Re: [ccp4bb] Who is using 64-bit Linux?
I myself recently had the misfortune of trying to get a java program relying on the (apparently 32-bit only) JMF package to run on 64-bit linux. This wasted almost an entire week of my life! I tried downgrading the operating system to 32-bit, but that reduced the number of CPUs available in the system from 24 to 8. Still don't know why that is (I'm not all that familiar with Ubuntu, and don't want to be), but I imagine one could call that a performance hit. On the whole, however, I have not seen any significant performance advantage of 64 over 32 bit running crystallography programs side-by-side on equivalent hardware. I have also been unimpressed with the supposed memory access advantages of 64 bit. I had to do a LOT of recompiling programs in order to create maps or MTZ files bigger than 2 GB, and I also still have certain programs running out of virtual memory at 4GB as well. Despite the fact that the relevant machine has 48 GB of RAM and 80 GB of swap. I tell you. Technology just doesn't work. -James Holton MAD Scientist On 4/4/2012 2:21 AM, Takanori Nakane wrote: Dear Tim, 64-bit is about memory addressing - why would you expect a performance boost? I have wondered where this notion originated from. The x86_64 architecture has more registers than 32bit (x86) architecture. Register access is faster than memory access so the more data programs can put on registers, the faster it runs. Best regards, Takanori Nakane
Re: [ccp4bb] Who is using 64-bit Linux?
I tell you. Technology just doesn't work. developers and user's don't, technology is usually ok, but I feel your pain.
Re: [ccp4bb] Who is using 64-bit Linux?
On Apr 13, 2012, at 1:24 PM, James Holton wrote: I tried downgrading the operating system to 32-bit, but that reduced the number of CPUs available in the system from 24 to 8. Still don't know why that is I'm probably wrong, but I'll guess that a 32 bit operating system can only spare 3 of those bits to address CPUs ;-) James
Re: [ccp4bb] Who is using 64-bit Linux?
No, that's a limit set by the ubuntu 32 bit kernel maintainers when they configured and compiled the kernel (again, see my comment about the problem being with developers and users). I think the limit is 256 for x86, 4096 for ia64 (itanium), even old versions of RHEL supported 16 and 32 logical CPUs for x86 : http://support.bull.com/ols/product/system/linux/redhat/help/kbf/g/inst/PrKB11417 http://cateee.net/lkddb/web-lkddb/NR_CPUS.html On Fri, Apr 13, 2012 at 3:08 PM, James Stroud xtald...@gmail.com wrote: On Apr 13, 2012, at 1:24 PM, James Holton wrote: I tried downgrading the operating system to 32-bit, but that reduced the number of CPUs available in the system from 24 to 8. Still don't know why that is I'm probably wrong, but I'll guess that a 32 bit operating system can only spare 3 of those bits to address CPUs ;-) James
Re: [ccp4bb] Who is using 64-bit Linux?
On the whole, however, I have not seen any significant performance advantage of 64 over 32 bit running crystallography programs side-by-side on equivalent hardware. I have also been unimpressed with the supposed memory access advantages of 64 bit. I had to do a LOT of recompiling programs in order to create maps or MTZ files bigger than 2 GB, and I also still have certain programs running out of virtual memory at 4GB as well. Despite the fact that the relevant machine has 48 GB of RAM and 80 GB of swap. Eventually all of the programs using cute memory tricks to deal with the restrictions of 70s, 80s, and early 90s systems will be patched, or replaced by ones which don't use these acrobatics. But I don't think it'll be anytime soon. Pete I tell you. Technology just doesn't work. -James Holton MAD Scientist On 4/4/2012 2:21 AM, Takanori Nakane wrote: Dear Tim, 64-bit is about memory addressing - why would you expect a performance boost? I have wondered where this notion originated from. The x86_64 architecture has more registers than 32bit (x86) architecture. Register access is faster than memory access so the more data programs can put on registers, the faster it runs. Best regards, Takanori Nakane
Re: [ccp4bb] Who is using 64-bit Linux?
Hi David I'm curious - do you mean running on a 32-bit Centos box or running the 32-bit Mosflm executable on a 64-bit Centos box? We did have one report of problems with the 32-bit exe on a 64-bit box, which (seemingly) randomly gave one of two different results (either the same failure or success) - but that was fixed in the beta we released in July last year, and didn't occur with the 64-bit exe at all. We really are grateful to people who tell us about the bugs they find rather than try to struggle on in silence! Funny enough I can't get iMosflm running reliably on 32 bit CentOS 5 or CentOS 6 and I can on 64 bits versions. We have all running (CCP4, Coot, iMosflm, XDS, phenix, best, etc, etc) running in 64 bit and intent to move all user computers to uniform 64 bit environment on the next shutdown as it is more difficult to support both 32 and 64 bit enviroment. David -- David Aragao, PhD | Research Fellow - MX | Australian Synchrotron p: (03) 8540 4121 | f: (03) 8540 4200 | m: 0467 775 203 david.ara...@synchrotron.org.au | www.synchrotron.org.au 800 Blackburn Road, Clayton, Victoria 3168, Australia Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Who is using 64-bit Linux?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Tom, 64-bit is about memory addressing - why would you expect a performance boost? I have wondered where this notion originated from. Cheers, Tim On 04/03/12 22:07, Tom Peat wrote: We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett [rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPfAmoUxlJ7aRr7hoRArGeAKDgsoIKEADDo6ycaJBpLf6W9tnCFACeOSM6 1gZUOKKWkQ6Ioo+pQkPtw4Y= =DdSc -END PGP SIGNATURE-
Re: [ccp4bb] Who is using 64-bit Linux?
Hello Tim, I believe the notion comes about as one can thread 64 instead of 32 addresses concurrently, thereby boosting performance. If it has no performance boost, why would they bother? Cheers, tom -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Wednesday, 4 April 2012 6:43 PM To: Peat, Tom (CMSE, Parkville) Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Who is using 64-bit Linux? -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Tom, 64-bit is about memory addressing - why would you expect a performance boost? I have wondered where this notion originated from. Cheers, Tim On 04/03/12 22:07, Tom Peat wrote: We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett [rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPfAmoUxlJ7aRr7hoRArGeAKDgsoIKEADDo6ycaJBpLf6W9tnCFACeOSM6 1gZUOKKWkQ6Ioo+pQkPtw4Y= =DdSc -END PGP SIGNATURE-
Re: [ccp4bb] Who is using 64-bit Linux?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Tom, because there are PCs out there with more than 200GB RAM, as well as programs and systems that make use of them. As far as I understand a 32-bit compiled kernel would have not possibility to address anything beyong 4GB. Regards, Tim On 04/04/12 10:53, Tom Peat wrote: Hello Tim, I believe the notion comes about as one can thread 64 instead of 32 addresses concurrently, thereby boosting performance. If it has no performance boost, why would they bother? Cheers, tom -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Wednesday, 4 April 2012 6:43 PM To: Peat, Tom (CMSE, Parkville) Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Who is using 64-bit Linux? Dear Tom, 64-bit is about memory addressing - why would you expect a performance boost? I have wondered where this notion originated from. Cheers, Tim On 04/03/12 22:07, Tom Peat wrote: We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett [rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPfA/AUxlJ7aRr7hoRAmfDAKDleNNb2BVxcNIHg7x81ks3gK5BpACgzQ9J DwQDnMorze1xjTZ+0qqacEg= =wVwe -END PGP SIGNATURE-
Re: [ccp4bb] Who is using 64-bit Linux?
Dear Tim, 64-bit is about memory addressing - why would you expect a performance boost? I have wondered where this notion originated from. The x86_64 architecture has more registers than 32bit (x86) architecture. Register access is faster than memory access so the more data programs can put on registers, the faster it runs. Best regards, Takanori Nakane
Re: [ccp4bb] Who is using 64-bit Linux?
A 32 bit Linux OS with PAE enabled (which is all of the current Linux distros) can actually address 64 Gb of memory, but no more than 3 Gb per process. 3 Gb may not be that much of a limitation for many processes, so large performance increases on a 64-bit system compared to a 32-bit may be difficult to observe in practice for now. Roger Rowlett On Apr 4, 2012 5:09 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Tom, because there are PCs out there with more than 200GB RAM, as well as programs and systems that make use of them. As far as I understand a 32-bit compiled kernel would have not possibility to address anything beyong 4GB. Regards, Tim On 04/04/12 10:53, Tom Peat wrote: Hello Tim, I believe the notion comes about as one can thread 64 instead of 32 addresses concurrently, thereby boosting performance. If it has no performance boost, why would they bother? Cheers, tom -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Wednesday, 4 April 2012 6:43 PM To: Peat, Tom (CMSE, Parkville) Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Who is using 64-bit Linux? Dear Tom, 64-bit is about memory addressing - why would you expect a performance boost? I have wondered where this notion originated from. Cheers, Tim On 04/03/12 22:07, Tom Peat wrote: We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett [rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPfA/AUxlJ7aRr7hoRAmfDAKDleNNb2BVxcNIHg7x81ks3gK5BpACgzQ9J DwQDnMorze1xjTZ+0qqacEg= =wVwe -END PGP SIGNATURE-
Re: [ccp4bb] Who is using 64-bit Linux?
Thanks everyone for the info. To summarize, it looks like 64-bit Linux is not the issue it was a few years ago for crystallography software. Many typically used crystallography packages are compiled for 64 bit now and the ia32 libs typically provide compatibility for those not yet compiled as 64 bit binaries. Cheers, Roger Rowlett On Apr 4, 2012 6:06 AM, Roger Rowlett rrowl...@colgate.edu wrote: A 32 bit Linux OS with PAE enabled (which is all of the current Linux distros) can actually address 64 Gb of memory, but no more than 3 Gb per process. 3 Gb may not be that much of a limitation for many processes, so large performance increases on a 64-bit system compared to a 32-bit may be difficult to observe in practice for now. Roger Rowlett On Apr 4, 2012 5:09 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Tom, because there are PCs out there with more than 200GB RAM, as well as programs and systems that make use of them. As far as I understand a 32-bit compiled kernel would have not possibility to address anything beyong 4GB. Regards, Tim On 04/04/12 10:53, Tom Peat wrote: Hello Tim, I believe the notion comes about as one can thread 64 instead of 32 addresses concurrently, thereby boosting performance. If it has no performance boost, why would they bother? Cheers, tom -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Wednesday, 4 April 2012 6:43 PM To: Peat, Tom (CMSE, Parkville) Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Who is using 64-bit Linux? Dear Tom, 64-bit is about memory addressing - why would you expect a performance boost? I have wondered where this notion originated from. Cheers, Tim On 04/03/12 22:07, Tom Peat wrote: We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett [rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPfA/AUxlJ7aRr7hoRAmfDAKDleNNb2BVxcNIHg7x81ks3gK5BpACgzQ9J DwQDnMorze1xjTZ+0qqacEg= =wVwe -END PGP SIGNATURE-
Re: [ccp4bb] Who is using 64-bit Linux?
Hi All, I did quite a bit of performance comparison with XDS between two centOS 5 (64 vs 32) and did notice performance boost when writing results to a remote NFS directory. Interestingly, using same OSs writing locally the performance boost was not noticeable. At the time I thought that somehow the temporary files that XDS was creating on the 32bit OS were better handled in memory instead. This off course was done using 32bit compiled XDS vs 64 bit compiled XDS. I did not try to run the 32bit XDS on the 64 bit OS. Maybe I should. This was done on particular machines configuration and would not generalize to all programs and situations. On the topic of 64 bit vs 32 which to choose? Funny enough I can't get iMosflm running reliably on 32 bit CentOS 5 or CentOS 6 and I can on 64 bits versions. We have all running (CCP4, Coot, iMosflm, XDS, phenix, best, etc, etc) running in 64 bit and intent to move all user computers to uniform 64 bit environment on the next shutdown as it is more difficult to support both 32 and 64 bit enviroment. David -- David Aragao, PhD | Research Fellow - MX | Australian Synchrotron p: (03) 8540 4121 | f: (03) 8540 4200 | m: 0467 775 203 david.ara...@synchrotron.org.au | www.synchrotron.org.au 800 Blackburn Road, Clayton, Victoria 3168, Australia From: Roger Rowlett [rrowl...@colgate.edu] Sent: 04 April 2012 20:13 Subject: Re: Who is using 64-bit Linux? Thanks everyone for the info. To summarize, it looks like 64-bit Linux is not the issue it was a few years ago for crystallography software. Many typically used crystallography packages are compiled for 64 bit now and the ia32 libs typically provide compatibility for those not yet compiled as 64 bit binaries. Cheers, Roger Rowlett On Apr 4, 2012 6:06 AM, Roger Rowlett rrowl...@colgate.edumailto:rrowl...@colgate.edu wrote: A 32 bit Linux OS with PAE enabled (which is all of the current Linux distros) can actually address 64 Gb of memory, but no more than 3 Gb per process. 3 Gb may not be that much of a limitation for many processes, so large performance increases on a 64-bit system compared to a 32-bit may be difficult to observe in practice for now. Roger Rowlett On Apr 4, 2012 5:09 AM, Tim Gruene t...@shelx.uni-ac.gwdg.demailto:t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Tom, because there are PCs out there with more than 200GB RAM, as well as programs and systems that make use of them. As far as I understand a 32-bit compiled kernel would have not possibility to address anything beyong 4GB. Regards, Tim On 04/04/12 10:53, Tom Peat wrote: Hello Tim, I believe the notion comes about as one can thread 64 instead of 32 addresses concurrently, thereby boosting performance. If it has no performance boost, why would they bother? Cheers, tom -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.demailto:t...@shelx.uni-ac.gwdg.de] Sent: Wednesday, 4 April 2012 6:43 PM To: Peat, Tom (CMSE, Parkville) Cc: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Who is using 64-bit Linux? Dear Tom, 64-bit is about memory addressing - why would you expect a performance boost? I have wondered where this notion originated from. Cheers, Tim On 04/03/12 22:07, Tom Peat wrote: We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304tel:%2B613%209662%207304 +614 57 539 419tel:%2B614%2057%20539%20419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett [rrowl...@colgate.edumailto:rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers
[ccp4bb] Who is using 64-bit Linux?
The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] Who is using 64-bit Linux?
We use the 64 bit Centos (Red Hat) distro and CCP4, Coot, etc seem to work fine on this. I can't say I notice a big performance boost from the 64 bit side of things. Maybe I'm just impatient. cheers, tom Tom Peat Biophysics Group CSIRO, CMSE 343 Royal Parade Parkville, VIC, 3052 +613 9662 7304 +614 57 539 419 tom.p...@csiro.au From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett [rrowl...@colgate.edu] Sent: Wednesday, April 04, 2012 5:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] Who is using 64-bit Linux?
Whatever you do, make sure you have enough bottled water before the next doomsday: http://en.wikipedia.org/wiki/Year_2038_problem I am using 64-bit linux almost exclusively for some time now. XRD software works fine, no lingering issues that I can report. ia32-libs do the trick for 32-bit binaries. On Tue, 2012-04-03 at 15:57 -0400, Roger Rowlett wrote: The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Who is using 64-bit Linux?
I have RHEL62-64 in a win 7-64 8GB desktop VMware installation. CCP4, ccp4i, coot, and shelxcde beta executables run fine. There were issues with the coot package installation due to unresolved dependencies and my ignorance thereof, but I think a working RHEL62-64 compatible package is available now, the coot wiki has latest info. I could not get Xtalview running, probably some xterm thing beyond my grasp, which also screws up the latest hkl2mapV0.3, V0.2 runs fine. Free intel ifort runs great. The great part about the VM ware installation is that I also got it running on a win7-64 8GB laptop by simply copying the virtual RHEL machine (files). That alone saved a few day's work. Also the Unity feature of VMware is a blast. BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett Sent: Tuesday, April 03, 2012 12:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] Who is using 64-bit Linux?
We have been using 64 bit Linux for several years. I'm not aware of any lingering issues with the 64 bit-ness. Linux is always sprinkling in a few new bugs, but I don't know of any current issues with 32 bit vs. 64 bit. On 04/03/12 15:57, Roger Rowlett wrote: The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Who is using 64-bit Linux?
Hi Roger CCP4 and Mosflm work fine in my testing - I do builds for Linux and Macs, both 32 and 64 bits. I wouldn't expect to see a difference in performance (and don't see anything significant in practice). One thing - I think you will need to install 32-bit compatibility libraries for some of the code that is dynamically linked and has been built as 32-bit, e.g. I think ActiveTcl distros might need them (for iMosflm). On 3 Apr 2012, at 20:57, Roger Rowlett wrote: The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Who is using 64-bit Linux?
Fedora and RHEL 64-bit work well and run pretty much all the standard programs (CCP4/Coot/Phenix/CNS/SHELX). By installing the relevant 32-bit libraries you can also run older programs if need be. On a related note, XtalView will work on Fedora/RHEL if you install/compile the appropriate XView library files. For more info, check out: http://www.physionet.org/physiotools/xview/ Hope that helps, Kip On Tue, 3 Apr 2012 17:01:30 -0400 David Schuller dj...@cornell.edu wrote: We have been using 64 bit Linux for several years. I'm not aware of any lingering issues with the 64 bit-ness. Linux is always sprinkling in a few new bugs, but I don't know of any current issues with 32 bit vs. 64 bit. On 04/03/12 15:57, Roger Rowlett wrote: The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Who is using 64-bit Linux?
Roger, My lab is using 64 bit distros of SUSE and Linux Mint and hasn't had any compatibility issues that I can recall. Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry h...@hawaii.edu Date:Tue, 3 Apr 2012 15:57:40 -0400 From:Roger Rowlett rrowl...@colgate.edu Subject: Who is using 64-bit Linux? The time has come for me to upgrade my Linux OS to something more recent for me and my student workstations. A 32-bit distro is certainly conservative and compatible with CCP4 and Coot, but it seems like that solution hobbles my hardware and puts some limitations on available memory, even with PAE enabled. So who is using a 64-bit distro these days, and are there lingering issues of compatibility and dependency hell with commonly used XRD software, like CCP4, Coot, iMOSFLM etc.? Ubuntu 12.04 LTS (beta) actually works OK with one simple workaround for the global menu for CCP4 and Coot, and wine compatibility is fine for running CrysalisPro in the same environment, so it's really comes down to whether or not the extra performance of a 64-bit OS is worth the pain of compatibility issues for XRD software. Any thoughts? Cheers, ___ Roger S. Rowlett Gordon Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
