Re: AMD dual core vs Intel core 2 quad
On Wed, Feb 06, 2008 at 04:44:41PM +, Jo Shields wrote: To be specific: when I run molecular dynamics (MD) on Debian amd64 with my shared memory Thunder with 2 AMD dual core, parallelization support OpenMPI (everything compiled with Intel ifort/icc), the MD program sees 4 cpus and top -i indicates four cpu at work. The gain with respect to running MD in serial mode is about threefold, i.e. the parallelization is not bad at all. What can I expect - from this viewpoint - with four Intel Core 2 quad? - but the achilles heel of the Intel platform is memory contention, and for heavily memory-bound codes, scalability will be poor. Conversely, for CPU-bound codes, performance will be SIGNIFICANTLY better. Roughly speaking, using a 4-way GROMACs job as an example, the same job could complete about 25% faster, clock for clock, on Intel. A bit offtopic, but maybe Francesco would benefit from a PS3 if (big IF) you can fit your computations in 256MB and can do a decent job of programming the SPUs. Or maybe even faster (and more memory) a GPU. -- Daniel Tryba -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: DG965ss
On Thu, Feb 07, 2008 at 05:07:22PM +0100, Dr. Helmut G. Enders wrote: I still have one strange error. When I do a apt-get install large deb file, e.g. linux-image-2.6..., this file is corrupted (apt-get said gzip: invalid compressed data). If I fetch this deb-file with wget into /var/cache/apt/archives and do an apt-get install package it worked. I tried within my net some filetransfers without a problem. So the interface seems to be ok. And apt-get from my other maschine with the same net/firewall to the same mirror worked smoothly. Do you use a http proxy? I have had my proxy get out of sync and end up caching a bad Packages file, so every time it downloaded it the proxy gave me the wrong one and I got messages that the checksum on the downloaded package was wrong when in fact the package was right but Packages.gz was corrupt. Forcing the proxy to refresh the file solved the problem (as did turning of the use of the proxy temporarily). -- Len Sorensen -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: DG965ss
On Thu, 7 Feb 2008, Dr. Helmut G. Enders wrote: I tried an amd64 installation on an Intel DG965SS board with 8GByte. The system is very very slow (installation more than 1 day.) and I got corrupt files from the net (e.g. apt-get update). Justin Piszcz: Use the following boot option: append=mem=8832M Yes it works, thanks. I wouldn't touch the BIOS Justin. You are right, I first changed back in the bios. Tt worked with the mem problem, but I got a lot of new troubles. So I ruefully come back to your advice and updated the bios to the new version again and with your option it worked nearly perfect. Even my grub problem with the raid controller (3ware) disappeared. I still have one strange error. When I do a apt-get install large deb file, e.g. linux-image-2.6..., this file is corrupted (apt-get said gzip: invalid compressed data). If I fetch this deb-file with wget into /var/cache/apt/archives and do an apt-get install package it worked. I tried within my net some filetransfers without a problem. So the interface seems to be ok. Strange, do you use an http proxy by any chance? Also you could try a different mirror just incase there was some temporal weirdness. I assume you ran the latest version of memtest86 and let it cook for some time? And apt-get from my other maschine with the same net/firewall to the same mirror worked smoothly. Helmut -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED] -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
DG965SS
Justin Piszcz: ... I assume you ran the latest version of memtest86 and let it cook for some time? Grub said 28: does not fit into memory? and I have *no* floppy :-(. I'll try to burn the image onto a cd. Helmut -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: DG965SS
On Thu, 7 Feb 2008, Dr. Helmut G. Enders wrote: Justin Piszcz: ... I assume you ran the latest version of memtest86 and let it cook for some time? Grub said 28: does not fit into memory? and I have *no* floppy :-(. I'll try to burn the image onto a cd. Helmut -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED] I am curious of the results :) If its good ram, probably http proxy or other misc error, else you got bad ram :) Justin. -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: AMD dual core vs Intel core 2 quad
On Wed, Feb 06, 2008 at 11:59:14PM -0800, Francesco Pietra wrote: Together with other suggestions that were kindly provided, that above makes an alluring prospect for me. Thanks. My point of view is that when a 8xxx series is offered, they already have a 8 series ready for offer. I rely much on the quality of the software, too, in particular the algorithm for parallelization and the model, i.e., for MD the force field. Bad ones fight against any advancement in hardware. I would be much indebted for a clarification of details, at the reader convenience. 8xx series (without their box/fan) are found for little. Should the four 8xx be the same clock? (as they are found as single, or at most as pairs). Also, is the box/fan specific of the 8xx series or can I use the box/fan for the 2xx I have? (and only look for two additional boxes/fans). I believe that they have to be the same speed, and in general it is recommended that they be the same revision (stepping) as well. If they have the same code on the box, then they should be good to work together. In the European union - where I am - a four-way mainboard for 8xx and 184 pin ECC is not easy to find. Worldwide, I came across brand new Supermicro H8QCE-B Quad Opteron 800 Dual Server motherboard and Supermicro CK804 Quad Opteron 800 Dual Server motherboard at an affordable price (though as much as $200 are charged for shipping). The problem is that the old DDR based systems are obsolete and the DDR2 based ones are the ones currently made. No one wants to stock obsolete equipment making it hard to find. As to the mainboard, which specifications should I check in order that there is no too narrow bottleneck for the 8xx cpus and ECC 400MHz? Optionally, it might help to have a connection to make a cluster with an 8-way server, should I decide one day to transfer my private server to my institution. The standard interconnects on the opteron ought to be plenty to handle the memory bandwidth. Can different memory slots (8 2GB ECC and 8 1GB ECC, all 400MHz and same voltage) be assembled into the 16 slots of the mainboard? Yes. Preferably you should balance the ram between the CPUs if possible, but most important is to make the dual channel work so each bank has to be matched. If you have 24GB, you could put 6GB per CPU with 3GB per bank on each CPU. of course ram is probably (not sure about registered ecc ram) cheap enough that it really is a rather insignificant part of the cost of a full system. It may make more sense to go for the new style 8xxx instead with new ram. DDR2 has more bandwidth than your current ram, so if your application uses a lot of ram that could make a big difference. After all if you want 8 cores, that could be done with either 2 opteron 2300 series, or 4 8000 or 8xx series, or 2 8300 series. 4 8300 series would of course give you 16 cores on a 4 socket board. Looking at prices I see a quad core opteron 2350 is around $400, while an 8350 is around $1200. A dual core opteron 870 costs about $600 (so half the cores of a 2350 at the same clock speed for 50% more money). So to get 8 cores you could get a dual socket board with two 2350's for $800 for CPUs, while for an 870 you would need a 4 socket board and $2400 worth of CPUs. How much ram could you buy for the difference? A two socket board is likely to be a lot less than a four socket board as well, and being the new 2xxx series with DDR2 it is likely to be much easier to find. DDR2 ram also costs less than DDR ram these days. You can get a dual socket system that holds up to 32GB DDR2 ram with 2xxx series CPUs for about $400, like for example this one (no idea how good it is): http://www.directcanada.com/products/?sku=10530BD5632vpn=KFN4-DREmanufacture=ASUS Basicly it can be VERY expensive to try to reuse old parts. -- Len Sorensen -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
DG965ss
I tried an amd64 installation on an Intel DG965SS board with 8GByte. The system is very very slow (installation more than 1 day.) and I got corrupt files from the net (e.g. apt-get update). Justin Piszcz: Use the following boot option: append=mem=8832M Yes it works, thanks. I wouldn't touch the BIOS Justin. You are right, I first changed back in the bios. Tt worked with the mem problem, but I got a lot of new troubles. So I ruefully come back to your advice and updated the bios to the new version again and with your option it worked nearly perfect. Even my grub problem with the raid controller (3ware) disappeared. I still have one strange error. When I do a apt-get install large deb file, e.g. linux-image-2.6..., this file is corrupted (apt-get said gzip: invalid compressed data). If I fetch this deb-file with wget into /var/cache/apt/archives and do an apt-get install package it worked. I tried within my net some filetransfers without a problem. So the interface seems to be ok. And apt-get from my other maschine with the same net/firewall to the same mirror worked smoothly. Helmut -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
