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0.cloud-introduction.Rmd
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---
title: "Cloud Introduction"
author: "Data Carpentry"
date: "Tuesday, March 24, 2015"
---
## Learning Objectives
* Describe reasons why using a remote computer system is useful.
* Understand terms related to cloud and high-performance (HPC) computing.
* Describe the differences between HPC and cloud computing.
* Access resources related to HPC and cloud computing.
### What are some of reasons to access a remote computer system?
* Your computer does not have enough resources to run the desired analysis (memory, processors, disk space, network bandwidth).
* You want to produce results faster than your computer can.
* You cannot install software in your computer (application does not have support for your operating system, conflicts with other existing applications)
### Main Computational Resources
* Find how much disk space is available in your system. Check that you have enough space to get and extract the input file of :
```{r, eval=FALSE}
df -h
wget http://www.hpa-bioinformatics.org.uk/lgp/resource/Sample280.fastq.gz
ls -lah Sample280.fastq.gz
gunzip Sample280.fastq.gz
ls -lah Sample280.fastq
```
The output on iPlant Atmosphere:
```{r, eval=FALSE}
--2015-03-25 09:40:33-- http://www.hpa-bioinformatics.org.uk/lgp/resource/Sample280.fastq.gz
Resolving www.hpa-bioinformatics.org.uk... 194.74.226.185
Connecting to www.hpa-bioinformatics.org.uk|194.74.226.185|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 215949113 (206M) [application/x-gzip]
Saving to: \u201cSample280.fastq.gz\u201d
100%[==========================================================================================>] 215,949,113 213K/s in 16m 48s
2015-03-25 09:57:21 (209 KB/s) - \u201cSample280.fastq.gz\u201d saved [215949113/215949113]
-rw-r--r-- 1 dnasubway01 iplant-everyone 206M Jun 29 2011 Sample280.fastq.gz
-rw-r--r-- 1 dnasubway01 iplant-everyone 627M Jun 29 2011 Sample280.fastq
```
The output on Amazon EC2:
```{r, eval=FALSE}
--2015-03-25 15:30:23-- http://www.hpa-bioinformatics.org.uk/lgp/resource/Sample280.fastq.gz
Resolving www.hpa-bioinformatics.org.uk (www.hpa-bioinformatics.org.uk)... 194.74.226.185
Connecting to www.hpa-bioinformatics.org.uk (www.hpa-bioinformatics.org.uk)|194.74.226.185|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 215949113 (206M) [application/x-gzip]
Saving to: \u2018Sample280.fastq.gz\u2019
Sample280.fastq.gz 100%[===============================================================>] 205.94M 376KB/s in 9m 23s
2015-03-25 15:39:46 (375 KB/s) - \u2018Sample280.fastq.gz\u2019 saved [215949113/215949113]
-rw-rw-r-- 1 ec2-user ec2-user 206M Jun 29 2011 Sample280.fastq.gz
-rw-rw-r-- 1 ec2-user ec2-user 627M Jun 29 2011 Sample280.fastq
```
The output on Azure:
```{r, eval=FALSE}
--2015-03-25 14:37:18-- http://www.hpa-bioinformatics.org.uk/lgp/resource/Sample280.fastq.gz
Resolving www.hpa-bioinformatics.org.uk... 194.74.226.185
Connecting to www.hpa-bioinformatics.org.uk|194.74.226.185|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 215949113 (206M) [application/x-gzip]
Saving to: \u201cSample280.fastq.gz\u201d
100%[===========================================================================================================================================>] 215,949,113 216K/s in 16m 26s
2015-03-25 14:53:44 (214 KB/s) - \u201cSample280.fastq.gz\u201d saved [215949113/215949113]
-rw-r--r--. 1 root root 206M Jun 29 2011 Sample280.fastq.gz
-rw-r--r--. 1 root root 627M Mar 25 14:57 Sample280.fastq
```
* Find how many cores and processors are available in your system:
```{r, eval=FALSE}
cat /proc/cpuinfo
```
```{r, eval=FALSE}
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 44
model name : Westmere E56xx/L56xx/X56xx (Nehalem-C)
stepping : 1
cpu MHz : 2400.084
cache size : 4096 KB
fpu : yes
fpu_exception : yes
cpuid level : 11
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon rep_good unfair_spinlock pni pclmulqdq vmx ssse3 cx16 pcid sse4_1 sse4_2 popcnt aes hypervisor lahf_lm
bogomips : 4800.16
clflush size : 64
cache_alignment : 64
address sizes : 40 bits physical, 48 bits virtual
power management:
processor : 1
vendor_id : GenuineIntel
cpu family : 6
model : 44
model name : Westmere E56xx/L56xx/X56xx (Nehalem-C)
stepping : 1
cpu MHz : 2400.084
cache size : 4096 KB
fpu : yes
fpu_exception : yes
cpuid level : 11
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon rep_good unfair_spinlock pni pclmulqdq vmx ssse3 cx16 pcid sse4_1 sse4_2 popcnt aes hypervisor lahf_lm
bogomips : 4800.16
clflush size : 64
cache_alignment : 64
address sizes : 40 bits physical, 48 bits virtual
power management:
```
On an Amazon EC2 instance, the following output shows availability of 2 Intel Xeon processors:
```{r, eval=FALSE}
cat /proc/cpuinfo
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 62
model name : Intel(R) Xeon(R) CPU E5-2670 v2 @ 2.50GHz
stepping : 4
microcode : 0x415
cpu MHz : 2494.060
cache size : 25600 KB
physical id : 0
siblings : 2
core id : 0
cpu cores : 2
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm xsaveopt fsgsbase smep erms
bogomips : 4988.12
clflush size : 64
cache_alignment : 64
address sizes : 46 bits physical, 48 bits virtual
power management:
processor : 1
vendor_id : GenuineIntel
cpu family : 6
model : 62
model name : Intel(R) Xeon(R) CPU E5-2670 v2 @ 2.50GHz
stepping : 4
microcode : 0x415
cpu MHz : 2494.060
cache size : 25600 KB
physical id : 0
siblings : 2
core id : 1
cpu cores : 2
apicid : 2
initial apicid : 2
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology eagerfpu pni pclmulqdq ssse3 cx16 pcid sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm xsaveopt fsgsbase smep erms
bogomips : 4988.12
clflush size : 64
cache_alignment : 64
address sizes : 46 bits physical, 48 bits virtual
power management:
```
On an Microsoft Azure instance, the following output shows availability of 2 Intel Xeon processors:
```{r, eval=FALSE}
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 63
model name : Intel(R) Xeon(R) CPU E5-2698B v3 @ 2.00GHz
stepping : 2
cpu MHz : 1995.365
cache size : 40960 KB
physical id : 0
siblings : 4
core id : 0
cpu cores : 4
apicid : 0
initial apicid : 0
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx lm constant_tsc rep_good unfair_spinlock pni pclmulqdq ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm abm xsaveopt fsgsbase bmi1 avx2 smep bmi2 erms
bogomips : 3990.73
clflush size : 64
cache_alignment : 64
address sizes : 42 bits physical, 48 bits virtual
power management:
processor : 1
vendor_id : GenuineIntel
cpu family : 6
model : 63
model name : Intel(R) Xeon(R) CPU E5-2698B v3 @ 2.00GHz
stepping : 2
cpu MHz : 1995.365
cache size : 40960 KB
physical id : 0
siblings : 4
core id : 1
cpu cores : 4
apicid : 1
initial apicid : 1
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx lm constant_tsc rep_good unfair_spinlock pni pclmulqdq ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm abm xsaveopt fsgsbase bmi1 avx2 smep bmi2 erms
bogomips : 3990.73
clflush size : 64
cache_alignment : 64
address sizes : 42 bits physical, 48 bits virtual
power management:
processor : 2
vendor_id : GenuineIntel
cpu family : 6
model : 63
model name : Intel(R) Xeon(R) CPU E5-2698B v3 @ 2.00GHz
stepping : 2
cpu MHz : 1995.365
cache size : 40960 KB
physical id : 0
siblings : 4
core id : 2
cpu cores : 4
apicid : 2
initial apicid : 2
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx lm constant_tsc rep_good unfair_spinlock pni pclmulqdq ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm abm xsaveopt fsgsbase bmi1 avx2 smep bmi2 erms
bogomips : 3990.73
clflush size : 64
cache_alignment : 64
address sizes : 42 bits physical, 48 bits virtual
power management:
processor : 3
vendor_id : GenuineIntel
cpu family : 6
model : 63
model name : Intel(R) Xeon(R) CPU E5-2698B v3 @ 2.00GHz
stepping : 2
cpu MHz : 1995.365
cache size : 40960 KB
physical id : 0
siblings : 4
core id : 3
cpu cores : 4
apicid : 3
initial apicid : 3
fpu : yes
fpu_exception : yes
cpuid level : 13
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx lm constant_tsc rep_good unfair_spinlock pni pclmulqdq ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm abm xsaveopt fsgsbase bmi1 avx2 smep bmi2 erms
bogomips : 3990.73
clflush size : 64
cache_alignment : 64
address sizes : 42 bits physical, 48 bits virtual
power management:
```
* Find how many processes are running in your system, and how much resources is each consuming:
```{r, eval=FALSE}
top
```
* Find how long it takes to run an application:
```{r, eval=FALSE}
time <your_application>
```
* For example, let's measure the time it takes to separate the R1 sequences into a separate file:
```{r, eval=FALSE}
time awk "/\/1$/{print; getline; print}" Sample280.fastq > Sample280_1.fastq
```
The output on iPlant Atmosphere, Amazon EC2, and Microsoft Azure are shown respectively below, indicating that EC2 took half of the time of Azure.
```{r, eval=FALSE}
real 0m20.893s
user 0m19.573s
sys 0m1.309s
real 0m14.856s
user 0m14.260s
sys 0m0.592s
real 0m36.294s
user 0m12.762s
sys 0m0.432s
```
### Distributed System Definitions and stacks:
(Note that many definitions exist for these terms)
* Distributed application: an application that can be executed on a distributed system platform (e.g., mpiBLAST)
* Distributed system platform: software layers that facilitates coordination and management of a distributed system (e.g., queue-based system, and MapReduce)
* Distributed system:
* High Performance Computing (HPC): large assemble of physical machines and a homogeneous operating system (e.g., your institutions' HPC, XSEDE's HPC)
* Cloud Computing: virtual machines, distributed platforms and/or applications offered as a service (e.g., Amazon Web Services, Microsoft Azure, Google Cloud Computing)
* Virtual machine (VM): software computer that like a physical computer can run an operating system and applications
* Operating system (OS): the basic software layer that allows execution and management of applications
* Physical machine: the hardware (processors, memory, disk and network)
### HPC vs. Cloud:
| HPC | Cloud |
|:----|:------|
| User account on the system | root account on the system |
| Limited control of the system | Full control of the system |
| Central shared file system | Local file system |
| Jobs submitted into a queue | Jobs executed on each resource |
| Account-based isolation | OS-based isolation |
| Batch-oriented execution of applications | support for batch or interactive applications |
| Request for resource and time allocation | Pay-per-use |
| etc. | etc.|
### Resources:
* Cloud computing offerings:
* Amazon EC2: http://aws.amazon.com/ec2/
* Microsoft Azure: https://azure.microsoft.com/en-us/
* Google Cloud Platform: https://cloud.google.com/
* iPlant's Atmosphere: http://www.iplantcollaborative.org/ci/atmosphere
* iPlant's help page: https://pods.iplantcollaborative.org/wiki/display/atmman/Atmosphere+Manual+Table+of+Contents
* HPC offerings:
* XSEDE: https://www.xsede.org/high-performance-computing