In [1]:

!date

Wed Apr 27 14:26:11 PDT 2016

In [2]:

%%bash
system_profiler SPSoftwareDataType

Software:

    System Software Overview:

      System Version: OS X 10.9.5 (13F34)
      Kernel Version: Darwin 13.4.0
      Boot Volume: Hummingbird
      Boot Mode: Normal
      Computer Name: hummingbird
      User Name: Sam (Sam)
      Secure Virtual Memory: Enabled
      Time since boot: 9 days 4:31

In [3]:

%%bash
#Uses grep to exclude lines that display serial number and hardware UUID
system_profiler SPHardwareDataType | grep -v [SH][ea]


      Model Name: Xserve
      Model Identifier: Xserve3,1
      Processor Name: Quad-Core Intel Xeon
      Processor Speed: 2.26 GHz
      Number of Processors: 2
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache (per Processor): 8 MB
      Memory: 24 GB
      Processor Interconnect Speed: 5.86 GT/s
      Boot ROM Version: XS31.0081.B06
      SMC Version (system): 1.43f4
      LOM Revision: 1.1.8

Show same file in each of three locations¶

In [4]:

%%bash
#Local copy of file
ls -lh /Volumes/Data/Sam/scratch/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz

-rw-r--r--  1 Sam  admin   3.0G Apr 27 14:25 /Volumes/Data/Sam/scratch/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz

In [5]:

%%bash
#External HDD copy of file
ls -lh /Volumes/toaster/sam/scratch/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz

-rw-r--r--  1 Sam  staff   3.0G Apr 27 14:21 /Volumes/toaster/sam/scratch/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz

In [6]:

%%bash
#Server (Owl) copy of file
ls -lh /Volumes/owl_web/nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz

-rw-rw-rw-  1 Sam  staff   3.0G Jan 25 02:30 /Volumes/owl_web/nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz

Gunzip all three files and send output to /dev/null (i.e. data is not saved when directed here)¶

In [7]:

%%bash
time gunzip -c /Volumes/Data/Sam/scratch/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz > /dev/null

real	1m7.447s
user	1m5.863s
sys	0m1.136s

In [8]:

%%bash
time gunzip -c /Volumes/toaster/sam/scratch/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz > /dev/null

real	1m6.946s
user	1m5.822s
sys	0m1.121s

In [9]:

%%bash
time gunzip -c /Volumes/owl_web/nightingales/O_lurida/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.gz > /dev/null

real	1m7.371s
user	1m5.826s
sys	0m1.201s

Surprisingly we don't see much speed difference (comparing the "real" time) between the the three file locations. Let's try with a significantly larger file¶

Show same file in each of three locations¶

In [10]:

%%bash
#Local copy of file
ls -lh /Volumes/Data/Sam/scratch/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz

-rw-r--r--  1 Sam  admin    17G Apr 27 14:53 /Volumes/Data/Sam/scratch/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz

In [11]:

%%bash
#External HDD copy of file
ls -lh /Volumes/toaster/sam/scratch/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz

-rw-r--r--  1 Sam  staff    17G Apr 27 14:57 /Volumes/toaster/sam/scratch/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz

In [12]:

%%bash
#Server (Owl) copy of file
ls -lh /Volumes/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz

-rw-r--r--  1 Sam  staff    17G Apr 22 04:21 /Volumes/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz

Gunzip all three files and send output to /dev/null (i.e. data is not saved when directed here)¶

In [13]:

%%bash
#Local copy of file
time gunzip -c /Volumes/Data/Sam/scratch/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz > /dev/null

real	6m45.887s
user	6m34.177s
sys	0m8.973s

In [14]:

%%bash
#External HDD copy of file
time gunzip -c /Volumes/toaster/sam/scratch/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz > /dev/null

real	7m54.975s
user	6m51.899s
sys	0m31.495s

In [15]:

%%bash
#Server (Owl) copy of file
time gunzip -c /Volumes/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz > /dev/null

real	13m52.376s
user	6m38.746s
sys	0m27.947s

With the larger file, there is a large difference in speed (comparing "real" time). Seems to show that dealing with files housed on the server is much slower than handling files locally.¶