- developers-list - monetdb.org

Re: [Monetdb-developers] C-Store as MySQL storage engine
by Daniel J Abadi 26 Aug '07

26 Aug '07

Hi Dossy, There is no source repository/patch submission system in C-Store like you'd see in a mature open source community project. C-Store is only designed to be used as tool by academic researchers to look at the properties of column-oriented database query execution. It is far from a complete database system and parts of the code are quite rudimentary. Further, it has been neglected recently as many of the people who used to code for C-Store are now coding for Vertica. However, I like the idea of using a column-oriented database as a storage engine for MySQL. The thought actually crossed my mind as well recently when I read about Solid using their database as a storage engine for MySQL. My recommendation is that you look into the Monet instead of C-Store, however (http://monetdb.cwi.nl/) They have a far more complete open source column-oriented database. BTW: I came across your blog entry on Vertica recently. IMO, Vertica is much more than Sybase IQ, with far more advanced compression schemes, and the query executer is better able to take advantage of the column-oriented layout (data is kept in columns as long as possible and operated on as such). I think Vertica is about 10 times as fast as IQ. Your blog entry says you have been in contact recently with the director of sales at Vertica who can probably give you more information. D On Fri, 24 Aug 2007, Dossy Shiobara wrote: > Hi! > > Thanks for the work on C-Store and releasing it as open source under the > BSD license. > > Is there a source repository for the project? What's the process for > submitting patches, etc.? > > I'm currently working on using/adapting C-Store as a storage engine for > MySQL. I anticipate needing to make a series of changes to the C-Store > 0.2 code to make this possible and I'd like to try and get those into > the official source tree. > > Thanks, > > -- Dossy > > -- > Dossy Shiobara | dossy(a)panoptic.com | http://dossy.org/ > Panoptic Computer Network | http://panoptic.com/ > "He realized the fastest way to change is to laugh at your own > folly -- then you can let go and quickly move on." (p. 70) > >

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Re: [Monetdb-developers] Monet crashes with {sum} and {avg}
by Stefan Manegold 24 Aug '07

24 Aug '07

On Fri, Aug 24, 2007 at 11:00:05AM -0400, Agustin Schapira wrote: > Hi Niels, > > Sorry for the late reply --I have been travelling. > > Thanks a lot for the fix. I'm glad that the bug was easy to find and > correct. Which file should I change in the Mars-SuperBall > distribution? Is it > MonetDB4-server/MonetDB4/src/monet/monet_multiplex.mx yep, that's the file. Please let us konw, in case there are any problems with the patch --- I'm not sure, whether there might have been other changes to this file in CVS since the tarbaal was made. > And then should I re-run the monetdb-install.sh script? By the way, > is it possible to can have the script do all the make in a directory > other than /tmp, so I can keep the intermediate files around and I > don't have to recompile EVERYTHING whenever I make a change? I'm not familiar at all with the monetdb-install.sh script, but Niels and/or Fabian can probably help. Stefan > Thanks for the quick fix! > > -- Agustin > > > > >Hi Agustin, > > > >You found an interesting bug. The interpret_setaggr implementation has > >indeed many cases. One set of cases uses an intermediate bat in > >a strait forward (normal inserts) way. This case is the one you > >trigger. > >As soon as many values exist in your input bat the intermediate may > >need extending which happens. > >Now many of the other cases don't used the nested bat in such a > >clean way, but do 'dirty' tricks, such as reusing the heaps of your > >input > >bat. Therefor at the end of interpret_setaggr the nested (bats) are > >cleared by restoring the initial contend. > > > >As you can see restoring the 'initial' contend of the normal > >inserts with > >extends is a problem. I now have a fix for this which I hope to > >check in > >soon. > > > > > >Index: monet_multiplex.mx > >=================================================================== > >RCS file: /cvsroot/monetdb/MonetDB4/src/monet/monet_multiplex.mx,v > >retrieving revision 1.4 > >diff -u -r1.4 monet_multiplex.mx > >--- monet_multiplex.mx 20 Feb 2007 11:32:16 -0000 1.4 > >+++ monet_multiplex.mx 22 Aug 2007 19:06:44 -0000 > >@@ -1430,7 +1430,7 @@ > > BAT *b, *nested, *nested_rev, *histo = 0, *extent = 0, *ret > >= 0; > > size_t minpos; > > int ret_val = -1, varsize, head_type, hidden_vartype = 0; > >- int prop_key, prop_sorted = 0; > >+ int prop_key, prop_sorted = 0, restore = 1; > > GDKfcn direct_call = NULL, packed_call = NULL; > > ValRecord argv_bak; > > BUN p, q, r, s; > >@@ -1688,6 +1688,7 @@ > > assert(batbuns->base!=(ptr)1); > > nested->batDeleted = nested->batInserted = batbuns- > >>base; > > > >+ restore = 0; > > if (direct_call == NULL) { > > if (GDKdebug & 131072) > > THRprintf(GDKout, "setaggr impl: > >non-optimized hash\n"); > >@@ -1814,8 +1815,16 @@ > > argv[1] = argv_bak; > > > > /* undo all our hacks in nested before freeing it */ > >- *(BATstore*) nested = nested_bak; > >- *(BAT*) nested_rev = nested_rev_bak; > >+ if (restore) { > >+ *(BATstore*) nested = nested_bak; > >+ *(BAT*) nested_rev = nested_rev_bak; > >+ } else { > >+ BATstore *n = (BATstore*)nested; > >+ nested->H = &n->H; > >+ nested->T = &n->T; > >+ nested_rev->H = &n->T; > >+ nested_rev->T = &n->H; > >+ } > > BBPreclaim(nested); > > > > if (ret_val < 0) { > > > > > > > >Niels > >> > >>I am having more difficulties with {sum} and {avg}. The problems > >>happen both on 4.16.2 and 4.18.0, on Linux and OS X, compiled with > >>32- and 64- bits, with and without optimizations. > >> > >>I have been able to isolate the problem and write a simple test case > >>that shows the error. The attached file has the contents of a BAT; if > >>you save it and then run the following script: > >> > >>module(ascii_io); > >>var b:=bat(str,int).import(<filename>); > >>var x:={sum}(b); > >> > >>then you will get the following error: > >> > >>*** glibc detected *** double free or corruption (!prev): > >>0x00000000006a6360 *** > >> > >>and Monet will crash. > >> > >>The failing free is called from line 1819 of MonetDB4/src/monet/ > >>monet_multiplex.mx. It's inside the 'interpret_setaggr' function, and > >>it happens only with the 'non-optimized hash' implementation of > >>setaggr starting on line 1694 (in fact, if you sort the BAT before > >>calling {sum}, there will be no error. The same is true for example > >>when you call {count}, which uses a different implementation of > >>setaggr to process the {}). > >> > >>The failing free appears within the 'bunins_failed' label (line > >>1800), which in turn is called by the loop that processes the > >>aggregate when, I think, its call to 'bunins_unary' fails. Here's the > >>failing code, starting on line 1694: > >> > >> BATloopFast(extent, p, q, yy) { > >> [...] > >> if (BATprepareHash(b)) > >> goto bunins_failed; > >> HASHloop(b, b->hhash, hh, last) { > >> r = BUNptr(b, hh); > >> @:bunins_unary(r,hh)@ > >> } > >> [...] > >> } > >> > >>I don't understand why @:bunins_unary(r,hh)@ should fail. I have > >>noticed, however, that if I remove the last couple of lines from the > >>attached file then the call to {sum} doesn't crash. These last two > >>lines are exactly the same as others, so it's not their particular > >>value that matters, but rather the number of rows in the BAT with the > >>"Other" head value. > >> > >>Do you have any suggestions? Any other information that I can provide > >>to help you fix the problem? > >> > >>Thanks a lot again, > >> > >>-- Agustin > >> > >> > >>PS: On OS X, instead of the crash you get an error message "malloc: > >>*** Deallocation of a pointer not malloced: 0x281ee00; This could be > >>a double free(), or free() called with the middle of an allocated > >>block", but for all practical purposes it's the same: the free() is > >>called from the same place in interpret_setaggr. The difference is > >>just in the way the Mac equivalent of glibc handles the double free. > >> > > > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 > >>"Course",1 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>>"Other",1 > >>"Other",1 > >>"Other",1 > >>"Other",1 > >>"Other",1 > >>"Other",1 > >>"Other",1 > >>"Other",1 > >>"Other",1 > >>"Other",1 > >>"Other",1 > >>"Other",1 > > > >> > >> > >> > > > >>--------------------------------------------------------------------- > >>---- > >>This SF.net email is sponsored by: Splunk Inc. > >>Still grepping through log files to find problems? Stop. > >>Now Search log events and configuration files using AJAX and a > >>browser. > >>Download your FREE copy of Splunk now >> http://get.splunk.com/ > >>_______________________________________________ > >>Monetdb-developers mailing list > >>Monetdb-developers(a)lists.sourceforge.net > >>https://lists.sourceforge.net/lists/listinfo/monetdb-developers > > > > > >-- > > > >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 -- | 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 |

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[Monetdb-developers] Monet crashes with {sum} and {avg}
by Agustin Schapira 22 Aug '07

22 Aug '07

Hi, I am having more difficulties with {sum} and {avg}. The problems happen both on 4.16.2 and 4.18.0, on Linux and OS X, compiled with 32- and 64- bits, with and without optimizations. I have been able to isolate the problem and write a simple test case that shows the error. The attached file has the contents of a BAT; if you save it and then run the following script: module(ascii_io); var b:=bat(str,int).import(<filename>); var x:={sum}(b); then you will get the following error: *** glibc detected *** double free or corruption (!prev): 0x00000000006a6360 *** and Monet will crash. The failing free is called from line 1819 of MonetDB4/src/monet/ monet_multiplex.mx. It's inside the 'interpret_setaggr' function, and it happens only with the 'non-optimized hash' implementation of setaggr starting on line 1694 (in fact, if you sort the BAT before calling {sum}, there will be no error. The same is true for example when you call {count}, which uses a different implementation of setaggr to process the {}). The failing free appears within the 'bunins_failed' label (line 1800), which in turn is called by the loop that processes the aggregate when, I think, its call to 'bunins_unary' fails. Here's the failing code, starting on line 1694: BATloopFast(extent, p, q, yy) { [...] if (BATprepareHash(b)) goto bunins_failed; HASHloop(b, b->hhash, hh, last) { r = BUNptr(b, hh); @:bunins_unary(r,hh)@ } [...] } I don't understand why @:bunins_unary(r,hh)@ should fail. I have noticed, however, that if I remove the last couple of lines from the attached file then the call to {sum} doesn't crash. These last two lines are exactly the same as others, so it's not their particular value that matters, but rather the number of rows in the BAT with the "Other" head value. Do you have any suggestions? Any other information that I can provide to help you fix the problem? Thanks a lot again, -- Agustin PS: On OS X, instead of the crash you get an error message "malloc: *** Deallocation of a pointer not malloced: 0x281ee00; This could be a double free(), or free() called with the middle of an allocated block", but for all practical purposes it's the same: the free() is called from the same place in interpret_setaggr. The difference is just in the way the Mac equivalent of glibc handles the double free.

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[Monetdb-developers] (no subject)
by Chantola Kit 22 Aug '07

22 Aug '07

Hi MonetDB-developers: I have tried to install Pathfinder on my Fedora7 many times and used all the kind of installations from both Tarball and sourceforge, but I fail to install it and always get error as bellow: grep: /home/sjoerd/Monet-Stable/lib/libbat.la: No such file or directory /bin/sed: can't read /home/sjoerd/Monet-Stable/lib/libbat.la: No such file or directory libtool: link: `/home/sjoerd/Monet-Stable/lib/libbat.la' is not a valid libtool archive make[4]: *** [lib_pf_support.la] Error 1 make[4]: Leaving directory `/root/Desktop/MonetDBInstall/runtime' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/root/Desktop/MonetDBInstall/runtime' make[2]: *** [all] Error 2 make[2]: Leaving directory `/root/Desktop/MonetDBInstall/runtime' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/root/Desktop/MonetDBInstall' make: *** [all] Error 2 It would be grateful if you can help me to solve this problem. I am looking forward to hearing from you. Tola -- Department of Computer Science Graduate School of Systems and Information Engineering University of Tsukuba Ibaraki, Tsukuba city, Japan

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[Monetdb-developers] SQL Stable branch is closed: it is being prepared for bug-fix release
by Sjoerd Mullender 21 Aug '07

21 Aug '07

From today, the Stable branch of sql is closed for all checkins unless approved by myself or Stefan. We are going to prepare a bug-fix release. Note that the development branch (HEAD branch) is open for normal business. -- Sjoerd Mullender

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[Monetdb-developers] Pathfinder installation error
by Chantola Kit 21 Aug '07

21 Aug '07

Dear MonetDBs: I have problem of installing pathfinder. Even though I try to install all MonetDBs such as MonetDB, MonetDB-client, MonetDB4-server, MonetDB5-server, MonetDB-SQL, I cannot install MonetDB4-XQuery. Every time, I use command "make" for Pathfinder, I got some errors which unable me to install Pathfinder as follow: grep: /home/sjoerd/Monet-Stable/lib/libbat.la: No such file or directory /bin/sed: can't read /home/sjoerd/Monet-Stable/lib/libbat.la: No such file or directory libtool: link: `/home/sjoerd/Monet-Stable/lib/libbat.la' is not a valid libtool archive make[4]: *** [lib_pf_support.la] Error 1 make[4]: Leaving directory `/root/Desktop/MonetDBInstall/runtime' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/root/Desktop/MonetDBInstall/runtime' make[2]: *** [all] Error 2 make[2]: Leaving directory `/root/Desktop/MonetDBInstall/runtime' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/root/Desktop/MonetDBInstall' make: *** [all] Error 2 I am looking forward to hearing from you. Best regards, Tola -- Department of Computer Science Graduate School of Systems and Information Engineering University of Tsukuba Ibaraki, Tsukuba city, Japan

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[Monetdb-developers] Installation problem
by Chantola Kit 17 Aug '07

17 Aug '07

Dear monetdb developers: I try to install MonetDB many times on Fedora7 using MonetDB-Mars-SuperBall, but I have the same problem which unables me to connect to server. 1. When I go to Mserver it was: [root@localhost ~]# Mserver # Monet Database Server V4.18.0 # Copyright (c) 1993-2007, CWI. All rights reserved. # Compiled for i686-redhat-linux-gnu/32bit with 32bit OIDs; dynamically linked. # Visit http://monetdb.cwi.nl/ for further information. MonetDB> But, then, I open MapiClient, there is an error like below: [root@localhost ~]# MapiClient -q MAPI = monetdb@localhost:50000 ACTION= mapi_start_talking ERROR = !MALException:setScenario:Scenario 'mil' not initialized 2. When I go to mserver5, it was: MonetDB>[root@localhost ~]# mserver5 # MonetDB Server v5.0.0 # Copyright (c) 1993-2007 CWI, all rights reserved # Compiled for i686-redhat-linux-gnu/32bit with 32bit OIDs dynamically linked # dbname:demo # Visit http://monetdb.cwi.nl/ for further information #warning: please don't forget to set your vault key! #(see /usr/local/etc/monetdb5.conf) > Then, I open MapiClient: [root@localhost ~]# MapiClient -q MAPI = monetdb@localhost:50000 ACTION= mapi_start_talking ERROR = !MALException:setScenario:Scenario 'mil' not initialized [root@localhost ~]# Could you help me to solve the problems? I am looking forward to hearing from you. Tola -- Department of Computer Science Graduate School of Systems and Information Engineering University of Tsukuba Ibaraki, Tsukuba city, Japan

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Re: [Monetdb-developers] [Monetdb-checkins] clients/src/mapiclient MapiClient.mx, , 1.54, 1.55
by Fabian Groffen 16 Aug '07

16 Aug '07

On 16-08-2007 18:49:48 +0000, Martin Kersten wrote: > Update of /cvsroot/monetdb/clients/src/mapiclient > In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv14690 > > Modified Files: > MapiClient.mx > Log Message: > > > Index: MapiClient.mx This commit looks pretty dangerous. Can you elaborate/explain?

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Re: [Monetdb-developers] [Monetdb-checkins] clients/src/java/scripts Makefile.ag, Clients_1-18, 1.3, 1.3.6.1 mjclient.bat.in, Clients_1-18, 1.1, 1.1.6.1 mjclient.in, Clients_1-18, 1.3, 1.3.6.1
by Sjoerd Mullender 16 Aug '07

16 Aug '07

Fabian wrote: > Update of /cvsroot/monetdb/clients/src/java/scripts > In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv31067/scripts > > Modified Files: > Tag: Clients_1-18 > Makefile.ag mjclient.bat.in mjclient.in > Log Message: > Merged HEAD into Clients_1-18 These checkins look like *incompatible* changes to the stable branch. That is not allowed. The whole idea of the stable branch is that you don't have to worry about changes, you can just use the old code with the new version. If you change the name of a file, you can't do that. > > Index: mjclient.bat.in > =================================================================== > RCS file: /cvsroot/monetdb/clients/src/java/scripts/mjclient.bat.in,v > retrieving revision 1.1 > retrieving revision 1.1.6.1 > diff -u -d -r1.1 -r1.1.6.1 > --- mjclient.bat.in 8 Jan 2007 14:03:39 -0000 1.1 > +++ mjclient.bat.in 16 Aug 2007 10:52:44 -0000 1.1.6.1 > @@ -21,4 +21,4 @@ > @rem Future versions might inspect a database of eligible servers > @rem to direct the interaction to the proper ports. > > -call java -jar @datadir@\MonetDB\lib\@JDBCCLIENT_JAR@ %* > +call java -jar @datadir@\MonetDB\lib\jdbcclient.jar %* > > Index: mjclient.in > =================================================================== > RCS file: /cvsroot/monetdb/clients/src/java/scripts/mjclient.in,v > retrieving revision 1.3 > retrieving revision 1.3.6.1 > diff -u -d -r1.3 -r1.3.6.1 > --- mjclient.in 3 Jan 2007 12:17:27 -0000 1.3 > +++ mjclient.in 16 Aug 2007 10:52:44 -0000 1.3.6.1 > @@ -23,4 +23,4 @@ > # to direct the interaction to the proper ports. > > prefix=@prefix@ > -exec java -jar @datadir@/MonetDB/lib/@JDBCCLIENT_JAR@ $* > +exec java -jar @datadir@/MonetDB/lib/jdbcclient.jar $* > > Index: Makefile.ag > =================================================================== > RCS file: /cvsroot/monetdb/clients/src/java/scripts/Makefile.ag,v > retrieving revision 1.3 > retrieving revision 1.3.6.1 > diff -u -d -r1.3 -r1.3.6.1 > --- Makefile.ag 8 Jan 2007 14:03:39 -0000 1.3 > +++ Makefile.ag 16 Aug 2007 10:52:43 -0000 1.3.6.1 > @@ -17,12 +17,14 @@ > MTSAFE > > scripts_sh = { > - NOINST > + COND = NOT_WIN32 > + DIR = bindir > EXT = "" > SOURCES = mjclient.in > } > > scripts_bat = { > - NOINST > + COND = NATIVE_WIN32 > + DIR = bindir > SOURCES = mjclient.bat.in > } > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > Monetdb-checkins mailing list > Monetdb-checkins(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/monetdb-checkins -- Sjoerd Mullender

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Re: [Monetdb-developers] [Monetdb-checkins] clients/src/mapiclient MapiClient.mx, , 1.41, 1.42
by Martin Kersten 15 Aug '07

15 Aug '07

Fabian Groffen wrote: > On 15-08-2007 11:24:47 +0000, Martin Kersten wrote: >> - case 'e': >> + case 'E': >> echoquery = 1; >> continue; >> case 'f': >> @@ -1253,7 +1243,7 @@ >> setFormatter(s); >> continue; >> } >> - case 'x': >> + case 'e': >> exit_on_error = 1; > > I suggest haveing -e for echo. > > exit_on_error should not be necessary, if you assume the following: > 1) the language being used has control for errors itself, e.g. SQL's > auto-commit, or > 2) an error should not happen in batches, thus > 3) the client continues executing when reading from stdin, but dies on > the first error when reading from file > > Don't know how much this would affect testweb, but somewhere I feel it > is only in an interactive session sensible to continue after an error. According to Stefan this does not affect the test web. The feature will be dropped on the next commit

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