[ome-devel] Server build questions.
josh.moore at gmx.de
josh.moore at gmx.de
Fri Feb 26 13:42:41 GMT 2010
> > From: "Ingvar Lagerstedt" <Ingvar at ebi.ac.uk>
> > Date: 26 February 2010 11:33:40 GMT
> > To: "Will Moore" <will at lifesci.dundee.ac.uk>
> > Subject: Re: EMAN2-OMERO scripts
> > Reply-To: Ingvar at ebi.ac.uk
> >
> > Hi Will,
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.
> > 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:
c++ --version
and
VERBOSE=1 ./build.py -f components/tools/OmeroCpp/build.xml tools-dist
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)
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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 ?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
> >
> >> 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 ? 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
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