Open Microscopy Environment

Hello:

Has anyone had any success installing/deploying server on os x 10.7? There have been several changes (unbeknownst to me before beginning this odyssey on 10.7) from the 10.6 version.

After much effort, it seems I have Postgresql 8.3.4 working, but it looks like OMERO is having trouble with the Ice-3.3.1 binaries (unfortunately I don't have the logs handy right now, I'll have to follow up with these).

So I tried to compile all the Ice dependencies from source, from the Zero-C Ice dependencies download. That worked fine until I got to Ice itself, which fails to compile. I've tried this new, not-working-with-Ice 10.7 clang compiler, and managed to install the legacy gcc 4.2 and neither one has been successful. I also applied this patch

http://www.zeroc.com/forums/bug-reports ... ilers.html

and was unsuccessful in getting Ice-3.3.1 working. The patch application belched up many errors, something about 'chunks' and didn't seem to solve the compilation errors.

It took several days of tinkering, scouring the web, changing permissions, seeking tribal knowledge just to get Postgresql 8.3 working and I've been compiling dependencies to dependencies but have had little success. After my preliminary testing on Os 10.6 on a laptop (and deciding an Apple server would be a good idea because it would be straightforward to set up and manage), Os X 10.7 on my new box has rocked my world and shut me down completely. It is a nightmare. I may have to switch to a plan b and start from scratch with a linux box, but I thought I would check with the community.

Has anyone out there had any success installing an OMERO server on OS X 10.7?

Thanks,
Karl G.

keg wrote:Has anyone had any success installing/deploying server on os x 10.7? There have been several changes (unbeknownst to me before beginning this odyssey on 10.7) from the 10.6 version.

How are you installing dependencies? Have you tried homebrew yet?

After much effort, it seems I have Postgresql 8.3.4 working, but it looks like OMERO is having trouble with the Ice-3.3.1 binaries (unfortunately I don't have the logs handy right now, I'll have to follow up with these).

So I tried to compile all the Ice dependencies from source, from the Zero-C Ice dependencies download. That worked fine until I got to Ice itself, which fails to compile. I've tried this new, not-working-with-Ice 10.7 clang compiler,

Just a heads up, we're also working on backporting patches from Ice 3.4 to 3.3 to enable a clang compile on Lion. See https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=1070&p=3878&hilit=lion#p3888p

... and managed to install the legacy gcc 4.2 and neither one has been successful. I also applied this patch

http://www.zeroc.com/forums/bug-reports ... ilers.html

and was unsuccessful in getting Ice-3.3.1 working. The patch application belched up many errors, something about 'chunks' and didn't seem to solve the compilation errors.

It took several days of tinkering, scouring the web, changing permissions, seeking tribal knowledge just to get Postgresql 8.3 working and I've been compiling dependencies to dependencies but have had little success. After my preliminary testing on Os 10.6 on a laptop (and deciding an Apple server would be a good idea because it would be straightforward to set up and manage), Os X 10.7 on my new box has rocked my world and shut me down completely. It is a nightmare. I may have to switch to a plan b and start from scratch with a linux box, but I thought I would check with the community.

Has anyone out there had any success installing an OMERO server on OS X 10.7?

We're very sorry to hear that you've had such a rough time. As soon as we get clang-built Ice 3.3 binaries, we'll certainly make them available for download. That being said, for other dependencies I'd encourage you to try homebrew. After having used MacPorts, we can highly suggest it. Further, if you are just evaluating OMERO and don't plan to go into production until, say, the summer, you could use the development version which has support for Ice 3.4, which we have gotten to build on Lion.

Let us know how else we might help.

Cheers,
~Josh

Ice binaries are ready for 10.7. Read more.

~Josh

Fantastic. Thanks for tips and the availability of Ice binaries; I'll give them a try. I know this was not trivial to build (at least from my perspective) so I'm really grateful for the assist.

It's been a few years since I've relied on OS X heavily, so I have to admit Homebrew is something I was unaware of. I'll definitely try this Homebrew approach at my next opportunity. I've messed around with macports in the past and I recall some frustration, so I avoided macports this time around and tried to do this all with manual building and installs (except Postgresql, I used their binary installer, which was no problem on 10.6 but I got caught by suprise with 10.7). I installed the apple java from their developer site. I'm not sure what other option(s) are out there. I've gone down so many rabbit holes on this 10.7 initiation experience I doubt I could ever repeat what I did to get things configured to this point.

I'm convinced the OMERO project will enable biomedical studies on an entirely new scale and level of sophistication, so keep up this great work. Thanks again.

Hello All:

I still seem to be having some trouble getting OMERO 4.3 running on OS X 10.7.

I tried the Ice binaries posted (much thanks) but ran into errors about being built for 64-bit architecture (which doesn't make sense seeing as this is a 64 bit intel Core i5 machine)--I figured it must have been something I messed up with all my previous hacksaw work trying to build ICE dependencies, trying different compilers, compiler flags etc. So I did a clean install of os 10.7 (no small task in itself: you need to know the double secret key combination, reboot while holding down the keys, have liberal web access, let the box verify itself and download the os over several hours--no recovery usb or cd provided or hard drive partition with the os).

Fast forward a day, and I've got a clean install of os x 10.7, developer tools, developer command line extensions installed, apple java development installed, now with a keyboard, internet connection and monitor because remote desktop and closed network was hopeless.

So I followed the homebrew bootstrap script instructions, ran brew doctor, fixed the few small issues, and things seemed to go fine until trying to download the tar ball for OMERO 4.3:
#****************************************************************************************************************************
RoyalMarsden-CTC-Database:OMERO.homebrew kgarsha$ ~/apps/OMERO.libs/bin/brew install omero43
==> Downloading https://github.com/joshmoore/openmicros ... ll/v.4.3.4
0.0%
curl: (22) The requested URL returned error: 404
Error: Download failed: https://github.com/joshmoore/openmicros ... ll/v.4.3.4

#****************************************************************************************************************************
I cloned the homebrew repo but haven't been able to figure out how to build OMERO:
#****************************************************************************************************************************
RoyalMarsden-CTC-Database:OMERO kgarsha$ cd ~/code/projects/OMERO
RoyalMarsden-CTC-Database:OMERO kgarsha$ ls
OMERO.homebrew openmicroscopy
RoyalMarsden-CTC-Database:OMERO kgarsha$ cd openmicroscopy
RoyalMarsden-CTC-Database:openmicroscopy kgarsha$ ls
LICENSE.txt build.py docs ivy.xml sql
README.txt build.xml etc lib test.xml
build.bat components examples omero.class
RoyalMarsden-CTC-Database:openmicroscopy kgarsha$ pico README.tx
RoyalMarsden-CTC-Database:openmicroscopy kgarsha$ pico README.txt
RoyalMarsden-CTC-Database:openmicroscopy kgarsha$ python build.py
Error getting version for BUILD_NUMBER=

BUILD FAILED
/Users/kgarsha/code/projects/omero/openmicroscopy/build.xml:36: The following error occurred while executing this line:
/Users/kgarsha/code/projects/omero/openmicroscopy/components/antlib/resources/global.xml:290: Execute failed: java.io.IOException: Cannot run program "slice2java": error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
at java.lang.Runtime.exec(Runtime.java:593)
at org.apache.tools.ant.taskdefs.Execute$Java13CommandLauncher.exec(Execute.java:827)
at org.apache.tools.ant.taskdefs.Execute.launch(Execute.java:445)
at org.apache.tools.ant.taskdefs.Execute.execute(Execute.java:459)
at org.apache.tools.ant.taskdefs.ExecTask.runExecute(ExecTask.java:635)
at org.apache.tools.ant.taskdefs.ExecTask.runExec(ExecTask.java:676)
at org.apache.tools.ant.taskdefs.ExecTask.execute(ExecTask.java:502)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:390)
at org.apache.tools.ant.helper.ProjectHelper2.parse(ProjectHelper2.java:168)
at org.apache.tools.ant.taskdefs.ImportTask.importResource(ImportTask.java:216)
at org.apache.tools.ant.taskdefs.ImportTask.execute(ImportTask.java:162)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:390)
at org.apache.tools.ant.helper.ProjectHelper2.parse(ProjectHelper2.java:179)
at org.apache.tools.ant.ProjectHelper.configureProject(ProjectHelper.java:80)
at org.apache.tools.ant.Main.runBuild(Main.java:786)
at org.apache.tools.ant.Main.startAnt(Main.java:218)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at omero.startAnt(omero.java:285)
at omero.main(omero.java:313)
Caused by: java.io.IOException: error=2, No such file or directory
at java.lang.UNIXProcess.forkAndExec(Native Method)
at java.lang.UNIXProcess.<init>(UNIXProcess.java:53)
at java.lang.ProcessImpl.start(ProcessImpl.java:91)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
... 35 more

Total time: 1 second
#****************************************************************************************************************************
In the event it may help, I will follow up with the terminal session below so you can see what transpired while running the OMERO homebrew scripts (I can't upload any sort of txt or pdf document using upload attachment). Thanks for any help and advice you may be able to offer.
#****************************************************************************************************************************
Best Regards,
Karl
#****************************************************************************************************************************

Karl's Homebrew attempt:
#*******************************************************************************************************************************
won't work unfortunately--I can't append because it is too many characters, and I can't attach any files.

I can send directly if you tell me where to send the output.

Hi Karl,

A couple of things:
* You can always post your results to https://gist.github.com/ if they are too long for the forums.
* My github repository was missing the new v.4.3.4. "install omero43" should now work. Sorry about that.
* The error you are seeing while trying to run "python build.py" is

Code: Select all

Cannot run program "slice2java": error=2, No such file or directory


which means that "~/apps/OMERO.libs/bin/" is not on your PATH variable.

Hope that helps,
~Josh

Hi Josh:

I still seem to be having trouble getting the omero install itself. When I try the brew install approach I get the following (I think the MD5 checksum must have changed):
#************************************************************************************
RoyalMarsden-CTC-Database:OMERO.libs kgarsha$ ~/apps/OMERO.libs/bin/brew install omero43
sh: line 1: 496 Trace/BPT trap: 5 /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild -version 2> /dev/null
sh: line 1: 502 Trace/BPT trap: 5 xcodebuild -version 2> /dev/null
==> Downloading https://github.com/joshmoore/openmicros ... ll/v.4.3.4
######################################################################## 100.0%
Error: MD5 mismatch
Expected: c5b32ba1452ae2e038c1fc9b5760c811
Got: 07a7d76ee9c13f89adf7d2d0038fac21
Archive: /Library/Caches/Homebrew/omero43-4.3.tgz
(To retry an incomplete download, remove the file above.)
#**********************************************************************************
There is no omero43 installed after this error :
#**********************************************************************************
RoyalMarsden-CTC-Database:~ kgarsha$ cd $OMEROLIBS/Cellar/
RoyalMarsden-CTC-Database:Cellar kgarsha$ ls -a
. berkeley-db46 hdf5 mcpp szip
.. ccache jpeg pkg-config zeroc-ice33
RoyalMarsden-CTC-Database:Cellar kgarsha$
#***********************************************************************************
RoyalMarsden-CTC-Database:Cellar kgarsha$ cd $OMEROLIBS/bin
RoyalMarsden-CTC-Database:bin kgarsha$
lsactivate h5ls pilfile.py
activate.csh h5mkgrp pilfont.py
activate.fish h5perf_serial pilprint.py
activate_this.py h5redeploy pip
brew h5repack pip-2.7
ccache h5repart pkg-config
cjpeg h5stat ptdump
cython h5unjam ptrepack
djpeg icebox python
dumpdb iceboxadmin python2.7
easy_install iceca rdjpgcom
easy_install-2.7 icegridadmin slice2cpp
f2py icegridnode slice2cs
gif2h5 icegridregistry slice2docbook
glacier2router icepatch2calc slice2freeze
h52gif icepatch2client slice2freezej
h5c++ icepatch2server slice2html
h5cc icestormadmin slice2java
h5copy icestormmigrate slice2py
h5debug jpegtran slice2rb
h5diff mcpp transformdb
h5dump nctoh5 wrjpgcom
h5import pilconvert.py
h5jam pildriver.py
#***************************************************************************************
I'm still having trouble using the python build script also:
#***************************************************************************************
RoyalMarsden-CTC-Database:openmicroscopy kgarsha$ python build.py
Error occurred during initialization of VM
Unable to load native library: libjava.jnilib
#****************************************************************************************
I suppose the other thing to try would be to download the OSX binary server and try to copy the directories to the correct locations, but I have a feeling that things will be smoother if the last bit with homebrew installation gets sorted. I see this process is being updated; but I'm not sure if I need to go through the procedure again to update everything. When I run:
#******************************************************************************************
RoyalMarsden-CTC-Database:OMERO.libs kgarsha$ brew install omero43
Error: No available formula for omero43
RoyalMarsden-CTC-Database:OMERO.libs kgarsha$
#******************************************************************************************
it looks like my formulas are out of sync with the latest scripts. Maybe I'll try this but please let me know if you have any tips. There are still some significant gaps in my knowledge of how this works.

Thanks for your help,

Best,
Karl

Hi Karl,

For omero43, you can update the Homebrew alternate formulas using:

Code: Select all

~/apps/OMERO.libs/bin/brew untap openmicroscopy/alt
~/apps/OMERO.libs/bin/brew tap openmicroscopy/alt

Once you enter the following commands, you should get something like

remote: Counting objects: 492, done.
remote: Compressing objects: 100% (257/257), done.
remote: Total 492 (delta 253), reused 404 (delta 207)
Receiving objects: 100% (492/492), 81.47 KiB, done.
Resolving deltas: 100% (253/253), done.
Warning: Could not tap openmicroscopy/alt/ice over mxcl/master/ice
Warning: Could not tap openmicroscopy/alt/mcpp over mxcl/master/mcpp
Tapped 4 formula

Try installing omero43 using brew install again and let us know it you still get a mismatch.

For the python build.py error, it could be a dynamic library error. What is the value of your DYLD_LIBRARY_PATH?

Code: Select all

echo $DYLD_LIBRARY_PATH

Cheers,
Sébastien

Hi,

I still can't seem to get omero to install from homebrew. Below (2nd append) is the output from the 'untap/tap' suggestion that was kindly provided. Apparently I still get an MD5 mismatch.

thanks for any insight you may have to how I can get around this.

Directly below is what my ~/.profile looks like:

#**************************************************************************************
export OMEROLIBS=~/apps/OMERO.libs
export OMERO_HOME=$OMEROLIBS/Cellar/omero43/4.3/
export ICE_CONFIG=$OMERO_HOME/etc/ice.config
export ICE_HOME=$OMEROLIBS/Cellar/zero-ice33
export PYTHONPATH=$OMERO_HOME/lib/python:$ICE_HOME/3.3.1/python

export PATH=/usr/local/bin:$OMEROLIBS/bin:$OMERO_HOME/bin:/usr/local/lib/node_module$
export DYLD_LIBRARY_PATH=$OMEROLIBS/lib
#**************************************************************************************
RoyalMarsden-CTC-Database:bin kgarsha$ brew untap openmicroscopy/alt
Untapped 4 formula
RoyalMarsden-CTC-Database:bin kgarsha$ brew tap openmicroscopy/alt
Cloning into '/usr/local/Library/Taps/openmicroscopy-alt'...
remote: Counting objects: 492, done.
remote: Compressing objects: 100% (258/258), done.
remote: Total 492 (delta 253), reused 403 (delta 206)
Receiving objects: 100% (492/492), 81.54 KiB, done.
Resolving deltas: 100% (253/253), done.
Warning: Could not tap openmicroscopy/alt/ice over mxcl/master/ice
Warning: Could not tap openmicroscopy/alt/mcpp over mxcl/master/mcpp
Tapped 4 formula
RoyalMarsden-CTC-Database:bin kgarsha$ brew install omero43
sh: line 1: 2541 Trace/BPT trap: 5 /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild -version 2> /dev/null
sh: line 1: 2548 Trace/BPT trap: 5 xcodebuild -version 2> /dev/null
sh: line 1: 2562 Trace/BPT trap: 5 /Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild -version 2> /dev/null
sh: line 1: 2568 Trace/BPT trap: 5 xcodebuild -version 2> /dev/null
==> Downloading https://github.com/openmicroscopy/openm ... ll/v.4.3.4
Already downloaded: /Library/Caches/Homebrew/omero43-4.3.tgz
Error: MD5 mismatch
Expected: c5b32ba1452ae2e038c1fc9b5760c811
Got: 07a7d76ee9c13f89adf7d2d0038fac21
Archive: /Library/Caches/Homebrew/omero43-4.3.tgz
(To retry an incomplete download, remove the file above.)
RoyalMarsden-CTC-Database:bin kgarsha$