From: Phil Evans
Is there any opinion or experience about whether Lion is ready for crystallographic use? Should I "upgrade"?
Phil
----------
From: Jason Vertrees
Phil,
MacPyMOL works fine on Lion.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
----------
From: William Scott
Hi Phil:
I've found few, if any advantages. I fear for the future.
I've had problems getting coot to run stereo due to the X11 implementation in 10.7. Apart from that, no major problems with crystallographic software.
Lion greedily uses memory, and any computer I have with less than 4 gig of memory has become extremely sluggish as a consequence of the "upgrade." Ideally, you need 8 gig.
Even with that, on my 2010 mini that I use for music playback, I regressed to 10.6.8, because of the audio interface. (It seems less robust, more prone to dropouts and now lacks integer mode output).
Sara has been screaming at me for the last two weeks (nothing us usual in of itself) because Apple decided to get rid of "Save As".
Xcode and the compiler set is free again on 10.7.
I've put some suggestions here for how to get rid of the most annoying new features:
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes
All the best,
Bill
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
----------
From: Jacob Keller
I have noticed, in new versions of OSes, that there generally is
rampant violation of the concept of "if it ain't broken, don't fix."
Shouldn't there be more moments of delight, when you see they have
solved a previous poorly-engineered feature with an elegant solution?
But a lot of the time, you have to try to figure out how to do what
you did in the last version in this version, albeit for no net gain.
Back to punch cards!
The Friday Curmudgeon
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
*******************************************
----------
From: William Scott
I forgot to mention how delightful the spelling auto-"correction" feature can be. (It should have read "nothing unusual in and of itself").
That, at least, can be turned off.
----------
From: Patrick Loll
Still doesn't beat my all-time favorite, an early Microsoft spell-checker that changed "diffract" to "defrocked."
----------
From: Frances C. Bernstein
Shoshana Wodak once told me that Word kept suggesting
Shoeshine Kodak as the correct spelling of her name.
I just tried my copy of Word and it seems to have improved.
Frances
=====================================================
**** Bernstein + Sons
* * Information Systems Consultants
**** 5 Brewster Lane, Bellport, NY 11713-2803
* * ***
**** * Frances C. Bernstein
=====================================================
----------
From: Jacques-Philippe Colletier
Hi,
Overall, the transition from 10.6 is seemingless, crystallographically-wise.
Of course you need to have the new XCode 4.1 installed, and you should also download new, 10.7-dedicated 64bits gcc/gfortran/g77 bundles from http://hpc.sourceforge.net/
And then, CNS, Phenix, CCP4, etc... will just run perfect.
I had to reinstall Coot -- but that's minor.
(Mac)Pymol also works fine, yet (for some reason) uses a lot of resources even when idle.
As per the Upsalla Soft. Factory programs, you'll have to recompile then using the above mentioned bundles, or get already compiled binaries from Mark Harris.
You'll also need to recompile Gromacs (and fftw3) if you're using it -- but it then works great.
I agree with W. Scott on the fact that the new OS is really greedy in terms of resources.
I surely wont upgrade my other, older mac computers that run just fine on 10.6.
But if you have a new Mac, Lion is is really neat.
Best
Jacques
Le Sep 10, 2011 à 2:09 AM, William Scott a écrit :
----------
From: harry powell
Hi
My two ha'porth.
If you are thinking of "upgrading" your sole Mac software development box to Lion I'd say "don't do it unless you like a lot of pain". Anything built on Snow Leopard should run okay on Lion (my Tiger builds seem okay on 10.4, 10.5, 10.6...), so unless you really have an over-riding need to move to 10.7, I'd hang fire.
If you're only running applications and not developing, you can always shout at the developers if things go wrong.
My plan is to install Lion on a spare bootable disk and see what happens - if all else fails, at least I can ignore the upgrade until Apple release 10.7.1, 10.7.2, etc and fix most of their screw-ups.
Harry
--
Dr Harry Powell,
MRC Laboratory of Molecular Biology,
Hills Road,
Cambridge,
CB2 0QH
----------
From: Jürgen Bosch
One really nice feature though comes with what Bill's wife hates. No worries about saving an edited file in many programs. The background versioning is great no more needs of having my_manuscript_###1.doc :-) one file to handle them all. And you can go back to older versions of course. The only disturbing feature about this integrated auto backup is sometimes your Mac goes idle before you can typebecause it is saving another version. This is particularly annoying when you edit large Keynote files.
Jürgen
......................
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
----------
From: Herbert J. Bernstein
Dear Colleagues,
Lion is an reality all developers have to live with. While I
agree that it would be a bad idea to update one's primary
development environment to Lion, it does seem a good idea to have
at least one system with sufficient memory, disk and good enough
graphics and the new UI (user interface) to be able to wring out
problems, especially on the UI side.
So the question is: Is a new MacBook Pro or new MacBook Air
sufficient for such testing, or is something heftier with a
studio display necessary?
Regards,
Herbert
--
=====================================================
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
=====================================================
----------
From: Bosch, Juergen
----------
From: Sean Seaver
Dear Herbert,
I've come across quite a few people that are using mac books as their main development computer. This site ( http://usesthis.com/ ) can be an good way to learn about various setups. A popular trend seems to be using a mac book along with the apple thunderbolt display for more screen real estate.
Take Care,
Sean Seaver
P212121
http://store.p212121.com/
----------
From: Phil Evans
I use my MBP with external screen, keyboard & mouse all the time. The new ones are fast, & mine should easily cope with Lion
My question about Lion was because
1. on the one hand as far as I can see Bill Scott only builds latest stand-alone Coots (0.7...) for Lion, and these don't work on 10.6 (is this true Bill?)
2. on the other hand, I had a report that ccp4mg doesn't work on Lion (is that true Stuart?)
and I need both of these (and don't fancy building either myself)
Phil (still on 10.6)
----------
From: William G. Scott
Dear Phil (and everyone):
1. I've now got automated build systems for coot for 10.7.1 and 10.6.8. I just haven't had a chance to get the 10.6.8 one on line. I'll try to do this today. (Also, the last few haven't build due to a change in the code with which the compiler can't cope, but hopefully that will be a thing of the past soon.)
2. Most things build on 10.6.X will run on 10.7.X. I haven't opened ccp4mg, but will give it a try after I wake up.
3. I've had trouble with stereo on coot with 10.7.1, but, oddly, the problem goes away if I have a second monitor.
If you update to 10.7, keep a clone of 10.6 just in case it drives you nuts. There are all sorts of perverse changes, and (unlike the reversal in scrolling direction) not a lot of over-ride options.
I guess this is a glimpse of the post-Jobs era, albeit one provided from an inconvenient vista.
Peace and joy,
Bill
On Sep 16, 2011, at 6:33 AM, William G. Scott wrote:
> Dear Phil (and everyone):
>
> 1. I've now got automated build systems for coot for 10.7.1 and 10.6.8. I just haven't had a chance to get the 10.6.8 one on line. I'll try to do this today. (Also, the last few haven't build due to a change in the code with which the compiler can't cope, but hopefully that will be a thing of the past soon.)
>
> 2. Most things build on 10.6.X will run on 10.7.X. I haven't opened ccp4mg, but will give it a try after I wake up.
>
>
> 3. I've had trouble with stereo on coot with 10.7.1, but, oddly, the problem goes away if I have a second monitor.
>
> If you update to 10.7, keep a clone of 10.6 just in case it drives you nuts. There are all sorts of perverse changes, and (unlike the reversal in scrolling direction) not a lot of over-ride options.
>
> I guess this is a glimpse of the post-Jobs era, albeit one provided from an inconvenient vista.
>
> Peace and joy,
>
> Bill
----------
From: Peter Keller
I guess this is one of them:
How Apple's Lion won't let you trash documents
The operating system for the nanny state?
http://www.reghardware.com/2011/09/07/apple_mac_os_x_lion_the_nanny_os/
One of the reasons why I'm sticking with Snow Lepoard for now....
Regards,
Peter.
--
Peter Keller
Global Phasing Ltd.,
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom
----------
From: Andreas Förster
I've bitched enough about all things Mac, but this one's just too good to pass on (from the article that Peter linked to):
"The fundamental issue here is Lion's assumption that you don't know what you're doing, and it's going to ensure you're protected from cock-ups that, in your ignorance, you may make."
The first half of that sentence has always been my major gripe with Mac OS. If there just were a Pro version for those that know what they're doing, but the iPadification of computing goes exactly the opposite way.
Andreas Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk
----------
From: Richard Gillilan
Listening to Jobs speak recently, I got the distinct impression that the end of the era of general desktop computers "PC's" may be on the horizon. Of course that's iPad sales rhetoric, but it may be that the public moves away from general computers and that surely will have implications for scientific computing.
Richard
----------
From: Adrian Goldman
Of course this has to be the case. I think most of us walk around with with mobile phones that have memory and processing power more powerful than all of the computers available before 1990.
Some of the things that seem difficult in Lion and are nanny-state-ish such as automatic file versioning (not that I am running Lion yet, mind) - well is it the case that all of the experts on the CCP4BB have _never_ deleted a file they didn't mean to delete? _Never_ had Word (O, Coot) crash taking with it 6 hours worth of changes that should have been saved but weren't?
If so, I feel humbled because I have made these mistakes and more.
Adrian
----------
From: Peter Keller
There is nothing nanny-state-ish (or indeed new) about automatic file
versioning. VMS (which was the major operating system that CCP4
targetted in the pre-Unix days) had it in the 1980's and I don't recall
anyone moaning about it at the time. As you say, it could be a lifesaver
if you overwrote something by mistake. VMS allowed you to purge old
versions completely though, whereas Lion doesn't: that is the
difference.
Is there any opinion or experience about whether Lion is ready for crystallographic use? Should I "upgrade"?
Phil
----------
From: Jason Vertrees
Phil,
MacPyMOL works fine on Lion.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
----------
From: William Scott
Hi Phil:
I've found few, if any advantages. I fear for the future.
I've had problems getting coot to run stereo due to the X11 implementation in 10.7. Apart from that, no major problems with crystallographic software.
Lion greedily uses memory, and any computer I have with less than 4 gig of memory has become extremely sluggish as a consequence of the "upgrade." Ideally, you need 8 gig.
Even with that, on my 2010 mini that I use for music playback, I regressed to 10.6.8, because of the audio interface. (It seems less robust, more prone to dropouts and now lacks integer mode output).
Sara has been screaming at me for the last two weeks (nothing us usual in of itself) because Apple decided to get rid of "Save As".
Xcode and the compiler set is free again on 10.7.
I've put some suggestions here for how to get rid of the most annoying new features:
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes
All the best,
Bill
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
----------
From: Jacob Keller
I have noticed, in new versions of OSes, that there generally is
rampant violation of the concept of "if it ain't broken, don't fix."
Shouldn't there be more moments of delight, when you see they have
solved a previous poorly-engineered feature with an elegant solution?
But a lot of the time, you have to try to figure out how to do what
you did in the last version in this version, albeit for no net gain.
Back to punch cards!
The Friday Curmudgeon
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
*******************************************
----------
From: William Scott
I forgot to mention how delightful the spelling auto-"correction" feature can be. (It should have read "nothing unusual in and of itself").
That, at least, can be turned off.
----------
From: Patrick Loll
Still doesn't beat my all-time favorite, an early Microsoft spell-checker that changed "diffract" to "defrocked."
----------
From: Frances C. Bernstein
Shoshana Wodak once told me that Word kept suggesting
Shoeshine Kodak as the correct spelling of her name.
I just tried my copy of Word and it seems to have improved.
Frances
=====================================================
**** Bernstein + Sons
* * Information Systems Consultants
**** 5 Brewster Lane, Bellport, NY 11713-2803
* * ***
**** * Frances C. Bernstein
=====================================================
----------
From: Jacques-Philippe Colletier
Hi,
Overall, the transition from 10.6 is seemingless, crystallographically-wise.
Of course you need to have the new XCode 4.1 installed, and you should also download new, 10.7-dedicated 64bits gcc/gfortran/g77 bundles from http://hpc.sourceforge.net/
And then, CNS, Phenix, CCP4, etc... will just run perfect.
I had to reinstall Coot -- but that's minor.
(Mac)Pymol also works fine, yet (for some reason) uses a lot of resources even when idle.
As per the Upsalla Soft. Factory programs, you'll have to recompile then using the above mentioned bundles, or get already compiled binaries from Mark Harris.
You'll also need to recompile Gromacs (and fftw3) if you're using it -- but it then works great.
I agree with W. Scott on the fact that the new OS is really greedy in terms of resources.
I surely wont upgrade my other, older mac computers that run just fine on 10.6.
But if you have a new Mac, Lion is is really neat.
Best
Jacques
Le Sep 10, 2011 à 2:09 AM, William Scott a écrit :
----------
From: harry powell
Hi
My two ha'porth.
If you are thinking of "upgrading" your sole Mac software development box to Lion I'd say "don't do it unless you like a lot of pain". Anything built on Snow Leopard should run okay on Lion (my Tiger builds seem okay on 10.4, 10.5, 10.6...), so unless you really have an over-riding need to move to 10.7, I'd hang fire.
If you're only running applications and not developing, you can always shout at the developers if things go wrong.
My plan is to install Lion on a spare bootable disk and see what happens - if all else fails, at least I can ignore the upgrade until Apple release 10.7.1, 10.7.2, etc and fix most of their screw-ups.
--
Dr Harry Powell,
MRC Laboratory of Molecular Biology,
Hills Road,
Cambridge,
CB2 0QH
----------
From: Jürgen Bosch
One really nice feature though comes with what Bill's wife hates. No worries about saving an edited file in many programs. The background versioning is great no more needs of having my_manuscript_###1.doc :-) one file to handle them all. And you can go back to older versions of course. The only disturbing feature about this integrated auto backup is sometimes your Mac goes idle before you can typebecause it is saving another version. This is particularly annoying when you edit large Keynote files.
Jürgen
......................
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
----------
From: Herbert J. Bernstein
Dear Colleagues,
Lion is an reality all developers have to live with. While I
agree that it would be a bad idea to update one's primary
development environment to Lion, it does seem a good idea to have
at least one system with sufficient memory, disk and good enough
graphics and the new UI (user interface) to be able to wring out
problems, especially on the UI side.
So the question is: Is a new MacBook Pro or new MacBook Air
sufficient for such testing, or is something heftier with a
studio display necessary?
Regards,
Herbert
=====================================================
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
=====================================================
----------
From: Bosch, Juergen
Regarding MBP versus MBA, one of my graduate students just got a new MBA and her machine is much faster than my MBP 2.8 GHz Intel Core 2 Duo with 4 GB RAM. Both machines are running Lion.
The new MBA is hot, only disadvantage you can't lock it down, there's no option for it.
Jürgen
......................
Jürgen Bosch
Johns Hopkins University
----------
From: Sean Seaver
Dear Herbert,
I've come across quite a few people that are using mac books as their main development computer. This site ( http://usesthis.com/ ) can be an good way to learn about various setups. A popular trend seems to be using a mac book along with the apple thunderbolt display for more screen real estate.
Take Care,
Sean Seaver
P212121
http://store.p212121.com/
----------
From: Phil Evans
I use my MBP with external screen, keyboard & mouse all the time. The new ones are fast, & mine should easily cope with Lion
My question about Lion was because
1. on the one hand as far as I can see Bill Scott only builds latest stand-alone Coots (0.7...) for Lion, and these don't work on 10.6 (is this true Bill?)
2. on the other hand, I had a report that ccp4mg doesn't work on Lion (is that true Stuart?)
and I need both of these (and don't fancy building either myself)
Phil (still on 10.6)
----------
From: William G. Scott
Dear Phil (and everyone):
1. I've now got automated build systems for coot for 10.7.1 and 10.6.8. I just haven't had a chance to get the 10.6.8 one on line. I'll try to do this today. (Also, the last few haven't build due to a change in the code with which the compiler can't cope, but hopefully that will be a thing of the past soon.)
2. Most things build on 10.6.X will run on 10.7.X. I haven't opened ccp4mg, but will give it a try after I wake up.
3. I've had trouble with stereo on coot with 10.7.1, but, oddly, the problem goes away if I have a second monitor.
If you update to 10.7, keep a clone of 10.6 just in case it drives you nuts. There are all sorts of perverse changes, and (unlike the reversal in scrolling direction) not a lot of over-ride options.
I guess this is a glimpse of the post-Jobs era, albeit one provided from an inconvenient vista.
Peace and joy,
Bill
On Sep 16, 2011, at 6:33 AM, William G. Scott wrote:
> Dear Phil (and everyone):
>
> 1. I've now got automated build systems for coot for 10.7.1 and 10.6.8. I just haven't had a chance to get the 10.6.8 one on line. I'll try to do this today. (Also, the last few haven't build due to a change in the code with which the compiler can't cope, but hopefully that will be a thing of the past soon.)
>
> 2. Most things build on 10.6.X will run on 10.7.X. I haven't opened ccp4mg, but will give it a try after I wake up.
>
>
> 3. I've had trouble with stereo on coot with 10.7.1, but, oddly, the problem goes away if I have a second monitor.
>
> If you update to 10.7, keep a clone of 10.6 just in case it drives you nuts. There are all sorts of perverse changes, and (unlike the reversal in scrolling direction) not a lot of over-ride options.
>
> I guess this is a glimpse of the post-Jobs era, albeit one provided from an inconvenient vista.
>
> Peace and joy,
>
> Bill
----------
From: Peter Keller
I guess this is one of them:
How Apple's Lion won't let you trash documents
The operating system for the nanny state?
http://www.reghardware.com/2011/09/07/apple_mac_os_x_lion_the_nanny_os/
One of the reasons why I'm sticking with Snow Lepoard for now....
Regards,
Peter.
--
Peter Keller
Global Phasing Ltd.,
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom
----------
From: Andreas Förster
I've bitched enough about all things Mac, but this one's just too good to pass on (from the article that Peter linked to):
"The fundamental issue here is Lion's assumption that you don't know what you're doing, and it's going to ensure you're protected from cock-ups that, in your ignorance, you may make."
The first half of that sentence has always been my major gripe with Mac OS. If there just were a Pro version for those that know what they're doing, but the iPadification of computing goes exactly the opposite way.
Andreas Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk
----------
From: Richard Gillilan
Listening to Jobs speak recently, I got the distinct impression that the end of the era of general desktop computers "PC's" may be on the horizon. Of course that's iPad sales rhetoric, but it may be that the public moves away from general computers and that surely will have implications for scientific computing.
Richard
----------
From: Adrian Goldman
Of course this has to be the case. I think most of us walk around with with mobile phones that have memory and processing power more powerful than all of the computers available before 1990.
Some of the things that seem difficult in Lion and are nanny-state-ish such as automatic file versioning (not that I am running Lion yet, mind) - well is it the case that all of the experts on the CCP4BB have _never_ deleted a file they didn't mean to delete? _Never_ had Word (O, Coot) crash taking with it 6 hours worth of changes that should have been saved but weren't?
If so, I feel humbled because I have made these mistakes and more.
Adrian
----------
From: Peter Keller
There is nothing nanny-state-ish (or indeed new) about automatic file
versioning. VMS (which was the major operating system that CCP4
targetted in the pre-Unix days) had it in the 1980's and I don't recall
anyone moaning about it at the time. As you say, it could be a lifesaver
if you overwrote something by mistake. VMS allowed you to purge old
versions completely though, whereas Lion doesn't: that is the
difference.
No comments:
Post a Comment