omero 5.4 installation issues

[mayav]

First issue ion Configure:

OMERO.server/bin/omero config set omero.data.dir "$OMERO_DATA_DIR"

System need Install Pillow

And next issue is installation as omero is failed , the output is added here, root user works good

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Configuring OMERO.web
The following steps are run as the omero system user.

Install other OMERO.web dependencies using pip:

pip install -r OMERO.server/share/web/requirements-py27.txt

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Exception:
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "/usr/lib/python2.7/site-packages/pip/commands/install.py", line 342, in                                                                              run
    prefix=options.prefix_path,
  File "/usr/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in insta                                                                             ll
    **kwargs
  File "/usr/lib/python2.7/site-packages/pip/req/req_install.py", line 851, in i                                                                             nstall
    self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
  File "/usr/lib/python2.7/site-packages/pip/req/req_install.py", line 1064, in                                                                              move_wheel_files
    isolated=self.isolated,
  File "/usr/lib/python2.7/site-packages/pip/wheel.py", line 345, in move_wheel_                                                                             files
    clobber(source, lib_dir, True)
  File "/usr/lib/python2.7/site-packages/pip/wheel.py", line 316, in clobber
    ensure_dir(destdir)
  File "/usr/lib/python2.7/site-packages/pip/utils/__init__.py", line 83, in ens                                                                             ure_dir
    os.makedirs(path)
  File "/usr/lib64/python2.7/os.py", line 157, in makedirs
    mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/usr/lib/python2.7/site-packages/django'


[mayav]

Hi
I installed omero 5.4 based on the document given below url

https://docs.openmicroscopy.org/omero/5 ... ice36.html
https://docs.openmicroscopy.org/omero/5 ... ce3.6.html


webserver runs good, but webclient gives error.

here with i attach the bin/omero admin diagnostics

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[b]bin/omero admin diagnostics[/b]

================================================================================
OMERO Diagnostics (admin) 5.4.0-ice36-b74
================================================================================

Commands:   java -version                  1.8.0     (/usr/bin/java)
Commands:   python -V                      2.7.5     (/usr/bin/python)
Commands:   icegridnode --version          3.6.4     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.6.4     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.6.5     (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 3479, enabled)
Server:     DropBox                        active (pid = 3499, enabled)
Server:     FileServer                     active (pid = 3504, enabled)
Server:     Indexer-0                      active (pid = 3505, enabled)
Server:     MonitorServer                  active (pid = 3506, enabled)
Server:     OMERO.Glacier2                 active (pid = 3511, enabled)
Server:     OMERO.IceStorm                 active (pid = 3535, enabled)
Server:     PixelData-0                    active (pid = 3543, enabled)
Server:     Processor-0                    active (pid = 3552, enabled)
Server:     Tables-0                       active (pid = 3545, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /home/omero/OMERO.server-5.4.0-ice36-b74/var/log exists
Log files:  Blitz-0.log                    1.0 MB        errors=17   warnings=19
Log files:  DropBox.log                    4.0 KB        errors=0    warnings=1
Log files:  FileServer.log                 0.0 KB
Log files:  Indexer-0.log                  4.0 KB
Log files:  MonitorServer.log              2.0 KB
Log files:  OMEROweb.lock                  0.0 KB
Log files:  OMEROweb.log                   0.0 KB        errors=0    warnings=1
Log files:  PixelData-0.log                5.0 KB
Log files:  Processor-0.log                119.0 KB      errors=0    warnings=1
Log files:  Tables-0.log                   3.0 KB        errors=0    warnings=1
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB        errors=1    warnings=2
Log files:  master.out                     0.0 KB
Log files:  Total size                     1.88 MB


Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/root/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/OMERO'                       Exists? True      Is writable? True
OMERO temp dir:'/home/omero/omero/tmp'        Exists? True      Is writable? True   (Size: 0)

JVM settings: Blitz-${index}                -Xmx2497m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx1665m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx2497m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx1665m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions


And

bin/omero config get --hide-password

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omero.data.dir=/OMERO
omero.db.name=omero_database
omero.db.pass=********
omero.db.user=maya
omero.web.application_server=wsgi-tcp

When i try to open the locahost/webclient/ it shows nginx error! The page you are looking for is not found.

[kennethgillen]

Hi Mayav,

To start with, could you please send us your OMERO logs as a zip, via https://www.openmicroscopy.org/qa2/qa/upload/

* OMERO.server logs: /home/omero/OMERO.server-5.4.0-ice36-b74/var/log

Thanks,

Kenny

[mayav]

Yes we send the log.tgz file to you via https://www.openmicroscopy.org/qa2/qa/upload/

https://www.openmicroscopy.org/qa2/qa/feedback/18090/

[kennethgillen]

Hi,

The first thing to ask: did you turn off PostgreSQL at the same time as stopping OMERO?

Immediately after OMERO is given a request to shut down, there are errors as follows

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2017-10-11 11:32:35,837 ERROR [ome.services.db.SelfCorrectingDataSource]
java.sql.SQLException: unable to get a connection
Caused by: org.postgresql.util.PSQLException: The connection attempt failed.
Caused by: java.net.SocketException: Network is unreachable (connect failed)


These are unusual, and shouldn't occur.

Also, I notice

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(      main) Max Memory (MB):   =   2220
(      main) OS Memory (MB):    =  15881

You might like to give OMERO more memory - since your server has 16GB. See [1] for more on that topic. Our recommendations and requirements are at [2] - something like 6-8GB would be more reasonable for Blitz alone.

[1] https://docs.openmicroscopy.org/omero/5 ... y-settings
[2] https://docs.openmicroscopy.org/omero/5 ... ments.html

Kenny

[mayav]

The first thing to ask: did you turn off PostgreSQL at the same time as stopping OMERO?


No

Sure we do assign more memory.

Now what is the solution for current situation ? Any clue ?

Can you suggest the Server installation Document ?
We have Cent OS 7(Minimal Installation) with 16 GB RAM and 2 TB HDD

[kennethgillen]

Code: Select all

OSError: [Errno 13] Permission denied

If this was while running

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pip install -r OMERO.server/share/web/requirements-py27.txt

- could you confirm which operating system user you ran this as when you first installed? Our docs state this should be run as your OMERO system user. If this was run as the OMERO system user the first time, there should not be a permissions issue when re-running as that user.

You can verify this as follows:

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ls -al /usr/lib/python2.7/site-packages/ | grep django

Thanks,

Kenny

[mayav]

I mentioned it in this thread OMERO user show Permission Denied So i choose root user

pip install -r OMERO.server/share/web/requirements-py27.txt

During omero user it show following error

Code: Select all

Exception:
Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "/usr/lib/python2.7/site-packages/pip/commands/install.py", line 342, in                                                                              run
    prefix=options.prefix_path,
  File "/usr/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in insta                                                                             ll
    **kwargs
  File "/usr/lib/python2.7/site-packages/pip/req/req_install.py", line 851, in i                                                                             nstall
    self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
  File "/usr/lib/python2.7/site-packages/pip/req/req_install.py", line 1064, in                                                                              move_wheel_files
    isolated=self.isolated,
  File "/usr/lib/python2.7/site-packages/pip/wheel.py", line 345, in move_wheel_                                                                             files
    clobber(source, lib_dir, True)
  File "/usr/lib/python2.7/site-packages/pip/wheel.py", line 316, in clobber
    ensure_dir(destdir)
  File "/usr/lib/python2.7/site-packages/pip/utils/__init__.py", line 83, in ens                                                                             ure_dir
    os.makedirs(path)
  File "/usr/lib64/python2.7/os.py", line 157, in makedirs
    mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/usr/lib/python2.7/site-packages/django'

[mayav]

ls -al /usr/lib/python2.7/site-packages/ | grep django

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drwxr-xr-x. 17 root root   4096 Oct 11 10:59 django
drwxr-xr-x.  2 root root   4096 Oct 11 10:59 django_pipeline-1.3.20.dist-info
drwxr-xr-x.  5 root root   4096 Oct 11 10:59 django_redis
drwxr-xr-x.  2 root root   4096 Oct 11 10:59 django_redis-4.8.0.dist-info


[kennethgillen]

Hi Mayav,

Your OMEROweb.log submitted is almost totally empty. You mention you get some errors from OMERO.web - can you please paste us those as well?

Thanks,

Kenny