVER_HELP_EMAIL is not_set
FOLLOW_SYMLINKS is not_set
Found exisiting NCWMS_BASE: https://localhost:8080
Starting the BES
Caught plugin exception during initialization of csv module:
    BESCatalogDirectory - root directory /usr/share/hyrax does not exist
Could not initialize the modules to get the log contexts.
Caught plugin exception during initialization of csv module:
    BESCatalogDirectory - root directory /usr/share/hyrax does not exist
The beslistener status is not 'BESLISTENER_RUNNING' (it is '24747808')  the master pid was not changed.
besdaemon: server cannot mount at first try (core dump). Please correct problems on the process manager /usr/bin/beslistener
BES PID file exists but process not running, cleaning up
FAILED: The BES daemon did not appear to start

I don't understand how this is possible, if I extract the container filesystem I can see that there is a directory called /usr/share/hyrax. Removing the -volume flag works fine, but then I cannot serve my data.

[gajowi]

Is the problem that the direction cannot be read/accessed (and the error message is close but not quite right)?

Gareth

On Mon, 22 Jun 2020, 11:17 pm Alberto Torres, notifications@github.com wrote:

When I run:

docker run --volume /home/user:/usr/share/hyrax opendap/hyrax

I get the following error:

############################## HYRAX ################################## Greetings, I am root. SERVER_HELP_EMAIL is not_set FOLLOW_SYMLINKS is not_set Found exisiting NCWMS_BASE: https://localhost:8080 Starting the BES Caught plugin exception during initialization of csv module: BESCatalogDirectory - root directory /usr/share/hyrax does not exist Could not initialize the modules to get the log contexts. Caught plugin exception during initialization of csv module: BESCatalogDirectory - root directory /usr/share/hyrax does not exist The beslistener status is not 'BESLISTENER_RUNNING' (it is '24747808') the master pid was not changed. besdaemon: server cannot mount at first try (core dump). Please correct problems on the process manager /usr/bin/beslistener BES PID file exists but process not running, cleaning up FAILED: The BES daemon did not appear to start

I don't understand how this is possible, if I extract the container filesystem I can see that there is a directory called /usr/share/hyrax. Removing the -volume flag works fine, but then I cannot serve my data.

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[albertotb]

Do you mean /usr/share/hyrax? it should be accessible, I'm using the official opendap/hyrax:latest image, I'm not building it myself

If you ment /home/user what permissions does it need? It belongs to the docker group and to the user running the container. I also tried with several directories with no luck

[ndp-opendap]

I think that /home/user needs to be mounted with read permission for the "bes" user. Adding the permissions to the volume command like this: --volume /home/user:/usr/share/hyrax:ro Might be the thing.

[albertotb]

I tried adding the permissions but I'm getting the same error. I'm a little bit confused, the 'bes' user lives in the container, how would /home/user, a directory located in the host machine, know about the "bes" user? Maybe I'm missing something

On Tue, 23 Jun 2020 at 20:20, Nathan Potter notifications@github.com wrote:

I think that /home/user needs to be mounted with read permission for the "bes" user. Adding the permissions to the volume command like this: --volume /home/user:/usr/share/hyrax:ro Might be the thing.

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[ndp-opendap]

The bes user is not known to your system, but what you can do is use the user and/or group IDs of the BES user by number. In the Docker container you can see in /etc/passwd the bes user entry:

bes:x:999:997:BES daemon:/var/log/bes:/sbin/nologin

So what you can do on your system would be:

chown -R 999:997 /home/user

If that's too heavy handed you could just do the group, assuming you also set all the things to be group readable:

chgrp -R /home/usr
chmod -R g+r /home/user

Does that make sense?

[albertotb]

I just tried in a fresh VM and everything works fine. Clearly is an OS related problem, but a very strange one. If I can reproduce it again I will try your suggestion and report back here.

[ndp-opendap]

I will close this for now if the problem reappears please let us know!