Open Microscopy Environment

Hi Everybody,

I tried to use Omero.insight to connect to a freshly installed virtualbox omero but without success.
Here is what I did:
I downloaded omero-vm-4.4.6.ova form the page http://cvs.openmicroscopy.org.uk/snapshots/omero/virtualbox/ and followed the instructions from http://www.openmicroscopy.org/site/support/omero4/users/virtual-appliance.html .

Then I started the virtualBox and the server booted with success.

I successfully connected to it using ssh command

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ssh omero@localhost -p 2222

(root is alos working).

I also could access to the server using the web interface at this address: http://localhost:8080/webclient/

Then I downloaded the Omero.insight client and ran it:

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~/bin/OMERO.clients-4.4.6-ice33-b102.linux$ ./OMEROinsight_unix.sh

I configured the server to be localhost and use the port 4064

I used the Username root with password omero but after a while is popup the message saying that the network is down.


Here is my iptables configuration:

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sudo iptables -L -n
Chain INPUT (policy ACCEPT)
target     prot opt source               destination         
ACCEPT     tcp  --  0.0.0.0/0            0.0.0.0/0            tcp dpt:4063
ACCEPT     tcp  --  0.0.0.0/0            0.0.0.0/0            tcp dpt:4064
ACCEPT     tcp  --  0.0.0.0/0            0.0.0.0/0            tcp dpt:443
ACCEPT     tcp  --  0.0.0.0/0            0.0.0.0/0            tcp dpt:80

Chain FORWARD (policy ACCEPT)
target     prot opt source               destination         

Chain OUTPUT (policy ACCEPT)
target     prot opt source               destination


I previously wiped everything to make sure my previous iptables configuration won't interfere with the connection by running the following script using sudo:

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#!/bin/sh
echo "Stopping firewall and allowing everyone..."
iptables -F
iptables -X
iptables -t nat -F
iptables -t nat -X
iptables -t mangle -F
iptables -t mangle -X
iptables -P INPUT ACCEPT
iptables -P FORWARD ACCEPT
iptables -P OUTPUT ACCEPT


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sudo chmod +x stop.fw
sudo ./stop.fw

Then I followed the recommendations given on this page to make sure ports 4064 and 4063 are open http://www.openmicroscopy.org/site/support/omero4/sysadmins/server-security.html

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iptables -P INPUT drop
iptables -A INPUT -p tcp --dport 4063 -j ACCEPT
iptables -A INPUT -p tcp --dport 4064 -j ACCEPT
iptables -A INPUT -p tcp --dport 443 -j ACCEPT
iptables -A INPUT -p tcp --dport 80 -j ACCEPT


But without success.

Logs located in /home/omero/OMERO.server/var/log/ on the server couln't give me any usefull information on what's going on.

I looks like I missed something in the configuration but I could find what...
Could someone guide me to find a fix?

Benjamin

Hi Benjamin,

Did the host machine lose it's internet connectivity at all while you were using the Insight client?

I have experienced this while using the OMERO virtualbox server running locally when the laptop has no internet connection. This is due to a compromise that had to be made due to Java 1.5. (https://trac.openmicroscopy.org.uk/ome/ticket/10409)

Best,

Kenny

kennethgillen wrote:Hi Benjamin,

Did the host machine lose it's internet connectivity at all while you were using the Insight client?

No, the internet connection on the host machine was continuously on, it's my main desktop and has a fixed ethernet connection. The only think I could think is that proxy is configured on this computer (running Ubuntu 12.10) but is is not supposed to interfere.

Thanks for your answer
Benjamin

Hi Benjamin,

Could you try connecting to the OMERO server from the host machine via telnet / openssl??

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telnet localhost 4063

Does telnet connect and if so what output do you see? Expect something like the following

Connected to localhost.
Escape character is '^]'.
IceP

And for SSL:

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openssl s_client -debug -connect localhost:4064 -no_tls1 -no_ssl3 -no_ssl2

Do you see something like:

CONNECTED(00000003)
13953:error:140740BF:SSL routines:SSL23_CLIENT_HELLO:no protocols available

Many Thanks,

Kenny

Hi Kenny,

So I could telnet to it:

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~$ telnet localhost 4063
Trying ::1...
Trying 127.0.0.1...
Connected to localhost.
Escape character is '^]'.
IceP




And for SSL:

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$ openssl s_client -debug -connect localhost:4064 -no_tls1 -no_ssl3 -no_ssl2
CONNECTED(00000003)
write to 0x1a56cf0 [0x1a57860] (226 bytes => 226 (0xE2))
0000 - 16 03 01 00 dd 01 00 00-d9 03 02 51 3a 19 8d b7   ...........Q:...
0010 - ea d1 f3 9e c2 16 a3 1d-b6 64 3c c8 47 f2 11 af   .........d<.G...
0020 - 18 90 f8 e9 c8 ab af 03-a2 11 fd 00 00 66 c0 14   .............f..
0030 - c0 0a c0 22 c0 21 00 39-00 38 00 88 00 87 c0 0f   ...".!.9.8......
0040 - c0 05 00 35 00 84 c0 12-c0 08 c0 1c c0 1b 00 16   ...5............
0050 - 00 13 c0 0d c0 03 00 0a-c0 13 c0 09 c0 1f c0 1e   ................
0060 - 00 33 00 32 00 9a 00 99-00 45 00 44 c0 0e c0 04   .3.2.....E.D....
0070 - 00 2f 00 96 00 41 c0 11-c0 07 c0 0c c0 02 00 05   ./...A..........
0080 - 00 04 00 15 00 12 00 09-00 14 00 11 00 08 00 06   ................
0090 - 00 03 00 ff 02 01 00 00-49 00 0b 00 04 03 00 01   ........I.......
00a0 - 02 00 0a 00 34 00 32 00-0e 00 0d 00 19 00 0b 00   ....4.2.........
00b0 - 0c 00 18 00 09 00 0a 00-16 00 17 00 08 00 06 00   ................
00c0 - 07 00 14 00 15 00 04 00-05 00 12 00 13 00 01 00   ................
00d0 - 02 00 03 00 0f 00 10 00-11 00 23 00 00 00 0f 00   ..........#.....
00e0 - 01 01                                             ..
read from 0x1a56cf0 [0x1a5cdc0] (7 bytes => 7 (0x7))
0000 - 15 03 01 00 02 02 28                              ......(
140160181737120:error:14077102:SSL routines:SSL23_GET_SERVER_HELLO:unsupported protocol:s23_clnt.c:697:
---
no peer certificate available
---
No client certificate CA names sent
---
SSL handshake has read 7 bytes and written 226 bytes
---
New, (NONE), Cipher is (NONE)
Secure Renegotiation IS NOT supported
Compression: NONE
Expansion: NONE

An i'm also not able to connect to the web interface anymore to http://localhost:8080/webclient
even with proxy option disabled (using firefox).
Here is a screenshot of the virtualbox configuration.

I also remove all rules in iptables by running the following script:

#!/bin/sh
echo "Stopping firewall and allowing everyone..."
iptables -F
iptables -X
iptables -t nat -F
iptables -t nat -X
iptables -t mangle -F
iptables -t mangle -X
iptables -P INPUT ACCEPT
iptables -P FORWARD ACCEPT
iptables -P OUTPUT ACCEPT

Thanks,
Benjamin

CORRECTION : I can connect to the web interface via the address http://localhost:8080/webclient

Benjamin

Hi Benjamin,

Glad to hear you can connect to the Web interface.

The Insight client should connect if you can telnet to the server, so I suggest it would be worth trying to connect again being sure that your host machine has Internet connectivity.

If you still receive the warning about connectivity, can you please reply with your java type and version?

Many thanks,

Kenny

Hi Kenny,
So unfortunately, I cannot connect using the omero insight client (see screenshot attached) even though telnet, openssl and we interface are working fine.

I do have a proxy set on my machine using the proxy_http and proxy_https variables.
Using

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env no_proxy='*'

before the command line like the following:

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env no_proxy='*' ./OMEROinsight_unix.sh

do not solve the problem.

Here is my java version:

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$ java -version
java version "1.6.0_27"
OpenJDK Runtime Environment (IcedTea6 1.12.3) (6b27-1.12.3-0ubuntu1~12.04.1)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

I do have internet connectivity since I right now posting this message to the OMERO forum

Thanks for your help,

Benjamin

Hi Benjamin,

Sorry you are having so much trouble: Insight should really connect - could you please help us see where the issue is by sending us the log files? We can then work out what's going wrong, and hopefully fix it.

The Insight client, which you're having trouble with, will be logging to your host machine's $HOME/omero/log

And if possible, could you [g/]zip up the whole directory of logs from the OMERO server from the appliance? If you can, that'd be fantastic.

/home/omero/OMERO.server/var/log

You may use the following system for uploading the logs: http://qa.openmicroscopy.org.uk/qa/upload/

Many thanks for your patience and assistance.

Best,

Kenny

Details on Logging: http://www.openmicroscopy.org/site/support/omero4/developers/logging.html

Hi Benjamin,

You may also like to try swapping JVM - openJDK 1.7 if it's available, or oracle java may produce different results.

Best,

Kenny