[Biojava-dev] build problem

Wed Aug 11 18:49:28 EDT 2010

thanks, still working on making it even faster...
A

On Wed, Aug 11, 2010 at 3:44 PM, George Waldon <gwaldon at geneinfinity.org> wrote:
> Andreas:
>
> Just for your intention, here are my today's build times. I am down to 9 min 21 s. This has very improved. Thank you very much.
>
> George
>
> ------------------------------------------------------------------------
> biojava ............................................... SUCCESS [3.938s]
> bytecode .............................................. SUCCESS [6.657s]
> core .................................................. SUCCESS [47.960s]
> alignment ............................................. SUCCESS [3.024s]
> blast ................................................. SUCCESS [24.915s]
> biojava3-structure .................................... SUCCESS [5:09.755s]
> das ................................................... SUCCESS [40.210s]
> sequence .............................................. SUCCESS [0.126s]
> sequence-core ......................................... SUCCESS [3.359s]
> sequence-rna .......................................... SUCCESS [0.364s]
> sequence-biosql ....................................... SUCCESS [1.763s]
> sequence-fasta ........................................ SUCCESS [0.324s]
> sequence-blastxml ..................................... SUCCESS [2.905s]
> sequencing ............................................ SUCCESS [5.447s]
> phylo ................................................. SUCCESS [4.051s]
> biosql ................................................ SUCCESS [4.305s]
> gui ................................................... SUCCESS [2.787s]
> biojava3-core ......................................... SUCCESS [6.502s]
> biojava3-phylo ........................................ SUCCESS [3.124s]
> biojava3-structure-gui ................................ SUCCESS [5.339s]
> biojava3-alignment .................................... SUCCESS [4.594s]
> biojava3-genome ....................................... SUCCESS [2.657s]
> biojava3-protmod ...................................... SUCCESS [1:13.620s]
> biojava3-ws ........................................... SUCCESS [2.078s]
> ------------------------------------------------------------------------
> ------------------------------------------------------------------------
> BUILD SUCCESSFUL
> ------------------------------------------------------------------------
> Total time: 9 minutes 21 seconds
> Finished at: Wed Aug 11 15:29:57 PDT 2010
> Final Memory: 83M/370M
>
>
>
>
>>----- ------- 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
>>---------------------------------------------------
>>--------------------
>

-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------