Open Microscopy Environment

Posted: **Wed Apr 21, 2010 6:27 pm**

Hi, I installed OMERO.server (except OMERO.web) and the clients insight, editor and importer on an XP machine. This part seems to work fine. I then tried to install the OmeroMatlab toolbox (using Matlab R2009a) and that's where I run into problems. I cannot establish a session. In Matlab, I get the following errors:

>> loadOmero
--------------------------
OmeroMatlab Toolbox
Beta-4.2.0-DEV-r6687-b3099
--------------------------
>> c=omero.client('localhost')

c =

omero.client@df46a

>> s=c.createSession('user', 'password')
??? Java exception occurred:
Ice.ConnectionRefusedException

error = 0

at IceInternal.Network.doFinishConnect(Network.java:417)

at IceSSL.TransceiverI.initialize(TransceiverI.java:37)

at Ice.ConnectionI.initialize(ConnectionI.java:1536)

at Ice.ConnectionI.socketReady(ConnectionI.java:1116)

at Ice.ConnectionI$SocketReadyCallback.socketReady(ConnectionI.java:2299)

at IceInternal.SelectorThread.run(SelectorThread.java:203)

at IceInternal.SelectorThread$HelperThread.run(SelectorThread.java:273)

Caused by: java.net.ConnectException: Connection refused: no further information

at sun.nio.ch.SocketChannelImpl.checkConnect(Native Method)

at sun.nio.ch.SocketChannelImpl.finishConnect(Unknown Source)

at IceInternal.Network.doFinishConnect(Network.java:393)

... 6 more

the diagnostics look as follows:

C:\omero_dist>bin\omero admin diagnostics

================================================================================

OMERO Diagnostics Beta-4.1.1-r5927-b91
================================================================================

Commands: java -version 1.6.0 (C:\WINDOWS\system32\java.EXE)
Commands: python -V 2.6.5 (C:\Python26\python.EXE)
Commands: icegridnode --version 3.4.0 (C:\Program Files\ZeroC\Ice-3.4.0\bin\icegridnode.EXE)
Commands: icegridadmin --version 3.4.0 (C:\Program Files\ZeroC\Ice-3.4.0\bin\icegridadmin.EXE)
Commands: psql --version 8.4.3 (C:\Program Files\PostgreSQL\8.4\bin\psql.EXE)

Server: icegridnode running
Server: Blitz-0 active (pid = 2272, enabled)
Server: DropBox inactive (disabled)
Server: FSServer inactive (disabled)
Server: Indexer-0 active (pid = 2328, enabled)
Server: OMERO.Glacier2 active (pid = 2372, enabled)
Server: OMERO.IceStorm inactive (disabled)
Server: Processor-0 inactive (disabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)
Server: Web inactive (enabled)

Log dir: C:\omero_dist\var\log exists

Log files: Blitz-0.log 2.0 MB errors=20 warnings=716
Log files: DropBox.log n/a
Log files: FSServer.log n/a
Log files: Indexer-0.log 369.0 KB errors=63 warnings=45

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: master.err 0.0 KB
Log files: master.out 0.0 KB
Log files: Total size 3.35 MB

Everything is run on the same machine. For >> s=c.createSession('user', 'password') I am using the same user name and password I use to connect to the server using the other clients (e.g. insight). I have tried to establish a session using all the other possibilities listed in loadOmero.m but all have failed. Do I need to configure SSL settings? Or get Omero.IceStorm running (how do I do that?) before I can use OmeroMatlab?

Any help would be highly appreciated.

tuco

Posted: **Thu Apr 22, 2010 12:13 pm**

No, you shouldn't have to do anything special. Can you give me the output of:

Code: Select all: netstat -an ping -n 1 localhost

Posted: **Thu Apr 22, 2010 1:59 pm**

Here they are:

C:\omero_dist>netstat -an

Active Connections

Proto Local Address Foreign Address State
TCP 0.0.0.0:135 0.0.0.0:0 LISTENING
TCP 0.0.0.0:445 0.0.0.0:0 LISTENING
TCP 0.0.0.0:1064 0.0.0.0:0 LISTENING
TCP 0.0.0.0:1084 0.0.0.0:0 LISTENING
TCP 0.0.0.0:3686 0.0.0.0:0 LISTENING
TCP 0.0.0.0:3702 0.0.0.0:0 LISTENING
TCP 0.0.0.0:4063 0.0.0.0:0 LISTENING
TCP 0.0.0.0:5225 0.0.0.0:0 LISTENING
TCP 0.0.0.0:5226 0.0.0.0:0 LISTENING
TCP 0.0.0.0:5432 0.0.0.0:0 LISTENING
TCP 0.0.0.0:6000 0.0.0.0:0 LISTENING
TCP 0.0.0.0:8008 0.0.0.0:0 LISTENING
TCP 127.0.0.1:1032 0.0.0.0:0 LISTENING
TCP 127.0.0.1:1032 127.0.0.1:3455 ESTABLISHED
TCP 127.0.0.1:1034 0.0.0.0:0 LISTENING
TCP 127.0.0.1:1035 0.0.0.0:0 LISTENING
TCP 127.0.0.1:1035 127.0.0.1:3670 ESTABLISHED
TCP 127.0.0.1:1041 0.0.0.0:0 LISTENING
TCP 127.0.0.1:1042 0.0.0.0:0 LISTENING
TCP 127.0.0.1:1045 0.0.0.0:0 LISTENING
TCP 127.0.0.1:1045 127.0.0.1:3718 ESTABLISHED
TCP 127.0.0.1:1049 0.0.0.0:0 LISTENING
TCP 127.0.0.1:1050 127.0.0.1:1051 ESTABLISHED
TCP 127.0.0.1:1051 127.0.0.1:1050 ESTABLISHED
TCP 127.0.0.1:1052 127.0.0.1:1053 ESTABLISHED
TCP 127.0.0.1:1053 127.0.0.1:1052 ESTABLISHED
TCP 127.0.0.1:1055 127.0.0.1:1056 ESTABLISHED
TCP 127.0.0.1:1056 127.0.0.1:1055 ESTABLISHED
TCP 127.0.0.1:1057 127.0.0.1:1058 ESTABLISHED
TCP 127.0.0.1:1058 127.0.0.1:1057 ESTABLISHED
TCP 127.0.0.1:1059 127.0.0.1:1060 ESTABLISHED
TCP 127.0.0.1:1060 127.0.0.1:1059 ESTABLISHED
TCP 127.0.0.1:1061 127.0.0.1:1062 ESTABLISHED
TCP 127.0.0.1:1062 127.0.0.1:1061 ESTABLISHED
TCP 127.0.0.1:1068 0.0.0.0:0 LISTENING
TCP 127.0.0.1:1069 127.0.0.1:1070 ESTABLISHED
TCP 127.0.0.1:1070 127.0.0.1:1069 ESTABLISHED
TCP 127.0.0.1:1071 127.0.0.1:1072 ESTABLISHED
TCP 127.0.0.1:1072 127.0.0.1:1071 ESTABLISHED
TCP 127.0.0.1:1074 127.0.0.1:1075 ESTABLISHED
TCP 127.0.0.1:1075 127.0.0.1:1074 ESTABLISHED
TCP 127.0.0.1:1076 127.0.0.1:1077 ESTABLISHED
TCP 127.0.0.1:1077 127.0.0.1:1076 ESTABLISHED
TCP 127.0.0.1:1078 127.0.0.1:1079 ESTABLISHED
TCP 127.0.0.1:1079 127.0.0.1:1078 ESTABLISHED
TCP 127.0.0.1:1080 127.0.0.1:1081 ESTABLISHED
TCP 127.0.0.1:1081 127.0.0.1:1080 ESTABLISHED
TCP 127.0.0.1:1095 0.0.0.0:0 LISTENING
TCP 127.0.0.1:1107 127.0.0.1:5226 ESTABLISHED
TCP 127.0.0.1:1192 127.0.0.1:1193 ESTABLISHED
TCP 127.0.0.1:1193 127.0.0.1:1192 ESTABLISHED
TCP 127.0.0.1:1196 127.0.0.1:1197 ESTABLISHED
TCP 127.0.0.1:1197 127.0.0.1:1196 ESTABLISHED
TCP 127.0.0.1:2219 0.0.0.0:0 LISTENING
TCP 127.0.0.1:2221 127.0.0.1:6000 ESTABLISHED
TCP 127.0.0.1:2223 127.0.0.1:6000 ESTABLISHED
TCP 127.0.0.1:2225 127.0.0.1:6000 ESTABLISHED
TCP 127.0.0.1:3455 127.0.0.1:1032 ESTABLISHED
TCP 127.0.0.1:3464 127.0.0.1:5432 ESTABLISHED
TCP 127.0.0.1:3647 127.0.0.1:3648 ESTABLISHED
TCP 127.0.0.1:3648 127.0.0.1:3647 ESTABLISHED
TCP 127.0.0.1:3670 127.0.0.1:1035 ESTABLISHED
TCP 127.0.0.1:3687 127.0.0.1:3688 ESTABLISHED
TCP 127.0.0.1:3688 127.0.0.1:3687 ESTABLISHED
TCP 127.0.0.1:3689 127.0.0.1:3690 ESTABLISHED
TCP 127.0.0.1:3690 127.0.0.1:3689 ESTABLISHED
TCP 127.0.0.1:3691 127.0.0.1:4063 ESTABLISHED
TCP 127.0.0.1:3692 127.0.0.1:3693 ESTABLISHED
TCP 127.0.0.1:3693 127.0.0.1:3692 ESTABLISHED
TCP 127.0.0.1:3694 127.0.0.1:3695 ESTABLISHED
TCP 127.0.0.1:3695 127.0.0.1:3694 ESTABLISHED
TCP 127.0.0.1:3696 127.0.0.1:3697 ESTABLISHED
TCP 127.0.0.1:3697 127.0.0.1:3696 ESTABLISHED
TCP 127.0.0.1:3698 127.0.0.1:3699 ESTABLISHED
TCP 127.0.0.1:3699 127.0.0.1:3698 ESTABLISHED
TCP 127.0.0.1:3701 127.0.0.1:5432 ESTABLISHED
TCP 127.0.0.1:3703 127.0.0.1:3704 ESTABLISHED
TCP 127.0.0.1:3704 127.0.0.1:3703 ESTABLISHED
TCP 127.0.0.1:3705 127.0.0.1:3706 ESTABLISHED
TCP 127.0.0.1:3706 127.0.0.1:3705 ESTABLISHED
TCP 127.0.0.1:3707 127.0.0.1:4063 ESTABLISHED
TCP 127.0.0.1:3708 127.0.0.1:3709 ESTABLISHED
TCP 127.0.0.1:3709 127.0.0.1:3708 ESTABLISHED
TCP 127.0.0.1:3710 127.0.0.1:3711 ESTABLISHED
TCP 127.0.0.1:3711 127.0.0.1:3710 ESTABLISHED
TCP 127.0.0.1:3712 127.0.0.1:3713 ESTABLISHED
TCP 127.0.0.1:3713 127.0.0.1:3712 ESTABLISHED
TCP 127.0.0.1:3714 127.0.0.1:3715 ESTABLISHED
TCP 127.0.0.1:3715 127.0.0.1:3714 ESTABLISHED
TCP 127.0.0.1:3716 127.0.0.1:4061 ESTABLISHED
TCP 127.0.0.1:3717 127.0.0.1:5432 ESTABLISHED
TCP 127.0.0.1:3718 127.0.0.1:1045 ESTABLISHED
TCP 127.0.0.1:4061 0.0.0.0:0 LISTENING
TCP 127.0.0.1:4061 127.0.0.1:3669 TIME_WAIT
TCP 127.0.0.1:4061 127.0.0.1:3672 TIME_WAIT
TCP 127.0.0.1:4061 127.0.0.1:3673 TIME_WAIT
TCP 127.0.0.1:4061 127.0.0.1:3674 TIME_WAIT
TCP 127.0.0.1:4061 127.0.0.1:3675 TIME_WAIT
TCP 127.0.0.1:4061 127.0.0.1:3676 TIME_WAIT
TCP 127.0.0.1:4061 127.0.0.1:3677 TIME_WAIT
TCP 127.0.0.1:4061 127.0.0.1:3678 TIME_WAIT
TCP 127.0.0.1:4061 127.0.0.1:3679 TIME_WAIT
TCP 127.0.0.1:4061 127.0.0.1:3680 TIME_WAIT
TCP 127.0.0.1:4061 127.0.0.1:3681 TIME_WAIT
TCP 127.0.0.1:4061 127.0.0.1:3682 TIME_WAIT
TCP 127.0.0.1:4061 127.0.0.1:3716 ESTABLISHED
TCP 127.0.0.1:4063 127.0.0.1:3691 ESTABLISHED
TCP 127.0.0.1:4063 127.0.0.1:3707 ESTABLISHED
TCP 127.0.0.1:5152 0.0.0.0:0 LISTENING
TCP 127.0.0.1:5152 127.0.0.1:3510 CLOSE_WAIT
TCP 127.0.0.1:5226 127.0.0.1:1107 ESTABLISHED
TCP 127.0.0.1:5432 127.0.0.1:3464 ESTABLISHED
TCP 127.0.0.1:5432 127.0.0.1:3701 ESTABLISHED
TCP 127.0.0.1:5432 127.0.0.1:3717 ESTABLISHED
TCP 127.0.0.1:6000 127.0.0.1:2221 ESTABLISHED
TCP 127.0.0.1:6000 127.0.0.1:2223 ESTABLISHED
TCP 127.0.0.1:6000 127.0.0.1:2225 ESTABLISHED
TCP 127.0.0.1:8005 0.0.0.0:0 LISTENING
TCP 130.132.19.147:139 0.0.0.0:0 LISTENING
TCP 130.132.19.147:1084 130.132.19.147:3700 ESTABLISHED
TCP 130.132.19.147:3683 134.36.65.53:80 TIME_WAIT
TCP 130.132.19.147:3684 134.36.65.53:80 TIME_WAIT
TCP 130.132.19.147:3700 130.132.19.147:1084 ESTABLISHED
UDP 0.0.0.0:162 *:*
UDP 0.0.0.0:445 *:*
UDP 0.0.0.0:500 *:*
UDP 0.0.0.0:1028 *:*
UDP 0.0.0.0:1101 *:*
UDP 0.0.0.0:1104 *:*
UDP 0.0.0.0:4500 *:*
UDP 127.0.0.1:123 *:*
UDP 127.0.0.1:1026 *:*
UDP 127.0.0.1:1188 *:*
UDP 127.0.0.1:1900 *:*
UDP 127.0.0.1:2220 *:*
UDP 127.0.0.1:2222 *:*
UDP 127.0.0.1:2224 *:*
UDP 127.0.0.1:2226 *:*
UDP 130.132.19.147:123 *:*
UDP 130.132.19.147:137 *:*
UDP 130.132.19.147:138 *:*
UDP 130.132.19.147:1900 *:*

C:\omero_dist>ping -n 1 localhost

Pinging ErdemDesktop [127.0.0.1] with 32 bytes of data:

Reply from 127.0.0.1: bytes=32 time<1ms TTL=128

Ping statistics for 127.0.0.1:
Packets: Sent = 1, Received = 1, Lost = 0 (0% loss),
Approximate round trip times in milli-seconds:
Minimum = 0ms, Maximum = 0ms, Average = 0ms

Posted: **Thu Apr 22, 2010 2:35 pm**

Thanks. All I can think of then is that somehow name resolution inside Matlab is not working correctly. Can you try 127.0.0.1 or the IP address of your workstation instead of localhost?

Posted: **Mon Apr 26, 2010 4:05 pm**

Hi, I tried both suggestions, none worked. I also updated Matlab to 2010a version and that didn't help either.
Could the problem have anything to do with the fact that the processor.py functionality is disabled in the windows installation? Do I need to install/activate the processor? If so, how do I do that?
thanks

tuco

Posted: **Mon Apr 26, 2010 4:23 pm**

No, you don't require the processor for Matlab functionality. All very odd, this is something that we use fairly routinely so I can't imagine why you're having the connection issues that you are.

What might be tripping you up is the usage of Ice 3.4, we currently do not support Ice 3.4.

Posted: **Mon Apr 26, 2010 7:41 pm**

I have installed ice 3.3.1 and changed the environment variables accordingly (I did not remove 3.4). I could not get icegridnode (and consequently the server) running. I re-ran the OMERO database initialization script (

Code: Select all: >bin\omero bd script

) and re-initialized the database, etc. and tried again to start the server, in vain:

C:\omero_dist>bin\omero admin start
No descriptor given. Using etc\grid\windefault.xml
[SC] CreateService SUCCESS

SERVICE_NAME: OMERO.master
TYPE : 10 WIN32_OWN_PROCESS
STATE : 2 START_PENDING
(NOT_STOPPABLE,NOT_PAUSABLE,IGNORES_SHUTDOWN)
WIN32_EXIT_CODE : 0 (0x0)
SERVICE_EXIT_CODE : 0 (0x0)
CHECKPOINT : 0x0
WAIT_HINT : 0x7d0
PID : 4000
FLAGS :

Waiting on startup. Use CTRL-C to exit
.............................Failed to startup after 5 minutes

C:\omero_dist>bin\omero admin diagnostics

================================================================================
OMERO Diagnostics Beta-4.1.1-r5927-b91
================================================================================

Commands: java -version 1.6.0 (C:\WINDOWS\system32\java.EXE)
Commands: python -V 2.6.5 (C:\Python26\python.EXE)
Commands: icegridnode --version 3.3.1 (C:\Ice-3.3.1-VC90\bin\icegridnode.EXE)
Commands: icegridadmin --version 3.3.1 (C:\Ice-3.3.1-VC90\bin\icegridadmin.EXE)
Commands: psql --version 8.4.3 (C:\Program Files\PostgreSQL\8.4\bin\psql.EXE)

Server: icegridnode not started

Log dir: C:\omero_dist\var\log exists

Log files: Blitz-0.log 8.0 MB errors=29 warnings=4997
Log files: DropBox.log n/a
Log files: FSServer.log n/a
Log files: Indexer-0.log 644.0 KB errors=76 warnings=87
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: master.err 0.0 KB
Log files: master.out 0.0 KB
Log files: Total size 8.87 MB

any idea what I am doing wrong?

On the XP SP3 machine I am using I also have cygwin installed. Do you think it might be a good idea to start from scratch and install everything under cygwin (especially for installing OMERO.web later)?

Posted: **Tue Apr 27, 2010 7:21 am**

You must use the exact Python and Ice binaries that match and I can't remember what the VC90 version was compiled against. If you use the VC80 MSI you'll need to use the Python version that we specify on the website.

In short I suspect you have a library mismatch. You can have a look in C:\omero_dist\var\log and see if there's anything specific in master.err, master.log or Blitz-0.log that might help you out.

Posted: **Tue Apr 27, 2010 4:53 pm**

It seems the problem was that I had to remove ice 3.4 (VC90 uses python 2.6). Now I can start omero server:

C:\omero_dist>bin\omero admin start
Creating c:\omero_dist\var\master
Initializing c:\omero_dist\var\log
Creating c:\omero_dist\var\registry
No descriptor given. Using etc\grid\windefault.xml

SERVICE_NAME: OMERO.master
TYPE : 10 WIN32_OWN_PROCESS
STATE : 2 START_PENDING
(NOT_STOPPABLE,NOT_PAUSABLE,IGNORES_SHUTDOWN)
WIN32_EXIT_CODE : 0 (0x0)
SERVICE_EXIT_CODE : 0 (0x0)
CHECKPOINT : 0x0
WAIT_HINT : 0x7d0
PID : 3672
FLAGS :

Waiting on startup. Use CTRL-C to exit
.
C:\omero_dist>bin\omero admin diagnostics

================================================================================
OMERO Diagnostics Beta-4.1.1-r5927-b91
================================================================================

Commands: java -version 1.6.0 (C:\WINDOWS\system32\java.EXE)
Commands: python -V 2.6.5 (C:\Python26\python.EXE)
Commands: icegridnode --version 3.3.1 (C:\Ice-3.3.1-VC90\bin\icegridnode.EXE)
Commands: icegridadmin --version 3.3.1 (C:\Ice-3.3.1-VC90\bin\icegridadmin.EXE)
Commands: psql --version 8.4.3 (C:\Program Files\PostgreSQL\8.4\bin\psql.EXE)

Server: icegridnode running
Server: Blitz-0 active (pid = 2216, enabled)
Server: DropBox active (pid = 2212, enabled)
Server: FSServer active (pid = 980, enabled)
Server: Indexer-0 active (pid = 2220, enabled)
Server: OMERO.Glacier2 active (pid = 1516, enabled)
Server: OMERO.IceStorm active (pid = 2644, enabled)
Server: Processor-0 active (pid = 1564, enabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)
Server: Web inactive (enabled)

Log dir: C:\omero_dist\var\log exists

Log files: Blitz-0.log 14.0 KB
Log files: DropBox.log 1.0 KB
Log files: FSServer.log 1.0 KB errors=0 warnings=1
Log files: Indexer-0.log 1.0 KB
Log files: OMEROweb.log n/a
Log files: Processor-0.log 0.0 KB
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB
Log files: master.out 0.0 KB
Log files: Total size 0.02 MB

somehow other things such as the processor are active now, too.

As for the original problem of failing to start a session in OmeroMatlab: I was using OmeroMatlab 4.2.0 (latest). I downloaded 4.1.2 and now it works:

>> p = java.util.Properties();
p.setProperty('omero.host', 'localhost');
p.setProperty('omero.user', 'user');
p.setProperty('omero.pass', 'pass');
c = loadOmero(p)
--------------------------
OmeroMatlab Toolbox
Beta-4.1.2-DEV-r6648-b113
--------------------------

c =

omero.client@1a5d193

>> s = c.createSession

s =

session-a5f280c0-6bb4-4ed5-a3de-06f6ec1373da/cbdd267a-082b-45e3-8d48-66441519da38 -t:tcp -h 130.132.19.147 -p 1199

>> g=s.createGateway()

g =

"cbdd267a-082b-45e3-8d48-66441519da38/82:84:13:93:1524a340:1283fefc553:-7ffaomero.api.Gateway" -t:tcp -h 130.132.19.147 -p 1199

(using the user and pass I use to connect insight). So there seems to be a problem in the 4.2.0 toolbox.

thanks for all the help

tuco

Posted: **Wed Apr 28, 2010 6:41 am**

No problem with the toolbox really. 4.2.0 will use the SSL and the SSL port 4064 for all authentication with the server unless forced to only use 4063.

Open Microscopy Environment

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