Cost Effectiveness Analysis (CEA) of running Ray on Amazon EC2

- 
Sample: SRA001125
URL: http://trace.ddbj.nig.ac.jp/DRASearch/submission?acc=SRA001125
DNA reads: 34911784 (2 * 17455892)
Read length (nt): 36
Technology: Illumina Genome Analyzer

API name: m1.large
2 Ray processes
Running time: 05:28:46
Pricing: 0.260 $ / h
Cost: 1.560 $

API name: m3.xlarge
4 Ray processes
Running time: 02:31:34
Pricing: 0.580 $ / h
Cost: 1.730 $

API name: cc2.8xlarge
32 Ray processes
Running time: 00:54:06
Pricing: 2.400 / h 
Cost: 2.400 $

Conclusions:

1. You get your results faster if you pay more.

2. For cc2.8xlarge, 33% (00:19:40) of the time was loading sequences from EBS.
That's a lot !

3. The scalability on this problem is not that good because the
problem size is not very large.

4. Amazon EC2 is really affordable for de novo assemblies of bacterial genomes. 
 
 
 
If you want to try these tests yourself => http://github.com/sebhtml/Ray-in-Amazon-EC2-CLOUD

Comments

Post a Comment

Popular posts from this blog

A survey of the burgeoning industry of cloud genomics

-
Image
I like lists. Here is a list of companies in the cloud genomics industry. Table 1: Companies acting in the industry of cloud genomics. The list is in no particular order. Company Products People Founded Link GenoSpace, LLC - GenoSpace platform - John Quackenbush (CEO) 2011 https://www.genospace.com/ DNAnexus, Inc. - DNAnexus Platform - DNAnexus Platform SDK (a.k.a. dx-toolkit) - Serafim Batzoglou (co-founder) - Andreas Sundquist (co-founder and CTO) - a bunch of other famous people in the field 2009 https://dnanexus.com/ Seven Bridges Genomics, Inc. - IGOR - IGOR Python SDK - Igor Bogicevic (CTO) 2009 https://www.sbgenomics.com/ BGI - EasyGenomics - Xing Xu (Senior Product Manager) Introduced in 2012 https://www.easygenomics.com/ Illumina, Inc. - BaseSpace™ - BaseSpace API - Alex Dickinson (SVP of Cloud Genomics) Introduced in 2011 https://basespace.illumina.com/ Era7 Information Technologies SLU - BG7
Read more

Generating neural machine instructions for multi-head attention

-
  An animal can do training and inference every day of its existence until the day of its death. A forward pass is all you need.   Here is the current model configuration that I use for multi-head attention:         let sequence_length = 6;         let vocab_size = 20;         let n_embd = 64;         let num_heads = 8; You can see the full model here: https://github.com/sebhtml/novigrad/blob/8df6192829edd9cda3a221e12affa770fbda2a1b/src/models/mega_man_attention.rs The struct uses Embedding, MultiHeadAttention, Linear, Softmax: struct MegaManAttentionModel {     input_shape: Vec<usize>,     output_shape: Vec<usize>,     vocab_size: usize,     sequence_length: usize,     embedding: Embedding,     multi_head_attention: MultiHeadAttention,     linear: Linear,     softmax: Softmax, } The instructions generated by Novigrad are below. Notes: - INSTRUCTION    MatMul    t170 t166    t171     means that we do a matrix multiplication between tensors t170 and t166 and the result is wr
Read more

Adding ZVOL VIRTIO disks to a guest running on a host with the FreeBSD BHYVE hypervisor

-
On atlantis.domain (my FreeBSD BHYVE hypervisor host), I use these commands: Install FreeBSD on a 10G disk. vm create -s 10G guestname   vm install FreeBSD-12.1-RELEASE-amd64-memstick.img vm console guestname Add 8 30GB zvol-based disks vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname You will need to do vm poweroff guestname vm start guestname because the guest does not seem to see the 8 30GB without power cycling. (rebooting won't work) *** If you want the boot disk (the one create by "vm create") to be a zvol, you must edit the template: root@atlantis:~ # zfs snapshot tank/vm-bhyve@2020-06-11-2145 root@atlantis:~ # mount -t zfs tank/vm-bhyve@2020-06-11-2145 /tank/vm-bhyve@2020-06-11-2145 r
Read more