Opened 9 years ago

Closed 8 years ago

#2 closed task (wontfix)

tutorial_viz fails processing R script

Reported by: johren@bbn.com Owned by: somebody
Priority: minor Milestone:
Component: OML Version: SPIRAL4
Keywords: Cc:
Dependencies:

Description

I am getting a failure when running tutorial_viz.sh. It seems to be choking on the size column from the mydata1 query result that is used in the throughput calculation in the R script.

I am using an OML server that I installed on pc41.emulab.net. This OML server is running the following package versions:

ii liboml2-0 2.8.0-ubuntu1 OML: The Orbit Measurement Library ii oml2-server 2.8.0-ubuntu1 OML measurement server ii libocomm0 2.8.0-ubuntu1 OComm: Orbit Communications Library

The command line used to run the OML server:

oml2-server --listen=3003 --data-dir=/users/johren/gimi --logfile=/users/johren/oml_server.log -H /users/johren/oml2-server-hook.sh

Failure output:

geniuser@UserWorkspace:~/Tutorials/GIMI/common$ ./tutorial_viz.sh johGIM1208011452 spawn sudo cp oml.html /var/www/ [sudo] password for geniuser:

R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i686-pc-linux-gnu (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

library(RSQLite)

Loading required package: DBI

con <- dbConnect(dbDriver("SQLite"), dbname = "johGIM1208011452.sq3") dbListTables(con)

[1] "_experiment_metadata" "_senders" "iperf_connection" [4] "iperf_losses" "iperf_transfer"

dbReadTable(con,"iperf_transfer")

oml_sender_id oml_seq oml_ts_client oml_ts_server pid connection_id

1 1 1 5.388446 7.034676 2062 6 2 2 1 6.606245 8.252811 2067 8 3 1 2 10.387249 12.032514 2062 6 4 2 2 11.606227 13.251819 2067 8 5 1 3 15.396865 17.042427 2062 6 6 2 3 16.607787 18.254453 2067 8 7 1 4 20.399311 22.045674 2062 6 8 2 4 21.612378 23.257894 2067 8 9 1 5 25.393106 27.038274 2062 6 10 2 5 26.607296 28.253705 2067 8 11 1 6 30.393661 32.039437 2062 6 12 2 6 31.613645 33.259031 2067 8 13 1 7 35.400952 37.048213 2062 6 14 2 7 36.603534 38.248871 2067 8 15 1 8 40.399306 42.045168 2062 6 16 2 8 41.601858 43.247054 2067 8 17 1 9 45.399324 47.046108 2062 6 18 1 10 50.395998 52.040854 2062 6 19 1 11 55.393171 57.039082 2062 6 20 1 12 60.400803 62.047121 2062 6 21 1 13 65.400208 67.046627 2062 6 22 1 14 70.388585 72.035083 2062 6 23 1 15 75.397092 77.042288 2062 6 24 2 9 46.600728 82.028875 2067 8 25 2 10 51.613374 82.036833 2067 8 26 2 11 56.599619 82.036876 2067 8 27 2 12 61.612575 82.036913 2067 8 28 2 13 66.601414 82.036949 2067 8 29 2 14 71.599163 82.036985 2067 8 30 2 15 76.609512 82.037022 2067 8 31 1 16 80.390716 82.037105 2062 6 32 2 16 81.599319 92.624815 2067 8 33 2 17 86.610173 92.630121 2067 8 34 2 18 91.604479 93.250640 2067 8 35 2 19 96.607112 105.685087 2067 8 36 2 20 101.599617 105.692035 2067 8 37 2 21 106.603068 108.249677 2067 8 38 2 22 111.615701 113.263163 2067 8 39 2 23 116.617748 118.263564 2067 8 40 2 24 121.597823 123.243652 2067 8 41 2 25 126.602973 128.249522 2067 8 42 1 17 85.393593 131.392774 2062 6 43 1 18 90.407232 131.399109 2062 6 44 1 19 95.388469 131.399152 2062 6 45 1 20 100.399700 131.399189 2062 6 46 1 21 105.393090 131.399318 2062 6 47 1 22 110.397234 131.399355 2062 6 48 1 23 115.403025 131.399391 2062 6 49 1 24 120.396397 131.399427 2062 6 50 1 25 125.399631 131.399463 2062 6 51 1 26 130.398120 132.043302 2062 6 52 2 26 131.601005 133.246357 2067 8 53 1 27 135.399982 137.045201 2062 6 54 2 27 136.610649 138.257299 2067 8 55 1 28 140.394563 142.041513 2062 6 56 2 28 141.608232 143.255436 2067 8 57 1 29 145.392405 147.038047 2062 6 58 2 29 146.612987 148.259507 2067 8 59 1 30 150.410938 152.057521 2062 6 60 2 30 151.619340 153.265825 2067 8 61 1 31 155.388956 157.034715 2062 6 62 2 31 156.603905 158.250641 2067 8 63 1 32 160.398588 162.043859 2062 6 64 2 32 161.607325 163.253567 2067 8 65 1 33 165.398681 167.045113 2062 6 66 2 33 166.610207 168.256586 2067 8 67 1 34 170.403420 172.049875 2062 6 68 2 34 171.614491 173.260053 2067 8 69 1 35 175.394490 177.039719 2062 6 70 2 35 176.603477 178.249917 2067 8 71 1 36 180.398909 182.044008 2062 6 72 2 36 181.606246 183.252053 2067 8 73 1 37 185.394913 187.040491 2062 6 74 2 37 186.605241 188.250960 2067 8 75 1 38 190.392186 192.037597 2062 6 76 2 38 191.606984 193.252478 2067 8 77 1 39 195.388672 197.035118 2062 6 78 2 39 196.604814 198.251633 2067 8 79 1 40 200.388130 202.035147 2062 6 80 2 40 201.603799 203.249238 2067 8

begin_interval end_interval size

1 0 5 00, 00, 00, 00, 7c, b8, 00, 00 2 0 5 00, 00, 00, 00, 2b, 10, 00, 00 3 5 10 00, 00, 00, 00, 8f, 94, 00, 00 4 5 10 00, 00, 00, 00, 38, ae, 00, 00 5 10 15 00, 00, 00, 00, ba, 70, 00, 00 6 10 15 00, 00, 00, 00, 3d, 54, 00, 00 7 15 20 00, 00, 00, 00, 81, e4, 00, 00 8 15 20 00, 00, 00, 00, 51, e6, 00, 00 9 20 25 00, 00, 00, 00, 70, 78, 00, 00 10 20 25 00, 00, 00, 00, 5d, 5e, 00, 00 11 25 30 00, 00, 00, 00, 73, f8, 00, 00 12 25 30 00, 00, 00, 00, 58, 94, 00, 00 13 30 35 00, 00, 00, 00, 6d, 64, 00, 00 14 30 35 00, 00, 00, 00, 50, 78, 00, 00 15 35 40 00, 00, 00, 00, 6f, 92, 00, 00 16 35 40 00, 00, 00, 00, 53, f0, 00, 00 17 40 45 00, 00, 00, 00, 6a, be, 00, 00 18 45 50 00, 00, 00, 00, 74, 32, 00, 00 19 50 55 00, 00, 00, 00, 72, c6, 00, 00 20 55 60 00, 00, 00, 00, 71, e6, 00, 00 21 60 65 00, 00, 00, 00, 71, a6, 00, 00 22 65 70 00, 00, 00, 00, 73, 14, 00, 00 23 70 75 00, 00, 00, 00, 6e, 4e, 00, 00 24 40 45 00, 00, 00, 00, 59, 6a, 00, 00 25 45 50 00, 00, 00, 00, 61, d8, 00, 00 26 50 55 00, 00, 00, 00, 5b, 92, 00, 00 27 55 60 00, 00, 00, 00, 54, 20, 00, 00 28 60 65 00, 00, 00, 00, 4e, 7e, 00, 00 29 65 70 00, 00, 00, 00, 50, d8, 00, 00 30 70 75 00, 00, 00, 00, 4f, 28, 00, 00 31 75 80 00, 00, 00, 00, 6f, cc, 00, 00 32 75 80 00, 00, 00, 00, 50, fc, 00, 00 33 80 85 00, 00, 00, 00, 54, 98, 00, 00 34 85 90 00, 00, 00, 00, 52, 20, 00, 00 35 90 95 00, 00, 00, 00, 4f, a6, 00, 00 36 95 100 00, 00, 00, 00, 4f, 48, 00, 00 37 100 105 00, 00, 00, 00, 51, 98, 00, 00 38 105 110 00, 00, 00, 00, 4f, 88, 00, 00 39 110 115 00, 00, 00, 00, 50, ec, 00, 00 40 115 120 00, 00, 00, 00, 57, 7e, 00, 00 41 120 125 00, 00, 00, 00, 4f, 2e, 00, 00 42 80 85 00, 00, 00, 00, 74, 60, 00, 00 43 85 90 00, 00, 00, 00, 72, 70, 00, 00 44 90 95 00, 00, 00, 00, 71, 9a, 00, 00 45 95 100 00, 00, 00, 00, 74, b6, 00, 00 46 100 105 00, 00, 00, 00, 6a, b4, 00, 00 47 105 110 00, 00, 00, 00, 73, 3c, 00, 00 48 110 115 00, 00, 00, 00, 74, 7a, 00, 00 49 115 120 00, 00, 00, 00, 6f, 4a, 00, 00 50 120 125 00, 00, 00, 00, 75, 50, 00, 00 51 125 130 00, 00, 00, 00, 6c, c8, 00, 00 52 125 130 00, 00, 00, 00, 53, 50, 00, 00 53 130 135 00, 00, 00, 00, 72, 62, 00, 00 54 130 135 00, 00, 00, 00, 54, a0, 00, 00 55 135 140 00, 00, 00, 00, 70, 86, 00, 00 56 135 140 00, 00, 00, 00, 58, 62, 00, 00 57 140 145 00, 00, 00, 00, 6e, 8a, 00, 00 58 140 145 00, 00, 00, 00, 51, 14, 00, 00 59 145 150 00, 00, 00, 00, 71, f6, 00, 00 60 145 150 00, 00, 00, 00, 4f, 92, 00, 00 61 150 155 00, 00, 00, 00, 71, 28, 00, 00 62 150 155 00, 00, 00, 00, 50, 44, 00, 00 63 155 160 00, 00, 00, 00, 70, 50, 00, 00 64 155 160 00, 00, 00, 00, 4f, 60, 00, 00 65 160 165 00, 00, 00, 00, 73, ba, 00, 00 66 160 165 00, 00, 00, 00, 50, 40, 00, 00 67 165 170 00, 00, 00, 00, 70, 10, 00, 00 68 165 170 00, 00, 00, 00, 51, 20, 00, 00 69 170 175 00, 00, 00, 00, 71, 06, 00, 00 70 170 175 00, 00, 00, 00, 53, bc, 00, 00 71 175 180 00, 00, 00, 00, 71, ae, 00, 00 72 175 180 00, 00, 00, 00, 54, d8, 00, 00 73 180 185 00, 00, 00, 00, 7d, 90, 00, 00 74 180 185 00, 00, 00, 00, 4f, 60, 00, 00 75 185 190 00, 00, 00, 00, 71, d8, 00, 00 76 185 190 00, 00, 00, 00, 4f, ec, 00, 00 77 190 195 00, 00, 00, 00, 75, de, 00, 00 78 190 195 00, 00, 00, 00, 4f, 84, 00, 00 79 195 200 00, 00, 00, 00, 80, 12, 00, 00 80 195 200 00, 00, 00, 00, 56, c0, 00, 00

mydata1 <- dbGetQuery(con, "select

oml_sender_id,begin_interval,size,end_interval from iperf_transfer where oml_sender_id=1")

intervals1 <- mydata1$end_interval - mydata1$begin_interval throughput1 <- abs(mydata1$size)/intervals1/1024/1024*8

Error in abs(mydata1$size) :

Non-numeric argument to mathematical function

Execution halted spawn sudo cp johGIM1208011452.png /var/www/ [sudo] password for geniuser: cp: cannot stat `johGIM1208011452.png': No such file or directory

Change History (2)

comment:1 Changed 9 years ago by johren@bbn.com

Priority: majorminor
Type: defecttask

When I had OML server version 2.8.0, the size column in the iperf_transfer table is of type BLOB. The R script cannot handle data of this type in its calculations. I had to install version 2.8.1 to make the size column type UNSIGNED BIGINT. This should be documented in the tutorial instructions in case others try to use their own OML server.

comment:2 Changed 8 years ago by johren@bbn.com

Resolution: wontfix
Status: newclosed

No longer using tutorial_viz. Cleaning up old tickets as we revive the ticket tracking in GIMI.

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