Open Microscopy Environment

Posted: **Tue Sep 09, 2014 11:19 am**

Hi all,

I am (finally!) in the process of updating omero to omero 5 (my install seem to be broken, but I though I'd upgrade to the latest version before reporting anything) and the prerequities situation on windows server 2008 is a bit complex so I thought I would ask: what is the recomended setup? In particular:
-the upgrade page mention a ice 3.5 compiled (by OME) against python 2.7 for windows but does not recommend it; has any issues been found or can I go ahead?
-is java8 officially supported starting 5.0.4? in particular ice mention java6 and 7 but not 8 in it's compatibility page...
-anything else I should be wary of? I currently use psql 9.1, that should be fine...

I seemed to have random issues with mismatch of version of stuff recently (see other thread), so I though I'd try to go for the most recent version I can...

Many thanks

A.

Posted: **Wed Sep 10, 2014 8:58 am**

Hi,

With regard to using the OME-compiled Ice 3.5 with Python 2.7, there are no known issues at this point. However, this combination (on Windows) hasn't yet had much real-world testing, and we don't have daily automated testing in place for this combination yet (it's pending). This combination is tested daily on MacOS and Linux, though, and has been tested manually on Windows. It's not recommended simply because of that--it's unlikely that there will be additional problems, but our internal support for it is not as extensive as for the other combinations at this point. But it should work without problems.

With regard to Java 8, 5.0.4 should work fine with Java 8 on both client and server.

PostgreSQL 9.1 is absolutely fine. 9.2 and 9.3 will also work if you wanted to upgrade.

If you use python 2.7 on a 64-bit system, I'd recommend a 64-bit python with additional modules installed from http://www.lfd.uci.edu/~gohlke/pythonlibs/ and the 64-bit OME Ice build.

If you aren't already, we also recommend running the OMERO service under a dedicated system account.

Regards,
Roger

Posted: **Fri Sep 12, 2014 5:02 pm**

thanks for the info. I went for your ice3.5 and python2.7, and OMERO fails with that looks like a version/path problem. The PATH/PYTHONPATH seems fine though so I am not sure what went wrong, if somebody got an idea...

The error:

Code: Select all: PS C:\Users\omero\Desktop\OMERO.server-5.0.4-ice35-b43> .\bin\omero admin start ******************************************************************************** ERROR: Could not import omero.cli! (DLL load failed: The specified module could not be found.) 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=C:\Users\omero\Desktop\OMERO.server-5.0.4-ice35-b43 VERSION=2.7.8 (default, Jun 30 2014, 16:08:48) [MSC v.1500 64 bit (AMD64)] OMERO_HOME=None PYTHONPATH=['C:\\Users\\omero\\Desktop\\OMERO.server-5.0.4-ice35-b43\\lib\\python', 'C:\\Users\\omero\\Desktop\\ OMERO.server-5.0.4-ice35-b43\\var\\lib', 'C:\\Users\\omero\\Desktop\\OMERO.server-5.0.4-ice35-b43\\bin', 'C:\\Users\\ome ro\\Ice-3.5.1-2-win-x64-Release\\python', 'C:\\Users\\omero\\Desktop\\OMERO.server-5.0.4-ice35-b43\\lib\\python', 'C:\\W indows\\system32\\python27.zip', 'C:\\Python27\\DLLs', 'C:\\Python27\\lib', 'C:\\Python27\\lib\\plat-win', 'C:\\Python27 \\lib\\lib-tk', 'C:\\Python27', 'C:\\Python27\\lib\\site-packages', 'C:\\Python27\\lib\\site-packages\\win32', 'C:\\Pyth on27\\lib\\site-packages\\win32\\lib', 'C:\\Python27\\lib\\site-packages\\Pythonwin', 'C:\\Users\\omero\\Desktop\\OMERO. server-5.0.4-ice35-b43\\lib\\fallback']

The PYTHONPATH:

Code: Select all: PS C:\Users\omero\Desktop\OMERO.server-5.0.4-ice35-b43> (Get-ChildItem Env:PYTHONPATH).value C:\Users\omero\Ice-3.5.1-2-win-x64-Release\python;C:\Users\omero\Desktop\OMERO.server-5.0.4-ice35-b43\lib\python

and PATH:

Code: Select all: PS C:\Users\omero\Desktop\OMERO.server-5.0.4-ice35-b43> (Get-ChildItem Env:PATH).value C:\Windows\system32\WindowsPowerShell\v1.0\;C:\Python27\;C:\Python27\Scripts;C:\Users\omero\Desktop\OMERO.server-5.0.4- ice35-b43\bin;C:\Users\omero\Ice-3.5.1-2-win-x64-Release\bin;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C: \Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\MySQL\MySQL Server 5.1\bin

many thanks...

Posted: **Mon Sep 15, 2014 8:58 am**

Looking at the information you provided, you already tried everything obvious which I would have suggested.

It looks like you have the 64-bit Ice build and you have PYTHONPATH set correctly to use the Ice modules and you have PATH set correctly to pick up the ice programs and DLLs. I'm assuming you have a 64-bit python installed here; if you don't that's the obvious problem. Some suggestions:

- can you run "slice2cpp --version" or "icegridnode --version"?
- can you run python and then import the Ice module?

Code: Select all: % python Python 2.7.6 (default, Mar 22 2014, 22:59:56) [GCC 4.8.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import Ice >>>

This should show up any problems with PATH or PYTHONPATH. If the import fails then the PYTHONPATH is incorrect or the DLLs won't load into the python process due to a mismatch. This can be due to a 32/64-bit mismatch or due to not being able to load or conflicting with other DLLs, e.g. mismatched Python build or Ice libraries. Maybe try removing the OMERO path from PYTHONPATH so that it's only got the Ice module path in there and see if you can manually import the rest; bin/omero should handle the OMERO modules for you.

Regards,
Roger

Posted: **Mon Sep 15, 2014 1:07 pm**

There is indeed a problem when importing Ice, but python is 64bit and python path seem ok... icegridnode --version does not output anything, but it does seem to be finding the right one:

PS C:\Windows\system32> python
Python 2.7.8 (default, Jun 30 2014, 16:08:48) [MSC v.1500 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import Ice
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\omero\Ice-3.5.1-2-win-x64-Release\python\Ice.py", line 47, in <module>
import IcePy
ImportError: DLL load failed: The specified module could not be found.
>>> import sys
>>> sys.path
['', 'C:\\Users\\omero\\Ice-3.5.1-2-win-x64-Release\\python', 'C:\\Windows\\system32\\python27.zip', 'C:\\Python27\\DLLs
', 'C:\\Python27\\lib', 'C:\\Python27\\lib\\plat-win', 'C:\\Python27\\lib\\lib-tk', 'C:\\Python27', 'C:\\Python27\\lib\\
site-packages', 'C:\\Python27\\lib\\site-packages\\win32', 'C:\\Python27\\lib\\site-packages\\win32\\lib', 'C:\\Python27
\\lib\\site-packages\\Pythonwin']
>>> exit()
PS C:\Windows\system32> icegridnode --version
PS C:\Windows\system32> get-command icegridnode

CommandType Name Definition
----------- ---- ----------
Application icegridnode.exe C:\Users\omero\Ice-3.5.1-2-win-x64-Release\bin\i...

I tried to take all the other python prereq in 64bits as well, could it be that I missed one? Or the python version is newer than yours? I must admit I do not know enough about python to know where to look really...

If troubles continue, I guess I can try the ice3.4-python2.6 combo, if that is where the pb comes from?
Many thanks for your help, it does come at the worst time as well (as usual).

Posted: **Mon Sep 15, 2014 2:12 pm**

Could you try adding

Code: Select all: C:\Users\omero\Ice-3.5.1-2-win-x64-Release\python\bin

and/or

Code: Select all: C:\Users\omero\Ice-3.5.1-2-win-x64-Release\python\lib

to your PATH variable?

Cheers

Simon

Posted: **Mon Sep 15, 2014 2:14 pm**

So after putting icepy.pyd through dependency walker, it turned out I was missing the msvc redristributable. I love windows.

Now to the next error (sorry):

PS C:\Users\omero\Desktop\OMERO.server-5.0.4-ice35-b43> .\bin\omero admin start
No descriptor given. Using etc\grid\windefault.xml
Installing OMERO.master Windows service.
Successfully installed OMERO.master Windows service.
OMERO.master service startup failed: (2) The system cannot find the file specified.
OMERO.master service deleted.

The first time it had a few lines about changing a configuration from a default, but the value it found seemed to make sense (I did not kept the log of that, sorry). 'etc\grid\windefault.xml' seem to be making sense as well...

The diagnostics in case that helps:

PS C:\Users\omero\Desktop\OMERO.server-5.0.4-ice35-b43> omero admin diagnostics

================================================================================
OMERO Diagnostics 5.0.4-ice35-b43
================================================================================

Commands: java -version 1.8.0 (C:\Windows\system32\java.EXE)
Commands: python -V 2.7.8 (C:\Python27\python.EXE)
Commands: icegridnode --version 3.5.1 (C:\Users\omero\Ice-3.5.1-2-win-x64-Release\bin\icegridnode.EXE)
Commands: icegridadmin --version 3.5.1 (C:\Users\omero\Ice-3.5.1-2-win-x64-Release\bin\icegridadmin.EXE)
Commands: psql --version not found

Server: icegridnode not started

Cannot list deployed applications.

Log dir: C:\Users\omero\Desktop\OMERO.server-5.0.4-ice35-b43\var\log exists

Log files: Blitz-0.log n/a
Log files: DropBox.log n/a
Log files: FileServer.log n/a
Log files: Indexer-0.log n/a
Log files: MonitorServer.log n/a
Log files: OMEROweb.log n/a
Log files: Processor-0.log n/a
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: Total size 0.00 MB

Error while parsing logs

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=(unset)
Environment:PATH=C:\Windows\system32\WindowsPowerShell\v1.0\;C:\Users\omero\Ice-3.5.1-2-win-x64-Release\bin;C:\Python27\
;C:\Python27\Scripts;C:\Users\omero\Desktop\OMERO.server-5.0.4-ice35-b43\bin;C:\Windows\system32;C:\Windows;C:\Windows\S
ystem32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\MySQL\MySQL Server 5.1\bin
Environment:PYTHONPATH=C:\Users\omero\Ice-3.5.1-2-win-x64-Release\python;C:\Users\omero\Desktop\OMERO.server-5.0.4-ice35
-b43\lib\python
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: 'E:\\OMERO' Exists? True Is writable? True
OMERO temp dir: 'C:\Users\omero\AppData\Roaming\omero\tmp' Exists? True Is writable? True (Size: 0)
OMERO.web status... [NOT STARTED]
PS C:\Users\omero\Desktop\OMERO.server-5.0.4-ice35-b43>

Many thanks...

Posted: **Mon Sep 15, 2014 2:20 pm**

Are you starting OMERO as a Windows administrator? Sometimes you need to use an elevated Command Prompt (Right click, Run as Administrator) even if you're already logged in as an admin.

Simon

Posted: **Mon Sep 15, 2014 2:46 pm**

I was using a elevated prompt, but forgot to restart the server for the changes in the path to take hold. God I love windows, did I say that already? Good to see some things never change :/...

Anyway, it works now, thanks for the help.
Now to fight with IIS...

Posted: **Mon Sep 15, 2014 5:18 pm**

my apologies for spamming the forums, that update is definitely going less smoothly than I had hoped (and given my previous experience under windows my hopes where not that high.)

A few things I had to do, just in case it helps somebody else:
-I had to reinstall isapi_wsgi, as I had resinstalled python. (Maybe mention it in the python requirement? I though it was a windows thing to be done only once)
-the isapi_wsgi.exe for some reason wanted to install itself onto python2.5, so I installed from source
-after 'omero web iis', localhost/omero gives an error 403 forbidden; I added IUSR and iis_iusrs as authorised users for the omero server folder. (that I had to do each time, btw)

And now I have a 'HTTP Error 500.0 - Internal Server Error'. None of the omero logs seem to be touched, the iis logs shows nothing either. I tried restarting omero and resetting iis without effects...

As usual, many thanks for any help
A.

Open Microscopy Environment

OMERO5 on windows and versions of stuff

OMERO5 on windows and versions of stuff

Re: OMERO5 on windows and versions of stuff

Re: OMERO5 on windows and versions of stuff

Re: OMERO5 on windows and versions of stuff

Re: OMERO5 on windows and versions of stuff

Re: OMERO5 on windows and versions of stuff

Re: OMERO5 on windows and versions of stuff

Re: OMERO5 on windows and versions of stuff

Re: OMERO5 on windows and versions of stuff

Re: OMERO5 on windows and versions of stuff