[ome-users] OMERO client install attempt under Mac OS X 10.6 - would appreciate some help on the client login popup

Taylor, Ronald C ronald.taylor at pnl.gov
Mon Jun 7 22:25:51 BST 2010 

 
Ken, Jeremy, other OMERO users,

I think I am very close to getting (finally) OMERO running on at least one machine. I have been following Ken's Mac 10.6 install manual, except instead of creating a separate omero account I have been doing the install in my pre-existing "RT" account. 

This is being done on my own personal Mac, just upgraded to 10.6. (Waiting on a OS 10.6 upgrade to a larger Mac server in our lab.)

I have apparently installed everything for the OMERO server correctly this time. I do an
 
  omero admin start
And
  omero admin diagnostics

And the diagnostics appear OK, from what I can gather.

However, I cannot bring up the client successfully. I have not yet installed the OMERO web server - from what I understand, that is not required to get a client connection on the same machine, and the server-client combination is the thing I want to test as fast as possible. Do I have that correct - I can use the client before installing the web server?

Presuming I could manage without the web server for my test, I went ahead and installed the OMERO client zip file OMERO.clients-Beta4.1.1.mac.zip, which matches the server release.

I then double-clicked on the OMERO.insight icon in the client directory. Got the popup. This is where my current problem is.

When I earlier installed the server and ran
   bin/omero db script

I gave the server the root password of "omero". Also, the omero Postgres account was named "omero" and has the password "omero". All this is being done in my Mac OS account of "RT".

My problem now is I can't get past the popup. I enter "omero" for the Username and "omero" for the Password. Is that the correct thing to do? Does my OS account of "RT" come into play here in any way?

Also - the client popup window says that I need to "Add a new server". Don't know what this means. When I click on that option I get an empty text box, followed by something for a port that defaults to "4063". Have no idea how to fill this out.

As I write this, my MacBook is not connected to the net - personal machines are not allowed on the lab intranet. So - it does not any IP address to put in. I tried entering "localhost", but that did not work.

What server is this entry panel referring to - the server started by "omero admin start"? Does that come up by default on port 4063? Or does this refer the OMERO web server, which I have not set up yet? Do I need to set up the web server before getting the client app to work?

I checked they OMERO clients User Guide. Sadly, cannot find anything useful on how to fill out the initial log in screen! In sect 2.2 it says

"When you start OMERO.importer, you will be asked to log in (See Figure 2.2-1). The
administrator who set up OMERO can provide you with a user account and the address of
the OMERO.server where your images will be stored.
You provide the address of the OMERO server by selecting the button and entering the
details in the form provided."

Well - duh. Unforunately, I'm the admin and I don't know how to provide myself with the correct account name and server address to use.

Would very much appreciate some help - hopefully OMERO users (who have logged in!) can answer these questions in just a couple sentences.

  - Ron

___________________________________________
Ronald Taylor, Ph.D.
Computational Biology & Bioinformatics Group
Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, Mail Stop J4-33
Richland, WA  99352 USA
Office:  509-372-6568
Email: ronald.taylor at pnl.gov

-----Original Message-----
From: Taylor, Ronald C 
Sent: Thursday, June 03, 2010 11:26 AM
To: 'Arcieri, Kenneth (NIH/NICHD) [V]'; ome-users at lists.openmicroscopy.org.uk; 'callan at lifesci.dundee.ac.uk'
Cc: Taylor, Ronald C
Subject: RE: [ome-users] Mcpp install failure during OMERO install attempt under Mac OS X 10.6

 
Chris, Ken,

Well, whoops. I did not see the suggested edit to internal.H on p. 6 of Ken's document. Just made the edit, ran make and make install, and mcpp appears to install normally. 

As for checking the README in the ThirdParty directory as Chris suggested - yep, I was doing that - that was actually my main reference document for installing these particular libs, and that's why I forgot to check Ken's instructions. Unfortunately, the README has nothing on patching or modifying the internal.H file for mcpp. It does tell you how to run configure for mcpp under Mac OS X, which I guess gave me a false sense of security. That is, wouldn't there be an additional note saying the "make" will fail unless internal.H is modified? Because, jeez, it will fail. I think the README needs some elaboration in the mcpp section! (I also checked the README in the mcpp directory - no help there.) 

BTW - the ThirdParty README does tell you how to patch BerkeleyDB, which I did successfully. But those are the only patches given.

Anyhoo - I'm continuing with the OMERO install using Ken's guide for OS X 10.6 (while reading it more closely). 

Thanks for the prompt help, everybody.
Ron

___________________________________________
Ronald Taylor, Ph.D.
Computational Biology & Bioinformatics Group Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, Mail Stop J4-33
Richland, WA  99352 USA
Office:  509-372-6568
Email: ronald.taylor at pnl.gov

-----Original Message-----
From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Arcieri, Kenneth (NIH/NICHD) [V]
Sent: Thursday, June 03, 2010 6:46 AM
To: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Mcpp install failure during OMERO install attempt under Mac OS X 10.6

Hello Listserv!

I just thought I would chime in on this.  

The reason why we did everything from source was so that we knew what was being installed where and what dependencies were being used. If you use an RPM or any other type of automatic installer, make sure you know where the files are going so that you can use them for other dependencies or for OMERO itself.

As for MCPP.  When you download the "Third Party" tarball from ICE's site for 3.3.1 (3.4.x will NOT work now unless Chris says otherwise), look into the readme file included with that on how to patch MCPP correctly.  On top of that patch, delete the lines from that header file as outlined in my install guide.  

If you have any questions about the install guide let me know!

-Ken

-----Original Message-----
From: Chris Allan [mailto:callan at lifesci.dundee.ac.uk]
Sent: Thursday, June 03, 2010 3:58 AM
To: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Mcpp install failure during OMERO install attempt under Mac OS X 10.6


On 3 Jun 2010, at 01:58, Taylor, Ronald C wrote:

> 
> Hello folks,

Hi Ron.

> 
> Haven't heard back yet on the two questions I sent last Tuesday to the list on my not-yet-completed OMERO install under Red Hat Linux. In the meantime, I thought I would try an entirely separate installation of OMERO on my Mac laptop, using Ken Arcieri's instructions on how to install under OS X 10.6.
> 
> Things were going smoothly - I installed Postgres, then many of the libraries. And then I got to mcpp (ver  2.7.2)  in the ThirdParty software download.

Did you perform the edits to the MCPP source outlined in Ken's document?

> 
> That mcpp install fails when I try to install according to the ThirdParty directory's  README.
> 
> I run configure like this:
> 
> ./configure  CFLAGS=fno-common  --enable-mcpplib  --disable-shared  
> --prefix=/Library/mcpp/Versions/2.7.2
> 
> and it appears to run OK.
> 
> But I then run "make" and get error msgs:
> 
> In file included from main.c:42:
> Internal.H:561: error  expected declaration specifiers or '...' before 
> numeric constant  ...  followed by a couple more errors reported on 
> line 561
> 
> Looking up mcpp at SourceForge, I found this note:
>  "On Linux ... and Mac OS X the system's standard headers have certain defects, and some workarounds are necessary for mcpp. Refer to section 3.9.9. in the manual"
> 
> I checked the HTML manual. From what I gather, the problems relate to stddef.h and limits.h? And to a compiler independent build? Not sure if I have that right. In any event, the manual does not tell you how to fix the install. But the SourceForge site says that there is a Mac disk image file available for the mcpp install. Though if I want to make sure I can uninstall it, I have to use the associated "port" file to install it - which will mean installing MacPorts on my laptop. Which I'm willing to do, if the Mac  disk image version of mcpp will work for Ice and Omero. Will it?

Presumably, you'd have to try it. Those of us here who are on 10.6 have either compiled it manually (using our own or Ken's suggested patch) or used MacPorts. 

> 
> Also: I found another web page at http://mcpp.darwinports.com that describes a Portfile for mcpp and says that there is a known set of patch files for mcpp 2.7.2. The page lists three:
>   patch-src__internal.H
>   patch-scr__system.H
>   fix-core-dumps.patch
> 
> Since one of the patch files has the same name as where the error appeared in the "make" run, I presume that that patch and maybe the others are needed in order for the "make" to work OK. However, I haven't been able to find the patch files themselves. Does anybody know how I should best proceed (and where the patch files are)?

A suggested patch is in Ken's document.

> (I did not have to deal with this in my Linux install - I ran an RPM to install mcpp  that our local sysadmin people had already downloaded into our AFS file system.) If the three patch files are available someplace, should I try patching with them, and then rerunning "make"? Or should I try the Mac disk image?

All of those options should work, really it's up to you as to what you feel most comfortable deploying.

> 
> Cheers,
>   Ron

-Chris

> 
> ___________________________________________
> Ronald Taylor, Ph.D.
> Computational Biology & Bioinformatics Group Pacific Northwest 
> National Laboratory
> 902 Battelle Boulevard
> P.O. Box 999, Mail Stop J4-33
> Richland, WA  99352 USA
> Office:  509-372-6568
> Email: ronald.taylor at pnl.gov
> 
> 
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

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