[Biojava-dev] build problem

Tue Aug 10 00:04:39 UTC 2010

I think you are right and these files are not downloaded again. Here are the tests that consume significant time; maybe you can figure out which process is slow:

Running org.biojava.bio.structure.align.fatcat.TestFlexibleRotationMatrices
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 63.145 sec

Running org.biojava.bio.structure.align.FlipAFPChainTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 35.688 sec

Running org.biojava.bio.structure.align.fatcat.TestOutputStrings
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 129.81 sec

Running org.biojava.bio.structure.align.fatcat.AFPChainSerialisationTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 131.016 sec

Running org.biojava3.protmod.structure.ProteinModificationParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 530.036 sec

George

>----- ------- Original Message ------- -----
>From: Andreas Prlic <andreas at sdsc.edu>
>To: George Waldon <gwaldon at geneinfinity.org>
>Sent: Mon, 9 Aug 2010 15:48:18
>
>Seems your times are comparable with the build
>machine. The files are
>downloaded and store in local temporary directories
>(as provided by
>System.getProperty("java.io.tmpdir") ) If that tmp
>directory changes,
>the files will have to be re-loaded again,
>otherwise they will be
>re-used and the code runs quicker. Seems the VM is
>changing the tmp
>dir location frequently. Anybody has a suggestion
>how to define a more
>"stable" tmp dir locations? Otherwise I will put
>all required test
>files into the test resources dir ...
>
>Andreas
>
>
>
>On Mon, Aug 9, 2010 at 3:20 PM, George Waldon
><gwaldon at geneinfinity.org> wrote:
>> Here is my summary and some of the timings are
>pretty good (simple HP laptop with a dual core):
>>
>>
>---------------------------------------------------
>---------------------
>> Reactor Summary:
>>
>---------------------------------------------------
>---------------------
>> biojava
>...............................................
>SUCCESS [3.820s]
>> bytecode
>..............................................
>SUCCESS [6.022s]
>> core
>..................................................
>SUCCESS [52.822s]
>> alignment
>.............................................
>SUCCESS [4.332s]
>> blast
>.................................................
>SUCCESS [27.453s]
>> biojava3-structure
>.................................... SUCCESS
>[7:33.228s]
>> das
>...................................................
>SUCCESS [18.456s]
>> sequence
>..............................................
>SUCCESS [0.122s]
>> sequence-core
>......................................... SUCCESS
>[3.974s]
>> sequence-rna
>.......................................... SUCCESS
>[0.313s]
>> sequence-biosql
>....................................... SUCCESS
>[2.735s]
>> sequence-fasta
>........................................ SUCCESS
>[0.324s]
>> sequence-blastxml
>..................................... SUCCESS
>[3.339s]
>> sequencing
>............................................
>SUCCESS [5.637s]
>> phylo
>.................................................
>SUCCESS [5.084s]
>> biosql
>................................................
>SUCCESS [6.344s]
>> gui
>...................................................
>SUCCESS [6.552s]
>> biojava3-core
>......................................... SUCCESS
>[8.477s]
>> biojava3-phylo
>........................................ SUCCESS
>[3.596s]
>> biojava3-structure-gui
>................................ SUCCESS [8.283s]
>> biojava3-alignment
>.................................... SUCCESS
>[6.002s]
>> biojava3-genome
>....................................... SUCCESS
>[3.933s]
>> biojava3-protmod
>...................................... SUCCESS
>[8:59.048s]
>> biojava3-ws
>........................................... SUCCESS
>[1.367s]
>>
>---------------------------------------------------
>---------------------
>>
>---------------------------------------------------
>---------------------
>> BUILD SUCCESSFUL
>>
>---------------------------------------------------
>---------------------
>> Total time: 19 minutes 33 seconds
>> Finished at: Mon Aug 09 13:48:00 PDT 2010
>> Final Memory: 116M/363M
>>
>---------------------------------------------------
>---------------------
>>
>> The long time comes apparently from fetching all
>these files. I tried the build last week on a
>different network after removing the faulty test as
>suggested by Scott and I had similar timing. This
>could be an issue with NetBeans in fact. If someone
>has experienced such long delays, it would be
>interesting to know in which conditions this
>occurred.
>>
>> Thanks again,
>>
>> George
>>
>>>----- ------- Original Message ------- -----
>>>From: Andreas Prlic <andreas at sdsc.edu>
>>>To: George Waldon <gwaldon at geneinfinity.org>
>>>Sent: Mon, 9 Aug 2010 14:27:27
>>>
>>>That seems like a very long time... on the
>>>automated build server the
>>>times look like below:
>>>
>>>If the structure module takes so much time, I
>>>wonder if you are behind
>>>a very slow network? Some of the junit tests
>fetch
>>>PDB files from a
>>>public ftp server and I wonder if there is a
>>>networking issue. Having
>>>said this, the two slowest modules are structure
>>>and protmod. We will
>>>try to cut down the time spent on those tests...
>>>
>>>Andreas
>>>
>>>
>>>INFO] biojava
>>>...............................................
>>>SUCCESS [21.430s]
>>>[INFO] bytecode
>>>..............................................
>>>SUCCESS [44.778s]
>>>[INFO] core
>>>.................................................
>.
>>>SUCCESS
>>>[4:54.691s]
>>>[INFO] alignment
>>>.............................................
>>>SUCCESS [48.048s]
>>>[INFO] blast
>>>.................................................
>>>SUCCESS
>>>[1:20.263s]
>>>[INFO] biojava3-structure
>>>.................................... SUCCESS
>>>[8:12.412s]
>>>[INFO] das
>>>.................................................
>..
>>>SUCCESS
>>>[1:13.103s]
>>>[INFO] sequence
>>>..............................................
>>>SUCCESS [18.176s]
>>>[INFO] sequence-core
>>>......................................... SUCCESS
>>>[47.424s]
>>>[INFO] sequence-rna
>>>..........................................
>SUCCESS
>>>[28.770s]
>>>[INFO] sequence-biosql
>>>....................................... SUCCESS
>>>[47.032s]
>>>[INFO] sequence-fasta
>>>........................................ SUCCESS
>>>[29.075s]
>>>[INFO] sequence-blastxml
>>>..................................... SUCCESS
>>>[44.392s]
>>>[INFO] sequencing
>>>............................................
>>>SUCCESS [49.520s]
>>>[INFO] phylo
>>>.................................................
>>>SUCCESS [48.459s]
>>>[INFO] biosql
>>>................................................
>>>SUCCESS [57.503s]
>>>[INFO] gui
>>>.................................................
>..
>>>SUCCESS [58.610s]
>>>[INFO] biojava3-core
>>>......................................... SUCCESS
>>>[1:05.398s]
>>>[INFO] biojava3-phylo
>>>........................................ SUCCESS
>>>[46.623s]
>>>[INFO] biojava3-structure-gui
>>>................................ SUCCESS
>>>[1:06.737s]
>>>[INFO] biojava3-alignment
>>>.................................... SUCCESS
>>>[54.682s]
>>>[INFO] biojava3-genome
>>>....................................... SUCCESS
>>>[49.844s]
>>>[INFO] biojava3-protmod
>>>...................................... SUCCESS
>>>[10:05.171s]
>>>[INFO] biojava3-ws
>>>...........................................
>SUCCESS
>>>[44.379s]
>>>
>>>
>>>On Mon, Aug 9, 2010 at 1:52 PM, George Waldon
>>><gwaldon at geneinfinity.org> wrote:
>>>> Thanks to all for the fixing.
>>>>
>>>> The build took 19 minutes and 33 seconds, of
>>>which 16 min and 32 s were for the structure
>>>modules! This sounds a bit long to me. Is-this
>>>expected?
>>>>
>>>> George
>>>>
>>>>>----- ------- Original Message ------- -----
>>>>>From: Andreas Prlic <andreas at sdsc.edu>
>>>>>To: George Waldon <gwaldon at geneinfinity.org>
>>>>>Sent: Mon, 9 Aug 2010 12:35:56
>>>>>
>>>>>If you update the class, this should be fixed
>>>now.
>>>>>Was a problem with
>>>>>a hard coded /tmp path...
>>>>>
>>>>>Andreas
>>>>>
>>>>>
>>>>>
>>>>>On Mon, Aug 9, 2010 at 12:26 PM, George Waldon
>>>>><gwaldon at geneinfinity.org> wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I am getting the following failures in
>>>>>org.biojava.bio.structure.align.benchmark.Multi
>pl
>>>eA
>>>>>lignmentTest:
>>>>>>
>>>>>> Fetching
>>>>>ftp://ftp.wwpdb.org/pub/pdb/data/structures/all
>/p
>>>db
>>>>>/pdb1hcy.ent.gz
>>>>>> writing to \tmp\hc\pdb1hcy.ent.gz
>>>>>> java.io.FileNotFoundException:
>>>>>\tmp\hc\pdb1hcy.ent.gz (The system cannot find
>>>the
>>>>>path specified)
>>>>>> ...
>>>>>>
>>>>>> and
>>>>>>
>>>>>> Fetching
>>>>>ftp://ftp.wwpdb.org/pub/pdb/data/structures/all
>/p
>>>db
>>>>>/pdb1nls.ent.gz
>>>>>> writing to \tmp\nl\pdb1nls.ent.gz
>>>>>> java.io.FileNotFoundException:
>>>>>\tmp\nl\pdb1nls.ent.gz (The system cannot find
>>>the
>>>>>path specified)
>>>>>> at java.io.FileOutputStream.open(Native
>Method)
>>>
>>>>>> at
>>>>>java.io.FileOutputStream.<init>(FileOutputStrea
>m.
>>>ja
>>>>>va:179)
>>>>>> at
>>>>>java.io.FileOutputStream.<init>(FileOutputStrea
>m.
>>>ja
>>>>>va:131)
>>>>>> at
>>>>>org.biojava.bio.structure.io.PDBFileReader.down
>lo
>>>ad
>>>>>PDB(PDBFileReader.java:430)
>>>>>> ...
>>>>>>
>>>>>> Does anyone has a solution for this? I am
>>>>>building from within NetBeans.
>>>>>>
>>>>>> Thanks,
>>>>>> George
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>--
>>>>>-----------------------------------------------
>--
>>>--
>>>>>--------------------
>>>>>Dr. Andreas Prlic
>>>>>Senior Scientist, RCSB PDB Protein Data Bank
>>>>>University of California, San Diego
>>>>>(+1) 858.246.0526
>>>>>-----------------------------------------------
>--
>>>--
>>>>>--------------------
>>>>
>>>
>>>
>>>
>>>--
>>>-------------------------------------------------
>--
>>>--------------------
>>>Dr. Andreas Prlic
>>>Senior Scientist, RCSB PDB Protein Data Bank
>>>University of California, San Diego
>>>(+1) 858.246.0526
>>>-------------------------------------------------
>--
>>>--------------------
>>
>
>
>
>-- 
>---------------------------------------------------
>--------------------
>Dr. Andreas Prlic
>Senior Scientist, RCSB PDB Protein Data Bank
>University of California, San Diego
>(+1) 858.246.0526
>---------------------------------------------------
>--------------------