developers-list July 2006

developers-list@monetdb.org

14 participants
19 discussions

[Monetdb-developers] Unable to shred 1gb xml file (OS: Not enough space)

by kla gw

Hi, I tried MonetDB/XQuery to shred a 1gb xml file, but it failed. Following is the error message: MonetDB>shred_doc("D:xbench/output/DC1000catalog.xml", "DC1000catalog.xml"); !ERROR: MT_mmap: MapViewOfFile(6b4, 2, 0, 0, 442499072, 0) failed !OS: Not enough space !GDKmmap(442499072) fail => BBPtrim(enter) usage[mem=101297568,vm=794361856] I use windows XP Professional version 2002 service pack 2, Pentium 4 CPU, 2.40GHz, 512 MB of RAM. Previously I tried to shred 100mb xml file, and it took 18.532 sec. For this 1 gb file, I left it overnight so I don't know how long it takes till the error message occurs. Can please help me to solve this problem? Regards, Klarinda Below is the complete error message: MonetDB>shred_doc("D:xbench/output/DC1000catalog.xml", "DC1000catalog.xml"); !ERROR: MT_mmap: MapViewOfFile(6b4, 2, 0, 0, 442499072, 0) failed !OS: Not enough space !GDKmmap(442499072) fail => BBPtrim(enter) usage[mem=101297568,vm=794361856] # !mallinfo.arena = 15613828 !mallinfo.ordblks = 46134 !mallinfo.smblks = 15492 !mallinfo.hblkhd = 0 !mallinfo.hblks = 0 !mallinfo.usmblks = 13718408 !mallinfo.fsmblks = 899720 !mallinfo.uordblks = 950740 !mallinfo.fordblks = 44960 #BBPTRIM_ENTER: memsize=101297568,vmsize=794361856 #BBPTRIM: memtarget=0 vmtarget=1073741824 #TRIMSCAN: mem=0 vm=1, start=1, limit=1 #TRIMSCAN: 145030 0=tmp_35 (#0) #TRIMSCAN: 145059 1=tmp_36 (#0) #TRIMSCAN: 145088 2=tmp_37 (#0) #TRIMSCAN: 145146 3=tmp_41 (#0) #TRIMSCAN: 149075 4=doc_query (#0) #TRIMSCAN: 149092 5=doc_sema (#0) #TRIMSCAN: 155215 6=tmp_374 (#0) #TRIMSCAN: 155218 7=prop_pre_39 (#0) #TRIMSCAN: 157895 8=tmp_533 (#0) #TRIMSCAN: 157898 9=prop_pre_310 (#0) #TRIMSCAN: end at 1 (size=628) #TRIMSELECT: dirty = 0 #TRIMSELECT: candidate=tmp_35 BAT*=03D6A230 # (cnt=0, mode=1024, refs=0, wait=0, parent=0, lastused=145030,145030 ,145030) #TRIMSELECT: keep tmp_35 [224,0] bytes [224,0] dirty target(mem=0 vm=1073741824) #TRIMSELECT: candidate=tmp_36 BAT*=03D66E60 # (cnt=0, mode=1024, refs=0, wait=0, parent=0, lastused=145059,145059 ,145059) #TRIMSELECT: keep tmp_36 [224,0] bytes [224,0] dirty target(mem=0 vm=1073741824) #TRIMSELECT: candidate=tmp_37 BAT*=058080B0 # (cnt=0, mode=1024, refs=0, wait=0, parent=0, lastused=145088,145088 ,145088) #TRIMSELECT: keep tmp_37 [224,0] bytes [224,0] dirty target(mem=0 vm=1073741824) #TRIMSELECT: candidate=tmp_41 BAT*=058066F0 # (cnt=0, mode=1024, refs=0, wait=0, parent=0, lastused=145146,145146 ,145146) #TRIMSELECT: keep tmp_41 [224,0] bytes [224,0] dirty target(mem=0 vm=1073741824) #TRIMSELECT: candidate=doc_query BAT*=057F9D10 # (cnt=0, mode=1024, refs=0, wait=0, parent=0, lastused=149075,149075 ,149075) #TRIMSELECT: keep doc_query [224,0] bytes [224,0] dirty target(mem=0 vm=10737418 24) #TRIMSELECT: candidate=doc_sema BAT*=05845370 # (cnt=0, mode=1024, refs=0, wait=0, parent=0, lastused=149092,149092 ,149092) #TRIMSELECT: keep doc_sema [224,0] bytes [224,0] dirty target(mem=0 vm=107374182 4) #TRIMSELECT: candidate=tmp_374 BAT*=03D722F0 # (cnt=0, mode=4096, refs=0, wait=0, parent=0, lastused=155215,155215 ,155215) #TRIMSELECT: keep tmp_374 [224,0] bytes [0,0] dirty target(mem=0 vm=1073741824) #TRIMSELECT: candidate=prop_pre_39 BAT*=05845CD0 # (cnt=0, mode=4096, refs=0, wait=0, parent=0, lastused=155218,155218 ,155218) #TRIMSELECT: keep prop_pre_39 [224,0] bytes [0,0] dirty target(mem=0 vm=10737418 24) #TRIMSELECT: candidate=tmp_533 BAT*=0583C598 # (cnt=0, mode=4096, refs=0, wait=0, parent=0, lastused=157895,157895 ,157895) #TRIMSELECT: keep tmp_533 [224,0] bytes [0,0] dirty target(mem=0 vm=1073741824) #TRIMSELECT: candidate=prop_pre_310 BAT*=057F7E70 # (cnt=0, mode=4096, refs=0, wait=0, parent=0, lastused=157898,157898 ,157898) #TRIMSELECT: keep prop_pre_310 [224,0] bytes [0,0] dirty target(mem=0 vm=1073741 824) #TRIMSELECT: end #TRIMSELECT: dirty = 1 #TRIMSELECT: candidate=tmp_35 BAT*=03D6A230 # (cnt=0, mode=1024, refs=0, wait=0, parent=0, lastused=145030,145030 ,145030) #TRIMSELECT: delete tmp_35 from trimlist (does not match trim needs) #TRIMSELECT: candidate=tmp_36 BAT*=03D66E60 # (cnt=0, mode=1024, refs=0, wait=0, parent=0, lastused=145059,145059 ,145059) #TRIMSELECT: delete tmp_36 from trimlist (does not match trim needs) #TRIMSELECT: candidate=tmp_37 BAT*=058080B0 # (cnt=0, mode=1024, refs=0, wait=0, parent=0, lastused=145088,145088 ,145088) #TRIMSELECT: delete tmp_37 from trimlist (does not match trim needs) #TRIMSELECT: candidate=tmp_41 BAT*=058066F0 # (cnt=0, mode=1024, refs=0, wait=0, parent=0, lastused=145146,145146 ,145146) #TRIMSELECT: delete tmp_41 from trimlist (does not match trim needs) #TRIMSELECT: candidate=doc_query BAT*=057F9D10 # (cnt=0, mode=1024, refs=0, wait=0, parent=0, lastused=149075,149075 ,149075) #TRIMSELECT: delete doc_query from trimlist (does not match trim needs) #TRIMSELECT: candidate=doc_sema BAT*=05845370 # (cnt=0, mode=1024, refs=0, wait=0, parent=0, lastused=149092,149092 ,149092) #TRIMSELECT: delete doc_sema from trimlist (does not match trim needs) #TRIMSELECT: candidate=tmp_374 BAT*=03D722F0 # (cnt=0, mode=4096, refs=0, wait=0, parent=0, lastused=155215,155215 ,155215) #TRIMSELECT: delete tmp_374 from trimlist (does not match trim needs) #TRIMSELECT: candidate=prop_pre_39 BAT*=05845CD0 # (cnt=0, mode=4096, refs=0, wait=0, parent=0, lastused=155218,155218 ,155218) #TRIMSELECT: delete prop_pre_39 from trimlist (does not match trim needs) #TRIMSELECT: candidate=tmp_533 BAT*=0583C598 # (cnt=0, mode=4096, refs=0, wait=0, parent=0, lastused=157895,157895 ,157895) #TRIMSELECT: delete tmp_533 from trimlist (does not match trim needs) #TRIMSELECT: candidate=prop_pre_310 BAT*=057F7E70 # (cnt=0, mode=4096, refs=0, wait=0, parent=0, lastused=157898,157898 ,157898) #TRIMSELECT: delete prop_pre_310 from trimlist (does not match trim needs) #TRIMSELECT: end #BBPTRIM: no more unload candidates! #BBPTRIM_EXIT: memsize=95140356,vmsize=794361856 !GDKmmap(442499072) fail => BBPtrim(ready) usage[mem=101297568,vm=794361856] # !mallinfo.arena = 15613828 !mallinfo.ordblks = 46134 !mallinfo.smblks = 15492 !mallinfo.hblkhd = 0 !mallinfo.hblks = 0 !mallinfo.usmblks = 13718408 !mallinfo.fsmblks = 899720 !mallinfo.uordblks = 950740 !mallinfo.fordblks = 44960 !ERROR: MT_mmap: MapViewOfFile(6b0, 2, 0, 0, 442499072, 0) failed !OS: Not enough space !ERROR: GDKload: cannot mmap(): name=05\552, ext=theap.priv !OS: Not enough space !ERROR: GDKload failed: name=05\552, ext=theap.priv !ERROR: shredder.mx:append_str2bat: APPEND-STR[PROP_TEXT](final foxes since the silent, quick realms should breach never sheaves--ruthless, daring waters beneat h the close asymptotes c), BUNappend fails !ERROR: CMDshred2bats: operation failed. MonetDB>

15 years, 11 months

[Monetdb-developers] Partitioning

by moredata＠fastmail.net

Hello, I've been following the developments of MonetDB off and on. It seems to me that there is a real emphasis on developing XML-related functionality, and less so for BI-related functionality. I wanted to ask if there are any plans to allow tables to be partitioned by some condition. This would have a couple of benefits. A table could be broken out into several BAT files, one for each condition met. That would allow you to potentially overcome the 2 GB BAT file limitation on 32 bit systems. And of course, when adding intelligence into the optimizer for this, it could examine the conditions of queries and potentially eliminate entire BAT files to scan. For example, assume you have a table with a column named sometype, and chose sometype for partitioning. Sometype has 10 possible values. Physically, MonetDB would create 10 different BAT files for each column, corresponding to each possible value. When a query is executed with a condition like "sometype = 1", the optimizer is smart enough to know it need only use 1 set of the bat files, and not all 10, significantly reducing the amount of data that needs to be examined. If you are familiar with PostgreSQL, they introduced something like this called Constraint Exclusion Partitioning (also, MySQL has some partitioning functionality in its new beta). Each partition is treated as a subtable of a main parent table. You are required to insert directly into the proper subtable, but querying on the main parent table will determine which subtables are required to be examined in processing the query. Their scheme is not entirely convenient with loading up data, but it is quite flexible in setting up arbitrary conditions on the subtables. Are there any such plans to do something similar? At what state is this in? I believe I saw something about Partitioning on the roadmap several months ago. The MonetDB home page mentions OLAP, and it would seem to me that a feature like this is critical if MonetDB really wants to handle large data volume Business Intelligence queries. Thanks. -- moredata(a)fastmail.net -- http://www.fastmail.fm - Choose from over 50 domains or use your own

15 years, 12 months

[Monetdb-developers] CVS and Monet5

by Luis Zarrabeitia

Hi again. The checkout instructions on the website cvs -d:pserver:anonymous@monetdb.cvs.sourceforge.net:/cvsroot/monetdb checkout buildtools MonetDB sql checks out Monet4.1x rather than Monet5 / Monet4.99. How do I checkout the later? I made some changes to 4.1x that I'd like to try on 4.99 before submitting them (they are so short that I feel I made a MAJOR mistake somewhere, so I'll be testing them at least one more day). Btw, should I submit the .diffs to this list? Zarrabeitia.

15 years, 12 months

[Monetdb-developers] Partitioning

by moredata＠fastmail.net

Hello, I've been following the developments of MonetDB off and on. It seems to me that there is a real emphasis on XML-related functionality, and less so for BI-related functionality. I wanted to ask if there are any plans to allow tables to be partitioned by some condition. This would have a couple of benefits. A table could be broken out into several BAT files, one for each condition met. That would allow you to potentially overcome the 2 GB BAT file limitation on 32 bit systems. And of course, when adding intelligence into the optimizer for this, it could examine the conditions of queries and potentially eliminate entire BAT files to scan. For example, assume you table tab with a column named sometype, and used sometype for partitioning. Sometype has 10 possible values. Physically, MonetDB would create 10 different BAT files for each column, corresponding to each possible value. When a query is executed with a condition like "sometype = 1", the optimizer is smart enough to know it need only use 1 set of the bat files, and not all 10, significantly reducing the amount of data that needs to be examined. If you are familiar with PostgreSQL, they introduced something like this called Constraint Exclusion Partitioning. Each partition is treated as a subtable of a main parent table. You are required to insert directly into the proper subtable, but querying on the main parent table will determine which subtables are required to be examined in processing the query. Their scheme is not entirely convenient with loading up data, but it is quite flexible in setting up arbitrary conditions on the subtables. Are there any such plans to do something similar? At what state is this in? I believe I saw something about Partitioning on the roadmap several months ago. The MonetDB home page mentions OLAP, and it would seem to me that a feature like this is critical if MonetDB really wants to handle Business Intelligence type of queries. Thanks! -- moredata(a)fastmail.net -- http://www.fastmail.fm - Faster than the air-speed velocity of an unladen european swallow

16 years

Re: [Monetdb-developers] join performance issue!

by Stefan Manegold

On Tue, Jul 25, 2006 at 10:02:16PM +0200, Arjen P. de Vries wrote: > Wasn't the property checking always determined by debug flag 8? in general: yes. for join: no, at least not any more since the following checkin: =================================================================== 2003/08/06 - sjoerd: src/gdk/gdk_relop.mx,1.38 DDI Merge. This is the big one! Before tag: BeforeDDImerge, after tag: AfterDDImerge. The DDI merge is now made the official main branch; the CWI_DDI_merge branch is not to be used anymore. =================================================================== Well, Sjoerd just did the checking; the origin is most probabaly Peter. As I said, there are indeed good reasons to do the BATpropcheck (even with debug=0) for *arbitrary* joins, where we can hardly predict any result properties --- maybe, we should consider to not do it in those cases (especially fetchjoin), where we can predict the join result properties pretty well... Stefan > On 25/07/06, Martin Kersten <Martin.Kersten(a)cwi.nl> wrote: > > > > > > > >Stefan Manegold wrote: > >> Dear all, > >> > >> > >> - We should consider making this BATpropcheck in BATjoin and BATleftjoin > >> configurable from the outside, e.g., by adding an extra optional > >argument > >> to join() to request to skipping the BATpropcheck. > >> > >Instead of pollution of the calling interface, I think we should inject > >an explicit request to check/enforce properties. This one might also be > >focussed on those properties of interest according to the optimizer at > >that point. > > > >In M5: > > b:= algebra.join(BAT,BAT); > > bat.setProperties(b); > > > > ... > > bat.checkDenseProperty(b); > > bat.checkOrderProperty(b); > > bat.checkKeyProperty(b); > > > >But first, assess the use of the join(bat,bat) in our controlled > >code base. Please report on this. > > > >regards, Martin > > > > > > > -- > ==================================================================== > CWI, room C1.16 Centre for Mathematics and Computer Science > Kruislaan 413 Email: Arjen.de.Vries(a)cwi.nl > 1098 SJ Amsterdam tel: +31-(0)20-5924306 > The Netherlands fax: +31-(0)20-5924312 > ===================== http://www.cwi.nl/~arjen/ ==================== -- | Dr. Stefan Manegold | mailto:Stefan.Manegold@cwi.nl | | CWI, P.O.Box 94079 | http://www.cwi.nl/~manegold/ | | 1090 GB Amsterdam | Tel.: +31 (20) 592-4212 | | The Netherlands | Fax : +31 (20) 592-4312 |

16 years

[Monetdb-developers] join performance issue!

by Stefan Manegold

Dear all, to prevent you from falling into the same trap as I did this afternoon when trying to analyze, measure & compare positional (fetch-)join performance, here's a warning and my detailed story: WARNING: When running 'join(BAT,BAT);' in MIL or 'algebra.join(BAT,BAT);' in MAL, be aware that this includes not only the actual join algorithm, but also a BATpropcheck() call to check and set properties of the join result (ALWAYS, i.e., also with the default --debug=0 !) NOTE: The latter can easily be up to 85% (*eighty-five* percent!) of the time you measure with a simple wall-clock around the 'join(BAT,BAT);' or 'algebra.join(BAT,BAT);' (see details below) ! Detailed Story: Preparing to invent and implement another cache-aware/-friendly positional (fetch-)join algorithm for some special cases, I was trying to assess the performance of the current positional (fetch-)join algorithms for the following three cases: 1) join(ld,r); 2) join(lo,r); 3) join(lu,r); In all three cases, r is a [V(o)ID, INT] BAT, i.e., has a dense non-materialized head and a randomly distributed integer tail. ld, lo, lu are all [INT, OID] BATs with a randomly distributed integer tail, and an OID head that is in ld: dense (and marked so in the BAT header) (but materialized) in lo: ordered (actually also dense, but only marked ordered, not marked dense in the BAT header) in lu: unordered (random shuffle of an originally dense sequense) Thus, the three case trigger the use following join implementations, respectively: 1) densefetchjoin 2) orderedfetchjoin 3) defaultfetchjoin I used the same size (count) four BATs, and the join is a perfect 1:1 hit; hence the result is as big as the inputs. Here are the wall-clock times (in micro seconds) for BATs of 10000000 tuples MonetDB 4.13.1 (CVS HEAD) default compilation (gcc -g -O2) 64-bits and 64-bit OIDs 2 GHz AMD Athlon(tm) 64 X2 Dual Core Processor 3800+ 2 GB RAM 1) join(ld,r); 2065162 us 2) join(lo,r); 2090277 us 3) join(lu,r); 3058936 us A close look under the hood (i.e., in BATjoin in src/gdk/gdk_relop.mx) reveals the following split timings for the actual join (batjoin()) and the property checking (BATpropcheck()): batjoin() BATpropcheck() join() 1) join(ld,r); 275331 us 1774275 us 2065162 us (abs) 13.33 % 85.91 % 100.00 % (rel) 2) join(lo,r); 303311 us 1770722 us 2090277 us (abs) 14.51 % 84.71 % 100.00 % (rel) 3) join(lu,r); 1268057 us 1775788 us 3058936 us (abs) 41.45 % 58.05 % 100.00 % (rel) Well, there are some lessons to learn: - Be aware of the BATpropcheck when you measure join performance! - The "mandatory" BATpropcheck is only used for BATjoin and BATleftjoin in src/gdk/gdk_relop.mx --- at least as far as I know. - The "mandatory" BATpropcheck in BATjoin and BATleftjoin is there for a good reason: With joins, it's hard to guess the properties of the result (are head and/or tail sorted, dense, and or key/unique?) in general, but the performance of MonetDB highly depends on the availability of these properties; hence, while making the join (considerably) more expensive, the investment (might) pay-off with later operation on the join result. - We should consider making this BATpropcheck in BATjoin and BATleftjoin configurable from the outside, e.g., by adding an extra optional argument to join() to request to skipping the BATpropcheck. I hope you find this information useful... Stefan -- | Dr. Stefan Manegold | mailto:Stefan.Manegold@cwi.nl | | CWI, P.O.Box 94079 | http://www.cwi.nl/~manegold/ | | 1090 GB Amsterdam | Tel.: +31 (20) 592-4212 | | The Netherlands | Fax : +31 (20) 592-4312 |

16 years

[Monetdb-developers] (no subject)

by Dennis Rutjes

L.S, Sorry dat ik dit niet vanaf de SF bug entry kan doen, ik kan me momenteel niet aanmelden. Ik ben om monetDb te deployen op een windows machine(dual core 2 GIg), eesrt gebruikmakend van de release(msi) installer. Daarna kreeg ik na het importeren van 200 k records, de fout # Monet Database Server V4.12.0 # Copyright (c) 1993-2006, CWI. All rights reserved. # Compiled for i686-pc-win32/32bit with 32bit OIDs; dynamically linked. # Visit http://monetdb.cwi.nl/ for further information. !WARNING: BBPincref: range error 283 !WARNING: BBPincref: range error 284 !WARNING: BBPincref: range error 282 !WARNING: BBPincref: range error 285 Ik dacht misschien zijn er XP specifieke dll's die mee gecompileert dienen te worden. MicrovisualC++ EXPRESS gedownload(gratis tegenwoordig met windows SDK SP2 :-), met nmake in de NT directory gedraaid(Ja alle vooraf gestelde eisen aan voldaan python etc) krijg ik de volgende melding. D:\Development\Projects_C++\Monet_CVS\MonetDB\NT>nmake NEED_MX=1 Microsoft (R) Program Maintenance Utility Version 8.00.50727.42 Copyright (C) Microsoft Corporation. All rights reserved. python ".\configure.py" "." "D:\Development\Projects_C++\Monet_CVS\Monet DB\NT" monetdb_config.h.in > monetdb_config.h echo #ifndef UNISTD_H > unistd.h echo #define UNISTD_H >> unistd.h echo #include "io.h" >> unistd.h echo #define open _open >> unistd.h echo #define read _read >> unistd.h echo #define write _write >> unistd.h echo #define close _close >> unistd.h echo #define getpid _getpid >> unistd.h echo #define umask _umask >> unistd.h echo #endif >> unistd.h if exist ".\..\RunMserver.bat.in" python ".\configure.py" "." "D:\Develo pment\Projects_C++\Monet_CVS\MonetDB\NT" ".\..\RunMserver.bat.in" > RunMserver.b at if exist ".\..\RunMapiClient.bat.in" python ".\configure.py" "." "D:\Dev elopment\Projects_C++\Monet_CVS\MonetDB\NT" ".\..\RunMapiClient.bat.in" > RunMap iClient.bat if exist ".\..\RunMtest.bat.in" python ".\configure.py" "." "D:\Developm ent\Projects_C++\Monet_CVS\MonetDB\NT" ".\..\RunMtest.bat.in" > RunMtest.bat if exist ".\..\RunMapprove.bat.in" python ".\configure.py" "." "D:\Devel opment\Projects_C++\Monet_CVS\MonetDB\NT" ".\..\RunMapprove.bat.in" > RunMapprov e.bat "D:\EPF\Microsoft Visual studio 8\VC\BIN\nmake.exe" /nologo /f ".\..\Mak efile.msc" "prefix=D:\Development\Projects_C++\Monet_CVS\MonetDB\NT" all if not exist "src" mkdir "src" copy ".\..\src\Makefile.msc" "src\Makefile" 1 file(s) copied. cd "src" && "D:\EPF\Microsoft Visual studio 8\VC\BIN\nmake.exe" /nologo "prefix=D:\Development\Projects_C++\Monet_CVS\MonetDB\NT" all if not exist "common" mkdir "common" NMAKE : fatal error U1073: don't know how to make '".\..\..\src\common\Makefile. msc"' Stop. NMAKE : fatal error U1077: 'cd' : return code '0x2' Stop. NMAKE : fatal error U1077: '"D:\EPF\Microsoft Visual studio 8\VC\BIN\nmake.exe"' : return code '0x2' Stop. D:\Development\Projects_C++\Monet_CVS\MonetDB\NT> Is daar wat aan te doen?, ik ben niet zo'n C++ wizz. Met vriendelijke groet, Dennis Rutjes

16 years

[Monetdb-developers] Problem editing the .mx files.

by Luis Zarrabeitia

Hello. I need to pipe data into a monetdb database (something along the lines of 'myprocess | MapiClient -s "COPY ...."'. It doesn't seem to be possible out-of-the-box, so I wanted to poke around in the code to find out why and how to fix it (if needed), and hopefully submit a patch. I've been having a problem with that (playing with the code). I don't know how to 'compile' the modified .mx files in the sql module. I have both bison and flex installed, but the makefile uses the commands 'x' and 'l' to process the .mx, and I don't have any idea of what x and l are. So, in a nutshell, my question is: "How do I recompile the sql module after I modify the .mx files? What are 'x' and 'l'?" Regards, Zarrabeitia.

16 years

[Monetdb-developers] Time, Money, Keeping you from earning the Degree you deserve?

by money12542＠aol.com

16 years

[Monetdb-developers] native XML database and XML:DB driver

by Berny Linnemann

Hello, I thought lets send a new posting to specify my goal. I want to use monetDB asa native XML database embedded in a java application. Thats why I would like to know where I can find the textfile as mentioned in the article found in the next link: http://www.monetdb.nl/TechDocs/APIs/JDBC/node9.html In my first posting I mentioned I was tying to find the textfile in some files I downloaded. That were XQuery binaries and source files. Perhaps I was looking at the wrong location and could somebody tell where so find the needed textfile. With kind regards, Berny

16 years

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developers-list July 2006