Snow Leopard Compatibility

Despite there being few new major features Snow Leopard (Mac OS 10.6) has a number significant upgrades under the hood. Whilst many sites highlight issues with software I thought it would be very useful to have a list of scientific applications and problems or not.

So to start.

Spartan and ChemDraw are reported to have no issues under Snow Leopard.

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iNMR

From the developer...

"I have installed Snow Leopard and tested iNMR 3.2.1.
The program works normally and sends no error message. A few errors,
however, appears into the Console (a seldom used utility, part of Mac
OS X).
At this moment, these messages are completely obscure to me, yet I
will try to understand more of them in future.

In conclusion, I think that the current version of iNMR is READY to
run under the new OS. An update is not required."

MacPymol

I tested MacPymol on Mac OS X 10.6. It works fine.

Mostly fine

Partek Genomic Suite is not compatible unfortunately. I suspect it doesn't play well with the new version of Java SL hosts. Their support told me I'd have to wait for a SNow Leopard specific version and didn't mention any beta available.

So far it's the only scientific application I use that's not compatible.
Some of the applications that appear to be fine so far:

  • Ingenuity Pathway Analysis
  • ImageJ
  • Image SXM
  • Genesis
  • Laser Gene
  • Scientific Journal Information
  • Papers of course :-)
  • tfsearch14
  • EnzymeX
  • Delta Graph
  • Prism

I have plenty more, but I haven't tried them yet.

Visor doesn't work anymore

I use visor to access the terminal fatser when I'm working. It seems that visor doesn't work anymore.

EDIT: The problem comes from SIMBL and the developer is working on it. Good news :)

Aabel

Snow Leopard has broken some fundamental functions of dialog, causing crashes. Please note that a special upgrade of Aabel v3 for Snow-Leopard compatibility was released last night. This upgrade is critical for those who have installed or are going to use Snow Leopard, and is available on the Gigawiz website:

http://www.gigawiz.com/updates.html

Other working software

All of these seem to work:

Prism 5

UCSF Chimera 1.3.2577

SPDBV viewer 4.0.1

VMD 1.8.7

Seem to

Seem to work:
Electroacoustics Toolbox 2.1
Endnote XII
Papers
Matlab R2009
Igor pro 6
R

Don't work:
SPSS 17

Numpy + Scipy + matplotlib

after some hard time, found the solution for scientific computing with python on SL

http://blog.hyperjeff.net/?p=160

cheers

GeneSpring GX 10 - Agilent

I can't get GeneSpring GX 10 to work under 10.6 on any machine I've upgraded. It was always unsupported (but largely working) on 10.5, Agilent STILL only support it on 10.4.

I did raise this issue with Agilent, that they were soon to be two OS revisions behind on what they would support.

GeneSpring GX 11 is out soon, let's hope they've bothered to check Snow Leopard compatibility.

Cheers Agilent!

DataGraph (the latest beta

DataGraph (the latest beta at least) works fine
Also, the NMR programs Sparky and NMRPipe load fine and function normally based on basic testing... I'll update as I try more.

about GRAPHPAD Prism 5 and Snow Leopard...

please See:

http://www.graphpad.com/faq/viewfaq.cfm?faq=1206

Other programs

Does anyone know if these are working with Snow Leopard ?

- DNA strider
- 4peaks
- amplifiX
- serial cloner
- quantity one

Thanks.

4Peaks OK Serial cloner 1.3

4Peaks OK
Serial cloner 1.3 OK

PASW statistics 18

PASW (SPSS)17 don't work
PASW 18 (Trial version) seems to work fine

And these ?

Thanks for the reply.

Could you also test these for me ?

http://ifrjr.nord.univ-mrs.fr/AmplifX-Home-page?lang=en

And

Quantity One, from Biorad ?

Thanks a lot.

Does anyone use iWork'08 ? Does it work ? I don't want to update to the latest version.

COMSOL

COMSOL 3.5 works fine, no problems here.

Visor problem seems solved

In the webpage of visor it says this:

"Snow Leopard:: In Finder go to /Applications/Utilities/Terminal.app and right-click it, open "Get Info" dialog and check in "Open in 32-bit mode" "

I haven't tried, I was checking for what visor was.

jmp

Does anyone know if jmp works?
thx

Macports

Macports isn't ready for scientific computing on SL yet, particularly with python. Here's a list of utilities that are currently having issues (09-11-2009). Some of these are as a result of failure of dependencies and may fall in line when those are ironed out.

- gcc43
- atlas/lapack
- numpy
- scipy
- pymvpa

It should be noted that python 2.5 will build, but it does not build a framework build. This will result in failure of many gui oriented modules (e.g. matplotlib) using that interpreter. The latest on the Python bug trackers indicates python 2.5 is viewed as maintenance only and so no efforts will be made to get the framework build working.

Center for Cognitive Neuroscience, UCLA

LaTeXiT Services Component

The Services component of LaTeXiT is no longer available through the revamped Services menu in SL. Hope this gets fixed soon!

Various physics software packages

I just upgraded today, and the following programs were all fine - didn't have to be modified or recompiled, other than to do the optional install of Xcode to recover 'make':

Mathematica 7.0.1
Matlab R2009a
Evernote
Papers 1.9.3
MacTeX (TeXShop 2.18)
GEANT4
MCNP
Smultron

Calibre doesn't work though!

----

Hywel Owen
University of Manchester

ChemDraw not compatible with iWork under Snow Leopard

Snow Leopard has broken the ability to paste chemdraw structures into iWork documents. The structures get truncated and lose their ChemDraw format. They can no longer be copied back into ChemDraw for editing. So, Chemdraw is completely unusable with Keynote or Pages at the present time. Even the most recent ChemDraw 12 has this problem and it will be a while before Cambridgesoft provides a new version.

ChemDraw still does not work with Office 2008 under snow leopard (loss of Chemdraw format) but the structures do not get truncated.

This is frustrating to say the least. But I have a workaround. A rather clunky workaround, but it does work. I have tested this with Chemdraw 11 in snow leopard.

Copy the chemdraw to a Powerpoint 2004 document. Save it as a .ppt file. Open the powerpoint file in Keynote. You can then copy the chemdraw to other keynote documents or back to Chemdraw for editing.

Another good reason not to toss out Office 2004. I suspect the same will work with Word 2004/Pages but I have not tested it.

Round trip editing in ChemDraw

The problem is the fact Chemdraw now includes a PDF version on the clipboard when cut and pasting (in addtition to other formats) iWork documents seem to only select this part of the clipboard. If you go to Preference in Chemdraw and deselect "Add PDF to clipboard" you should be able to do round trip editing in iWork.

Not in Chemdraw 11

I can find no feature to add PDF to clipboard in ChemDraw 11. I presume this is a Chemdraw 12 feature? Can you please tell me if it still cuts off the structures using ChemDraw 12 with PDF turned off?

OS X Server + MySQL + Perl

Since I had some trouble with MySQL, after I upgraded to SL from a Leopard installation where I compiled my own MySQL server, I also installed MySQL (5.4b x86_64) by hand. Works now without a problem, from command line as well as with PHP. However, the Perl module DBD::mysql won't build with a myriad of errors...

Problems with Igor and Comsol

Contrary to postings by other people here, I am actually having issues with Igor (both 6.05A and 6.11) and Comsol 3.5a. Igor sometimes crashes when loading data (hard crash, no error message) while Comsol produces a "fatal error". I get the impression that both are related to memory issues, but that is just a guess (based, in part, on "out of memory" messages I get from Igor when there is actually enough memory available). Has anyone seen similar problems?

Other than that, some that seem to be fine here are:
*Papers
*Fugu
*Cisco VPN Client
*Adobe CS4
*Skype
*Aquamacs Emacs
*Evernote
*LabView (not that anyone cares...)
*Parallels
*TexShop
*Quicksilver
*Growl
*Xcode :))
*QT Creator; QT 4.5.2 (not entirely sure about all the QT libraries though)
*I did have issues with GSL but they might work again after reinstalling. Have not yet tried.

Cheers.

And these last two ? Help me switch ^_^ !

I was told by someone that iWork'08 works fine under Snow Leopard.
So that's one ticked off my list.

Could someone also test these for me ?

(Version 1.5.4)
http://ifrjr.nord.univ-mrs.fr/AmplifX-Home-page?lang=en

And

Quantity One, from Biorad ? Version 4.6.8 for MacOSX.

Thanks.

Mathematica 7.0.1 interface crashing when interfacing w/ files

I have noticed that the rainbow spinning wheel of death has appeared when I try and fetch a file path or open a file (i.e. the open file dialog box).This makes me suspect Snow Leapord as I didnt reinstall MMA after upgrade, going to do that now. Anyone else notice this??

ChemDraw 11 Not Compatible with SL

It is not possible to enter text in "Convert Name to Structure" when running Chemdraw 11 under SL. Since it looks like Chemdraw 11 will not see a fix, and upgrading is not an option right now, I am stuck with Leopard. Mind you, most of my testbanks do not work in SL either.

ChemDraw 11 not compatible with SL

It would seem multiple dialog boxes in ChemDraw 11 are broken under SL (I wonder how they managed this). There is a notice on the CS forums that 12.0.1 is SL compatible.

ChemBioDraw Update

Details of the 12.0.1 Update are here.

This update does not address the problem with round-trip editing.

Tested : work

Hi, I have tested them, and they are working fine.

Quantity One, Biorad, and AmplifX

bye.

STATA 10 works perfectly

Stata offers a 64bit Multi-processor update free of charge. This works just fine. No hickups, no problems.

MacPymol

Both MacPymol and UCSF Chimera support the 3D mouse Space Navigator under Snow Leopard.

Not strictly scientific but also important: Personal Backup 10.5.5 seems to have a few issues with Snow Leopards, crashing or not finishing sync correctly. Beware.

Aabel has been further updated

http://www.gigawiz.com/updates.html

CCNA Networking

Is snow leopard covered on the latest CCNA Networking certification exam? Has anyone taken the test since 10.6 was released?

Matlab-Mysql Interface

Since I have SnowLeopard (MacOS 10.6.2) and Matlab 7.9.0.529 (R2009b), I cannot correctly access the MySQL database from a Matlab session.

For compilation of mysql.cpp and generation of mysql.mexmaci64, I used the command:

mex -v -maci -I/usr/local/mysql/include -L/Applications/MATLAB_R2009b/bin/maci -lmysqlclient_r -L/usr/local/mysql/lib -lpthread mysql.cpp

Basic commands like:

data=mysql('select * from table1')

do not work. Maybe the compilation options have to be changed?
Thank you for consideration!