June 2007 - users-list

[MonetDB-users] create a database
by Matt Stucky 14 Jun '07

14 Jun '07

ok, i give up, how do i create a new database? that is, peer to the 'demo' database that comes with the initial install. 'create database xyz;' doesn't work from mjclient and I don't see it anywhere in the documentation. matt ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The Preacher Said: "Oh Lord, without you we are but dust!" And the Child Said: "What's butt dust?" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AOL & Yahoo IM: stuckym44 MSN Messenger: stuckym4 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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[MonetDB-users] But, for there to be more Jericho, we will need more viewers.
by Odom X. Samuel 14 Jun '07

14 Jun '07

CAON UP 45% In The Last Week! Chan-On International Inc. Symbol: CAON Close: $0.80 UP CAON continues to climb daily. Up 45% in the last 7 days as investors are excited about this company's new direction. Read the releases, consider the potential and get on CAON first thing Thursday! In success, there is the potential for more. It seemed as though things had quieted down on the set, but I guess in the end they thought it best to keep the wheels running smoothly. What can we expect this summer on all three series? Season seven is still a few months away, but it looks as though Smallville is already off to another exciting year. Washington's publicist Howard Bragman told TMZ that the actor received word from Shonda Rhimes that he has been fired due to what was described as a "pattern of problematic behavior. I am happy to report that CBS has officially renewed Jericho! Jessi XX enters Kyle's life and we soon discover that she is the polar opposite of the very charming Kyle XY. You got our attention; your emails and collective voice have been heard. Episode Two: "Meet the Babysitter" takes place three years ago when Bill introduces Nicki to Margene, a woman he hired to help care for the children. It seemed as though things had quieted down on the set, but I guess in the end they thought it best to keep the wheels running smoothly. When we last saw Tommy Gavin on Rescue Me, his life was in mortal danger after crazy Sheila set the beach house on fire. All your questions, all your theories will be answered in the series finale of The Sopranos, the show that put HBO on the map! >From his expressive eyes to his hilarious first words, the creators could not have chosen a better actor to play this fascinating character. We will count on you to rally around the show, to recruit new viewers with the same grass-roots energy, intensity and volume you have displayed in recent weeks. I wonder if Washington's firing had anything to do with Knight's new contract? Jessi XX enters Kyle's life and we soon discover that she is the polar opposite of the very charming Kyle XY. HBO is now offering fans of the hit series Big Love a chance to learn more about our favorite polygamists before season one began. You made a difference. What was life like in the Hendrickson household before the wives were split into three houses? Bill stops at nothing to find out who was responsible for Barb's outing. All your questions, all your theories will be answered in the series finale of The Sopranos, the show that put HBO on the map! I wonder if Washington's firing had anything to do with Knight's new contract? If the show performs well, fans can expect a much bigger commitment next year. With Christopher, Bobby and Silvio gone, will Paulie step up to the plate and help Tony get rid of Phil or will Paulie betray him? You made a difference. Season seven is still a few months away, but it looks as though Smallville is already off to another exciting year. We will let you know specifics when we have them so you can pass them on. As a result, CBS has ordered seven episodes of Jericho for mid-season next year. Season seven is still a few months away, but it looks as though Smallville is already off to another exciting year. Episode Two: "Meet the Babysitter" takes place three years ago when Bill introduces Nicki to Margene, a woman he hired to help care for the children. Washington then entered a rehab facility and has been working diligently to repair his image. Are the Sopranos in mortal danger? Washington's publicist Howard Bragman told TMZ that the actor received word from Shonda Rhimes that he has been fired due to what was described as a "pattern of problematic behavior. Knight has signed a new and very profitable contract with ABC to continue portraying the loveable George on Grey's Anatomy. Such is the case of the very lovely and talented actress Kari Matchett. Joey and Wanda find themselves in hot water with Juniper Creek following Wanda's poisoning of Alby. She'll quickly capture the interest of the evil Lex Luthor and becomes romantically involved with Jimmy Olsen. Stay tuned folks; this character promises to take this series to new and exciting heights! HBO is now offering fans of the hit series Big Love a chance to learn more about our favorite polygamists before season one began. Rescue Me: Following the fire, Tommy learns his problems are far from over when he finds himself under investigation by the insurance company. This beautiful and engaging actress couldn't be more excited about her new role as the mysterious Jessi XX, a character designed to be the polar opposite of her counterpart, Kyle XY. This beautiful and engaging actress couldn't be more excited about her new role as the mysterious Jessi XX, a character designed to be the polar opposite of her counterpart, Kyle XY. Are the Sopranos in mortal danger? We will count on you to rally around the show, to recruit new viewers with the same grass-roots energy, intensity and volume you have displayed in recent weeks. At this time, I cannot tell you the specific date or time period that Jericho will return to our schedule. Season seven is still a few months away, but it looks as though Smallville is already off to another exciting year. " That behavior would be the whole Isaiahgate scandal that began with a fight on the set with Patrick Dempsey in October and continuing after the Golden Globes in January. Washington's publicist Howard Bragman told TMZ that the actor received word from Shonda Rhimes that he has been fired due to what was described as a "pattern of problematic behavior. HBO is now offering fans of the hit series Big Love a chance to learn more about our favorite polygamists before season one began. I wonder if Washington's firing had anything to do with Knight's new contract? Let's hope he fairs better than the recently jailed Paris Hilton. Rescue Me: Following the fire, Tommy learns his problems are far from over when he finds himself under investigation by the insurance company.

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[MonetDB-users] newbie question, Debian install, can't connect
by Matt Stucky 12 Jun '07

12 Jun '07

downloaded the super tarball, installed from the top-level shell script, all seemed ok. mserver5 starts, io.print("test"); works as expected. but when I try to connect with mjclient i get: matt@debian5150:/root/MonetDB/bin$ ./mjclient -umonetdb -lsql password: Database connect failed: MALException:setScenario:Scenario 'sql' not initialized what am i doing wrong? thanks for the help in advance. matt ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The Preacher Said: "Oh Lord, without you we are but dust!" And the Child Said: "What's butt dust?" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AOL & Yahoo IM: stuckym44 MSN Messenger: stuckym4 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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[MonetDB-users] Fwd: MonetDB Error
by Venks 08 Jun '07

08 Jun '07

Niels/Fabian/Romulo, Thanks for all your replies. I rebooted the server and was able to bring up the database again. Next time, if this happens I will try to remove the locks. I tried to remove the file ".gdk_lock" but Linux wouldn't allow me to remove it. Meanwhile, let me do more tests and see why this is becoming an issue. If necessary as Niels suggested I will open a bug as the query actually crashed the server instead of just returning an error. Niels, Though I am joining all these tables, I have WHERE conditions on each table and the end result is actually 16,384 rows. I will do some more testing by changing the syntax of the query and see if it helps. Forwarded Conversation Subject: MonetDB Error ------------------------ From: Venks <venkatesh.mantha(a)gmail.com> To: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:12 AM I got the following error while trying to run a query joining 10 tables. These tables are all 2 or 3 column tables but do have on an average 10M rows in each table. =================== lin5 kernel: journal_get_undo_access: No memory for committed data mserver5: /scratch/monet.GNU.64.64.d.5883/MonetDB5/src/optimizer/opt_joinpath.mx:227: ALGjoinPath: Assertion `b' failed. ./startmonet.sh: line 2: 9488 Aborted $MONETDB5_PREFIX/bin/mserver5 --dbname=csdb --dbinit='include sql;' ====================== After the above error, I am unable to start the MonetDB database. I get the following error. !FATAL: GDKlockHome: Database lock '.gdk_lock' denied How can I re-start the server? Thanks, - Venks -------- From: Romulo Goncalves <R.A.Goncalves(a)cwi.nl> To: Venks <venkatesh.mantha(a)gmail.com> Cc: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:19 AM [Quoted text hidden]You need to remove your dbfarm and dblogs. Just do rm -fr $MONETDB5_PREFIX/var/* Regards, Romulo > > > How can I re-start the server? > > Thanks, > > - Venks > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > MonetDB-users mailing list > MonetDB-users(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/monetdb-users -------- From: Venks <venkatesh.mantha(a)gmail.com> To: Romulo Goncalves <R.A.Goncalves(a)cwi.nl> Cc: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:27 AM If I remove /var/* that will wipe-out my entire database. Correct? [Quoted text hidden] -------- From: Romulo Goncalves <R.A.Goncalves(a)cwi.nl> To: Venks <venkatesh.mantha(a)gmail.com> Cc: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:30 AM Venks wrote: > If I remove /var/* that will wipe-out my entire database. Correct? Yes. Regards, Romulo [Quoted text hidden] -------- From: Venks <venkatesh.mantha(a)gmail.com> To: Romulo Goncalves <R.A.Goncalves(a)cwi.nl> Cc: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:31 AM Is there any way I can restart MonetDB without loosing all my data? [Quoted text hidden] -------- From: Niels Nes <Niels.Nes(a)cwi.nl> To: Venks <venkatesh.mantha(a)gmail.com> Date: Fri, Jun 8, 2007 at 9:34 AM On Fri, Jun 08, 2007 at 09:12:50AM -0400, Venks wrote: > I got the following error while trying to run a query joining 10 > tables. These tables are all 2 or 3 column tables but do have on an > average 10M rows in each table. > > =================== > > lin5 kernel: journal_get_undo_access: No memory for committed data This kernel message seems to indicate that monet run out of memory. 10M^10 is really big, so unless you had a very selective join condition this will blow up to extreme big tables. > mserver5: /scratch/monet.GNU.64.64.d.5883/MonetDB5/src/optimizer/opt_joinpath.mx:227: > ALGjoinPath: Assertion `b' failed. > ./startmonet.sh: line 2: 9488 Aborted Afcourse a crash shouldn't happen. > $MONETDB5_PREFIX/bin/mserver5 --dbname=csdb --dbinit='include sql;' > > ====================== > > After the above error, I am unable to start the MonetDB database. I > get the following error. and after restarting it should normally work even with a crash. So these are bugs, could you report them. Together with a script or so which triggers it? Many thanks.. Niels > > > !FATAL: GDKlockHome: Database lock '.gdk_lock' denied > > > How can I re-start the server? > > Thanks, > > - Venks > [Quoted text hidden]-- Niels Nes, Centre for Mathematics and Computer Science (CWI) Kruislaan 413, 1098 SJ Amsterdam, The Netherlands room C0.02, phone ++31 20 592-4098, fax ++31 20 592-4312 url: http://www.cwi.nl/~niels e-mail: Niels.Nes(a)cwi.nl -------- From: Romulo Goncalves <R.A.Goncalves(a)cwi.nl> To: Venks <venkatesh.mantha(a)gmail.com> Cc: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:35 AM Venks wrote: > Is there any way I can restart MonetDB without loosing all my data? Of course. Just kill your server and start it again.. [goncalve@amelia Triggers]$ ps aux | grep mserver goncalve 27450 1.8 4.8 338904 99192 pts/0 Sl+ 15:34 0:00 mserver5 goncalve 27484 0.0 0.0 60240 708 pts/2 R+ 15:34 0:00 grep mserver [goncalve@amelia Triggers]$ kill -9 27450 [goncalve@amelia Triggers]$ ps aux | grep mserver goncalve 27491 0.0 0.0 60244 708 pts/2 S+ 15:34 0:00 grep mserver [goncalve@amelia Triggers]$ [Quoted text hidden] -------- From: Fabian Groffen <Fabian.Groffen(a)cwi.nl> Reply-To: monetdb-users(a)lists.sourceforge.net, monetdb-users(a)lists.sourceforge.net To: monetdb-users(a)lists.sourceforge.net Date: Fri, Jun 8, 2007 at 9:36 AM On 08-06-2007 09:31:45 -0400, Venks wrote: > Is there any way I can restart MonetDB without loosing all my data? Make sure there are no running mservers any more. If there still are, kill 'em all. Find the .gdk_lock file in your var/monetdb/... and remove it. Try to start MonetDB. (Preferably without the script so you can see what happens.) If it fails to load the BATs, the database has been corrupted. [Quoted text hidden] -------- From: Niels Nes <Niels.Nes(a)cwi.nl> To: Venks <venkatesh.mantha(a)gmail.com> Date: Fri, Jun 8, 2007 at 9:36 AM On Fri, Jun 08, 2007 at 09:31:45AM -0400, Venks wrote: > Is there any way I can restart MonetDB without loosing all my data? > > > >> > > > >> > After the above error, I am unable to start the MonetDB database. I > > >> > get the following error. > > >> > > > >> > > > >> > !FATAL: GDKlockHome: Database lock '.gdk_lock' denied If the lock is the only problem you could simply remove this, ie do a find $prefix/var/ -name .gdk_lock | xargs rm -f This will remove all gdk_lock files, so be sure there are no running Mserver/mserver5s. niels > > >> You need to remove your dbfarm and dblogs. > > >> > > >> Just do > > >> rm -fr $MONETDB5_PREFIX/var/* > > >> > > >> Regards, > > >> Romulo > > >> > > > >> > > > >> > How can I re-start the server? > > >> > > > >> > Thanks, > > >> > > > >> > - Venks > > >> > > > >> > > > >> ------------------------------------------------------------------------- > > >> > This SF.net email is sponsored by DB2 Express > > >> > Download DB2 Express C - the FREE version of DB2 express and take > > >> > control of your XML. No limits. Just data. Click to get it now. > > >> > http://sourceforge.net/powerbar/db2/ > > >> > _______________________________________________ > > >> > MonetDB-users mailing list > > >> > MonetDB-users(a)lists.sourceforge.net > > >> > https://lists.sourceforge.net/lists/listinfo/monetdb-users > > >> > > >> > > > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > MonetDB-users mailing list > MonetDB-users(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/monetdb-users [Quoted text hidden] --------

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[MonetDB-users] MonetDB Error
by Venks 08 Jun '07

08 Jun '07

I got the following error while trying to run a query joining 10 tables. These tables are all 2 or 3 column tables but do have on an average 10M rows in each table. =================== lin5 kernel: journal_get_undo_access: No memory for committed data mserver5: /scratch/monet.GNU.64.64.d.5883/MonetDB5/src/optimizer/opt_joinpath.mx:227: ALGjoinPath: Assertion `b' failed. ./startmonet.sh: line 2: 9488 Aborted $MONETDB5_PREFIX/bin/mserver5 --dbname=csdb --dbinit='include sql;' ====================== After the above error, I am unable to start the MonetDB database. I get the following error. !FATAL: GDKlockHome: Database lock '.gdk_lock' denied How can I re-start the server? Thanks, - Venks

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[MonetDB-users] Error during making buildtools (branch MonetDB_1-18)
by Ying Zhang 06 Jun '07

06 Jun '07

Hi all, I have just checked out the release branch and try to rebuild everything from scratch (on andorea). Making buildtools gives the following error: Making install in conf make[1]: Entering directory `/export/scratch1/zhang/monet/stable/buildtools/build-debug/conf' make[1]: *** No rule to make target `buildtools-config', needed by `all-am'. Stop. make[1]: Leaving directory `/export/scratch1/zhang/monet/stable/buildtools/build-debug/conf' make: *** [install-recursive] Error 1 Does anyone have an idea about this? I believe that building environment is clean. Thanks! Jennie

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[MonetDB-users] building monetdb5 on windows
by Colin Foss 05 Jun '07

05 Jun '07

Are there any plans to create a script similar to monetdb-install.sh for Windows?

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[MonetDB-users] XRPC problem: too many parameters
by Makoto YUI 02 Jun '07

02 Jun '07

Hi, I caught an error (see attached file) at the remote method invocation of XRPC. While I'm not sure whether my query is correct or not, is there imitation of parameters in XRPC? The query and dataset used in the evaluation are put on here. http://db-www.naist.jp/~makoto-y/tmp/xrpc.tgz Thanks, Makoto YUI P.S. To: list-admin please ignore previous mail from wrong address MAPI = monetdb@localhost:50000 QUERY = import module namespace test = "xrpc-test-function" at "/usr/share/MonetDB/xrpc/export/xrpc-mod.xq"; (: local database :) declare variable $blast-gb := fn:doc("blast-gb.xml")/result; declare variable $blast-uniprot := fn:doc("blast-uniprot.xml")/result; (: remote basebase :) declare variable $remote-endpoint := "xanadu.naist.jp"; let $gb_entry := (for $e in $blast-gb/BlastOutput let $hit := $e/BlastOutput_iterations/Iteration/Iteration_hits/Hit ERROR = !WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" !ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. MAPI = monetdb@localhost:50000 QUERY = import module namespace test = "xrpc-test-function" at "/usr/share/MonetDB/xrpc/export/xrpc-mod.xq"; (: local database :) declare variable $blast-gb := fn:doc("blast-gb.xml")/result; declare variable $blast-uniprot := fn:doc("blast-uniprot.xml")/result; (: remote basebase :) declare variable $remote-endpoint := "xanadu.naist.jp"; let $gb_entry := (for $e in $blast-gb/BlastOutput let $hit := $e/BlastOutput_iterations/Iteration/Iteration_hits/Hit ERROR = !ERROR: doLoopLiftedRPC: execution failed at all destinations mapi_query_part:1705:import module namespace test = "xrpc-test-function" at "/usr/share/MonetDB/xrpc/export/xrpc-mod.xq"; (: local database :) declare variable $blast-gb := fn:doc("blast-gb.xml")/result; declare variable $blast-uniprot := fn:doc("blast-uniprot.xml")/result; (: remote basebase :) declare variable $remote-endpoint := "xanadu.naist.jp"; let $gb_entry := (for $e in $blast-gb/BlastOutput let $hit := $e/BlastOutput_iterations/Iteration/Iteration_hits/Hit where $hit/Hit_num = 1 and $hit/Hit_hsps/Hsp/Hsp_evalue/text() <= 1.0e-8 return $e), $uniprot_entry := (for $e in $blast-uniprot/BlastOutput let $hit := $e/BlastOutput_iterations/Iteration/Iteration_hits/Hit where $hit/Hit_num = 1 and $hit/Hit_hsps/Hsp/Hsp_evalue/text() <= 1.0e-8 return $e) where $gb_entry/BlastOutput_query-def/text() = $uniprot_entry/BlastOutput_query-def/text() return <result> { let $gb-hit := $gb_entry/BlastOutput_iterations/Iteration/Iteration_hits/Hit, $gb-key := $gb-hit/Hit_gb/text() return let $genbank-remote-entries := execute at {$remote-endpoint} { test:q1($gb-key) } for $remote_entry at $pos in $genbank-remote-entries let $gb_definition := $remote_entry/INSDSeq_definition, $gb_feature := $remote_entry/INSDSeq_feature-table/INSDFeature, $blast_evalue := $gb-hit[Hit_gb/text() = $remote_entry/INSDSeq_accession-version/text()]/Hit_hsps/Hsp/Hsp_evalue return <genbank num="{ $pos }">{ $blast_evalue, $gb_definition, $gb_feature } </genbank> } </result> fetch next block: start at:2 got next block: length:269 text:XRPC_Client_Serialisation: 626 microsec !WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" !ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations got complete block: text:XRPC_Client_Serialisation: 626 microsec !WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" !ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:XRPC_Client_Serialisation: 626 microsec allocating new result set XRPC_Client_Serialisation: 626 microsec got complete block: text:!WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" !ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:!WARNING: doLoopLiftedRPC: error occurred during RPC call to "xanadu.naist.jp" allocating new result set got complete block: text:!ERROR: CMDhttp_post: too many parameters. !ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:!ERROR: CMDhttp_post: too many parameters. got complete block: text:!ERROR: CMDhttp_post: operation failed. !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:!ERROR: CMDhttp_post: operation failed. got complete block: text: !ERROR: doLoopLiftedRPC: execution failed at all destinations read_line: closing result set got complete block: text:!ERROR: doLoopLiftedRPC: execution failed at all destinations read_line:!ERROR: doLoopLiftedRPC: execution failed at all destinations allocating new result set fetch next block: start at:271 got next block: length:0 text: got complete block: text: read_line: closing result set closing result set Timer 1014.527 msec

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[MonetDB-users] Data Load Issue
by Venks 01 Jun '07

01 Jun '07

Hi, I am trying to load a 12.8 Million row table using COPY command. The table has about 256 columns. After 4 or 5 hours of running, the server terminated abruptly. I am running this on a AMD 64 Bit running Redhat Linux with 3GB of memory and lots of swap space. Any help in identifying the issue would be appreciated. Thanks, - Venks

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