>>> numbers = [1,2,3,4,5] >>> numpy.mean(numbers) Traceback (most recent call last): File "", line 1, in NameError: name 'numpy' is not defined >>> import numpy >>> numbers = [1,2,3,4,5] >>> numpy.mean(numbers) 3.0 >>> numpy.median(numbers) 3.0 >>> numpy.std(numbers) 1.4142135623730951
install numpy
[vagrant@localhost ~]$ python -V
Python 3.5.2
[vagrant@localhost ~]$ pip list
pip (8.1.1)
setuptools (20.10.1)
You are using pip version 8.1.1, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
[vagrant@localhost ~]$ pip install --upgrade pip
Collecting pip
Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB)
100% |████████████████████████████████| 1.3MB 478kB/s
Installing collected packages: pip
Found existing installation: pip 8.1.1
Uninstalling pip-8.1.1:
Successfully uninstalled pip-8.1.1
Successfully installed pip-9.0.1
[vagrant@localhost ~]$ pip install numpy
Collecting numpy
Downloading numpy-1.13.1-cp35-cp35m-manylinux1_x86_64.whl (16.9MB)
100% |████████████████████████████████| 16.9MB 54kB/s
Installing collected packages: numpy
Successfully installed numpy-1.13.1
vagrant upしようとした際に、error
コマンドラインで、vagrant upしようとしたら、error while executing `VBoxManage`と表示
>vagrant up
Bringing machine 'default' up with 'virtualbox' provider...
==> default: Importing base box 'bento/centos-6.8'...
==> default: Matching MAC address for NAT networking...
==> default: Checking if box 'bento/centos-6.8' is up to date...
==> default: A newer version of the box 'bento/centos-6.8' is available! You currently
==> default: have version '2.3.0'. The latest is version '2.3.4'. Run
==> default: `vagrant box update` to update.
==> default: Setting the name of the VM: FirstCentOs_default_1504414856800_6279
==> default: Clearing any previously set network interfaces...
==> default: Preparing network interfaces based on configuration...
default: Adapter 1: nat
default: Adapter 2: hostonly
==> default: Forwarding ports...
default: 22 (guest) => 2222 (host) (adapter 1)
==> default: Booting VM...
There was an error while executing `VBoxManage`, a CLI used by Vagrant
for controlling VirtualBox. The command and stderr is shown below.
Command: ["startvm", "6663a9a1-034a-4794-b88f-xxxxxxxxxxxx", "--type", "headless"]
困りますよね。別の仮想マシンを立ち上げましたが、同じように、error while executing `VBoxManage`と表示されたので、windowsのアプリから、Oracle VM VirtualBox 5.1.22をアンインストールして、Oracle VM VirtualBox 5.1.26を再度インストール。

今度は上手くいきました。
>vagrant up
Bringing machine 'default' up with 'virtualbox' provider...
==> default: Checking if box 'bento/centos-6.8' is up to date...
==> default: A newer version of the box 'bento/centos-6.8' is available! You currently
==> default: have version '2.3.0'. The latest is version '2.3.4'. Run
==> default: `vagrant box update` to update.
==> default: Clearing any previously set forwarded ports...
==> default: Clearing any previously set network interfaces...
==> default: Preparing network interfaces based on configuration...
default: Adapter 1: nat
default: Adapter 2: hostonly
==> default: Forwarding ports...
default: 22 (guest) => 2222 (host) (adapter 1)
==> default: Booting VM...
==> default: Waiting for machine to boot. This may take a few minutes...
default: SSH address: 127.0.0.1:2222
default: SSH username: vagrant
default: SSH auth method: private key
default: Warning: Connection reset. Retrying...
default: Warning: Connection aborted. Retrying...
default:
default: Vagrant insecure key detected. Vagrant will automatically replace
default: this with a newly generated keypair for better security.
default:
default: Inserting generated public key within guest...
default: Removing insecure key from the guest if it's present...
default: Key inserted! Disconnecting and reconnecting using new SSH key...
==> default: Machine booted and ready!
Numpy
Numpy
– functions useful for statistical analysis
– mean, median, standard deviation
Data Scientist
Hacking skills, Math & statistics knowledge, Substantive Expertise
Machine Learning, Data Science, Traditional Research
Raw data – processing – data set – statistical models / analysis – machine learning predictions – data driven products, reports visualization blogs
‘substantive expertise’
– knows which question to ask
– can interpret the data well
– understands structure of the data
– data scientist often work in team
Data science can solve problems you’d expect…
– netflix, social media, web apps, (okcupid, uber, etc)
bioin formatics, urban planning, a straphysics, public health, public health, sports
Tools to use
– Numpy
– multidimensional arrays + matrices
– mathematical functions
– Pandas
– handle data in a way suited to analysis
– similar to R
Both common among data scientists
Heavy Lifting Done by the run time
spow workers assign mappers
assign reducers
Issues to be handled by the run time
Master data structures
– location of files created by completed mapper
– score board of mapper/reducer assignment
– fault tolerance
* start new instances if no timely resonse
* completion message from redundant stragglers
– locality management
– task granlarity
– backup tasks
Content Delivery Networks
Napster started for music sharing
content hash, node-id where content stored
content-hash = 149 => <149, 80>
Name space {key-space, node-space}
content -> sha-1 -> unique 160-bit key, unique 160-bit node id
Objective:
APIs
– put key, getkey
CDN – an overlay network
routing table at A, name, node id, next
multimedia API
middleware
commodity OS
Parallel program
-pthreads: API for parallel programs
Distributed programs
-sockets: API for distributed programs
Conventional Distributed program
client – unix(socket) – server e.g. NFS
Novel multimedia Apps
sensor-based: sensors, distributed
sense -> prioritize -> process -> actuate
computationally intensive, real time
large-scale situation awareness
PTS Programming Model
Channel ch1 =
lookup(“video channel”)
while(1){
// get data
response γ =
ch1.get()
// process data
…
// produce output
ch2.put(item,
}
RioVista
RioVista
– performance-conscious design of persistent memory
Quicksilver
– making recovery a first class citizen in os design
LRVM Revisited
begin-xact, nomal program writes, end-xact
cpu, undo <- memory, cpu memory, memory data reda
CPU, application memory, File cache
mmap => normal application memory secomes rersistent
Crash Recovery
Treat like abort
– recover old image from undo log -> servives crashes since it is in RIO file cache
Crash during crash recovery?
– idempotency of recovery -> no problem
Server design
Server design
-persistent metadata m1, m2, ..mm
-normal data structures + code
=>
create external data segments to back persistent data structures
-apps manage their persistence needs
Designer’s choice to use single or multiple data segment
RVM Primitives
Initialization
– initialize(options)
– map(region, options)
– unmap(region)
Body of server code
– begin_xact (tid, restore_mode)
– set_range(tid, addr, size)
– end_xact(tid, connect, t_mode)
– abort_xact(tid)
GC to reduce log space
– flush()
– truncate()
bigin_xact(tid,mode); set range(tid, base_addr, #bytes); write meta data m1 write meta data m2 end_xact(tid, mode);
No action by LRVM
LRVM create redo log in memory
Redo log
-AV changes of different region between begin and end xact
Commit
Redo log, window of vulnerability
Log truncation
apply to data seg, read redo log
Log based striping
Client: memory, log seq, log fragments parity, LAN, storage services
Stripe Group, stripe group for x, y, z, L, M, N
-subset server into stripe group
-parallel client activities
-increased availability
-efficient log cleaning
Cache coherence
-single writer, multiple reader
-fileblock unit of coherence
write- request
-receive token
-manager revokes
Log cleaning
log segment evolution, writes to file blocks
– may belong to different files
Unix File System
{filename, offset} -> i-node -> data blocks on disk
Client node action
filename -> mmap -> metadata manager
Manager node actions
filename -> File Dir -> i-number -> i-map -> i-node a dir -> stripe group map -> storage server -> index node of logseg id -> stripe group map -> storage servers -> data blocks form -> storage severs
LRVM
– persistent memory layer in support of system service
Riovista
– performance conscious design of persistent – memory
Quicksilver
– making recovery a first clacks citizen in os design
Persistence
– need of os subsystems
– make virtual memory persistent
– subsystem designers 4 is performant
– use persistent logs to record changes to VM
VM -> replace VM
Implementation
Write(x)
DSM + OS coop x -> twin, original writable
Write project after release Twin, X’ diff run length
Non-page-based DSM
shared r/w -> dsm software -> <-data
library-based
-annotate shared variables
-coherence achons
inserted at point of access
API calls lang runtime
structured DSM
-APU for struct
-coherence action on app calls
DSM and speedup
LAN - DSM library - p -> mem
First NFS
-SUN, 1985
Client, LAN, Servers(student), file cache
DFS
no central server
-each file distributed across several nodes
DFS implemented across all disks in the network
Preliminaries: Striping a file to multiple disks
-increase I/O bandwidth by striping to parallel disks
-Failure protection by ECC
Log Structured File System
– Buffer changes to multiple files in one contiguous log segment data structure
– log segment to disk once a file up or periodically solves small write program
mods to x, mods to y, log segment written the disk
Eebra File System(uc-berkeley)
-combines LFS + RAID
use commodity hardware
-stripe by segment on multiple nodes’ disks in software
xFS – a DFS
-log based striping, cooperative caching, dynamic manageent of data, subsetting storage servers, distributed log cleaning
Traditional NFS with centralized server(s)
– memory content
* metadata, file cache, client caching divectory