can not install ice 3.6.3 on new Fresh omero server

[saleht]

Hallo all,

i am trying to install new test OMERO server, but i am facing an issue, it is not realted with Omero directly but maybe someone here face same issue,
i am trying to install ice 3.6.3, but it gives this error. i tried to google it but no success, any help, i would be so thank

sudo yum install ice-all-runtime ice-all-devel

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Loaded plugins: langpacks, product-id, search-disabled-repos, subscription-manager
epel/x86_64/metalink                                                                                                                |  25 kB  00:00:00     
epel                                                                                                                                | 4.3 kB  00:00:00     
pgdg96                                                                                                                              | 4.1 kB  00:00:00     
zeroc-ice-el7                                                                                                                       | 2.5 kB  00:00:00     
zeroc-ice-el7-noarch                                                                                                                | 2.4 kB  00:00:00     
zeroc-ice-el7-src                                                                                                                   | 2.4 kB  00:00:00     
(1/2): epel/x86_64/updateinfo                                                                                                       | 806 kB  00:00:00     
(2/2): epel/x86_64/primary_db                                                                                                       | 4.8 MB  00:00:00     
Resolving Dependencies
--> Running transaction check
---> Package ice-all-devel.x86_64 0:3.6.3-1.el7 will be installed
--> Processing Dependency: php-ice-devel(x86-64) = 3.6.3-1.el7 for package: ice-all-devel-3.6.3-1.el7.x86_64
--> Processing Dependency: libice-java(x86-64) = 3.6.3-1.el7 for package: ice-all-devel-3.6.3-1.el7.x86_64
--> Processing Dependency: libice-c++-devel(x86-64) = 3.6.3-1.el7 for package: ice-all-devel-3.6.3-1.el7.x86_64
---> Package ice-all-runtime.x86_64 0:3.6.3-1.el7 will be installed
--> Processing Dependency: php-ice(x86-64) = 3.6.3-1.el7 for package: ice-all-runtime-3.6.3-1.el7.x86_64
--> Processing Dependency: libicestorm3.6(x86-64) = 3.6.3-1.el7 for package: ice-all-runtime-3.6.3-1.el7.x86_64
--> Processing Dependency: libice3.6-c++(x86-64) = 3.6.3-1.el7 for package: ice-all-runtime-3.6.3-1.el7.x86_64
--> Processing Dependency: libfreeze3.6-c++(x86-64) = 3.6.3-1.el7 for package: ice-all-runtime-3.6.3-1.el7.x86_64
--> Processing Dependency: icepatch2(x86-64) = 3.6.3-1.el7 for package: ice-all-runtime-3.6.3-1.el7.x86_64
--> Processing Dependency: icegrid(x86-64) = 3.6.3-1.el7 for package: ice-all-runtime-3.6.3-1.el7.x86_64
--> Processing Dependency: icebox(x86-64) = 3.6.3-1.el7 for package: ice-all-runtime-3.6.3-1.el7.x86_64
--> Processing Dependency: ice-utils-java = 3.6.3-1.el7 for package: ice-all-runtime-3.6.3-1.el7.x86_64
--> Processing Dependency: glacier2(x86-64) = 3.6.3-1.el7 for package: ice-all-runtime-3.6.3-1.el7.x86_64
--> Running transaction check
---> Package glacier2.x86_64 0:3.6.3-1.el7 will be installed
---> Package ice-utils-java.noarch 0:3.6.3-1.el7 will be installed
---> Package icebox.x86_64 0:3.6.3-1.el7 will be installed
--> Processing Dependency: ice-utils = 3.6.3-1.el7 for package: icebox-3.6.3-1.el7.x86_64
---> Package icegrid.x86_64 0:3.6.3-1.el7 will be installed
---> Package icepatch2.x86_64 0:3.6.3-1.el7 will be installed
---> Package libfreeze3.6-c++.x86_64 0:3.6.3-1.el7 will be installed
--> Processing Dependency: libdb_cxx-5.3.so()(64bit) for package: libfreeze3.6-c++-3.6.3-1.el7.x86_64
---> Package libice-c++-devel.x86_64 0:3.6.3-1.el7 will be installed
--> Processing Dependency: ice-slice = 3.6.3-1.el7 for package: libice-c++-devel-3.6.3-1.el7.x86_64
---> Package libice-java.x86_64 0:3.6.3-1.el7 will be installed
--> Processing Dependency: libdb-java(x86-64) >= 5.3.21 for package: libice-java-3.6.3-1.el7.x86_64
---> Package libice3.6-c++.x86_64 0:3.6.3-1.el7 will be installed
---> Package libicestorm3.6.x86_64 0:3.6.3-1.el7 will be installed
---> Package php-ice.x86_64 0:3.6.3-1.el7 will be installed
--> Processing Dependency: php-common(x86-64) for package: php-ice-3.6.3-1.el7.x86_64
---> Package php-ice-devel.x86_64 0:3.6.3-1.el7 will be installed
--> Running transaction check
---> Package ice-slice.noarch 0:3.6.3-1.el7 will be installed
---> Package ice-utils.x86_64 0:3.6.3-1.el7 will be installed
--> Processing Dependency: libdb_cxx-5.3.so()(64bit) for package: ice-utils-3.6.3-1.el7.x86_64
---> Package libfreeze3.6-c++.x86_64 0:3.6.3-1.el7 will be installed
--> Processing Dependency: libdb_cxx-5.3.so()(64bit) for package: libfreeze3.6-c++-3.6.3-1.el7.x86_64
---> Package libice-java.x86_64 0:3.6.3-1.el7 will be installed
--> Processing Dependency: libdb-java(x86-64) >= 5.3.21 for package: libice-java-3.6.3-1.el7.x86_64
---> Package php-ice.x86_64 0:3.6.3-1.el7 will be installed
--> Processing Dependency: php-common(x86-64) for package: php-ice-3.6.3-1.el7.x86_64
--> Finished Dependency Resolution
Error: Package: libice-java-3.6.3-1.el7.x86_64 (zeroc-ice-el7)
           Requires: libdb-java(x86-64) >= 5.3.21
Error: Package: libfreeze3.6-c++-3.6.3-1.el7.x86_64 (zeroc-ice-el7)
           Requires: libdb_cxx-5.3.so()(64bit)
Error: Package: php-ice-3.6.3-1.el7.x86_64 (zeroc-ice-el7)
           Requires: php-common(x86-64)
Error: Package: ice-utils-3.6.3-1.el7.x86_64 (zeroc-ice-el7)
           Requires: libdb_cxx-5.3.so()(64bit)


[kennethgillen]

Hi,

libdb-java or the correct version should be available in `base`.

You could try cleaning yum's cache?

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yum clean all

And if you're still struggling - check what repos are enabled:

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yum repolist all

And make sure `base` is enabled.

Best,

Kenny

[saleht]

Hi Kenny,

thx for your answer it was so helpful ,

now after i did everything like what is written in Documentation
bin/omero admin start .. .works fine and i can log in from omero insight
for Omero web
i installed with virtualenv first of all omero web started and works fine
but after a reboot
bin/omero web start not working
i treid
source /home/omero/omerowebvenv/bin/activate
bin/omero web start not working
it gives

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ERROR: Could not import omero.cli! (No module named Ice)

        This means that your installation is incomplete. Contact
        the OME mailing lists for more information:

        http://www.openmicroscopy.org/site/community

        If you are building from source, please supply the build log
        as well as which version you are building from. If you
        downloaded a distribution, please provide which link you
        used.
       
********************************************************************************

        Debugging Info:
        --------------
        CWD=/home/omero/OMERO.py-5.3.2-ice36-b62
        VERSION=2.7.5 (default, Aug  2 2016, 04:20:16)  [GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
        OMERO_HOME=None
        PYTHONPATH=['/home/omero/OMERO.py-5.3.2-ice36-b62/lib/python', '/home/omero/OMERO.py-5.3.2-ice36-b62/var/lib', '/home/omero/OMERO.py-5.3.2-ice36-b62/bin', '/home/omero/omerowebvenv/lib64/python27.zip', '/home/omero/omerowebvenv/lib64/python2.7', '/home/omero/omerowebvenv/lib64/python2.7/plat-linux2', '/home/omero/omerowebvenv/lib64/python2.7/lib-tk', '/home/omero/omerowebvenv/lib64/python2.7/lib-old', '/home/omero/omerowebvenv/lib64/python2.7/lib-dynload', '/usr/lib64/python2.7', '/usr/lib/python2.7', '/home/omero/omerowebvenv/lib/python2.7/site-packages', '/home/omero/OMERO.py-5.3.2-ice36-b62/lib/fallback']


any suggestion ?, i believe that the problem related to virtualenv , becasue i am not so familier with it

[saleht]

i am getting also this when i am runnig
omero/bin web start

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Traceback (most recent call last):
  File "manage.py", line 56, in <module>
    execute_from_command_line(sys.argv)
  File "/usr/lib64/python2.7/site-packages/django/core/management/__init__.py", line 354, in execute_from_command_line
    utility.execute()
  File "/usr/lib64/python2.7/site-packages/django/core/management/__init__.py", line 328, in execute
    django.setup()
  File "/usr/lib64/python2.7/site-packages/django/__init__.py", line 18, in setup
    apps.populate(settings.INSTALLED_APPS)
  File "/usr/lib64/python2.7/site-packages/django/apps/registry.py", line 85, in populate
    app_config = AppConfig.create(entry)
  File "/usr/lib64/python2.7/site-packages/django/apps/config.py", line 86, in create
    module = import_module(entry)
  File "/usr/lib64/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
ImportError: No module named pipeline


bin/omero admin diagnostics

================================================================================
OMERO Diagnostics 5.3.2-ice36-b62
================================================================================

Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.5 (/usr/bin/python)
Commands: icegridnode --version 3.6.3 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.6.3 (/usr/bin/icegridadmin)
Commands: psql --version 9.6.3 (/usr/bin/psql)

Server: icegridnode running
Server: Blitz-0 active (pid = 2659, enabled)
Server: DropBox active (pid = 2671, enabled)
Server: FileServer active (pid = 2677, enabled)
Server: Indexer-0 active (pid = 2678, enabled)
Server: MonitorServer active (pid = 2680, enabled)
Server: OMERO.Glacier2 active (pid = 2686, enabled)
Server: OMERO.IceStorm active (pid = 2699, enabled)
Server: PixelData-0 active (pid = 2714, enabled)
Server: Processor-0 active (pid = 2716, enabled)
Server: Tables-0 active (pid = 2720, enabled)
Server: TestDropBox inactive (enabled)

Log dir: /home/omero/OMERO.server-5.3.2-ice36-b62/var/log exists
Log files: Blitz-0.log 8.0 MB errors=4 warnings=31
Log files: DropBox.log 32.0 KB errors=2 warnings=10
Log files: FileServer.log 4.0 KB
Log files: Indexer-0.log 44.0 KB errors=2 warnings=1
Log files: MonitorServer.log 17.0 KB
Log files: OMEROweb.lock 0.0 KB
Log files: OMEROweb.log 0.0 KB errors=0 warnings=2
Log files: PixelData-0.log 43.0 KB
Log files: Processor-0.log 727.0 KB errors=0 warnings=2
Log files: Tables-0.log 19.0 KB errors=0 warnings=2
Log files: TestDropBox.log n/a
Log files: master.err 23.0 KB errors=8 warnings=10
Log files: master.out 0.0 KB
Log files: Total size 9.08 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:'/data/OMERO' Exists? True Is writable? True
OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)

JVM settings: Blitz-${index} -Xmx1230m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx820m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx1230m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx820m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [NOT STARTED]
Django version: 1.8.6

[jmoore]

Hi Saleh,

what instructions are you following for the installation? I'm assuming you are on CentOS7 in which case I'd expect you to be following https://www.openmicroscopy.org/site/support/omero5.3/sysadmins/unix/install-web/walkthrough/omeroweb-install-centos7-ice3.6.html (which is linked from https://www.openmicroscopy.org/site/support/omero5.3/sysadmins/unix/server-centos7-ice36.html?highlight=pip). The command I'm wondering about in particular is:

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/home/omero/omerowebvenv/bin/pip install --upgrade -r /home/omero/OMERO.py/share/web/requirements-py27.txt


Have you done this?
~Josh.

[saleht]

Hi Josh,

it works now, i solved but i can not remember how , maybe i did what you wrote, anyway thx

cheers,
Saleh