Open Microscopy Environment

Hi! I have an exception I have been banging my head on for a while now. See below. It comes from Indexer and Pixelstore

* It is a userspace installation of Ice 3.5.1
* it's Red Hat Enterprise Linux Server release 6.5 (Santiago), java 1.7.0_55 (manually downloaded)
* this works on another Centos 6.5 (just copied over the files), java 1.7.0_55 (package)
* IPv6 is disabled and net.ipv6.bindv6only=0 (was default)

django runs well though, it just can't connect...

I assume it is a nitpicky system setting but any takes on which one?

cheers,
Johan


-------------


Ice.SocketException: java.net.SocketException: Protocol family unavailable
at IceInternal.Network.doBind(Network.java:251) ~[ice.jar:na]
at IceInternal.TcpAcceptor.<init>(TcpAcceptor.java:119) ~[ice.jar:na]
at IceInternal.TcpEndpointI.acceptor(TcpEndpointI.java:414) ~[ice.jar:na]
at IceInternal.IncomingConnectionFactory.<init>(IncomingConnectionFactory.java:376) ~[ice.jar:na]
at Ice.ObjectAdapterI.<init>(ObjectAdapterI.java:1028) ~[ice.jar:na]
at IceInternal.ObjectAdapterFactory.createObjectAdapter(ObjectAdapterFactory.java:160) ~[ice.jar:na]
at Ice.CommunicatorI.createObjectAdapter(CommunicatorI.java:77) ~[ice.jar:na]
at ome.services.blitz.Entry.start(Entry.java:202) [blitz.jar:na]
at ome.services.blitz.Entry.main(Entry.java:150) [blitz.jar:na]
Caused by: java.net.SocketException: Protocol family unavailable
at sun.nio.ch.Net.bind0(Native Method) ~[na:1.6.0_30]
at sun.nio.ch.Net.bind(Net.java:174) ~[na:1.6.0_30]
at sun.nio.ch.ServerSocketChannelImpl.bind(ServerSocketChannelImpl.java:139) ~[na:1.6.0_30]
at sun.nio.ch.ServerSocketAdaptor.bind(ServerSocketAdaptor.java:77) ~[na:1.6.0_30]
at IceInternal.Network.doBind(Network.java:245) ~[ice.jar:na]
... 8 common frames omitted

Hi Johan,

other than the IPv6 setting, etc/ is vanilla? Which OMERO version? Is there anything in master.out/master.err?

Cheers,
~Josh.

Hi Josh!

I don't have root on this machine, so it's a bit hard to tell what has been done. But - I think they have kept it as close to vanilla as possible, to ensure their support agreement with redhat (they have been very picky with only using official RPMs etc)

master.out is empty. However, here follows master.err:

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

Traceback (most recent call last):
File "lib/python/runTables.py", line 16, in <module>
import omero.tables
File "/net/isilonP/public/rw/homes/w3_rst01/OMERO.server-5.0.1-ice35-b21/lib/python/omero/tables.py", line 35, in <module>
tables = __import__("tables") # Pytables
ImportError: No module named tables
-! 05/28/14 14:18:06.023 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
Reference.cpp:1663: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @ BlitzAdapters'
-! 05/28/14 14:18:06.041 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
Reference.cpp:1663: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @ BlitzAdapters'
0 IceUtil::Exception::Exception(char const*, int) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIceUtil.so.35
1 Ice::LocalException::LocalException(char const*, int) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
2 Ice::NoEndpointException::NoEndpointException(char const*, int, std::string const&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
3 /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35(+0x55bcac) [0x7f9ae6c1ccac]
4 IceInternal::LocatorInfo::RequestCallback::response(IceInternal::Handle<IceInternal::LocatorInfo> const&, IceInternal::ProxyHandle<IceProxy::Ice::Object> const&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
5 IceInternal::LocatorInfo::Request::response(IceInternal::ProxyHandle<IceProxy::Ice::Object> const&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
6 Ice::CallbackNC_Locator_findAdapterById<IceInternal::LocatorInfo::Request>::__completed(IceInternal::Handle<Ice::AsyncResult> const&) const in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
7 Ice::AsyncResult::__response() in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
8 IceInternal::OutgoingAsync::__finished() in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
9 Ice::ConnectionI::dispatch(IceUtil::Handle<Ice::ConnectionI::StartCallback> const&, std::vector<Ice::ConnectionI::SentCallback, std::allocator<Ice::ConnectionI::SentCallback> > const&, unsigned char, int, int, IceInternal::Handle<IceInternal::ServantManager> const&, IceInternal::Handle<Ice::ObjectAdapter> const&, IceInternal::Handle<IceInternal::OutgoingAsync> const&, IceInternal::BasicStream&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
10 Ice::ConnectionI::message(IceInternal::ThreadPoolCurrent&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
11 IceInternal::ThreadPool::run(IceUtil::Handle<IceInternal::ThreadPool::EventHandlerThread> const&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
12 IceInternal::ThreadPool::EventHandlerThread::run() in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
13 /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIceUtil.so.35(+0x58c85) [0x7f9ae64a0c85]
14 /lib64/libpthread.so.0(+0x79d1) [0x7f9ae51bf9d1]
15 clone() in /lib64/libc.so.6
Traceback (most recent call last):
File "lib/python/runTables.py", line 16, in <module>
import omero.tables
File "/net/isilonP/public/rw/homes/w3_rst01/OMERO.server-5.0.1-ice35-b21/lib/python/omero/tables.py", line 35, in <module>
tables = __import__("tables") # Pytables
ImportError: No module named tables
-! 05/28/14 15:01:47.849 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
Reference.cpp:1663: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @ BlitzAdapters'
-! 05/28/14 15:01:47.883 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
Reference.cpp:1663: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @ BlitzAdapters'
0 IceUtil::Exception::Exception(char const*, int) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIceUtil.so.35
1 Ice::LocalException::LocalException(char const*, int) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
2 Ice::NoEndpointException::NoEndpointException(char const*, int, std::string const&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
3 /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35(+0x55bcac) [0x7f7b37717cac]
4 IceInternal::LocatorInfo::RequestCallback::response(IceInternal::Handle<IceInternal::LocatorInfo> const&, IceInternal::ProxyHandle<IceProxy::Ice::Object> const&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
5 IceInternal::LocatorInfo::Request::response(IceInternal::ProxyHandle<IceProxy::Ice::Object> const&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
6 Ice::CallbackNC_Locator_findAdapterById<IceInternal::LocatorInfo::Request>::__completed(IceInternal::Handle<Ice::AsyncResult> const&) const in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
7 Ice::AsyncResult::__response() in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
8 IceInternal::OutgoingAsync::__finished() in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
9 Ice::ConnectionI::dispatch(IceUtil::Handle<Ice::ConnectionI::StartCallback> const&, std::vector<Ice::ConnectionI::SentCallback, std::allocator<Ice::ConnectionI::SentCallback> > const&, unsigned char, int, int, IceInternal::Handle<IceInternal::ServantManager> const&, IceInternal::Handle<Ice::ObjectAdapter> const&, IceInternal::Handle<IceInternal::OutgoingAsync> const&, IceInternal::BasicStream&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
10 Ice::ConnectionI::message(IceInternal::ThreadPoolCurrent&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
11 IceInternal::ThreadPool::run(IceUtil::Handle<IceInternal::ThreadPool::EventHandlerThread> const&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
12 IceInternal::ThreadPool::EventHandlerThread::run() in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
13 /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIceUtil.so.35(+0x58c85) [0x7f7b36f9bc85]
14 /lib64/libpthread.so.0(+0x79d1) [0x7f7b35cba9d1]
15 clone() in /lib64/libc.so.6
Traceback (most recent call last):
File "lib/python/runTables.py", line 16, in <module>
import omero.tables
File "/net/isilonP/public/rw/homes/w3_rst01/OMERO.server-5.0.1-ice35-b21/lib/python/omero/tables.py", line 35, in <module>
tables = __import__("tables") # Pytables
ImportError: No module named tables
-! 05/28/14 15:45:28.973 OMERO.Glacier2: warning: unable to contact permissions verifier `BlitzVerifier@BlitzAdapters'
Reference.cpp:1663: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @ BlitzAdapters'
-! 05/28/14 15:45:29.018 OMERO.Glacier2: warning: unable to contact session manager `BlitzManager@BlitzAdapters'
Reference.cpp:1663: Ice::NoEndpointException:
no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @ BlitzAdapters'
0 IceUtil::Exception::Exception(char const*, int) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIceUtil.so.35
1 Ice::LocalException::LocalException(char const*, int) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
2 Ice::NoEndpointException::NoEndpointException(char const*, int, std::string const&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
3 /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35(+0x55bcac) [0x7f6502207cac]
4 IceInternal::LocatorInfo::RequestCallback::response(IceInternal::Handle<IceInternal::LocatorInfo> const&, IceInternal::ProxyHandle<IceProxy::Ice::Object> const&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
5 IceInternal::LocatorInfo::Request::response(IceInternal::ProxyHandle<IceProxy::Ice::Object> const&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
6 Ice::CallbackNC_Locator_findAdapterById<IceInternal::LocatorInfo::Request>::__completed(IceInternal::Handle<Ice::AsyncResult> const&) const in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
7 Ice::AsyncResult::__response() in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
8 IceInternal::OutgoingAsync::__finished() in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
9 Ice::ConnectionI::dispatch(IceUtil::Handle<Ice::ConnectionI::StartCallback> const&, std::vector<Ice::ConnectionI::SentCallback, std::allocator<Ice::ConnectionI::SentCallback> > const&, unsigned char, int, int, IceInternal::Handle<IceInternal::ServantManager> const&, IceInternal::Handle<Ice::ObjectAdapter> const&, IceInternal::Handle<IceInternal::OutgoingAsync> const&, IceInternal::BasicStream&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
10 Ice::ConnectionI::message(IceInternal::ThreadPoolCurrent&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
11 IceInternal::ThreadPool::run(IceUtil::Handle<IceInternal::ThreadPool::EventHandlerThread> const&) in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
12 IceInternal::ThreadPool::EventHandlerThread::run() in /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIce.so.35
13 /net/isilonP/public/rw/homes/w3_rst01/Ice-3.5.1/lib64/libIceUtil.so.35(+0x58c85) [0x7f6501a8bc85]
14 /lib64/libpthread.so.0(+0x79d1) [0x7f65007aa9d1]
15 clone() in /lib64/libc.so.6

The best I can tell from this thread on the ZeroC forums, you'll need to add:

Code: Select all

<property name="Ice.IPv6" value="0"/>


to

Code: Select all

<properties id="JavaServer">


in etc/grid/templates.xml (or similar).

If that works for you, please let us know.

All the best,
~Josh.

See also:

• http://www.zeroc.com/forums/help-center/6239-address-family-not-supported-protocol-family.html
• http://www.zeroc.com/forums/help-center/6184-address-family-not-supported-protocol.html

I can verify that this does the trick

Thanks!

Great to hear! Cheers, ~Josh