I have a couple of question around the topic "hardware requirements" for
a server which is intended to be bought and used as concept machine for
NGS-related jobs. It should be used for development of tools and
workflows (using Galaxy, sure) as well as platform for some "alpha"
users, who should learn to work on NGS data, which they just began to
This concept phase is planned to last 1-2 years. During this time main
memory and especially storage could be extended, the latter on a
per-project basis. We will start with a small team of 3 people for
supporting and developing Galaxy and system due to the user's
requirements, and the first group of users will bring in data,
scientific questions and hands-on work on their own data. Main task
(regarding system load) will be sequence alignment (BLAST, mapping tools
like BWA/Bowtie), and after that maybe some experimental sequence
clustering/de novo assembly for exome data. Additionally variant
detection in whatever form are targeted. Only active projects will be
stored locally, data no more in use will be stored elsewhere in the network.
So far for the setting, regarding the specs the following is intended:
- dual-CPU mainboard
- 256 GB RAM
- 20-30 TB HDD @ RAID6 (data)
- SSDs @ RAID5 (system, tmp)
Due to funding limitations it may be the case that RAM has to be
decreased to 128 GB, not solved is currently the question, if it will be
enough for those SSD bundle in RAID5, maybe we have to go for only two
of them in RAID1.
What we try to find out is, where in those described tasks the machine
would run into bottlenecks. What's pretty clear is that I/O is
everything, already by a theoretical point of view. But we also observed
that on a comparable machine (2x 3,33 Ghz Intel 6-core, 100GB RAM, 450
MB/s R/W to data RAID6).
The question of questions is right at the beginning of configuring a
system, if one should go for an AMD or an Intel architecture system. The
first offers more cores (8-12) at a lower frequency (~2,4 Ghz), the
latter less cores (6) with higher frequency (~3,3 Ghz). Due to the data
sheets, the Intel CPUs are on a per-core basis ~30% faster with integer
operations and ~50% faster with floating point. The risk we see with the
AMDs is on the one hand that the number of cores per socket could
saturate the memory controller, and on the other hand those jobs, which
can not or only poorly be parallelized need more time.
To bring all this to some distinct questions (don't feel forced to
answer all of them):
1. Using the described bioinformatics software: where are the potential
system bottlenecks? (connections between CPUs, RAM, HDDs)
2. What is the expected relation of integer-based and floating point
based calculations, which will be loading the CPU cores?
3. Regarding the architectural differences (strengths, weaknesses):
Would an AMD- or an Intel-System be more suitable?
4. How much I/O (read and write) can be expected at the memory
controllers? Which tasks are most I/O intensive (regarding RAM and/or HDDs)?
5. Roughly separated in mapping and clustering jobs: which amounts of
main memory can be expected to be required by a single job (given e.g.
Illumina exome data, 50x coverage)? As far as I know mapping should be
around 4 GB, clustering much more (may reach high double digits).
6. HDD access (R/W) is mainly in bigger blocks instead of masses of
short operations - correct?
All those questions are a bit rough and improved (yes, it IS a bit of a
chaos currently - sorry for that), but any clue to a single question
would help. "Unfortunately" we got the money to place the order for our
own hardware unexpectedly quick, and we are now forced to act. We want
to make as few cardinal errors as possible...
Thanks a lot in advance,
Sebastian Schaaf, M.Sc. Bioinformatics
Chair of Biometry and Bioinformatics
Department of Medical Information Sciences, Biometry and Epidemiology
University of Munich
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