[ccp4bb] Mac pro
Dear all, I am thinking of getting a apple Mac pro desktop computer. I was wondering does all crystallography programs run on it? I think there are Mac OSX version of CCP4, CNS, SHELX etc. But how about programs in the Uppsala software factory etc?. Also is it difficult to install these programs - are there problems? Is linux still a safer choice? sheemei
Re: [ccp4bb] Mac pro
Hi Sheemei. The majority of crystallography programs run under osx, including the Uppsala software factory stuff. Installation has always been very straight forward for me. Bill Scott's webpages will have everything you need to get started. http://sage.ucsc.edu/xtal/ Cheers, David 2009/1/6 Sheemei s...@purdue.edu: Dear all, I am thinking of getting a apple Mac pro desktop computer. I was wondering does all crystallography programs run on it? I think there are Mac OSX version of CCP4, CNS, SHELX etc. But how about programs in the Uppsala software factory etc?. Also is it difficult to install these programs - are there problems? Is linux still a safer choice? sheemei -- David C. Briggs PhD Father Crystallographer http://drdavidcbriggs.googlepages.com/home Skype: DocDCB
Re: [ccp4bb] Mac pro
Hi Sheemel, I assume you are waiting for today's announcements of the i7 core MacPro's ? If not wait another 6 hours before deciding to buy something. Jürgen On 6 Jan 2009, at 06:27, Sheemei wrote: Dear all, I am thinking of getting a apple Mac pro desktop computer. I was wondering does all crystallography programs run on it? I think there are Mac OSX version of CCP4, CNS, SHELX etc. But how about programs in the Uppsala software factory etc?. Also is it difficult to install these programs - are there problems? Is linux still a safer choice? sheemei - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Biochemistry and Molecular Biology, W8708 615 North Wolfe Street Baltimore, MD 21205 Phone: +1-410-614-4742
Re: [ccp4bb] Mac pro
I was much more enticed by the proposition of the MacBook Wheel: http://www.theonion.com/content/video/apple_introduces_revolutionary Get your orders in now - there's reportedly a 3-15 month waiting time... Derek ;-) On Jan 6, 2009, week2, at 13:14, JBosch wrote: Hi Sheemel, I assume you are waiting for today's announcements of the i7 core MacPro's ? If not wait another 6 hours before deciding to buy something. Jürgen On 6 Jan 2009, at 06:27, Sheemei wrote: Dear all, I am thinking of getting a apple Mac pro desktop computer. I was wondering does all crystallography programs run on it? I think there are Mac OSX version of CCP4, CNS, SHELX etc. But how about programs in the Uppsala software factory etc?. Also is it difficult to install these programs - are there problems? Is linux still a safer choice? sheemei - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Biochemistry and Molecular Biology, W8708 615 North Wolfe Street Baltimore, MD 21205 Phone: +1-410-614-4742
Re: [ccp4bb] Mac pro
The Mac Pro is what I use for all my crystallography calculations. The vast majority of programs run, the one major sticking point being the older version of HKL but I believe that HKL2000 may well run on OSX now. I use XDS and/or MOSFLM if I want to reprocess on this machine. With most packages the bad old days of actually having to edit the Makefile to install programs is past - you can either install via Fink (especially with all the fine work from Bill Scott) or via .dmg files and failing that most packages will compile with not too much pain. Coot did make the CPU almost glow on my MacBook when I installed all the dependencies via Fink back in early 2008, however. The principal problem with the Mac Pro is that it is difficult to get it to run stereo - the one supported configuration last time I checked was absurdly expensive. If you need stereo (and can actually find a CRT monitor) Linux supports a wider array of options, but I enjoy the relatively seamless integration of a conventional desktop environment with Unix on the Mac. There are also options for virtualization of Windoze and Linux via the software Parallels although I have yet to test this out. OSX has minor quirks, like the patch to make OSX treat e.g. the filenames MyJunkData.sca and myjunkdata.sca as the same file rather than the expected Unix behavior. But in practice I rarely find this to be an issue. Phil Jeffrey Princeton Sheemei wrote: Dear all, I am thinking of getting a apple Mac pro desktop computer. I was wondering does all crystallography programs run on it? I think there are Mac OSX version of CCP4, CNS, SHELX etc. But how about programs in the Uppsala software factory etc?. Also is it difficult to install these programs - are there problems? Is linux still a safer choice? sheemei
Re: [ccp4bb] Mac pro
with Unix on the Mac. There are also options for virtualization of Windoze and Linux via the software Parallels although I have yet to test this out. If you're trying to purchase a Mac so that you can run MS Office or other Windows only products without dual booting this is no longer necessary if you've got a Windows installation CD and a Linux system. I run Windows in Linux using Virtualbox (http://www.virtualbox.org) which is pretty much like a free version of VMWare Workstation. Do all of your research/graphics/modeling work on Linux and put it together using Adobe/MS publishing software in Windows running in VirtualBox. You can even share folders between the host Linux system and the guest Windows system without manually setting up a Samba server in Linux. VirtualBox doesn't support Direct3D so most Windows games won't work. I haven't tried OpenGL apps, but what's the point when you can just run these in Linux. HTH, Sabuj Pattanayek
Re: [ccp4bb] Mac pro
Hi I use Parallels on my Mac at home for both Windows XP and Ubuntu - it works fine for me when running the more number-crunching parts of CCP4 - haven't really looked at graphics programs like Coot MG. At work I'm running VMWare (Workstation 6.0.0) on a Linux box for Vista, and that, too, is fine. If anyone from Redmond is reading this, both my Windows licenses are legit. On 6 Jan 2009, at 17:55, Nathaniel Echols wrote: There are also options for virtualization of Windoze and Linux via the software Parallels although I have yet to test this out. Parallels is okay; I only use it for testing GUI code on Linux. It doesn't support multiple processors, which probably isn't necessary for most people. The graphics support was somewhat flaky in the past, but it now emulates 3D acceleration well enough to run Coot or PyMOL. I've heard anecdotal evidence that VMWare Fusion is better, but I've only used the Linux version. Unrelated advice: try iWork before spending a massive amount of money on MS Office. It's only about $40-$50 with the academic discount, and much less bloated. It'll still read and export Office documents, although I don't know how robust this is. -Nat Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Mac pro
I've heard anecdotal evidence that VMWare Fusion is better, but I've only used the Linux version. As a heavy user of both products under Mac OS X on an eight-core Mac Pro, I find VMWare to be far more robust and feature rich than Parallels. Regardless, only Parallels supports 3D OpenGL acceleration (Windows only). Accordingly, I use Parallels on the desktop (only) and VMWare everywhere else. Cheers, Warren -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Harry Powell Sent: Tuesday, January 06, 2009 10:08 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Mac pro Hi I use Parallels on my Mac at home for both Windows XP and Ubuntu - it works fine for me when running the more number-crunching parts of CCP4 - haven't really looked at graphics programs like Coot MG. At work I'm running VMWare (Workstation 6.0.0) on a Linux box for Vista, and that, too, is fine. If anyone from Redmond is reading this, both my Windows licenses are legit. On 6 Jan 2009, at 17:55, Nathaniel Echols wrote: There are also options for virtualization of Windoze and Linux via the software Parallels although I have yet to test this out. Parallels is okay; I only use it for testing GUI code on Linux. It doesn't support multiple processors, which probably isn't necessary for most people. The graphics support was somewhat flaky in the past, but it now emulates 3D acceleration well enough to run Coot or PyMOL. I've heard anecdotal evidence that VMWare Fusion is better, but I've only used the Linux version. Unrelated advice: try iWork before spending a massive amount of money on MS Office. It's only about $40-$50 with the academic discount, and much less bloated. It'll still read and export Office documents, although I don't know how robust this is. -Nat Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Mac pro
There are also options for virtualization of Windoze and Linux via the software Parallels although I have yet to test this out. Parallels is okay; I only use it for testing GUI code on Linux. It doesn't support multiple processors, which probably isn't necessary for most people. The graphics support was somewhat flaky in the past, but it now emulates 3D acceleration well enough to run Coot or PyMOL. I've heard anecdotal evidence that VMWare Fusion is better, but I've only used the Linux version. Unrelated advice: try iWork before spending a massive amount of money on MS Office. It's only about $40-$50 with the academic discount, and much less bloated. It'll still read and export Office documents, although I don't know how robust this is. -Nat
Re: [ccp4bb] Mac pro
I assume you are waiting for today's announcements of the i7 core MacPro's ? If not wait another 6 hours before deciding to buy something. hrmm, I was hoping store.apple.com was down due to modifications for this new item, it's back up but no new i7 mac pro ..
Re: [ccp4bb] mac pro configuration for crystallographic computing
I should apology for my unqualified remark (initiated by a personal note to me). I do appreciate and like grasp. From my experience, though, the appearance of an electrostatic surface representation is so much dependent on the parameters, on the input PDB-file (presence of ligands, waters, several copies), that I suppose many of the calculations could be replaced by a surface with a colour scheme based on acidic or basic residues without loss of information - I have met too many people who use software just as they would use Windows instead of understanding what they are really trying to do, and as soon as they see what they want to see the make a screen shot (not excluding me here). cheers, Tim -Original Message- From: Tim Grune [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Date: Thu, 21 Jun 2007 13:26:54 +1000 Subject: Re: [ccp4bb] mac pro configuration for crystallographic computing On Thursday 21 June 2007 06:50, Juergen Bosch wrote: I don't have one of those beast in my hands unfortunately. But I can verify that all except of HKL2000 (which I don't use, so I don't care/bother to check if there is an OS X version there) of the programs you mentioned run without any troubles. There's one more program I know that has not been ported to OS X and that is Grasp but there are other options to draw nice electrostatics. Grasp2 runs nicely in a Windows XP installation within Virtualbox under Linux. Since Virtualbox is also available for Mac (even though only as beta1-Version) one might get it to run under MacOSX And I think one can run Windows within MacOSX anyhow? (even though in my opinion one might as well use the gimp to paint your protein red-blue and still have about the same information content, but that's only my very personal opinion). Tim -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia
Re: [ccp4bb] mac pro configuration for crystallographic computing
Gretchen Meinke wrote: Hi-- I last saw some entries on the Mac Pro Xeon dated ~ April 2007. Were they purchased? Are you happy with them? Does ccp4, mosflm, hkl2000, coot run seamlessly on them? If so, what was the final cost and configuration (we would like stereo). How much memory should one get? Assuming Nuvision glasses for stereo, A CRT monitor (either NEC or Viewsonic) Based on previous readings, it still looks like the FX4500 is the only graphics card to support stereo for macs, correct? Thanks for any and all input. Gretchen Meinke I don't have one of those beast in my hands unfortunately. But I can verify that all except of HKL2000 (which I don't use, so I don't care/bother to check if there is an OS X version there) of the programs you mentioned run without any troubles. There's one more program I know that has not been ported to OS X and that is Grasp but there are other options to draw nice electrostatics. Regarding memory I would go for 1 GB per CPU and not less, otherwise you have a nice 4 core CPU but you are putting the brakes on if say 4 solve jobs run in parallel because they all need 500 MB or perhaps if you have larger problems to solve even larger than that. I'm running all my stuff from data processing to paper submission on my MacBook Pro 1.83 GHz with 2 GB of RAM. The only reason I leave my Mac is to sit in front of a Linux box running Coot in stereo. If you google for Stereo on Macintosh you will find a list of more than 1 graphics card which are stereo enabled on the Mac. the FX4500 is just the turbo card, there are also some from ATI which seem to work. But I'm not an expert in stereo graphics cards. Hope that helps. If you have further questions regarding Mac OS X don't hesitate to ask. I assume you are aware of the following web page: http://xanana.ucsc.edu/xtal/ Juergen -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002
Re: [ccp4bb] mac pro configuration for crystallographic computing
On Thursday 21 June 2007 06:50, Juergen Bosch wrote: I don't have one of those beast in my hands unfortunately. But I can verify that all except of HKL2000 (which I don't use, so I don't care/bother to check if there is an OS X version there) of the programs you mentioned run without any troubles. There's one more program I know that has not been ported to OS X and that is Grasp but there are other options to draw nice electrostatics. Grasp2 runs nicely in a Windows XP installation within Virtualbox under Linux. Since Virtualbox is also available for Mac (even though only as beta1-Version) one might get it to run under MacOSX And I think one can run Windows within MacOSX anyhow? (even though in my opinion one might as well use the gimp to paint your protein red-blue and still have about the same information content, but that's only my very personal opinion). Tim -- Tim Grune Australian Synchrotron 800 Blackburn Road Clayton, VIC 3168 Australia pgpFhY3yeObxL.pgp Description: PGP signature
Re: [ccp4bb] Mac Pro questions
Mischa, Though the FX4500 is expensive, it is (unfortunately) the only option for hardware stereo 3D. And with that card, I can personally attest to the fact that it is possible to have a 30 LCD and a ~22 stereo-capable CRT running simultaneously off of a single Mac Pro system. Thus, you can get the best of both worlds -- indeed, it is possible to direct MacPyMOL to open up in stereo 3D mode on the second display while still making simultaneous full use of the primary LCD for your other 2D work. Hopefully the same will prove true for Coot and O. Fantastic! Though I haven't had time yet to thoroughly benchmark the Octacore (having just opened the box 24 hours ago), I have run some head-to-head comparisons versus a dual-core 2 Ghz Opteron, and the initial results were staggering: PyMOL rendered a set of complex scenes nearly 7X faster on the Octacore Xeon than the dual-core Opteron. That is almost exactly what one would expect from clockspeed alone: 8x3 = 24 gHz of Xeon versus 2x2 = 4 gHz of Opteron. Honestly, that seems too good to believe, and yet I have not yet found a problem with those measurements. Though I can't speak to the other packages, PyMOL already supports multithreaded rendering and parallel geometry construction for multistate objects (trajectories) and/or scenes with multiple independent objects. In other words, if you have the cores to space, PyMOL can make use of them and will do so increasingly over the next couple of years as we add more parallelism into the code. For PyMOL rendering, eight cores cuts your wait time nearly in half (relative to four cores). Cheers, Warren -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Mischa Machius Sent: Tuesday, April 24, 2007 10:33 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Mac Pro questions Y'all - We are currently contemplating the purchase of a couple of Mac Pros. Apple has three graphics cards available. Initially, I was leaning towards the ATI Radeon X1900 XT 512MB, but read a lot of horror stories about that card overheating when taxed. I was wondering if anyone had such a setup and how it fares regarding general crystallographic work, i.e., running Coot, O, Pymol, etc. Would the NVIDIA GeForce 7300 GT be a better choice? I don't think we'll be going for the NVIDIA Quattro FX 4500. Also, I would appreciate it very much if anyone is willing to share their experience with other graphics cards, or to discuss whether it is worth getting an 8-core machine as opposed to a 4-core. Thanks so much. Best - MM Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353
