[ome-devel] Server build questions.
Ingvar Lagerstedt
Ingvar at ebi.ac.uk
Fri Feb 26 15:17:15 GMT 2010
Should have replied to the list, not just Josh.
---------------------------- Original Message ----------------------------
Subject: Re: [ome-devel] Server build questions.
From: "Ingvar Lagerstedt" <Ingvar at ebi.ac.uk>
Date: Fri, February 26, 2010 3:03 pm
To: josh.moore at gmx.de
--------------------------------------------------------------------------
Hi Josh,
>
> Hi Ingvar,
>
> > > I have started to look at your EMAN2 scripts. My previous
> > > checkout was for the tagged 4.1.0 release, so "svn up" did not do
what I thought. So I did a fresh checkout of the trunk, which by
the way do not have a "home" in the path, at least not when
accessing remotely. I am now at revision 6149.
>
> Right. A tag doesn't (shouldn't) change, so "svn up" would tend to do
nothing. A branch like:
>
> svn co http://svn.openmicroscopy.org.uk/svn/omero/branches/Beta4.1
>
> is periodically updated as we make fixes, and "svn up" would bring those
in. "svn switch" would allow you to move from your tag or branch to
trunk in order to not have to check everything out from scratch.
Thanks, that will save time in the future.
>
> > > The build does not finish. I had the same warnings in the 4.1.0
build, but as they have now turned in to errors - see the cc1plus
line below. So the questions are, is it is safe to ignore this
warning, and secondly if so, what is the easiest way to revert back
to the old behaviour of ignoring the warnings.
>
> Interesting. Despite the settings the build passes for me. What
> platform is this? Can you also send us the output of:
>
I am on a Mac OS X 10.6.2.
uname -a
Darwin ingvar.windows.ebi.ac.uk 10.2.0 Darwin Kernel Version 10.2.0: Tue
Nov 3 10:37:10 PST 2009; root:xnu-1486.2.11~1/RELEASE_I386 i386
> c++ --version
c++ (GCC) 4.5.0 20090910 (experimental)
Copyright (C) 2009 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.
I have at some point upgraded from gcc 4.2.0, but I think that was before
the last time I built Omero 4.1.0.
>
> and
>
> VERBOSE=1 ./build.py -f components/tools/OmeroCpp/build.xml tools-dist
Buildfile: components/tools/OmeroCpp/build.xml
Entering /Users/ingvar/Software/omero/omero/components/tools/OmeroCpp...
build:
Building with ICE_HOME=/opt/Ice-3.3.1-64
Debug setting: True (debug)
Using boost_unit_test_framework-mt
64-Bit build: True (detect)
scons: `src' is up to date.
tools-dist:
Building with ICE_HOME=/opt/Ice-3.3.1-64
Debug setting: True (debug)
Using boost_unit_test_framework-mt
64-Bit build: True (detect)
g++ -o target/omero/API.os -c -fPIC -Wall -ansi -Wno-long-long
-Wnon-virtual-dtor -Wno-unused-parameter -Wno-unused-function
-Wunused-variable -Wunused-value -Werror -O0 -g -DOMERO_API_EXPORTS
-D_REENTRANT -DDEBUG -Isrc -Itarget
-I/Users/ingvar/Software/omero/omero/components/blitz/generated
-I/opt/Ice-3.3.1-64/include -I/opt/local/include
-I/opt/Ice-3.3.1-64/include target/omero/API.cpp
cc1plus: warnings being treated as errors
target/omero/API.cpp: In member function ‘virtual Ice::DispatchStatus
IceDelegateD::omero::api::ServiceFactory::sharedResources(const
Ice::Context*)::_DirectI::run(Ice::Object*)’:
target/omero/API.cpp:83475:60: error: ‘virtual
omero::grid::SharedResourcesPrx
omero::api::ServiceFactory::sharedResources(const Ice::Current&)’ is
deprecated (declared at target/omero/API.h:32780)
target/omero/API.cpp: In member function ‘virtual Ice::DispatchStatus
IceDelegateD::omero::api::ServiceFactory::close(const
Ice::Context*)::_DirectI::run(Ice::Object*)’:
target/omero/API.cpp:83852:36: error: ‘virtual void
omero::api::ServiceFactory::close(const Ice::Current&)’ is deprecated
(declared at target/omero/API.h:32795)
target/omero/API.cpp: In member function ‘Ice::DispatchStatus
omero::api::ServiceFactory::___sharedResources(IceInternal::Incoming&,
const Ice::Current&)’:
target/omero/API.cpp:100717:76: error: ‘virtual
omero::grid::SharedResourcesPrx
omero::api::ServiceFactory::sharedResources(const Ice::Current&)’ is
deprecated (declared at target/omero/API.h:32780)
target/omero/API.cpp: In member function ‘Ice::DispatchStatus
omero::api::ServiceFactory::___close(IceInternal::Incoming&, const
Ice::Current&)’:
target/omero/API.cpp:100816:20: error: ‘virtual void
omero::api::ServiceFactory::close(const Ice::Current&)’ is deprecated
(declared at target/omero/API.h:32795)
scons: *** [target/omero/API.os] Error 1
BUILD FAILED
/Users/ingvar/Software/omero/omero/components/tools/OmeroCpp/build.xml:63:
The following error occurred while executing this line:
/Users/ingvar/Software/omero/omero/components/antlib/resources/global.xml:203:
exec returned: 2
Total time: 44 seconds
>
> When I run the above, I see:
>
> omero_trunk$ c++ --version
> c++ (GCC) 4.1.2 (Gentoo 4.1.2 p1.3)
> ...
>
> omero_trunk $ VERBOSE=1 ./build.py -f
components/tools/OmeroCpp/build.xml
> tools-dist
> Buildfile: components/tools/OmeroCpp/build.xml
> Entering /home/jmoore/omero_trunk/components/tools/OmeroCpp...
>
> build:
> Building with ICE_HOME=/opt/Ice-3.3.1
> Debug setting: True (debug)
> Using boost_unit_test_framework-mt
> 64-Bit build: True (detect)
> scons: `src' is up to date.
>
> tools-dist:
> Building with ICE_HOME=/opt/Ice-3.3.1
> Debug setting: True (debug)
> Using boost_unit_test_framework-mt
> 64-Bit build: True (detect)
>
> g++ -o target/omero/API.os -c -fPIC -Wall -ansi -Wno-long-long
> -Wnon-virtual-dtor -Wno-unused-parameter -Wno-unused-function
> -Wunused-variable -Wunused-value -Werror -O0 -g -DOMERO_API_EXPORTS
-D_REENTRANT -DDEBUG -Isrc -Itarget
> -I/home/jmoore/omero_trunk/components/blitz/generated
> -I/opt/Ice-3.3.1/include target/omero/API.cpp
>
> If you'd like to try disabling the errors, I've attached a patch for
components/blitz/blitz_tools.py. (See line 187)
>
All compiled OK with the patch.
Thanks,
Ingvar
>
> Cheers,
> ~J.
>
>
> > > Below is the end of the build log file.
> > > Cheers,
> > > Ingvar
> > >
> > > Compiling target/omero/model/XmlAnnotation.os
> > > Compiling target/omero/model/XmlAnnotationI.os
> > > Compiling target/omero/API.os
> > > cc1plus: warnings being treated as errors
> > > target/omero/API.cpp: In member function $,1rx(Bvirtual
> Ice::DispatchStatus
> > > IceDelegateD::omero::api::ServiceFactory::sharedResources(const
Ice::Context*)::_DirectI::run(Ice::Object*)$,1ry(B:
> > > target/omero/API.cpp:83475:60: error: $,1rx(Bvirtual
> > > omero::grid::SharedResourcesPrx
> > > omero::api::ServiceFactory::sharedResources(const
> Ice::Current&)$,1ry(B is
> > > deprecated (declared at target/omero/API.h:32780)
> > > target/omero/API.cpp: In member function $,1rx(Bvirtual
> Ice::DispatchStatus
> > > IceDelegateD::omero::api::ServiceFactory::close(const
> > > Ice::Context*)::_DirectI::run(Ice::Object*)$,1ry(B:
> > > target/omero/API.cpp:83852:36: error: $,1rx(Bvirtual void
omero::api::ServiceFactory::close(const Ice::Current&)$,1ry(B is
> deprecated
> > > (declared at target/omero/API.h:32795)
> > > target/omero/API.cpp: In member function
$,1rx(BIce::DispatchStatus
> > > omero::api::ServiceFactory::___sharedResources(IceInternal::Incoming&,
const Ice::Current&)$,1ry(B:
> > > target/omero/API.cpp:100717:76: error: $,1rx(Bvirtual
> > > omero::grid::SharedResourcesPrx
> > > omero::api::ServiceFactory::sharedResources(const
> Ice::Current&)$,1ry(B is
> > > deprecated (declared at target/omero/API.h:32780)
> > > target/omero/API.cpp: In member function
$,1rx(BIce::DispatchStatus
> > > omero::api::ServiceFactory::___close(IceInternal::Incoming&, const
Ice::Current&)$,1ry(B:
> > > target/omero/API.cpp:100816:20: error: $,1rx(Bvirtual void
omero::api::ServiceFactory::close(const Ice::Current&)$,1ry(B is
> deprecated
> > > (declared at target/omero/API.h:32795)
> > > scons: *** [target/omero/API.os] Error 1
> > >
> > >> Hi Ingvar,
> > >>
> > >> I remember that you wanted to try running the latest server and
> > >> test my EMAN2 scripts? I realise there are a few steps you'll
need to do...
> > >>
> > >> Are you currently running the latest server on your laptop?
> > >>
> > >> svn.openmicroscopy.org.uk/home/svn/omero/trunk If you check out
this code, then build by running ant in the root directory, it
should put the code in a folder called dist.
> > >>
> > >> You'll need to have the latest database (for storing ROIs on the
server). We don't have upgrade scripts to upgrade to this DB from
the previous one yet, since we haven't released this
> > >> version. The easiest thing to do is to dropdb and make a new one
using the $ bin/omero db script command as described here
> > >> https://www.openmicroscopy.org.uk/site/support/omero4/server/installation
> > >>
> > >>
> > >> For EMAN2 install....
> > >> http://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstall
> > >> I downloaded the latest EMAN2 dmg here
> > >> http://ncmi.bcm.edu/ncmi/software/counter_222/software_86
> > >>
> > >> I think the EMAN2 install includes numpy.
> > >> Try
> > >> $ python
> > >>>>> import numpy
> > >>
> > >> Also you'll need to configure your Python path as described on the
install pages, if you haven't done it already so that you can do
> > >>>>> import omero
> > >>
> > >> You will also need Python Imaging Library if you don't already
have
> > >> it
> > >> Some tips here:
> > >> http://www.openmicroscopy.org.uk/site/support/omero4/server/install-omero-4.1-on-mac-os-x-10.5
> > >>
> > >> The sample images I have been using are from
> > >> http://ami.scripps.edu/experiment/index.php Go to GroEL, view
06jul12a>> I downloaded image:
> > >> 00027gr_00065sq_00009hl_00003en.mrc Click to view the image, then
click the little save icon to download.
> > >>
> > >> Unfortunately, this image is too big to import with our current
importer. I had to open in ImageJ, change to 8 bit and save as
tiff, which you can import OK.
> > >>
> > >> You can draw ROIs
> > >> http://cvs.openmicroscopy.org.uk/snapshots/movies/omero-4-0/mov/MeasurementTool-DrawingROI.mov
and then go to the bottom of the "Inspector" tab to set the width
> and
> > >> height to be a square (I use 330 pixels).
> > >>
> > >>
> > >> I have written the Python scripts to be run by the scripting
service on the server. They need to be "uploaded" to the
> > >> server, so that the scripting service database is aware of them.
> > >>
> > >> You need to have the server running. Then, if you start in the
Omero src folder, you can do: $ cd
> > >> components/tools/OmeroPy/scripts $ python uploadscript.py -h
<host> -u <username> -p <password> -s EMAN2/boxer.py
> > >>
> > >> If you don't want to check out and build from source, you can get
> the
> > >> latest OMERO.server build from hudson
> > >> http://hudson.openmicroscopy.org.uk/job/OMERO/
> > >>
> > >> and you can find the scripts here
> > >> http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/tools/OmeroPy/scripts/
> > >>
> > >>
> > >> To run the boxer script, you'll need the ID that is printed out
when you upload the script above. I use this script to run the
boxer script, passing it a list of the image IDs for it to
process, in this case 101. You can see the image ID when you view
your imported image in Insight.
> > >>
> > >>
> > >> import omero
> > >> import getopt, sys, os, subprocess
> > >> import omero_api_IScript_ice
> > >> from omero.rtypes import *
> > >>
> > >> def run():
> > >>
> > >> # edit these manually, then run the script!
> > >> host = "localhost"
> > >> user = "root"
> > >> password = "omero"
> > >> scriptId = 152
> > >>
> > >> client = omero.client(host)
> > >> session = client.createSession(user, password)
> > >> scriptService = session.getScriptService()
> > >>
> > >> # edit the IDs of the images you want to process...
> > >> ids = [omero.rtypes.rint(101), ]
> > >> imageIds = omero.rtypes.rlist(ids)
> > >>
> > >> map = {
> > >> "imageIds": imageIds,
> > >> }
> > >>
> > >> argMap = omero.rtypes.rmap(map)
> > >> scriptService.runScript(scriptId, map)
> > >>
> > >>
> > >> if __name__ == "__main__":
> > >> run()
> > >>
> > >>
> > >> You can find output of the script (standard output and errors) in
the last 2 files under /OMERO/Files
> > >>
> > >> Good luck, and let me know if/when you need some help!
> > >>
> > >> Cheers,
> > >>
> > >> Will.
> > >>
> > >>
> > >>
> > >> On 22 Feb 2010, at 13:25, Ingvar Lagerstedt wrote:
> > >>
> > >>> Hi Will,
> > >>>
> > >>> It could be that I failed to clear out some class file from the
previous build. Took a couple of rounds to exclude enough files
to get down to a file that our mailer is happy with. I wrote my
own ant-file. Something like: ant compile-renderer ant dist
> > >>>
> > >>> should build it.
> > >>>
> > >>> Cheers,
> > >>> Ingvar
> > >>>
> > >>>
> > >>>> Hi Ingvar,
> > >>>>
> > >>>> I'm getting exactly the same error with this new jar, although I
have java 1.5. I wonder if something in your system is still
using 1.6? I don't really want to upgrade to 1.6 since
everything we release is built for java 1.5.
> > >>>>
> > >>>> You could just send me your code. Zip up the whole
> > >>>> OpenAstexViewer folder, just like they do on the web-site. Then
I can Open it as a new project and build it. Obviously this is
not a good long-term solution, but should work for now.
> > >>>>
> > >>>> Do you commit your code to a repository anywhere that I could
access
> > >>>> it from?
> > >>>>
> > >>>> Cheers,
> > >>>>
> > >>>> Will.
> > >>>>
> > >>>>
> > >>>> On 22 Feb 2010, at 12:13, Ingvar Lagerstedt wrote:
> > >>>>
> > >>>>> Hi Will,
> > >>>>>
> > >>>>> Could be that I compiled with java 1.6, and your java runtime
is slightly out of date. I am rather new to java, but that
seems like a reasonable first guess.
> > >>>>>
> > >>>>> I recompiled using java 1.4, attached, unless you want to
> upgrade.
> > >>>>>
> > >>>>> You are likely to run out of memory with the default jvm memory
settings. The Astex viewer is a bit of a memory black hole.
Use something like: java -Xmx1G -jar
> > >>>>> OpenAstexViewer.jar
> > >>>>>
> > >>>>> Hope this helps,
> > >>>>> Ingvar
> > >>>>>
> > >>>>>>
> > >>>>>> Hi Ingvar,
> > >>>>>>
> > >>>>>> I just tried to run the jar, but got this error....
> > >>>>>>
> > >>>>>> will$ java -jar OpenAstexViewer.jar Exception in thread "main"
java.lang.UnsupportedClassVersionError: Bad version number in
.class file at
> > >>>>>> java.lang.ClassLoader.defineClass1(Native Method) at
> > >>>>>> java.lang.ClassLoader.defineClass(ClassLoader.java:676) at java
> > >>>>>> .security.SecureClassLoader.defineClass(SecureClassLoader.java:
124)
> > >>>>>> at
java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
> > >>>>>> at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
at java.net.URLClassLoader$1.run(URLClassLoader.java:195) at
java.security.AccessController.doPrivileged(Native Method) at
java.net.URLClassLoader.findClass(URLClassLoader.java:188) at
java.lang.ClassLoader.loadClass(ClassLoader.java:317) at
> sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:280)
> > >>>>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:252) at
> java.lang.ClassLoader.loadClassInternal(ClassLoader.java:375)
> > >>>>>>
> > >>>>>> Hope you can see what is going on here?
> > >>>>>> Does this jar work for you?
> > >>>>>> Do I need to do something different?
> > >>>>>>
> > >>>>>> Many thanks,
> > >>>>>>
> > >>>>>> Will.
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>> On 22 Feb 2010, at 11:38, Ingvar Lagerstedt wrote:
> > >>>>>>
> > >>>>>>> Hi Will,
> > >>>>>>>
> > >>>>>>> As discussed last Friday I send you my current version of the
Astex
> > >>>>>>> Viewer.
> > >>>>>>> We are trying to do a merge of three EBI branches of the
> viewer,
> > >>>>>>> so
> > >>>>>>> here
> > >>>>>>> is likely to be changes in the near future...
> > >>>>>>>
> > >>>>>>> My current favourite test case is EMD_5036 available from:
http://www.ebi.ac.uk/pdbe-srv/emsearch/atlas/5036_summary.html
http://www.ebi.ac.uk/pdbe-srv/emsearch/atlas/5036_downloads.html
> > >>>>>>>
> > >>>>>>> The first link for the PDB ids, the second for the EM map.
> > >>>>>>>
> > >>>>>>> All the best,
> > >>>>>>> Ingvar
> > >>>>>>>
> > >>>>>>>> Hi Christoph, Ingvar, Jason,
> > >>>>>>>>
> > >>>>>>>> Just wanted to note a few points for discussion this
> afternoon.
> > >>>>>>>>
> > >>>>>>>> Here's a short presentation I did recently for our group
discussion:
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>> To summarise:
> > >>>>>>>> - There are several different directions I could work on at
this
> > >>>>>>>> point
> > >>>>>>>> Eg: Publication Web client?
> > >>>>>>>> EM submission client? (needs web import)
> > >>>>>>>> 3D viewer? (Client-side or server-side?)
> > >>>>>>>> EMAN2 $,1rs(B OMERO interaction?
> > >>>>>>>> Server stuff? Big Images, arbitrary planes/proj
> > >>>>>>>> OMERO.editor?
> > >>>>>>>> - What I do depends on:
> > >>>>>>>> The other members of OME team
> > >>>>>>>> EM project goals - needs some discussion
> > >>>>>>>>
> > >>>>>>>> - I included some slides from the EMEN2 WebEx demo the other
day, since there seems to be a lot of overlap with what they
are doing and what we are thinking of. How does their work
affect what we do?
> > >>>>>>>>
> > >>>>>>>> - I have been working on EMAN2 - OMERO integration (adding
EMAN2 functionality to the server via Python). Not sure if
this is something we want to pursue? Do we want users to
eventually use OMERO as their image repository for
> > >>>>>>>> single-particle workflow? - What are the benefits of this
that we can offer them? - If so, do we need to target more
than 1 application (EMAN2)? Spider? IMOD? BSoft? etc
> > >>>>>>>>
> > >>>>>>>> Speak later (3pm)?
> > >>>>>>>>
> > >>>>>>>> Cheers,
> > >>>>>>>>
> > >>>>>>>> Will .
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>> On 18 Feb 2010, at 08:28, Christoph Best wrote:
> > >>>>>>>>
> > >>>>>>>>> Hi Will and Jason,
> > >>>>>>>>>
> > >>>>>>>>> I am back at EBI tomorrow (Friday) afternoon, or we can
talk next week (except Wednesday and Friday since we are
conducting all-day interviews...).
> > >>>>>>>>>
> > >>>>>>>>> Best
> > >>>>>>>>> -Christoph
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
--
Ingvar Lagerstedt, PDBe, EMBL-EBI, Hinxton, UK
Ingvar at ebi.ac.uk
--
Ingvar Lagerstedt, PDBe, EMBL-EBI, Hinxton, UK
Ingvar at ebi.ac.uk
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