well this is something new, a very strange behavior in one of my tests cases:


List result = this.getEntityManager().createQuery("from " + LoggingEntityBean.class.getName() + " b").getResultList();
assertTrue(result.isEmpty() == false);

int size = result.size();
int exspected = testSize * addres.length;

logger.info(size);
logger.info(exspected);
assertTrue(size == exspected);


now why do I get this error message...

[17:37:02,007] [INFO ] [main] [LoggingServiceTest] [400]
[17:37:02,008] [INFO ] [main] [LoggingServiceTest] [200]

junit.framework.AssertionFailedError: null
at edu.ucdavis.genomics.metabolomics.binbase.logging.server.LoggingServiceTest.setUp(LoggingServiceTest.java:73)
at org.jmock.core.VerifyingTestCase.runBare(Unknown Source)
at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:81)
at com.intellij.rt.junit4.Junit4ClassSuite.run(Junit4ClassSuite.java:99)
at com.intellij.rt.execution.junit.JUnitStarter.main(JUnitStarter.java:40)



error in this line:

assertTrue(size == exspected);

ok it's supposed to fail because 200 isn't 400, but not with a NullPointer exception...

now I have been working with intellij for a bit over a week and it have to say it has it's highs and it's lows.

• refactoring is just great
• override/implment function works good
• I hate the code completion, it's just strange behavior wise
• the junit plugin is nice, but a bit strange
• the grails/groovy support is exceptional good
• the performance is good if I work on a single project, if I work on my average 40 projects at once it's impossible to work with
• nice support for for python, works quite well
• uml support is great
• ant based build are a nightmare, but we want to use maven anyway whenever, where ever
• maven plugin is great in therorie, but with complex pom's it's extremely slow.

conclusions:

• python development will be in intellij
• groovy development will be in intellij
• scala development will be in intellij
• java development will be in eclipse
• pom writing will be in intillij and I generate the project directly via 'mvn idea:idea eclipse:eclipse' instead of using the pom as project file
  

ok it's not hot in davis,

it's ridiculous hot, 47 Degree Celsius....

I mean seriously...

lesson:

• do not buy a car with black leather seats...
• do not buy a car with black leather...
• do not buy a car with black...
• do not buy a car with...
• do not buy a car...
• do not buy a...
• do not buy...
• do not...
• do...
• ...
• ..
• .

translation I hid in the office, enjoyed the AC and got some stuff done (Die hard, Die hard with a vengeance,...)

Also no smoked meat today, I will not sit for 12 hours next to this thing fighting with the heat during the day or the roaches at night.

Now time to run for a restaurant and get some tasty food. I'm in no mood to cook tonight.

mocking spring,

moved to Coding and More

ajax and grails

moved to Coding and More

to cancel flight's is fun...

Flight cost summary

Flight cost - 6/16/09

Airfare #XXXXXXXXXXXXX	$679.25
Flight cost	$679.25
Exchange cost - 6/25/09
Airfare #XXXXXXXXXXXXX	$688.78
Previous airfare	-$679.25
Airfare difference	$9.53
Orbitz exchange fee	$30.00
Airline change fee	$200.00
Total exchange cost	$239.53	USD

Grand total itinerary cost to-date	$918.78 USD

boy my checking account truly hates me right now...

so it look's like the raid is now running, so this next step would be an lvm2 layer on top of it.

I thought it would be easy, but...

/dev/sdc1: lseek 10448441413827256320 failed: Invalid argument

Incorrect metadata area header checksum

--- Physical volume ---

PV Name /dev/md3

VG Name data

PV Size 9.09 TB / not usable 3.25 MB

Allocatable yes

PE Size (KByte) 4096

Total PE 2384157

Free PE 2384157

Allocated PE 0

PV UUID 2EQH1i-BIYU-BDvH-sRb3-yruB-V15f-ZCTywN

"/dev/sdc1" is a new physical volume of "8.98 EB"

--- NEW Physical volume ---

PV Name /dev/sdc1

VG Name

PV Size 9.06 EB

Allocatable NO

PE Size (KByte) 0

Total PE 0

Free PE 0

Allocated PE 0

PV UUID 2;??-ƈ+-?m-s?b3-?ruB-V15f-ZCTywN

"/dev/sdn1" is a new physical volume of "64.01 PB"

--- NEW Physical volume ---

PV Name /dev/sdn1

VG Name

PV Size 64.01 PB

Allocatable NO

PE Size (KByte) 0

Total PE 0

Free PE 0

Allocated PE 0

PV UUID 2EQI1i-BHYU-BEvH-sRb3-yruB-V15f-ZCTywN

it looks like I just got promoted to a 64 Peta Byte server on the disk's sdn1 and 9.06 Exta Byte on sdc1.

Guess I got more harddrive space as I ordered...

So it look's like it's adding my disk's to the group instead of only my raid6 devices. The solution for this is to disable in the /etc/lvm/lvm.com the related disks:

filter = [ "r|/dev/cdrom|","r|/dev/sd*|" ]

Time for the next issue...

currently I'm fighting since 4 weeks with a retarded server, well whenever I got some time besides

• fixing bugs
• keeping the system running, because the main server is offline since 2 month now
• helping people with problems
• fighting with power outages
• fixing servers
• and actually coding doing research in the left over time

anyway for some reasons the raid system keeps failing all the time, specially it keeps forgetting it's devices.

So just some small things for me to remember for the next time...

• removing existing raid stuff: mdadm --zero-superblock /dev/sd[c,d,e,f,g,h,i,j,k,l,m,n,o,p]1
• stopping a raid: mdadm --stop /dev/md_d3
• getting some info's about the raid: mdadm --examine /dev/sd[c-p]1
• trying to assemble a raid: mdadm -v -A /dev/md_d3 /dev/sd[c,d,e,f,g,h,i,j,k,l,m,n,o,p]1
• creating a large raid0 for testing: mdadm --create --verbose --force /dev/md3 --level=raid0 --raid-devices=14 /dev/sd{c,d,e,f,g,h,i,j,k,l,m,n,o,p}1
• creating a raid6: mdadm --create --verbose --force --name=data /dev/md3 --level=raid6 --raid-devices=12 --spare-devices=2 /dev/sd{c,d,e,f,g,h,i,j,k,l,m,n,o,p}1
• storing the generated configuration: mdadm --examine --scan --config=mdadm.conf >> /etc/mdadm/mdadm.conf

solution: found here

now just wait a tiny bit for the rebuild...

md3 : active raid6 sdp1[13](S) sdo1[12](S) sdn1[11] sdm1[10] sdl1[9] sdk1[8] sdj1[7] sdi1[6] sdh1[5] sdg1[4] sdf1[3] sde1[2] sdd1[1] sdc1[0]

9765510400 blocks level 6, 64k chunk, algorithm 2 [12/12] [UUUUUUUUUUUU]

[>....................] resync = 0.7% (7591112/976551040) finish=1074.7min speed=15024K/sec

well since this month turned out to be much more pricey than planned

• ticket to germany 700$
• visa fee 200$
• conference fee 200$ (should get reimbursed in the next view weeks)
• smoker 350$ (including needed stuff like coal and wood)

and next month is going to be the same game

• rent deposit 500$
• last month rent 500$
• paying rent for 2 places 750-1000$

well I need a new cheap hobby, which won't cost more than 50$ a month and the eququiment should be also affordable/rentable.

Solution?

I will try to pick up free climbing, which will also help me to conquer my fear of heights. And also will try to survive on 500$ of food (so no more chocolate and soda)

so what's new,

• my experiment to live on 100$ a week worked quite well, only 2 days left and I still have 2 whole chickens in the freezer, which are going to visit the smoker tomorrow
• for some reasons my back is killing me time to try a different workout and I'm looking forward to swimming again
• booking a flight to germany and a visa appointment and screwing it up, now I have only a 2 day window to get my visa delivered
• trying to learn and understand ajax
• trying to work more with groovy and grails
• learning a new IDE (IntelliJ 8) and so far I love it
• switching from firefox to safari for internet related stuff, since firefox is so slow
• looking for a small ultra portable laptop with 10 hours of battery live

just another saturday, well since I decided to skip carmel this weekend and stay in davis, since friends are in town, well I decided to use this weekend and give the smoker a run for it's money.

So today we make trout spread for bagels and smoked trout.

• buy 4 trouts = 10$
• buy cottage cheese and cream cheese = 5$
• buy 12 bagels = 6$

ok now this is out of the way time to setup the smoker, this time we use apple wood chips to see how they work.

First we brine the trouts for an hour in sugar and salt (lesson for next time, brine 2 - 3 hours, they are a bit dry and needed a lot of salt), while setting up the fire. It turned out that the new york times is an aweful starter, so let's try another newspaper the next time.

The trouts are now happily smoking for 3 hours at 220-240 Fahrenheit and I use this time to be productive, equals watching cheesy movies.

Once the trout were done, we had one for lunch, put away one for dinner and mixed 2 for the spread.

• sellery
• onion
• garlic
• cottage cheese
• cream cheese

It turned out that my hand blender is broken, our other blender is not strong enough and a fork is a lot of work. So the spread is a bit chunky, but very tasty!
And I also have about 2 pound of spread now, which has to be eaten in the next 4 days, so 2 bagels for breakfast everyday and if somebody want's some spread, call me.
(It has some fishbones, blame the blender...)

About the smoked trout in general? It's is amaizingly tasty and quite a fat fish. I like it.

so the smoker finally arrived and so we started to cook our first dish.

The lesson of the day? It's not worth it to cook a single chicken, since you need way to much charcoal and wood for it. It was like 5$ worth of charcoal.

lesson 2:

one chicken is not enough, they are so damn tasty you want a second one 5 minutes later

how too?

• soak chicken in solution of salt and sugar for 2 hours
  
• try chicken
• put pepper on chicken
• preheat smoker to 250 degrees fahrenheit
• leave chicken in there for 3h
• try to understand where you need to put the thermometer and figure out why it constantly looses connection
• figure out a way to kill the coals and wood once you are done, since it makes me nervous as hell to leave the bbq on over night and going to bed
• carve the chicken, executed by ashley!

todo:

get more chickens and repeat!

step two:

the smoker is ordered and on its way...
and so is the meat thermometer

(no more dining out this month...)

step three:

get wood and charcoal

step four:

get some ribs and smoke them tomorrow night till the early morning

BBQ season has started and this year I will full fill my desire and buy a smoker.

But first time to read up where I can get what parts of beef and the parts for the smoker. Like wood and so.

You know, the usual...

well I'm back from phillidelphia and the first thing we did was a nice picnic in sacramento. We also looked at some town houses and discovered a small honey store.

It's amaizing how different honey can taste. From delicious to disgusting is just a spoon apart

• orange blossom - yummy
• clover - yummy
• sage - ok and very mild
• eucalyptus - disgusting
  
• several other kind's I can't remember

I only bought 2 pounds of honey, but it was so much cheaper than grocery stores.

...time to make some tea...

the last day in philli seems to follow a trend, it's raining and we are waiting impatiently for our flight and hope to be back in the warms of California soon.
It was a fun week, but pretty stressful. Short a day on the pool in the sun sounds great.

so it's always sunny in Philadelphia? Nah it's a freaking lie! Never believe in TV Shows! Why are I'm surrounded by thunderstorms and rain.

I should had brought shoes besides sandals...

Anyway the poster presentation is done and the response was quite nice. It also looks that everybody starts to agree with our point:

You need a database for your results!

So the last 7 years start to pay off. Several people congratulated us to the software we wrote and are highly impressed. I'm still surprised that I was brave enough to actually participate in the discussion, in front of 300 people about the different approaches to annotate massspecs. Who all have fancy titles and are accepted experts in the field of metabolomics.

What else, the first people which were fun to hangout with already left and so I have to work again tonight to find new people to talk too.

current location: philidelphia
current food: gyros
food of the last days: philli cheesesteaks
busy with: looking so far at 1400 posters, 1400 more are comming
mistake: not staying the weekend here and driving to new york = bad planning from me

why such a short post?

got no time, have to run to a talk and the internet is so damn unreliable...