Open Microscopy Environment

Posted: **Mon Jun 12, 2017 7:29 am**

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

Code: Select all: 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)

Posted: **Mon Jun 12, 2017 9:59 am**

Hi,

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

You could try cleaning yum's cache?

Code: Select all: yum clean all

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

Code: Select all: yum repolist all

And make sure `base` is enabled.

Best,

Kenny

Posted: **Mon Jun 19, 2017 10:28 am**

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

Code: Select all: 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

Posted: **Mon Jun 19, 2017 11:20 am**

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

Code: Select all: 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

Posted: **Tue Jun 20, 2017 9:49 am**

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:

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

Have you done this?
~Josh.

Posted: **Wed Jun 21, 2017 9:17 am**

Hi Josh,

it works now, i solved but i can not remember how

, maybe i did what you wrote, anyway thx

cheers,
Saleh

Open Microscopy Environment

can not install ice 3.6.3 on new Fresh omero server

can not install ice 3.6.3 on new Fresh omero server

Re: can not install ice 3.6.3 on new Fresh omero server

Re: can not install ice 3.6.3 on new Fresh omero server

Re: can not install ice 3.6.3 on new Fresh omero server

Re: can not install ice 3.6.3 on new Fresh omero server

Re: can not install ice 3.6.3 on new Fresh omero server