Help building dual Quad Core system for Protein Analysis

[tdido]

Greets, guys.

I'm about to build a system for my research. The tasks the system will perform will vary, from complex queries to big (up to 70GB) MySQL and Postgres databases, to protein alignment using BLAST, and so on.

I live in Argentina, and I have some limitations regarding the availability of parts. These are the options that I'm considering:

A) 2x Opteron 2350 on a Tyan S2927G2NR

B) 2x Xeon 5405 on a Supermicro X7DVL-i

I have not been able to find info to help me understand if the 16MB cache in the Xeons will be beneficial, for example.

Opinions, suggestions and alternatives regarding the choice of parts will be really welcome.

Thank you in advance!

 

[Siggy19]

Consider getting a powerful video card and running the research on there... looking at the Folding@Home figures, the parallelism available from a decent GPU wipes the floor with any regular CPU for that sort of work.

However, how to write code for it is a question you'll need to ask someone else !

 

[cjl]

Between those, I'd go for the Opterons. The i7 xeons would be faster than either, but the Opterons beat the older gen xeons quite handily in that kind of work.

 

[rescawen]

depends on your budget too ? Performance to money wise Id agree with cjl cause all the new products are always expensive

 

[tdido]

Yup, i7s will probably be too much for my budget, and are not available now, so I'll have to stick with one of those options... Seems like the Opterons are winning so far...

 

[daft]

is there really any budget worth noting with this build? and i would suggest 2x 2376 opteron cpus, same thermal limit, built on the 45nm process, and 300mhz faster than the 2350

 

[tdido]

Yup, there's a budget. Thing is, since I'm not in the US there's no way we can compare prices. I'll always be paying a lot more than you'd assume.

Just as an example, the best price on the 2350s I can get is $369...

 

[xthekidx]

Link the sites you would be buying from and we will try to work with your currency and proposed budget.

 

[tdido]

I uploaded the most complete price list I could get. You can find it here: http://www.tdido.com.ar/lista_05_01_2009.rar

Thanks!

 

[daft]

any ideas on how much RAM you will need for those programs. im assuming a lot, but im hoping for real numbers.

 

[xthekidx]

I uploaded the most complete price list I could get. You can find it here: http://www.tdido.com.ar/lista_05_01_2009.rar

Thanks!

all I got from that link was a bunch of this garbage:

Rar!�ϐs��
�������k8t@9�õª��� �(ŠŽnC<.:3� ���lista_05_01_2009.xls�ðxçh&ÍÌÕÖbfú¤·u%«Ç|¬Ý[¹špx_s3sG™@`°I«WR‘‡á @9¤ãñ×q·q´›M6ã}~Éø¤ºÜj7Æ8Û‘¸Üo©ÈÜru.¸ü~J6ãnDÖýùu`æ�<åUÝ‹�XÁÍûú»›óI
çåÕUÕÕr¹ÎW+”?ˆsþçûóœ®U×µ‹ßÑšcõûÿ•÷_Ú|·˜ï-çhóçú}ÓÎÝ··Ú‡ÿþ>3Ç|CêÃÖ?Õ³õÁö¿ÈÇÕÿõ+}BÞž÷÷Éþø.¾›Œnáý8~ûgß>ãyw+wKwkw‹z¥½ZÞ±nôÖyß®½jÞ¹o^·€·°[Ø­ì–ök{E¼¼%¼5¼E½ªÇ-í–ä-â­ã-íÖñÖòä­Ê[É[1nZÏV|³õ ,zÈ,ŠÉ,šÊ-hKC[Ê[˜·5nqm¶¹Ï"óˆ´U£-iIZRÙ«K[ ¶rÓš´å³Öž·Ej*µ´Ñ[IjKy«yË{…¼õ½Êßü-î–÷kS[MmEª,=éïZÒé­UoAn¢Úël-Yjël­ïÚZÂÖVÛ[ª·¢¶âÛ«u–ú¾…o¢[èÖúE½"Ϻáÿ[ÉÏ$�¿cÚ)¿ýìÆ,Ù,n;¹ã—ßüÓ|ÒGñ×ìkËÙýN7»ô{ωÿ0ýöƒÖÍ&y¤wh(î™f?Qæ[þõ¯8üa
?M‹¡÷·

 

[gkay09]

all I got from that link was a bunch of this garbage:

Rar!�ϐs��
�������k8t@9�õª��� �(ŠŽnC<.:3� ���lista_05_01_2009.xls�ðxçh&ÍÌÕÖbfú¤·u%«Ç|¬Ý[¹špx_s3sG™@`°I«WR‘‡á @9¤ãñ×q·q´›M6ã}~Éø¤ºÜj7Æ8Û‘¸Üo©ÈÜru.¸ü~J6ãnDÖýùu`æ�<åUÝ‹�XÁÍûú»›óI
çåÕUÕÕr¹ÎW+”?ˆsþçûóœ®U×µ‹ßÑšcõûÿ•÷_Ú|·˜ï-çhóçú}ÓÎÝ··Ú‡ÿþ>3Ç|CêÃÖ?Õ³õÁö¿ÈÇÕÿõ+}BÞž÷÷Éþø.¾›Œnáý8~ûgß>ãyw+wKwkw‹z¥½ZÞ±nôÖyß®½jÞ¹o^·€·°[Ø­ì–ök{E¼¼%¼5¼E½ªÇ-í–ä-â­ã-íÖñÖòä­Ê[É[1nZÏV|³õ ,zÈ,ŠÉ,šÊ-hKC[Ê[˜·5nqm¶¹Ï"óˆ´U£-iIZRÙ«K[ ¶rÓš´å³Öž·Ej*µ´Ñ[IjKy«yË{…¼õ½Êßü-î–÷kS[MmEª,=éïZÒé­UoAn¢Úël-Yjël­ïÚZÂÖVÛ[ª·¢¶âÛ«u–ú¾…o¢[èÖúE½"Ϻáÿ[ÉÏ$�¿cÚ)¿ýìÆ,Ù,n;¹ã—ßüÓ|ÒGñ×ìkËÙýN7»ô{ωÿ0ýöƒÖÍ&y¤wh(î™f?Qæ[þõ¯8üa
?M‹¡÷·

Well actually there is an excel sheet in the rar file...am getting it properly...do check it once more...

 

[gkay09]

stick with ur CPU and the MOBO suggestions...

Get 4 nos. of this memory

Memoria DDR2 FB-DIMM 667 Mhz PC-5400 SuperTalent 4096 MB Server Memory - $175X4
ie about 8GB for each processor...Will let u add more moidules later...
And 2 2GB modules are costlier than the single 4 GB module from ur list...

 

[tdido]

all I got from that link was a bunch of this garbage:

Rar!�ϐs��
�������k8t@9�õª��� �(ŠŽnC<.:3� ���lista_05_01_2009.xls�ðxçh&ÍÌÕÖbfú¤·u%«Ç|¬Ý[¹špx_s3sG™@`°I«WR‘‡á @9¤ãñ×q·q´›M6ã}~Éø¤ºÜj7Æ8Û‘¸Üo©ÈÜru.¸ü~J6ãnDÖýùu`æ�<åUÝ‹�XÁÍûú»›óI

That's probably the browser not knowing about rar files, and displaying the contents as plain text. You can find the uncompressed version here: http://www.tdido.com.ar/lista_05_01_2009.xls

Thanks!

 

[xthekidx]

Budget?

 

[tdido]

Around $3000, give or take...

 

[WR2]

You're on the right track with your initial choices.
Harpertown (54xx) and Barcelona (23xx) are pretty evenly matched. Barcelona does have a clock for clock advantage.
Either option would be a good choice.
When you compare the E5410 (2.33Ghz) against the similar priced 2350(2.0Ghz) it should be almost the same peformance.
E5405 system should end up using less power than the 2350 system and that could be the deciding factor if you'll be using your new system heavily.

 

[gkay09]

2x Opteron 2350 on a Tyan S2927G2NR

4x Memoria DDR2 FB-DIMM 667 Mhz PC-5400 SuperTalent 4096 MB Server Memory
(2 for each processor)

A gud ATX full tower case as ur Tyan mobo is a ATX board and nt an eATX...
Antec 1200

A very gud quality PSU...
Fuentes Thermaltake Tough Power 750W ATX 12V APFC EPS

Any normal display card...(If there are any vector graphics or rendering, get a workstation graphics card...)