YPD plate with glucose directly added

Make YPD plates with glucose directly added.

1. Dissolve 10g of BactoYeast extract in 500ml water
2. Dissolve 20g of BactoPeptone in the above solution
3. Dissolve 20g Dextrose in the above solution
4. Add 20g agar
5. Melt agar into solution in the microwave (skipped)
6. q.s. to 1000ml with water
7. Autoclave

See   http://www.thelabrat.com/protocols/YPDAgar.shtml

bio233, 20150930Tue, exam 1 review,

Exam 1, part 2, make up, bamboo pen

makeup open in class.

bio233 20150929Tue review of exam 1

bio233 20150929Tue review of exam 1

go over exam 1

make up exercises for part 2. Group exercise.

A few student sat alone, but I asked them to join a group nearby, they were welcomed by the groups.
In one group, students were explaining how to do unit conversions and scale conversions.

In another group, students were exchanging answers, and they were trying to gaming the test as a group. The group that were gaming the system quickly got all the correct answers. Unfortunately, they have missed the point of the entire makeup practice.

The students clearly enjoyed the group work to redo the exam.

NSF workshop information

http://www.nsf.gov/pubs/gpg/nsf04_23/2.jsp#IID7


An estimated total budget for the conference, together with an itemized statement of the amount of support requested from NSF (the NSF budget may include participant support for transportation (when appropriate), per diem costs, stipends, publication and other conference-related costs. (Note: participant support costs must be excluded from the indirect cost base.) See Chapter II, Section C.2.g.(v); and


http://www.nsf.gov/bio/mcb/confworkshopguidance.jsp

Allowable costs
http://www.nsf.gov/pubs/manuals/gpm05_131/gpm6.jsp

skin related GEO datasets

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68583
Comparative transcriptome profiling of human epidermis keratinocyte stem cells (KSC) versus keratinocyte progenitors (KP)
http://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE68583


Age-related methylation changes are associated with altered transcriptional circuitry [Methyl-seq]

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46450

http://www.ncbi.nlm.nih.gov/pubmed/24279375

Epigenetics Chromatin. 2013 Oct 31;6(1):36. doi: 10.1186/1756-8935-6-36.

Aging is associated with highly defined epigenetic changes in the human epidermis.

Raddatz G, Hagemann S, Aran D, Söhle J, Kulkarni PP, Kaderali L, Hellman A, Winnefeld M, Lyko F.

tissue specific gene expression data in mouse

MPSS mouse transcriptome analysis project, tissue reference

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1581

Red blood cell trait in African Americans

=> Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network

Zhao Chen1, Hua Tang3, Rehan Qayyum4, Ursula M. Schick5, Michael A. Nalls6, Robert

Handsaker7, Jin Li8, Yingchang Lu10, Lisa R. Yanek15, Brendan Keating16, Yan Meng18,

Frank J.A. van Rooij19, Yukinori Okada20,21,22, Michiaki Kubo23, Laura Rasmussen-Torvik24,

Margaux F. Keller25, Leslie Lange26, Michele Evans27, Erwin P. Bottinger11, Michael D.

Linderman12, Douglas M. Ruderfer13, Hakon Hakonarson8,9,17, George Papanicolaou28,

Alan B. Zonderman29, Omri Gottesman11, BioBank Japan Project, CHARGE Consortium,

Cynthia Thomson2, Elad Ziv30, Andrew B. Singleton25, Ruth J.F. Loos14, Patrick M.A.

Sleiman8,9,17, Santhi Ganesh31, Steven McCarroll32,33, Diane M. Becker4, James G. Wilson34,

Guillaume Lettre35 and Alexander P. Reiner5,36,∗

=> Genome-wide association study of white blood cell count in 16,388 African Americans: the continental origins and genetic epidemiology network (COGENT).

http://www.ncbi.nlm.nih.gov/pubmed/21738479

PLoS Genet. 2011 Jun;7(6):e1002108. doi: 10.1371/journal.pgen.1002108. Epub 2011 Jun 30.

FYE studying, note taking

VGA connector, dry-erasable marker, Playdough, beaker
Two beaker, play dough balls, large and small demo.

Soractive for discussions.

Note taking video as backup plans.

Note taking videoshttps://www.youtube.com/watch?v=UAhRf3U50lM
Cornell notes:  https://www.youtube.com/watch?v=w3pM5hEgBk4
Clarissa on Cornell notes: https://www.youtube.com/watch?v=Y4uzQEWj0X8

bio233 exam 1, part 2, open book exam.

bring papers for calculation question.

color code for the structure question
 white: C
 red:  O
 blue: N
 orange/yellow: P


Bring extra paper for students to show their process to get some partial credits.

bio386, 20150924Thu

linear regression, abline plot

go over previous exam1

XSEDE GORDON

https://portal.xsede.org/sdsc-gordon#running

MBryant 20150923Wed

Use the following code to get protein sequences and gene names from NCBI

echo -e "3119" | while read G; do curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=protein&id=${G}" | grep -A 1 "<Link>" | grep "<Id>" | cut -d '>' -f 2 | cut -d '<' -f 1 | while read S ; do curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=${S}&retmode=text&rettype=fasta" ; done;  done > _out3119.txt

See https://www.biostars.org/p/52652/

We decided to run this code individually for each id, because there are multiple output sequence for each NCBI gene ID. 

white and red blood cells

Red blood cells, photohemolysis
M. Al-Akhras, A new application of Gompertz function in photohemolysis: the effect of temperature on red blook cell hemolysis phtosensitized by protoporthyrin IX, Med Bio, Eng Comput. 2006, 44:703-710.  Figures are plotted as percentage of dead cells ~ time, i.e., 1-viability ~ time.

http://www.haematologica.org/content/early/2015/02/09/haematol.2014.116368.abstract

http://onlinelibrary.wiley.com/doi/10.1002/ajh.23982/abstract;jsessionid=0CA8BAF2EF87DAE6D642B2B5CE13CB1B.f02t04?userIsAuthenticated=false&deniedAccessCustomisedMessage=


Late stages of hematopoiesis and B cell lymphopoiesis are regulated by α-synuclein, a key player in Parkinson's disease
http://www.sciencedirect.com/science/article/pii/S0171298514001272

MSPnet academy, computational thinking

MSPnet Academy: Infusing Computational Thinking into Science Education Presenters: Irene Lee, Maureen Psaila-Dombrowski, Paige Prescott Sep 21, 2015 at 2:00 PM (Eastern) 
Description: The Santa Fe Institute has been developing programs and curricula that infuse computational thinking into Science education for the past 12 years. In this webinar we will describe how the study of Complex Adaptive Systems through computer modeling and simulation fits into existing science frameworks and classes, share information about our program and curricula, and describe the professional development needed to prepare Science teachers to address the computational thinking practices presented in the NRC framework and NGSS. Capacity is limited and access is first-come, first served. Please RSVP to confirm your attendance. Early admission (10 minutes prior to the scheduled starting time) will be granted to those who respond "yes". 
To RSVP, go to http://hub.mspnet.org/wr.cfm/454/202819/D8SBEHAc40Zv86aCYBGE.

travel policy, per diem rate

per diem rate

http://www.gsa.gov/portal/content/242627
2015 GSA rate

 
Atlanta rate:
http://www.gsa.gov/portal/category/100120

bio386, Tue, salary example

Go over salary example. Ask students to follow along. Some students were able to modify my code and apply it to different variables.
The EdX R course also prepared the students for R syntax.

Correlationhttps://class.coursera.org/rprog-032/forum/thread?thread_id=265

Announcement: Skip "program 2 assignment" on Coursera's R course.

youtube:
https://youtu.be/wrM2uA0NGNs

bio233 gram stain lab, Monday

Gram stain lab.

Sunday: 
I prepared the lab on Sunday.

Items: 
Distilled water

·      Slides, cover slips

·      Bunsen burners and lighter

·      Inoculating loops

·      Microscope (optional oil-immersion lenses, oil cleaner)

·      Lens wipers

·      Bibulous papers (Absorbent papers)

·      Wax pencil

·      Crystal violet

·      Gram iodine

·      Safranin 

·      95% EtOH

·      75% EthOH

·      Dropping pipettes

·      Shape collection box

·      Staining rack

·      Clips for staining

·      White paper towel to absorb the runoff

·      Kim wipes

Lab coat is recommended

Microscope with vertical adaptoer, smart phone stages. 

Monday  gram stain lab, 2pm-4:40pm

Many students did not know how to use microscope. 

There is a shortage of microscope with vertical adapters. 

flow cytometer models

http://www.aceabio.com/novocyte/novocyte-index.html

Accuri C6

http://www.emdmillipore.com/US/en/life-science-research/cell-analysis/flow-cytometry-instrumentation/9Iyb.qB.31gAAAFMiMw0iy0I,nav

bio233 20150917Thu go over problem sets

bio233 20150917Thu go over problem sets

Go over youtube tutorial on screen cast. Bonus points will be given to students for self-recording during exam.

bio386 20150917Thu, coursera coding assignment part1

Problem: Almost all students did not watch the coursera videos. they seem to expect to finish the assignment without going over the lecture videos.

bio386 20150917Thu, coursera coding assignment part1

MByant 20150916

Convert PDF into WORD.
MB manually copy-pasted Table 2 into an Excel file.

Get FASTA sequences using NCBI Gene ID

echo -e "19084\n112407\n18113" | while read G; do curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=protein&id=${G}" | grep -A 1 "<Link>" | grep "<Id>" | cut -d '>' -f 2 | cut -d '<' -f 1 | while read S ; do curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=${S}&retmode=text&rettype=fasta" ; done;  done

See https://www.biostars.org/p/52652/

HQ tested with 1029 and it returned the correct sequences. 

aging genomics resource

http://genomics.senescence.info/

http://pcwww.liv.ac.uk/~aging/publications.html

*** greenfield, netaging.pbs running results, each run is 6.5 SU

Conclusions: Each run is 8:30pm - 3am = 6.5 hours. 

20140914 8:30pm :: qsub netaging.pbs 

[hqin2@greenfield ms02GINPPI]$ cat netaging.pbs

#!/bin/bash

# Request 15 cores

#PBS -l nodes=1:ppn=15

#  Request 7days  of cpu time

#PBS -l walltime=7:00:00:00

module load R/3.2.1-mkl

echo hostname

pwd

cd /crucible/mc48o9p/hqin2/mactower-network-failure-simulation-master/ms02GINPPI

pwd

numactl -C +0 R --vanilla --slave -f net-aging-sim-20150915.R --args 92 92 0.02 1.0 2000  &

numactl -C +1 R --vanilla --slave -f net-aging-sim-20150915.R --args 93 93 0.02 1.0 2000  &

numactl -C +2 R --vanilla --slave -f net-aging-sim-20150915.R --args 94 94 0.02 1.0 2000  &

numactl -C +3 R --vanilla --slave -f net-aging-sim-20150915.R --args 95 95 0.02 1.0 2000  &

numactl -C +4 R --vanilla --slave -f net-aging-sim-20150915.R --args 96 96 0.02 1.0 2000  &

numactl -C +5 R --vanilla --slave -f net-aging-sim-20150915.R --args 97 97 0.02 1.0 2000  &

numactl -C +6 R --vanilla --slave -f net-aging-sim-20150915.R --args 98 98 0.02 1.0 2000  &

numactl -C +7 R --vanilla --slave -f net-aging-sim-20150915.R --args 99 99 0.02 1.0 2000  &

numactl -C +8 R --vanilla --slave -f net-aging-sim-20150915.R --args 100 100 0.02 1.0 2000  &

numactl -C +9 R --vanilla --slave -f net-aging-sim-20150915.R --args 101 101 0.02 1.0 2000  &

numactl -C +10 R --vanilla --slave -f net-aging-sim-20150915.R --args 102 102 0.02 1.0 2000  &

numactl -C +11 R --vanilla --slave -f net-aging-sim-20150915.R --args 103 103 0.02 1.0 2000  &

numactl -C +12 R --vanilla --slave -f net-aging-sim-20150915.R --args 92 92 0.01 1.0 2000  &

wait

[hqin2@greenfield ms02GINPPI]$ ll -th dipgin.ms02.output/9[2-9]/popages/*2000*

-rw-r--r-- 1 hqin2 mc48o9p 33K Sep 15 02:55 dipgin.ms02.output/96/popages/cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Sep15_025515.txt

-rw-r--r-- 1 hqin2 mc48o9p 33K Sep 15 02:55 dipgin.ms02.output/95/popages/cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Sep15_025509.txt

-rw-r--r-- 1 hqin2 mc48o9p 33K Sep 15 02:54 dipgin.ms02.output/98/popages/cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Sep15_025456.txt

-rw-r--r-- 1 hqin2 mc48o9p 34K Sep 15 02:54 dipgin.ms02.output/97/popages/cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Sep15_025451.txt

-rw-r--r-- 1 hqin2 mc48o9p 34K Sep 15 02:54 dipgin.ms02.output/94/popages/cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Sep15_025442.txt

-rw-r--r-- 1 hqin2 mc48o9p 33K Sep 15 02:54 dipgin.ms02.output/99/popages/cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Sep15_025409.txt

-rw-r--r-- 1 hqin2 mc48o9p 33K Sep 15 02:52 dipgin.ms02.output/92/popages/cutoff.4.p.1.lambda.0.01.popsize.2000.time.2015Sep15_025240.txt

-rw-r--r-- 1 hqin2 mc48o9p 33K Sep 15 02:52 dipgin.ms02.output/93/popages/cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Sep15_025211.txt

-rw-r--r-- 1 hqin2 mc48o9p 33K Sep 15 02:50 dipgin.ms02.output/92/popages/cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Sep15_025058.txt

[hqin2@greenfield ms02GINPPI]$ ll -th dipgin.ms02.output/10[234]/popages/*2000*

-rw-r--r-- 1 hqin2 mc48o9p 33K Sep 15 02:54 dipgin.ms02.output/102/popages/cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Sep15_025438.txt

-rw-r--r-- 1 hqin2 mc48o9p 33K Sep 15 02:53 dipgin.ms02.output/103/popages/cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Sep15_025353.txt

[hqin2@greenfield ms02GINPPI]$ cat netaging.pbs.o2350 | grep 2000 | grep "1.0"

[1] "101"  "101"  "0.02" "1.0"  "2000"

 "100"  "100"  "0.02" "1.0"  "2000"

[1] "94"   "94"   "0.02" "1.0"  "2000"

[1] "92"   "92"   "0.02" "1.0"  "2000"

 "103"  "0.02" "1.0"  "2000"

 "102"  "0.02" "1.0"  "2000"

 "1.0"  "2000"

[1] "97"   "97"   "0.02" "1.0"  "2000"

 "1.0"  "2000"

[1] "95"   "95"   "0.02" "1.0"  "2000"

[1] "96"   "96"   "0.02" "1.0"  "2000"

 "99"   "99"   "0.02" "1.0"  "2000"

 "92"   "92"   "0.01" "1.0"  "2000"

Genie technology

Genie technology and broaden participation

bio233 20150915Tue ch4 go over exam 1, part2 of fall 2014

Retrurn central dogma drawing back to students

Exam preparation

http://hongqinlab.blogspot.com/2015/09/bio233-ch4-mole-biol.html
http://hongqinlab.blogspot.com/2014/03/bio233-ch6-dna-helices-bases-3d.html
http://hongqinlab.blogspot.com/2014/09/bio233-20140930-ch5-continued-and-ch6.html
http://hongqinlab.blogspot.com/2015/01/bio125-tue-jan-20-2015-dna-structure.html

bio386, week 1, programming assignment

Problem: One student try to read in a file in a directory. "directory/file_name"

The first programming assignment of the Coursera is very challenging. Students started to have trouble to complete the programming assignment.

(in progress)(to do) network aging popSize=2000

[hqin2@greenfield ms02GINPPI]$ cat netaging.pbs 

#!/bin/bash

# Request 15 cores

#PBS -l nodes=1:ppn=15

#  Request 2:30 minutes of cpu time

#PBS -l walltime=7:00:00:00

module load R/3.2.1-mkl

echo hostname

pwd

cd /crucible/mc48o9p/hqin2/mactower-network-failure-simulation-master/ms02GINPPI

pwd

numactl -C +0 R --vanilla --slave -f net-aging-sim-20150915.R --args 92 92 0.02 1.0 2000  &

numactl -C +1 R --vanilla --slave -f net-aging-sim-20150915.R --args 93 93 0.02 1.0 2000  &

numactl -C +2 R --vanilla --slave -f net-aging-sim-20150915.R --args 94 94 0.02 1.0 2000  &

numactl -C +3 R --vanilla --slave -f net-aging-sim-20150915.R --args 95 95 0.02 1.0 2000  &

numactl -C +4 R --vanilla --slave -f net-aging-sim-20150915.R --args 96 96 0.02 1.0 2000  &

numactl -C +5 R --vanilla --slave -f net-aging-sim-20150915.R --args 97 97 0.02 1.0 2000  &

numactl -C +6 R --vanilla --slave -f net-aging-sim-20150915.R --args 98 98 0.02 1.0 2000  &

numactl -C +7 R --vanilla --slave -f net-aging-sim-20150915.R --args 99 99 0.02 1.0 2000  &

numactl -C +8 R --vanilla --slave -f net-aging-sim-20150915.R --args 100 100 0.02 1.0 2000  &

numactl -C +9 R --vanilla --slave -f net-aging-sim-20150915.R --args 101 101 0.02 1.0 2000  &

numactl -C +10 R --vanilla --slave -f net-aging-sim-20150915.R --args 102 102 0.02 1.0 2000  &

numactl -C +11 R --vanilla --slave -f net-aging-sim-20150915.R --args 103 103 0.02 1.0 2000  &

numactl -C +12 R --vanilla --slave -f net-aging-sim-20150915.R --args 92 92 0.01 1.0 2000  &

wait

[hqin2@greenfield ms02GINPPI]$ qsub netaging.pbs 

2350.greenfield.psc.xsede.org

[hqin2@greenfield ms02GINPPI]$ qstat

Job ID                    Name             User            Time Use S Queue

------------------------- ---------------- --------------- -------- - -----

2104.greenfield            newRunNew.job    ismini          134:54:1 R batch          

2314.greenfield            runjob           hchen7          21:41:25 R batch          

2350.greenfield            netaging.pbs     hqin2                  0 R batch          

[hqin2@greenfield ms02GINPPI]$ qstat

Job ID                    Name             User            Time Use S Queue

------------------------- ---------------- --------------- -------- - -----

2104.greenfield            newRunNew.job    ismini          134:54:1 R batch          

2314.greenfield            runjob           hchen7          21:41:25 R batch          

2350.greenfield            netaging.pbs     hqin2                  0 R batch          

[hqin2@greenfield ms02GINPPI]$ 

[hqin2@greenfield ms02GINPPI]$ 

[hqin2@greenfield ms02GINPPI]$ 

[hqin2@greenfield ms02GINPPI]$ qstat -a

greenfield.psc.xsede.org: 

                                                                                  Req'd    Req'd       Elap

Job ID                  Username    Queue    Jobname          SessID  NDS   TSK   Memory   Time    S   Time

----------------------- ----------- -------- ---------------- ------ ----- ------ ------ --------- - ---------

2104.greenfield.psc.xs  ismini      batch    newRunNew.job     83468     1     30    --  150:00:00 R 116:11:48

2314.greenfield.psc.xs  hchen7      batch    runjob           139085     1     15    --   24:00:00 R  21:41:55

2350.greenfield.psc.xs  hqin2       batch    netaging.pbs      48203     1     15    --  168:00:00 R  00:00:12

[hqin2@greenfield ms02GINPPI]$ 

backup files from crucial to my data directory (in progress)

$ tar cf /arc/users/hqin2/ms02GINPPI.tar ms02GINPPI/ & 

[1] 17265

[hqin2@greenfield mactower-network-failure-simulation-master]$ ps

  PID TTY          TIME CMD

 1519 pts/10   00:00:00 bash

17265 pts/10   00:00:00 tar

17280 pts/10   00:00:00 ps

There some runtime errors during the tar operation. Maybe some simulation jobs were killed prematurely. 

$ tar: ms02GINPPI/dipgin.ms02.output/43/ms02_43.tab: Read error at byte 0, while reading 7680 bytes: Connection timed out

$ tar: ms02GINPPI/dipgin.ms02.output/49/popages/cutoff.4.p.1.lambda.0.02.popsize.2000.time.2014Oct22_043941.txt: Read error at byte 0, while reading 8192 bytes: Connection timed out

$ tar: ms02GINPPI/dipgin.ms02.output/133/ms02_133.tab: Read error at byte 0, while reading 1536 bytes: Connection timed out

$ tar: ms02GINPPI/dipgin.ms02.output/372/ms02_372.tab: Read error at byte 0, while reading 1536 bytes: Connection timed out

tar: ms02GINPPI/dipgin.ms02.output/71/popages/cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Feb17_113337.txt: Read error at byte 0, while reading 6656 bytes: Connection timed out

tar: ms02GINPPI/dipgin.ms02.output/71/ms02_71.tab: Read error at byte 0, while reading 8704 bytes: Connection timed out

tar: ms02GINPPI/dipgin.ms02.output/645/ms02_645.tab: Read error at byte 0, while reading 6656 bytes: Connection timed out

tar: ms02GINPPI/dipgin.ms02.output/324/ms02_324.tab: Read error at byte 0, while reading 9216 bytes: Connection timed out

tar: ms02GINPPI/dipgin.ms02.output/50/ms02_50.tab: Read error at byte 0, while reading 5632 bytes: Connection timed out

tar: ms02GINPPI/dipgin.ms02.output/68/popages/cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Feb05_212237.txt: Read error at byte 0, while reading 2048 bytes: Connection timed out

tar: ms02GINPPI/dipgin.ms02.output/86/popages/cutoff.4.p.0.6.lambda.0.02.popsize.2000.time.2015Feb01_021709.txt: Read error at byte 0, while reading 512 bytes: Connection timed out

tar: ms02GINPPI/dipgin.ms02.output/62/popages/cutoff.4.p.0.6.lambda.0.01.popsize.2000.time.2014Dec04_123712.txt: Read error at byte 0, while reading 7168 bytes: Connection timed out

tar: ms02GINPPI/dipgin.ms02.output/528/ms02_528.tab: Read error at byte 0, while reading 512 bytes: Connection timed out

tar: ms02GINPPI/dipgin.ms02.output/7/ms02_7.tab: Read error at byte 0, while reading 8704 bytes: Connection timed out

tar: ms02GINPPI/dipgin.ms02.output/428/ms02_428.tab: Read error at byte 0, while reading 1024 bytes: Connection timed out

tar: ms02GINPPI/dipgin.ms02.output/18/ms02_18.tab: Read error at byte 0, while reading 4096 bytes: Connection timed out

*** parallel runs of net-aging-sim-20150915.R -> net-aging-sim-2015Sep15.R

[hqin2@greenfield ms02GINPPI]$ cat netaging.pbs

#!/bin/bash

# Request 15 cores

#PBS -l nodes=1:ppn=15

#  Request 2:30 minutes of cpu time

#PBS -l walltime=7:00:00:00

module load R/3.2.1-mkl

echo hostname

pwd

cd /crucible/mc48o9p/hqin2/mactower-network-failure-simulation-master/ms02GINPPI

pwd

numactl -C +0 R --vanilla --slave -f net-aging-sim-20150915.R --args 95 95 0.02 1.0 50  &

numactl -C +1 R --vanilla --slave -f net-aging-sim-20150915.R --args 96 96 0.02 1.0 50  &

numactl -C +2 R --vanilla --slave -f net-aging-sim-20150915.R --args 97 97 0.02 1.0 50  &

wait

[hqin2@greenfield ms02GINPPI]$ qstat -u hqin2 -a

greenfield.psc.xsede.org: 

                                                                                  Req'd    Req'd       Elap

Job ID                  Username    Queue    Jobname          SessID  NDS   TSK   Memory   Time    S   Time

----------------------- ----------- -------- ---------------- ------ ----- ------ ------ --------- - ---------

2343.greenfield.psc.xs  hqin2       batch    netaging.pbs      44687     1     15    --  168:00:00 R  00:03:56

[hqin2@greenfield ms02GINPPI]$ ll -t dipgin.ms02.output/9[567]/popages/*0.02*

-rw-r--r-- 1 hqin2 mc48o9p 848 Sep 14 19:26 dipgin.ms02.output/97/popages/cutoff.4.p.1.lambda.0.02.popsize.50.time.2015Sep14_192617.txt

-rw-r--r-- 1 hqin2 mc48o9p 845 Sep 14 19:26 dipgin.ms02.output/95/popages/cutoff.4.p.1.lambda.0.02.popsize.50.time.2015Sep14_192616.txt

-rw-r--r-- 1 hqin2 mc48o9p 846 Sep 14 19:26 dipgin.ms02.output/96/popages/cutoff.4.p.1.lambda.0.02.popsize.50.time.2015Sep14_192613.txt

[hqin2@greenfield ms02GINPPI]$ cat netaging.pbs

#!/bin/bash

# Request 15 cores

#PBS -l nodes=1:ppn=15

#  Request 2:30 minutes of cpu time

#PBS -l walltime=7:00:00:00

module load R/3.2.1-mkl

echo hostname

pwd

cd /crucible/mc48o9p/hqin2/mactower-network-failure-simulation-master/ms02GINPPI

pwd

numactl -C +0 R --vanilla --slave -f net-aging-sim-20150915.R --args 95 95 0.02 1.0 150  &

numactl -C +1 R --vanilla --slave -f net-aging-sim-20150915.R --args 96 96 0.02 1.0 150  &

numactl -C +2 R --vanilla --slave -f net-aging-sim-20150915.R --args 97 97 0.02 1.0 150  &

wait

[hqin2@greenfield ms02GINPPI]$ qstat -u hqin2

greenfield.psc.xsede.org: 

                                                                                  Req'd    Req'd       Elap

Job ID                  Username    Queue    Jobname          SessID  NDS   TSK   Memory   Time    S   Time

----------------------- ----------- -------- ---------------- ------ ----- ------ ------ --------- - ---------

2344.greenfield.psc.xs  hqin2       batch    netaging.pbs      45653     1     15    --  168:00:00 R  00:21:47

[hqin2@greenfield ms02GINPPI]$ qstat

Job ID                    Name             User            Time Use S Queue

------------------------- ---------------- --------------- -------- - -----

2344.greenfield            netaging.pbs     hqin2           01:07:54 R batch 

/*Great. The Elapse time is 21 minutes but my CPU time is 3 times of it. So, I am running job in paralle. */

[hqin2@greenfield ms02GINPPI]$ ll -th dipgin.ms02.output/9[567]/popages/*txt

-rw-r--r-- 1 hqin2 mc48o9p 2.5K Sep 14 20:05 dipgin.ms02.output/95/popages/cutoff.4.p.1.lambda.0.02.popsize.150.time.2015Sep14_200529.txt

-rw-r--r-- 1 hqin2 mc48o9p 2.5K Sep 14 20:05 dipgin.ms02.output/96/popages/cutoff.4.p.1.lambda.0.02.popsize.150.time.2015Sep14_200528.txt

-rw-r--r-- 1 hqin2 mc48o9p 2.5K Sep 14 20:05 dipgin.ms02.output/97/popages/cutoff.4.p.1.lambda.0.02.popsize.150.time.2015Sep14_200527.txt

-rw-r--r-- 1 hqin2 mc48o9p  848 Sep 14 19:26 dipgin.ms02.output/97/popages/cutoff.4.p.1.lambda.0.02.popsize.50.time.2015Sep14_192617.txt

-rw-r--r-- 1 hqin2 mc48o9p  845 Sep 14 19:26 dipgin.ms02.output/95/popages/cutoff.4.p.1.lambda.0.02.popsize.50.time.2015Sep14_192616.txt

-rw-r--r-- 1 hqin2 mc48o9p  846 Sep 14 19:26 dipgin.ms02.output/96/popages/cutoff.4.p.1.lambda.0.02.popsize.50.time.2015Sep14_192613.txt

/*The three popsize.150 files are generated simultaneously. */

*** parallel runs on greenfield, example.R and example.pbs

helen:ms02GINPPI hqin$ cat example.R 

#20150914 testing parallel jobs on greenfield

# R CMD BATCH ./example.R --args 2 35 red

rm(list=ls())

source("lifespan.r")

source("network.r")

#R -f file --args start end

options(echo=TRUE) # if you want see commands in output file

args <- commandArgs(trailingOnly = TRUE)

print(args)

# trailingOnly=TRUE means that only your arguments are returned, check:

# print(commandsArgs(trailingOnly=FALSE))

start = as.integer(args[1]); start; 

end = as.integer(args[2]); end; 

tag = args[3]

  

myhost = 'greenfield'  # 'byte' 'blacklight' 'mactower'

myhost = 'byte'  # 'byte' 'blacklight' 'mactower'

myhost = 'helen'  # 'byte' 'blacklight' 'helen'

mydir = "/crucible/mc48o9p/hqin2/mactower-network-failure-simulation-master/ms02GINPPI"

if (myhost == 'byte') {  mydir = "/Users/hqin/github/mactower-network-failure-simulation/ms02GINPPI"

} else if (myhost == 'helen') { mydir = "/Users/hqin/github/mactower-network-failure-simulation/ms02GINPPI";  

}

print(paste("current dir is:", mydir))

list.files()

getwd()

print(paste("Now setwd"))

setwd(mydir)

list.files()

debug = 0; 

x = start:end 

outfile = paste( tag, start, end, "tab", sep='.')

write.csv( x, outfile, row.names=F)

[hqin2@greenfield ms02GINPPI]$ cat example.pbs

#!/bin/bash

# Request 15 cores

#PBS -l nodes=1:ppn=15

#  Request 1hr of cpu time

#PBS -l walltime=0:00:01:00

module load R/3.2.1-mkl

echo hostname

pwd

cd /crucible/mc48o9p/hqin2/mactower-network-failure-simulation-master/ms02GINPPI

pwd

numactl -C +0 R --vanilla --slave -f ./example.R --args 1 199999 '_zero' &

numactl -C +1 R --vanilla --slave -f ./example.R --args 2 299999 '_one' &

numactl -C +2 R --vanilla --slave -f ./example.R --args 3 399999 '_two' &

numactl -C +3 R --vanilla --slave -f ./example.R --args 4 499999 '_three' &

numactl -C +4 R --vanilla --slave -f ./example.R --args 4 499999 '_four' &

numactl -C +5 R --vanilla --slave -f ./example.R --args 4 499999 '_five' &

numactl -C +6 R --vanilla --slave -f ./example.R --args 4 499999 '_six' &

numactl -C +7 R --vanilla --slave -f ./example.R --args 4 499999 '_seven' &

numactl -C +8 R --vanilla --slave -f ./example.R --args 4 499999 '_eight' &

numactl -C +9 R --vanilla --slave -f ./example.R --args 4 499999 '_nine' &

wait