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Re: [Monetdb-developers] [Monetdb-pf-checkins] pathfinder/tests/XRpc/Tests add_trusted.mil, XQuery_0-22, 1.2, 1.2.12.1
by Stefan Manegold 13 Feb '08

13 Feb '08

On Wed, Feb 13, 2008 at 02:50:03PM +0000, Ying Zhang wrote: > Update of /cvsroot/monetdb/pathfinder/tests/XRpc/Tests > In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv23952/tests/XRpc/Tests > > Modified Files: > Tag: XQuery_0-22 > add_trusted.mil > Log Message: > [ monetdb-Bugs-1892582 ] PF: XRpc does not work on Windows > > Don't use hard coded directory name, '/' as directory separator will not > work on Windows. Thanks --- although I have NOT released the CVS check-in lock for the branches, yet ... Stefan > Index: add_trusted.mil > =================================================================== > RCS file: /cvsroot/monetdb/pathfinder/tests/XRpc/Tests/add_trusted.mil,v > retrieving revision 1.2 > retrieving revision 1.2.12.1 > diff -u -d -r1.2 -r1.2.12.1 > --- add_trusted.mil 22 Feb 2007 11:34:56 -0000 1.2 > +++ add_trusted.mil 13 Feb 2008 14:50:00 -0000 1.2.12.1 > @@ -1,7 +1,7 @@ > module("pathfinder"); > module("unix"); > > -var TSTSRCDIR := getenv("TSTSRCBASE") + "/tests/XRpc/Tests"; > +var TSTSRCDIR := getenv("TSTSRCDIR"); > var TSTTRGDIR := getenv("TSTTRGDIR"); > > add_xrpc_trusted(TSTSRCDIR); > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Monetdb-pf-checkins mailing list > Monetdb-pf-checkins(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/monetdb-pf-checkins -- | 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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Re: [Monetdb-developers] monetdb/SQL development plan
by Marcin Zukowski 12 Feb '08

12 Feb '08

Hi Michael, Thank you for your interest in MonetDB. Since I'm not involved with the core MonetDB development, I forward this email to the monetdb-developers list. I'm sure the guys over there will be able to help you. All the best, Marcin Michael Yang wrote: > Hi Marcin, > > I saw that you're one of Peter's PhD students. I just got introduced > to MonetDB as a possible column-store solution for some time series I > work with. I'm in financial mathematics here at Princeton in the > Operations Research department. > > I am a heavy user of MS SQL Server and I use aggregate ranking > functions a lot - row_number(), rank(), etc. Could you give me a > rough estimate as to when MonetDB might add support for these > functions - LEAD(), LAG(), and X() over (partition by ... order by > ...). I see that it's in the development plan, but will it take 1 > year? 1 month? many years? > > Also, in the meantime is there a way you know to emulate these > aggregate functions using local variables in monetdb? > > thanks, > Michael Yang > > Princeton University Operations Research and Financial Engineering

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Re: [Monetdb-developers] [Monetdb-checkins] MonetDB4/src/modules/plain bat_arith.mx, MonetDB_4-22, 1.4.2.2, 1.4.2.3
by Stefan Manegold 12 Feb '08

12 Feb '08

my below fixes in MonetDB4/src/modules/plain/bat_arith.mx would need to be propagated / applied to MonetDB5/src/modules/kernel/batcalc.mx too, but a simple diff|patch does not work, and I haven't found time to do it by hand, yet, sorry ... Stefan On Sun, Feb 10, 2008 at 10:46:53PM +0000, Stefan Manegold wrote: > Update of /cvsroot/monetdb/MonetDB4/src/modules/plain > In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv13856 > > Modified Files: > Tag: MonetDB_4-22 > bat_arith.mx > Log Message: > > fixed bug > [ 1890131 ] PF: property error: incorrectly marked sorted! > http://sourceforge.net/tracker/index.php?func=detail&aid=1890131&group_id=5… > > fixed sortedness propagation for "const [op] BAT" & "BAT [op] const", > in particular three cases: > - substracting a BAT from a constant > yields a result with the input's sort order reversed > - dividing a BAT by a negative constant > yields a result with the input's sort order reversed > - for modulo (%) (also on) float & double > we cannot predict any result order > > > Index: bat_arith.mx > =================================================================== > RCS file: /cvsroot/monetdb/MonetDB4/src/modules/plain/bat_arith.mx,v > retrieving revision 1.4.2.2 > retrieving revision 1.4.2.3 > diff -u -d -r1.4.2.2 -r1.4.2.3 > --- bat_arith.mx 8 Feb 2008 15:02:14 -0000 1.4.2.2 > +++ bat_arith.mx 10 Feb 2008 22:46:51 -0000 1.4.2.3 > @@ -57,42 +57,42 @@ > .END bat_arith; > > @= operations > -@:@1_operation(bte,+,add,,0,2)@ > -@:@1_operation(bte,-,sub,,0,2)@ > -@:@1_operation(bte,*,mul,1,0,3)@ > -@:@1_operation(bte,/,div,1,1,1)@ > +@:@1_operation(bte,+,add,,0,(1|2))@ > +@:@1_operation(bte,-,sub,,0,(1|8))@ > +@:@1_operation(bte,*,mul,1,0,(16|32))@ > +@:@1_operation(bte,/,div,1,1,16)@ > @:@1_operation(bte,%,mod,1,1,0)@ > -@:@1_operation(sht,+,add,,0,2)@ > -@:@1_operation(sht,-,sub,,0,2)@ > -@:@1_operation(sht,*,mul,1,0,3)@ > -@:@1_operation(sht,/,div,1,1,1)@ > +@:@1_operation(sht,+,add,,0,(1|2))@ > +@:@1_operation(sht,-,sub,,0,(1|8))@ > +@:@1_operation(sht,*,mul,1,0,(16|32))@ > +@:@1_operation(sht,/,div,1,1,16)@ > @:@1_operation(sht,%,mod,1,1,0)@ > -@:@1_operation(int,+,add,,0,2)@ > -@:@1_operation(int,-,sub,,0,2)@ > -@:@1_operation(int,*,mul,1,0,3)@ > -@:@1_operation(int,/,div,1,1,1)@ > +@:@1_operation(int,+,add,,0,(1|2))@ > +@:@1_operation(int,-,sub,,0,(1|8))@ > +@:@1_operation(int,*,mul,1,0,(16|32))@ > +@:@1_operation(int,/,div,1,1,16)@ > @:@1_operation(int,%,mod,1,1,0)@ > -@:@1_operation(wrd,+,add,,0,2)@ > -@:@1_operation(wrd,-,sub,,0,2)@ > -@:@1_operation(wrd,*,mul,1,0,3)@ > -@:@1_operation(wrd,/,div,1,1,1)@ > +@:@1_operation(wrd,+,add,,0,(1|2))@ > +@:@1_operation(wrd,-,sub,,0,(1|8))@ > +@:@1_operation(wrd,*,mul,1,0,(16|32))@ > +@:@1_operation(wrd,/,div,1,1,16)@ > @:@1_operation(wrd,%,mod,1,1,0)@ > -@:@1_operation(lng,+,add,,0,2)@ > -@:@1_operation(lng,-,sub,,0,2)@ > -@:@1_operation(lng,*,mul,1,0,3)@ > -@:@1_operation(lng,/,div,1,1,1)@ > +@:@1_operation(lng,+,add,,0,(1|2))@ > +@:@1_operation(lng,-,sub,,0,(1|8))@ > +@:@1_operation(lng,*,mul,1,0,(16|32))@ > +@:@1_operation(lng,/,div,1,1,16)@ > @:@1_operation(lng,%,mod,1,1,0)@ > -@:@1_operation(flt,+,add,,0,2)@ > -@:@1_operation(flt,-,sub,,0,2)@ > -@:@1_operation(flt,*,mul,1,0,3)@ > -@:@1_operation(flt,/,div,1,1,1)@ > -@:@1_operation(dbl,+,add,,0,2)@ > -@:@1_operation(dbl,-,sub,,0,2)@ > -@:@1_operation(dbl,*,mul,1,0,3)@ > -@:@1_operation(dbl,/,div,1,1,1)@ > +@:@1_operation(flt,+,add,,0,(1|2))@ > +@:@1_operation(flt,-,sub,,0,(1|8))@ > +@:@1_operation(flt,*,mul,1,0,(16|32))@ > +@:@1_operation(flt,/,div,1,1,16)@ > +@:@1_operation(dbl,+,add,,0,(1|2))@ > +@:@1_operation(dbl,-,sub,,0,(1|8))@ > +@:@1_operation(dbl,*,mul,1,0,(16|32))@ > +@:@1_operation(dbl,/,div,1,1,16)@ > @:@1_redefine_OP()@ > -@:@1_operation(flt,%,mod,1,1,1,%)@ > -@:@1_operation(dbl,%,mod,1,1,1,%)@ > +@:@1_operation(flt,%,mod,1,1,0,%)@ > +@:@1_operation(dbl,%,mod,1,1,0,%)@ > > @* Implementation > @c > @@ -108,9 +108,13 @@ > @3: add, sub, mul, div, mod basic arithmetic operator name > @4: not used > @5: 0 / 1 disable/enable division by zero check > - @6: 0 / 1 / 2 disable/enable sorting propagation > - 1 propagate on bat,const > - 2 propagate also on const,bat > + @6: (bit pattern) disable/enable sorting propagation > + 1 propagate as-is on bat,const > + 2 propagate as-is on const,bat > + 4 propagate reverted on bat,const (not required/used!) > + 8 propagate reverted on const,bat > + 16 propagate as-is / reverted on bat,const if const >=0 / <0 > + 32 propagate as-is / reverted on const,bat if const >=0 / <0 > */ > @= c_operation > int > @@ -201,7 +205,6 @@ > if (bn == NULL) > return GDK_FAIL; > BATseqbase(bn,b->hseqbase); > - bn->tsorted = 0; > bq = (@1*)Tloc(b,BUNlast(b)); > bp = (@1*)Tloc(b,BUNfirst(b)); > s = bnp = (@1*)Tloc(bn,BUNlast(bn)); > @@ -225,13 +228,19 @@ > BATsetcount(bn, bnp-s); > if (!bn->batDirty) bn->batDirty = TRUE; > > - if (@6 == 2) > + if (@6 & 2) { > bn->tsorted = BATtordered(b); > - if (@6 == 3) { > - if (*v > 0) > + } else > + if (@6 & 8) { > + bn->tsorted = REVERT_SORTED(BATtordered(b)); > + } else > + if (@6 & 32) { > + if (*v >= 0) > bn->tsorted = BATtordered(b); > else > bn->tsorted = REVERT_SORTED(BATtordered(b)); > + } else { > + bn->tsorted = 0; > } > > *ret = bn; > @@ -264,15 +273,20 @@ > } > if (!b->batDirty) b->batDirty = TRUE; > > - if (@6 == 2) > + if (@6 & 2) { > b->tsorted = BATtordered(b); > - if (@6 == 3) { > - if (*v > 0) > + } else > + if (@6 & 8) { > + b->tsorted = REVERT_SORTED(BATtordered(b)); > + } else > + if (@6 & 32) { > + if (*v >= 0) > b->tsorted = BATtordered(b); > else > b->tsorted = REVERT_SORTED(BATtordered(b)); > - } else > + } else { > b->tsorted = 0; > + } > > BBPfix(b->batCacheid); > *ret = b; > @@ -294,7 +308,6 @@ > if( bn == NULL) > return GDK_FAIL; > BATseqbase(bn,b->hseqbase); > - bn->tsorted = 0; > bq = (@1*)Tloc(b,BUNlast(b)); > bp = (@1*)Tloc(b,BUNfirst(b)); > s = bnp = (@1*)Tloc(bn,BUNlast(bn)); > @@ -317,14 +330,21 @@ > } > BATsetcount(bn, bnp-s); > if (!bn->batDirty) bn->batDirty = TRUE; > - if (@6 == 2) > + > + if (@6 & 1) { > bn->tsorted = BATtordered(b); > - if (@6 == 3) { > - if (*v > 0) > + } else > + if (@6 & 4) { > + bn->tsorted = REVERT_SORTED(BATtordered(b)); > + } else > + if (@6 & 16) { > + if (*v >= 0) > bn->tsorted = BATtordered(b); > else > bn->tsorted = REVERT_SORTED(BATtordered(b)); > - } > + } else { > + bn->tsorted = 0; > + } > > *ret = bn; > return GDK_SUCCEED; > @@ -356,15 +376,21 @@ > } > } > if (!b->batDirty) b->batDirty = TRUE; > - if (@6 == 2) > + > + if (@6 & 1) { > b->tsorted = BATtordered(b); > - if (@6 == 3) { > - if (*v > 0) > + } else > + if (@6 & 4) { > + b->tsorted = REVERT_SORTED(BATtordered(b)); > + } else > + if (@6 & 16) { > + if (*v >= 0) > b->tsorted = BATtordered(b); > else > b->tsorted = REVERT_SORTED(BATtordered(b)); > - } else > + } else { > b->tsorted = 0; > + } > > BBPfix(b->batCacheid); > *ret = b; -- | 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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Re: [Monetdb-developers] [Monetdb-checkins]MonetDB/src/gdkgdk_utils.mx, MonetDB_1-22, 1.206, 1.206.2.1
by Peter Boncz 11 Feb '08

11 Feb '08

Hi Stefan Thanks for your response. However, as I have said, but let me say it as clear as possble: I am *sure* there is a bug still unfound in the way re-allocations are done when mem_bigsize redirects it into virtual memory. For this reason, at this stage, with the goal of a stable release, it is just my recommendation *not* to re-enable it. In M5 nor in M5. Peter Dear all, On Mon, Feb 11, 2008 at 02:54:59PM +0100, Peter Boncz wrote: > Hi Stefan, > > The pftijah bug was unrelated to vmalloc(), a relationship that I never > assumed. Indeed, that was (only) my mis-interpretation. Sorry. > The vmalloc() troubles occured, as you may recall, during the data > preparation of the sorted 100GB TPC-H. > > As it is entirely foreseeable that we at some point again will re-encounter an > OS with a malloc implementation that is prone to fragmentation, I'd keep the > vmalloc() code in for the moment (though in disabled state). Linux and Windows > do not need it. > > So, my advise is to for the monet let vmalloc() be disabled, until the issue > is properly investigated and a bugfix is found. Let's call it option (0). Ok. Just to sum up the current state. Please check, whether this is OK and consistent: a) Documentation in MonetDB4/conf/MonetDB.conf.in & MonetDB5/conf/monetdb5.conf.in says: " # gdk_mem_bigsize & gdk_vm_minsize will be set/limited to # 1/2 of the physically available amount of main-memory # during start-up in src/tools/Mserver.mx # memory chunks of size >= gdk_mem_bigsize (in bytes) will be mmaped anonymously #gdk_mem_bigsize=262144 # memory chunks of size >= gdk_vm_minsize (in bytes) will be mmaped; #gdk_vm_minsize=137438953472 " b) Documentation in ./monetweb/Docs/XQuery/MonetDB.conf.texi says " @item @code{gdk_mem_bigsize}: minimum size for memory-mapped columns, e.g. @code{262144}. @item @code{gdk_vm_minsize}: column size above which memory mapped files are used always, e.g. @code{1749291171} " c) MonetDB/src/common/monet_options.mx sets " set[i].kind = opt_builtin; set[i].name = strdup("gdk_mem_bigsize"); set[i].value = strdup("262144"); " d) MonetDB/src/common/monet_options.py.in sets " # gdk_mem_bigsize & gdk_vm_minsize will be set/limited to # 1/2 of the physically available amount of main-memory # during start-up in src/tools/Mserver.mx gdk_mem_bigsize = '256K' gdk_vm_minsize = '128G' " e) GDKinit() in MonetDB/src/gdk/gdk_utils.mx sets " if ((p = GDKgetenv("gdk_mem_bigsize"))) { /* when allocating >6% of all RAM; do so using vmalloc() iso malloc() */ lng max_mem_bigsize = GDK_mem_maxsize/16; /* sanity check to avoid memory fragmentation */ GDK_mem_bigsize = (size_t) MIN(max_mem_bigsize, strtol(p, NULL, 10)); } " f) GDKmallocmax() in MonetDB/src/gdk/gdk_utils.mx ignores GDK_mem_bigsize g) HEAPalloc() in MonetDB/src/gdk/gdk_heap.mx uses GDK_mem_bigsize as follows: " /* when using anonymous vm we malloc we need 64K chunks, also we * 20% extra malloc */ if (h->size > GDK_mem_bigsize) { h->maxsize = (size_t) ((double) h->maxsize * BATMARGIN) - 1; h->maxsize = (1 + (h->maxsize >> 16)) << 16; } " h) HEAPextend() in MonetDB/src/gdk/gdk_heap.mx uses GDK_mem_bigsize as follows: " /* extend a malloced heap, possibly switching over to file-mapped storage */ Heap bak = *h; int can_mmap = (h->filename && size >= GDK_mem_bigsize); int must_mmap = can_mmap && (size >= GDK_vm_minsize || (h->newstorage != STORE_MEM)); [...] if (can_mmap) { /* in anonymous vm, if have to realloc anyway, we reserve some extra space */ if (size > h->maxsize) { h->maxsize = (size_t) ((double) size * BATMARGIN); } /* when using anonymous vm we malloc we need 64K chunks */ h->maxsize = (1 + ((h->maxsize - 1) >> 16)) << 16; [...] /* too big: convert it to a disk-based temporary heap */ if (can_mmap) { char privext[PATHLENGTH], *of = h->filename; FILE *fp; h->filename = NULL; sprintf(privext, "%s.priv", ext); fp = GDKfilelocate(nme, "wb", privext); if (fp != NULL) { fclose(fp); /* a non-persistent heap: we create a .priv but *not* MMAP_PRIV !!! */ h->storage = STORE_MMAP; h->base = NULL; if (HEAPload(h, nme, privext, FALSE) >= 0) { memcpy(h->base, bak.base, bak.free); HEAPfree(&bak); return 0; } } GDKfree(of); } " i) MIL offers mem_bigsize() & mem_bigsize(lng) to get / set mem_bigsize in MonetDB4/src/modules/plain/sys.mx j) both MIL & MAL offer commands to set mem_maxsize and vm_minsize, however, only the MIL variants (still) related mem_maxsize & vm_minsize with mem_bigsize, while the MAL variants no longer do so: MonetDB4/src/modules/plain/sys.mx: " int set_mem_maxsize(lng *num) { @:num2sze(mem_maxsize)@ if (sze < GDK_mem_bigsize) set_mem_bigsize(num); GDK_mem_maxsize = MAX(GDK_mem_bigsize, sze); return GDK_SUCCEED; } int set_vm_minsize(lng *num) { @:num2sze(vm_minsize)@ if (sze < GDK_mem_bigsize) set_mem_bigsize(num); GDK_vm_minsize = MAX(GDK_mem_bigsize, sze); return GDK_SUCCEED; } " MonetDB5/src/modules/kernel/status.mx " int set_mem_maxsize(lng *num) { @:num2sze(mem_maxsize)@ #if 0 if (sze < GDK_mem_bigsize) set_mem_bigsize(num); GDK_mem_maxsize = MAX(GDK_mem_bigsize, sze); #endif GDK_mem_maxsize = sze; return GDK_SUCCEED; } int set_vm_minsize(lng *num) { @:num2sze(vm_minsize)@ #if 0 if (sze < GDK_mem_bigsize) set_mem_bigsize(num); GDK_vm_minsize = MAX(GDK_mem_bigsize, sze); #endif GDK_vm_minsize = sze; return GDK_SUCCEED; } " If all this is considered OK and consistent, we're done. Otherwise, we need to do what ever is required to get the code and documentation consistent, preferably before the release. Stefan > Peter > > > > > > > > > > > > > > > > > Dear all, > > since Roberto's bug appears to be fixed by Peter's ".priv" (vm_minsize > related) fixes (Thanks!), and disabling of vmalloc() (mem_bigsize related) > does not appear have any impact on this bug (just tested successfully both > with vmalloc() disabled and vmalloc() enabled), there are two ways to finish > this release (more or less) quickly: > > (1) finish the disabling of vmalloc() in all parts of the code as indicated > below (or better: remove all remains completely) --- this might need > some extra testing to ensure that it does not have any (significant) > impact on performance ... > > (2) for now (i.e., in the release branch) re-enable vmalloc(), and then > finish the removal of it (incl. extensive testing) in the development > trunk for th next release. > > Since I'm not completely aware of the impact of vmalloc(), I cannot really > make this decision --- the "save" back-up would IMHO be (2). > > Any other comments, opinions, suggestions, expertise? > > Thanks in advance! > > Stefan > > > On Sun, Feb 10, 2008 at 01:33:04PM +0100, Stefan Manegold wrote: > > Peter: Thanks for disabling mem_bigsize / vmalloc(). > > > > All: > > (a) > > Unfortunately, this does not (yet) solve > > [ 1872685 ] PF(tijah): HEAPsetmmap: Assertion `p' failed. > > http://sourceforge.net/tracker/index.php?func=detail&aid=1872685&group_id=5… > > > > But this appears to be more vm_minsize related than mem_bigsize related. > > > > > > (b) > > We should check all occurances of mem_bigsize and remove / "hide" those that > > have become irrelevant with the deactivation of mem_bigsize / vmalloc(): > > ======== > > $ cvsfiles * | egrep -v ' |/Tests/' | xargs grep -n --color 'mem_bigsize' > > -------- > > MonetDB4/conf/MonetDB.conf.in:29:# gdk_mem_bigsize & gdk_vm_minsize will be > set/limited to > > MonetDB4/conf/MonetDB.conf.in:32:# memory chunks of size >= gdk_mem_bigsize > (in bytes) will be mmaped anonymously > > MonetDB4/conf/MonetDB.conf.in:33:#gdk_mem_bigsize=262144 > > MonetDB5/conf/monetdb5.conf.in:33:# gdk_mem_bigsize & gdk_vm_minsize will be > set/limited to > > MonetDB5/conf/monetdb5.conf.in:36:# memory chunks of size >= gdk_mem_bigsize > (in bytes) will be mmaped anonymously > > MonetDB5/conf/monetdb5.conf.in:37:#gdk_mem_bigsize=262144 > > MonetDB/src/common/monet_options.mx:410: set[i].name = > strdup("gdk_mem_bigsize"); > > MonetDB/src/common/monet_options.py.in:39: # gdk_mem_bigsize & > gdk_vm_minsize will be set/limited to > > MonetDB/src/common/monet_options.py.in:42: gdk_mem_bigsize = '256K' > > MonetDB/src/gdk/gdk_heap.mx:121: if (h->size > GDK_mem_bigsize) { > > MonetDB/src/gdk/gdk_heap.mx:189: int can_mmap = (h->filename > && size >= GDK_mem_bigsize); > > MonetDB/src/gdk/gdk.mx:2210:gdk_export size_t GDK_mem_bigsize; /* size > after which we use VM rather than heap */ > > MonetDB/src/gdk/gdk_utils.mx:396:size_t GDK_mem_bigsize = 1 << 20; > > MonetDB/src/gdk/gdk_utils.mx:964:larger than GDK_mem_bigsize) to anonymous > virtual memory. The seamless > > MonetDB/src/gdk/gdk_utils.mx:1054: if (size > GDK_mem_bigsize) { > > MonetDB/src/gdk/gdk_utils.mx:1191: if (size <= GDK_mem_bigsize) { > > MonetDB/src/gdk/gdk_utils.mx:1529: if ((p = > GDKgetenv("gdk_mem_bigsize"))) { > > MonetDB/src/gdk/gdk_utils.mx:1531: lng max_mem_bigsize = > GDK_mem_maxsize/16; > > MonetDB/src/gdk/gdk_utils.mx:1534: GDK_mem_bigsize = (size_t) > MIN(max_mem_bigsize, strtol(p, NULL, 10)); > > monetweb/Docs/XQuery/MonetDB.conf.texi:115:@item @code{gdk_mem_bigsize}: > minimum size for memory-mapped columns, e.g. @code{262144}. > > MonetDB4/src/modules/plain/sys.mx:96:.COMMAND mem_bigsize() : lng = > get_mem_bigsize; > > MonetDB4/src/modules/plain/sys.mx:98:.COMMAND mem_bigsize(lng) : void = > set_mem_bigsize; > > MonetDB4/src/modules/plain/sys.mx:1430:get_mem_bigsize(lng *num) > > MonetDB4/src/modules/plain/sys.mx:1432: *num = GDK_mem_bigsize; > > MonetDB4/src/modules/plain/sys.mx:1437:set_mem_bigsize(lng *num) > > MonetDB4/src/modules/plain/sys.mx:1439: @:num2sze(mem_bigsize)@ > > MonetDB4/src/modules/plain/sys.mx:1440: GDK_mem_bigsize = MAX(32768, sze); > > MonetDB4/src/modules/plain/sys.mx:1462: if (sze < GDK_mem_bigsize) > > MonetDB4/src/modules/plain/sys.mx:1463: set_mem_bigsize(num); > > MonetDB4/src/modules/plain/sys.mx:1464: GDK_mem_maxsize = > MAX(GDK_mem_bigsize, sze); > > MonetDB4/src/modules/plain/sys.mx:1486: if (sze < GDK_mem_bigsize) > > MonetDB4/src/modules/plain/sys.mx:1487: set_mem_bigsize(num); > > MonetDB4/src/modules/plain/sys.mx:1488: GDK_vm_minsize = > MAX(GDK_mem_bigsize, sze); > > MonetDB5/src/modules/kernel/status.mx:405:get_mem_bigsize(lng *num) > > MonetDB5/src/modules/kernel/status.mx:407: *num = GDK_mem_bigsize; > > MonetDB5/src/modules/kernel/status.mx:412:set_mem_bigsize(lng *num) > > MonetDB5/src/modules/kernel/status.mx:414: @:num2sze(mem_bigsize)@ > > MonetDB5/src/modules/kernel/status.mx:415: GDK_mem_bigsize = MAX(32768, > sze); > > MonetDB5/src/modules/kernel/status.mx:439: if (sze < GDK_mem_bigsize) > > MonetDB5/src/modules/kernel/status.mx:440: set_mem_bigsize(num); > > MonetDB5/src/modules/kernel/status.mx:441: GDK_mem_maxsize = > MAX(GDK_mem_bigsize, sze); > > MonetDB5/src/modules/kernel/status.mx:466: if (sze < GDK_mem_bigsize) > > MonetDB5/src/modules/kernel/status.mx:467: set_mem_bigsize(num); > > MonetDB5/src/modules/kernel/status.mx:468: GDK_vm_minsize = > MAX(GDK_mem_bigsize, sze); > > monetweb/MonetDB/QuickTour/HelloWorld/content.shtml:42:[ "gdk_mem_bigsize", > "262144" > > ======== > > > > more tomorrow during MADAM ... > > > > Stefan > > > > > > On Sun, Feb 10, 2008 at 10:37:54AM +0100, Peter Boncz wrote: > > > no consequences. > > > > > > > > > > > > > > > Peter, > > > > > > What about the consequences in: > > > build/MonetDB/src/gdk/gdk_heap.c > > > build/MonetDB5/src/modules/kernel/status.c > > > build/MonetDB/src/gdk/gdk.h > > > > > > Peter Boncz wrote: > > > > Update of /cvsroot/monetdb/MonetDB/src/gdk > > > > In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv29651 > > > > > > > > Modified Files: > > > > Tag: MonetDB_1-22 > > > > gdk_utils.mx > > > > Log Message: > > > > disable use of vmalloc() > > > > > > > > > > > > > > > > Index: gdk_utils.mx > > > > =================================================================== > > > > RCS file: /cvsroot/monetdb/MonetDB/src/gdk/gdk_utils.mx,v > > > > retrieving revision 1.206 > > > > retrieving revision 1.206.2.1 > > > > diff -u -d -r1.206 -r1.206.2.1 > > > > --- gdk_utils.mx 14 Jan 2008 10:48:58 -0000 1.206 > > > > +++ gdk_utils.mx 9 Feb 2008 15:38:11 -0000 1.206.2.1 > > > > @@ -1050,6 +1050,7 @@ > > > > #endif > > > > } > > > > size = (size + 7) & ~7; /* round up to a multiple of eight */ > > > > +#if 0 > > > > if (size > GDK_mem_bigsize) { > > > > size_t newsize = size + sizeof(size_t) + sizeof(size_t); > > > > size_t newmax = MAX(*maxsize, newsize); > > > > @@ -1064,6 +1065,7 @@ > > > > *maxsize = newmax - (sizeof(size_t) + sizeof(size_t)); > > > > return (void *) s; > > > > } > > > > +#endif > > > > CHKMEM(size, 0); > > > > GDKmalloc_prefixsize(s, size); > > > > if (s == NULL) { > > > > > > > > > > > > ------------------------------------------------------------------------- > > > > This SF.net email is sponsored by: Microsoft > > > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > > > _______________________________________________ > > > > Monetdb-checkins mailing list > > > > Monetdb-checkins(a)lists.sourceforge.net > > > > https://lists.sourceforge.net/lists/listinfo/monetdb-checkins > > > > > > > > > > > > > ------------------------------------------------------------------------- > > > This SF.net email is sponsored by: Microsoft > > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > > _______________________________________________ > > > Monetdb-developers mailing list > > > Monetdb-developers(a)lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/monetdb-developers > > > > > > > > > > > > > > > > > > > -- > > | 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 | > > -- > | 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 | > > -- | 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] mem_bigsize
by Peter Boncz 11 Feb '08

11 Feb '08

Hi Stefan, Thanks for so much Grundlichkeit. It is appreciated. It seems that the comment in the XQuery documentation describing mem_bigsize is not correct. Given the current disabled status of mem_bigsize I will remove it. The behavior to limit mem_bigsize to the values of both mem_maxsize and vm_minsize I did not recall; but it probably makes sense. The rest is.. indeed correct. The repitition of configuration values in the python and monet_options has always bothered me, but I recall there was some reason why it cannot be avoided (though not what it was). However, I have spent the entire night&day, re-thinking the mmap-heap situation; and there are still some problems. I think it can be fixed once and for all, but it requires abandoning the X.priv approach to STORE_PRIV copy-on-write heaps in favor of always mapping the X file and writing into X.new files (which take preference over X files if encountered). But that also affects the BBP, the commit protocol. Peter Dear all, On Mon, Feb 11, 2008 at 02:54:59PM +0100, Peter Boncz wrote: > Hi Stefan, > > The pftijah bug was unrelated to vmalloc(), a relationship that I never > assumed. Indeed, that was (only) my mis-interpretation. Sorry. > The vmalloc() troubles occured, as you may recall, during the data > preparation of the sorted 100GB TPC-H. > > As it is entirely foreseeable that we at some point again will re-encounter an > OS with a malloc implementation that is prone to fragmentation, I'd keep the > vmalloc() code in for the moment (though in disabled state). Linux and Windows > do not need it. > > So, my advise is to for the monet let vmalloc() be disabled, until the issue > is properly investigated and a bugfix is found. Let's call it option (0). Ok. Just to sum up the current state. Please check, whether this is OK and consistent: a) Documentation in MonetDB4/conf/MonetDB.conf.in & MonetDB5/conf/monetdb5.conf.in says: " # gdk_mem_bigsize & gdk_vm_minsize will be set/limited to # 1/2 of the physically available amount of main-memory # during start-up in src/tools/Mserver.mx # memory chunks of size >= gdk_mem_bigsize (in bytes) will be mmaped anonymously #gdk_mem_bigsize=262144 # memory chunks of size >= gdk_vm_minsize (in bytes) will be mmaped; #gdk_vm_minsize=137438953472 " b) Documentation in ./monetweb/Docs/XQuery/MonetDB.conf.texi says " @item @code{gdk_mem_bigsize}: minimum size for memory-mapped columns, e.g. @code{262144}. @item @code{gdk_vm_minsize}: column size above which memory mapped files are used always, e.g. @code{1749291171} " c) MonetDB/src/common/monet_options.mx sets " set[i].kind = opt_builtin; set[i].name = strdup("gdk_mem_bigsize"); set[i].value = strdup("262144"); " d) MonetDB/src/common/monet_options.py.in sets " # gdk_mem_bigsize & gdk_vm_minsize will be set/limited to # 1/2 of the physically available amount of main-memory # during start-up in src/tools/Mserver.mx gdk_mem_bigsize = '256K' gdk_vm_minsize = '128G' " e) GDKinit() in MonetDB/src/gdk/gdk_utils.mx sets " if ((p = GDKgetenv("gdk_mem_bigsize"))) { /* when allocating >6% of all RAM; do so using vmalloc() iso malloc() */ lng max_mem_bigsize = GDK_mem_maxsize/16; /* sanity check to avoid memory fragmentation */ GDK_mem_bigsize = (size_t) MIN(max_mem_bigsize, strtol(p, NULL, 10)); } " f) GDKmallocmax() in MonetDB/src/gdk/gdk_utils.mx ignores GDK_mem_bigsize g) HEAPalloc() in MonetDB/src/gdk/gdk_heap.mx uses GDK_mem_bigsize as follows: " /* when using anonymous vm we malloc we need 64K chunks, also we * 20% extra malloc */ if (h->size > GDK_mem_bigsize) { h->maxsize = (size_t) ((double) h->maxsize * BATMARGIN) - 1; h->maxsize = (1 + (h->maxsize >> 16)) << 16; } " h) HEAPextend() in MonetDB/src/gdk/gdk_heap.mx uses GDK_mem_bigsize as follows: " /* extend a malloced heap, possibly switching over to file-mapped storage */ Heap bak = *h; int can_mmap = (h->filename && size >= GDK_mem_bigsize); int must_mmap = can_mmap && (size >= GDK_vm_minsize || (h->newstorage != STORE_MEM)); [...] if (can_mmap) { /* in anonymous vm, if have to realloc anyway, we reserve some extra space */ if (size > h->maxsize) { h->maxsize = (size_t) ((double) size * BATMARGIN); } /* when using anonymous vm we malloc we need 64K chunks */ h->maxsize = (1 + ((h->maxsize - 1) >> 16)) << 16; [...] /* too big: convert it to a disk-based temporary heap */ if (can_mmap) { char privext[PATHLENGTH], *of = h->filename; FILE *fp; h->filename = NULL; sprintf(privext, "%s.priv", ext); fp = GDKfilelocate(nme, "wb", privext); if (fp != NULL) { fclose(fp); /* a non-persistent heap: we create a .priv but *not* MMAP_PRIV !!! */ h->storage = STORE_MMAP; h->base = NULL; if (HEAPload(h, nme, privext, FALSE) >= 0) { memcpy(h->base, bak.base, bak.free); HEAPfree(&bak); return 0; } } GDKfree(of); } " i) MIL offers mem_bigsize() & mem_bigsize(lng) to get / set mem_bigsize in MonetDB4/src/modules/plain/sys.mx j) both MIL & MAL offer commands to set mem_maxsize and vm_minsize, however, only the MIL variants (still) related mem_maxsize & vm_minsize with mem_bigsize, while the MAL variants no longer do so: MonetDB4/src/modules/plain/sys.mx: " int set_mem_maxsize(lng *num) { @:num2sze(mem_maxsize)@ if (sze < GDK_mem_bigsize) set_mem_bigsize(num); GDK_mem_maxsize = MAX(GDK_mem_bigsize, sze); return GDK_SUCCEED; } int set_vm_minsize(lng *num) { @:num2sze(vm_minsize)@ if (sze < GDK_mem_bigsize) set_mem_bigsize(num); GDK_vm_minsize = MAX(GDK_mem_bigsize, sze); return GDK_SUCCEED; } " MonetDB5/src/modules/kernel/status.mx " int set_mem_maxsize(lng *num) { @:num2sze(mem_maxsize)@ #if 0 if (sze < GDK_mem_bigsize) set_mem_bigsize(num); GDK_mem_maxsize = MAX(GDK_mem_bigsize, sze); #endif GDK_mem_maxsize = sze; return GDK_SUCCEED; } int set_vm_minsize(lng *num) { @:num2sze(vm_minsize)@ #if 0 if (sze < GDK_mem_bigsize) set_mem_bigsize(num); GDK_vm_minsize = MAX(GDK_mem_bigsize, sze); #endif GDK_vm_minsize = sze; return GDK_SUCCEED; } " If all this is considered OK and consistent, we're done. Otherwise, we need to do what ever is required to get the code and documentation consistent, preferably before the release. Stefan > Peter > > > > > > > > > > > > > > > > > Dear all, > > since Roberto's bug appears to be fixed by Peter's ".priv" (vm_minsize > related) fixes (Thanks!), and disabling of vmalloc() (mem_bigsize related) > does not appear have any impact on this bug (just tested successfully both > with vmalloc() disabled and vmalloc() enabled), there are two ways to finish > this release (more or less) quickly: > > (1) finish the disabling of vmalloc() in all parts of the code as indicated > below (or better: remove all remains completely) --- this might need > some extra testing to ensure that it does not have any (significant) > impact on performance ... > > (2) for now (i.e., in the release branch) re-enable vmalloc(), and then > finish the removal of it (incl. extensive testing) in the development > trunk for th next release. > > Since I'm not completely aware of the impact of vmalloc(), I cannot really > make this decision --- the "save" back-up would IMHO be (2). > > Any other comments, opinions, suggestions, expertise? > > Thanks in advance! > > Stefan > > > On Sun, Feb 10, 2008 at 01:33:04PM +0100, Stefan Manegold wrote: > > Peter: Thanks for disabling mem_bigsize / vmalloc(). > > > > All: > > (a) > > Unfortunately, this does not (yet) solve > > [ 1872685 ] PF(tijah): HEAPsetmmap: Assertion `p' failed. > > http://sourceforge.net/tracker/index.php?func=detail&aid=1872685&group_id=5… > > > > But this appears to be more vm_minsize related than mem_bigsize related. > > > > > > (b) > > We should check all occurances of mem_bigsize and remove / "hide" those that > > have become irrelevant with the deactivation of mem_bigsize / vmalloc(): > > ======== > > $ cvsfiles * | egrep -v ' |/Tests/' | xargs grep -n --color 'mem_bigsize' > > -------- > > MonetDB4/conf/MonetDB.conf.in:29:# gdk_mem_bigsize & gdk_vm_minsize will be > set/limited to > > MonetDB4/conf/MonetDB.conf.in:32:# memory chunks of size >= gdk_mem_bigsize > (in bytes) will be mmaped anonymously > > MonetDB4/conf/MonetDB.conf.in:33:#gdk_mem_bigsize=262144 > > MonetDB5/conf/monetdb5.conf.in:33:# gdk_mem_bigsize & gdk_vm_minsize will be > set/limited to > > MonetDB5/conf/monetdb5.conf.in:36:# memory chunks of size >= gdk_mem_bigsize > (in bytes) will be mmaped anonymously > > MonetDB5/conf/monetdb5.conf.in:37:#gdk_mem_bigsize=262144 > > MonetDB/src/common/monet_options.mx:410: set[i].name = > strdup("gdk_mem_bigsize"); > > MonetDB/src/common/monet_options.py.in:39: # gdk_mem_bigsize & > gdk_vm_minsize will be set/limited to > > MonetDB/src/common/monet_options.py.in:42: gdk_mem_bigsize = '256K' > > MonetDB/src/gdk/gdk_heap.mx:121: if (h->size > GDK_mem_bigsize) { > > MonetDB/src/gdk/gdk_heap.mx:189: int can_mmap = (h->filename > && size >= GDK_mem_bigsize); > > MonetDB/src/gdk/gdk.mx:2210:gdk_export size_t GDK_mem_bigsize; /* size > after which we use VM rather than heap */ > > MonetDB/src/gdk/gdk_utils.mx:396:size_t GDK_mem_bigsize = 1 << 20; > > MonetDB/src/gdk/gdk_utils.mx:964:larger than GDK_mem_bigsize) to anonymous > virtual memory. The seamless > > MonetDB/src/gdk/gdk_utils.mx:1054: if (size > GDK_mem_bigsize) { > > MonetDB/src/gdk/gdk_utils.mx:1191: if (size <= GDK_mem_bigsize) { > > MonetDB/src/gdk/gdk_utils.mx:1529: if ((p = > GDKgetenv("gdk_mem_bigsize"))) { > > MonetDB/src/gdk/gdk_utils.mx:1531: lng max_mem_bigsize = > GDK_mem_maxsize/16; > > MonetDB/src/gdk/gdk_utils.mx:1534: GDK_mem_bigsize = (size_t) > MIN(max_mem_bigsize, strtol(p, NULL, 10)); > > monetweb/Docs/XQuery/MonetDB.conf.texi:115:@item @code{gdk_mem_bigsize}: > minimum size for memory-mapped columns, e.g. @code{262144}. > > MonetDB4/src/modules/plain/sys.mx:96:.COMMAND mem_bigsize() : lng = > get_mem_bigsize; > > MonetDB4/src/modules/plain/sys.mx:98:.COMMAND mem_bigsize(lng) : void = > set_mem_bigsize; > > MonetDB4/src/modules/plain/sys.mx:1430:get_mem_bigsize(lng *num) > > MonetDB4/src/modules/plain/sys.mx:1432: *num = GDK_mem_bigsize; > > MonetDB4/src/modules/plain/sys.mx:1437:set_mem_bigsize(lng *num) > > MonetDB4/src/modules/plain/sys.mx:1439: @:num2sze(mem_bigsize)@ > > MonetDB4/src/modules/plain/sys.mx:1440: GDK_mem_bigsize = MAX(32768, sze); > > MonetDB4/src/modules/plain/sys.mx:1462: if (sze < GDK_mem_bigsize) > > MonetDB4/src/modules/plain/sys.mx:1463: set_mem_bigsize(num); > > MonetDB4/src/modules/plain/sys.mx:1464: GDK_mem_maxsize = > MAX(GDK_mem_bigsize, sze); > > MonetDB4/src/modules/plain/sys.mx:1486: if (sze < GDK_mem_bigsize) > > MonetDB4/src/modules/plain/sys.mx:1487: set_mem_bigsize(num); > > MonetDB4/src/modules/plain/sys.mx:1488: GDK_vm_minsize = > MAX(GDK_mem_bigsize, sze); > > MonetDB5/src/modules/kernel/status.mx:405:get_mem_bigsize(lng *num) > > MonetDB5/src/modules/kernel/status.mx:407: *num = GDK_mem_bigsize; > > MonetDB5/src/modules/kernel/status.mx:412:set_mem_bigsize(lng *num) > > MonetDB5/src/modules/kernel/status.mx:414: @:num2sze(mem_bigsize)@ > > MonetDB5/src/modules/kernel/status.mx:415: GDK_mem_bigsize = MAX(32768, > sze); > > MonetDB5/src/modules/kernel/status.mx:439: if (sze < GDK_mem_bigsize) > > MonetDB5/src/modules/kernel/status.mx:440: set_mem_bigsize(num); > > MonetDB5/src/modules/kernel/status.mx:441: GDK_mem_maxsize = > MAX(GDK_mem_bigsize, sze); > > MonetDB5/src/modules/kernel/status.mx:466: if (sze < GDK_mem_bigsize) > > MonetDB5/src/modules/kernel/status.mx:467: set_mem_bigsize(num); > > MonetDB5/src/modules/kernel/status.mx:468: GDK_vm_minsize = > MAX(GDK_mem_bigsize, sze); > > monetweb/MonetDB/QuickTour/HelloWorld/content.shtml:42:[ "gdk_mem_bigsize", > "262144" > > ======== > > > > more tomorrow during MADAM ... > > > > Stefan > > > > > > On Sun, Feb 10, 2008 at 10:37:54AM +0100, Peter Boncz wrote: > > > no consequences. > > > > > > > > > > > > > > > Peter, > > > > > > What about the consequences in: > > > build/MonetDB/src/gdk/gdk_heap.c > > > build/MonetDB5/src/modules/kernel/status.c > > > build/MonetDB/src/gdk/gdk.h > > > > > > Peter Boncz wrote: > > > > Update of /cvsroot/monetdb/MonetDB/src/gdk > > > > In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv29651 > > > > > > > > Modified Files: > > > > Tag: MonetDB_1-22 > > > > gdk_utils.mx > > > > Log Message: > > > > disable use of vmalloc() > > > > > > > > > > > > > > > > Index: gdk_utils.mx > > > > =================================================================== > > > > RCS file: /cvsroot/monetdb/MonetDB/src/gdk/gdk_utils.mx,v > > > > retrieving revision 1.206 > > > > retrieving revision 1.206.2.1 > > > > diff -u -d -r1.206 -r1.206.2.1 > > > > --- gdk_utils.mx 14 Jan 2008 10:48:58 -0000 1.206 > > > > +++ gdk_utils.mx 9 Feb 2008 15:38:11 -0000 1.206.2.1 > > > > @@ -1050,6 +1050,7 @@ > > > > #endif > > > > } > > > > size = (size + 7) & ~7; /* round up to a multiple of eight */ > > > > +#if 0 > > > > if (size > GDK_mem_bigsize) { > > > > size_t newsize = size + sizeof(size_t) + sizeof(size_t); > > > > size_t newmax = MAX(*maxsize, newsize); > > > > @@ -1064,6 +1065,7 @@ > > > > *maxsize = newmax - (sizeof(size_t) + sizeof(size_t)); > > > > return (void *) s; > > > > } > > > > +#endif > > > > CHKMEM(size, 0); > > > > GDKmalloc_prefixsize(s, size); > > > > if (s == NULL) { > > > > > > > > > > > > ------------------------------------------------------------------------- > > > > This SF.net email is sponsored by: Microsoft > > > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > > > _______________________________________________ > > > > Monetdb-checkins mailing list > > > > Monetdb-checkins(a)lists.sourceforge.net > > > > https://lists.sourceforge.net/lists/listinfo/monetdb-checkins > > > > > > > > > > > > > ------------------------------------------------------------------------- > > > This SF.net email is sponsored by: Microsoft > > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > > _______________________________________________ > > > Monetdb-developers mailing list > > > Monetdb-developers(a)lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/monetdb-developers > > > > > > > > > > > > > > > > > > > -- > > | 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 | > > -- > | 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 | > > -- | 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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Re: [Monetdb-developers] [Monetdb-checkins] MonetDB/src/gdkgdk_utils.mx, MonetDB_1-22, 1.206, 1.206.2.1
by Peter Boncz 11 Feb '08

11 Feb '08

Hi Stefan, The pftijah bug was unrelated to vmalloc(), a relationship that I never assumed. The vmalloc() troubles occured, as you may recall, during the data preparation of the sorted 100GB TPC-H. As it is entirely foreseeable that we at some point again will re-encounter an OS with a malloc implementation that is prone to fragmentation, I'd keep the vmalloc() code in for the moment (though in disabled state). Linux and Windows do not need it. So, my advise is to for the monet let vmalloc() be disabled, until the issue is properly investigated and a bugfix is found. Let's call it option (0). Peter Dear all, since Roberto's bug appears to be fixed by Peter's ".priv" (vm_minsize related) fixes (Thanks!), and disabling of vmalloc() (mem_bigsize related) does not appear have any impact on this bug (just tested successfully both with vmalloc() disabled and vmalloc() enabled), there are two ways to finish this release (more or less) quickly: (1) finish the disabling of vmalloc() in all parts of the code as indicated below (or better: remove all remains completely) --- this might need some extra testing to ensure that it does not have any (significant) impact on performance ... (2) for now (i.e., in the release branch) re-enable vmalloc(), and then finish the removal of it (incl. extensive testing) in the development trunk for th next release. Since I'm not completely aware of the impact of vmalloc(), I cannot really make this decision --- the "save" back-up would IMHO be (2). Any other comments, opinions, suggestions, expertise? Thanks in advance! Stefan On Sun, Feb 10, 2008 at 01:33:04PM +0100, Stefan Manegold wrote: > Peter: Thanks for disabling mem_bigsize / vmalloc(). > > All: > (a) > Unfortunately, this does not (yet) solve > [ 1872685 ] PF(tijah): HEAPsetmmap: Assertion `p' failed. > http://sourceforge.net/tracker/index.php?func=detail&aid=1872685&group_id=5… > > But this appears to be more vm_minsize related than mem_bigsize related. > > > (b) > We should check all occurances of mem_bigsize and remove / "hide" those that > have become irrelevant with the deactivation of mem_bigsize / vmalloc(): > ======== > $ cvsfiles * | egrep -v ' |/Tests/' | xargs grep -n --color 'mem_bigsize' > -------- > MonetDB4/conf/MonetDB.conf.in:29:# gdk_mem_bigsize & gdk_vm_minsize will be set/limited to > MonetDB4/conf/MonetDB.conf.in:32:# memory chunks of size >= gdk_mem_bigsize (in bytes) will be mmaped anonymously > MonetDB4/conf/MonetDB.conf.in:33:#gdk_mem_bigsize=262144 > MonetDB5/conf/monetdb5.conf.in:33:# gdk_mem_bigsize & gdk_vm_minsize will be set/limited to > MonetDB5/conf/monetdb5.conf.in:36:# memory chunks of size >= gdk_mem_bigsize (in bytes) will be mmaped anonymously > MonetDB5/conf/monetdb5.conf.in:37:#gdk_mem_bigsize=262144 > MonetDB/src/common/monet_options.mx:410: set[i].name = strdup("gdk_mem_bigsize"); > MonetDB/src/common/monet_options.py.in:39: # gdk_mem_bigsize & gdk_vm_minsize will be set/limited to > MonetDB/src/common/monet_options.py.in:42: gdk_mem_bigsize = '256K' > MonetDB/src/gdk/gdk_heap.mx:121: if (h->size > GDK_mem_bigsize) { > MonetDB/src/gdk/gdk_heap.mx:189: int can_mmap = (h->filename && size >= GDK_mem_bigsize); > MonetDB/src/gdk/gdk.mx:2210:gdk_export size_t GDK_mem_bigsize; /* size after which we use VM rather than heap */ > MonetDB/src/gdk/gdk_utils.mx:396:size_t GDK_mem_bigsize = 1 << 20; > MonetDB/src/gdk/gdk_utils.mx:964:larger than GDK_mem_bigsize) to anonymous virtual memory. The seamless > MonetDB/src/gdk/gdk_utils.mx:1054: if (size > GDK_mem_bigsize) { > MonetDB/src/gdk/gdk_utils.mx:1191: if (size <= GDK_mem_bigsize) { > MonetDB/src/gdk/gdk_utils.mx:1529: if ((p = GDKgetenv("gdk_mem_bigsize"))) { > MonetDB/src/gdk/gdk_utils.mx:1531: lng max_mem_bigsize = GDK_mem_maxsize/16; > MonetDB/src/gdk/gdk_utils.mx:1534: GDK_mem_bigsize = (size_t) MIN(max_mem_bigsize, strtol(p, NULL, 10)); > monetweb/Docs/XQuery/MonetDB.conf.texi:115:@item @code{gdk_mem_bigsize}: minimum size for memory-mapped columns, e.g. @code{262144}. > MonetDB4/src/modules/plain/sys.mx:96:.COMMAND mem_bigsize() : lng = get_mem_bigsize; > MonetDB4/src/modules/plain/sys.mx:98:.COMMAND mem_bigsize(lng) : void = set_mem_bigsize; > MonetDB4/src/modules/plain/sys.mx:1430:get_mem_bigsize(lng *num) > MonetDB4/src/modules/plain/sys.mx:1432: *num = GDK_mem_bigsize; > MonetDB4/src/modules/plain/sys.mx:1437:set_mem_bigsize(lng *num) > MonetDB4/src/modules/plain/sys.mx:1439: @:num2sze(mem_bigsize)@ > MonetDB4/src/modules/plain/sys.mx:1440: GDK_mem_bigsize = MAX(32768, sze); > MonetDB4/src/modules/plain/sys.mx:1462: if (sze < GDK_mem_bigsize) > MonetDB4/src/modules/plain/sys.mx:1463: set_mem_bigsize(num); > MonetDB4/src/modules/plain/sys.mx:1464: GDK_mem_maxsize = MAX(GDK_mem_bigsize, sze); > MonetDB4/src/modules/plain/sys.mx:1486: if (sze < GDK_mem_bigsize) > MonetDB4/src/modules/plain/sys.mx:1487: set_mem_bigsize(num); > MonetDB4/src/modules/plain/sys.mx:1488: GDK_vm_minsize = MAX(GDK_mem_bigsize, sze); > MonetDB5/src/modules/kernel/status.mx:405:get_mem_bigsize(lng *num) > MonetDB5/src/modules/kernel/status.mx:407: *num = GDK_mem_bigsize; > MonetDB5/src/modules/kernel/status.mx:412:set_mem_bigsize(lng *num) > MonetDB5/src/modules/kernel/status.mx:414: @:num2sze(mem_bigsize)@ > MonetDB5/src/modules/kernel/status.mx:415: GDK_mem_bigsize = MAX(32768, sze); > MonetDB5/src/modules/kernel/status.mx:439: if (sze < GDK_mem_bigsize) > MonetDB5/src/modules/kernel/status.mx:440: set_mem_bigsize(num); > MonetDB5/src/modules/kernel/status.mx:441: GDK_mem_maxsize = MAX(GDK_mem_bigsize, sze); > MonetDB5/src/modules/kernel/status.mx:466: if (sze < GDK_mem_bigsize) > MonetDB5/src/modules/kernel/status.mx:467: set_mem_bigsize(num); > MonetDB5/src/modules/kernel/status.mx:468: GDK_vm_minsize = MAX(GDK_mem_bigsize, sze); > monetweb/MonetDB/QuickTour/HelloWorld/content.shtml:42:[ "gdk_mem_bigsize", "262144" > ======== > > more tomorrow during MADAM ... > > Stefan > > > On Sun, Feb 10, 2008 at 10:37:54AM +0100, Peter Boncz wrote: > > no consequences. > > > > > > > > > > Peter, > > > > What about the consequences in: > > build/MonetDB/src/gdk/gdk_heap.c > > build/MonetDB5/src/modules/kernel/status.c > > build/MonetDB/src/gdk/gdk.h > > > > Peter Boncz wrote: > > > Update of /cvsroot/monetdb/MonetDB/src/gdk > > > In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv29651 > > > > > > Modified Files: > > > Tag: MonetDB_1-22 > > > gdk_utils.mx > > > Log Message: > > > disable use of vmalloc() > > > > > > > > > > > > Index: gdk_utils.mx > > > =================================================================== > > > RCS file: /cvsroot/monetdb/MonetDB/src/gdk/gdk_utils.mx,v > > > retrieving revision 1.206 > > > retrieving revision 1.206.2.1 > > > diff -u -d -r1.206 -r1.206.2.1 > > > --- gdk_utils.mx 14 Jan 2008 10:48:58 -0000 1.206 > > > +++ gdk_utils.mx 9 Feb 2008 15:38:11 -0000 1.206.2.1 > > > @@ -1050,6 +1050,7 @@ > > > #endif > > > } > > > size = (size + 7) & ~7; /* round up to a multiple of eight */ > > > +#if 0 > > > if (size > GDK_mem_bigsize) { > > > size_t newsize = size + sizeof(size_t) + sizeof(size_t); > > > size_t newmax = MAX(*maxsize, newsize); > > > @@ -1064,6 +1065,7 @@ > > > *maxsize = newmax - (sizeof(size_t) + sizeof(size_t)); > > > return (void *) s; > > > } > > > +#endif > > > CHKMEM(size, 0); > > > GDKmalloc_prefixsize(s, size); > > > if (s == NULL) { > > > > > > > > > ------------------------------------------------------------------------- > > > This SF.net email is sponsored by: Microsoft > > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > > _______________________________________________ > > > Monetdb-checkins mailing list > > > Monetdb-checkins(a)lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/monetdb-checkins > > > > > > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by: Microsoft > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > _______________________________________________ > > Monetdb-developers mailing list > > Monetdb-developers(a)lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/monetdb-developers > > > > > > > > > > > > -- > | 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 | -- | 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 |

2 1

Re: [Monetdb-developers] [Monetdb-checkins] MonetDB/src/gdk gdk_utils.mx, MonetDB_1-22, 1.206, 1.206.2.1
by Peter Boncz 11 Feb '08

11 Feb '08

no consequences. Peter, What about the consequences in: build/MonetDB/src/gdk/gdk_heap.c build/MonetDB5/src/modules/kernel/status.c build/MonetDB/src/gdk/gdk.h Peter Boncz wrote: > Update of /cvsroot/monetdb/MonetDB/src/gdk > In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv29651 > > Modified Files: > Tag: MonetDB_1-22 > gdk_utils.mx > Log Message: > disable use of vmalloc() > > > > Index: gdk_utils.mx > =================================================================== > RCS file: /cvsroot/monetdb/MonetDB/src/gdk/gdk_utils.mx,v > retrieving revision 1.206 > retrieving revision 1.206.2.1 > diff -u -d -r1.206 -r1.206.2.1 > --- gdk_utils.mx 14 Jan 2008 10:48:58 -0000 1.206 > +++ gdk_utils.mx 9 Feb 2008 15:38:11 -0000 1.206.2.1 > @@ -1050,6 +1050,7 @@ > #endif > } > size = (size + 7) & ~7; /* round up to a multiple of eight */ > +#if 0 > if (size > GDK_mem_bigsize) { > size_t newsize = size + sizeof(size_t) + sizeof(size_t); > size_t newmax = MAX(*maxsize, newsize); > @@ -1064,6 +1065,7 @@ > *maxsize = newmax - (sizeof(size_t) + sizeof(size_t)); > return (void *) s; > } > +#endif > CHKMEM(size, 0); > GDKmalloc_prefixsize(s, size); > if (s == NULL) { > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Monetdb-checkins mailing list > Monetdb-checkins(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/monetdb-checkins >

2 2

Re: [Monetdb-developers] [Monetdb-checkins] MonetDB/src/gdk gdk_utils.mx, MonetDB_1-22, 1.206, 1.206.2.1
by Martin Kersten 10 Feb '08

10 Feb '08

Peter, What about the consequences in: build/MonetDB/src/gdk/gdk_heap.c build/MonetDB5/src/modules/kernel/status.c build/MonetDB/src/gdk/gdk.h Peter Boncz wrote: > Update of /cvsroot/monetdb/MonetDB/src/gdk > In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv29651 > > Modified Files: > Tag: MonetDB_1-22 > gdk_utils.mx > Log Message: > disable use of vmalloc() > > > > Index: gdk_utils.mx > =================================================================== > RCS file: /cvsroot/monetdb/MonetDB/src/gdk/gdk_utils.mx,v > retrieving revision 1.206 > retrieving revision 1.206.2.1 > diff -u -d -r1.206 -r1.206.2.1 > --- gdk_utils.mx 14 Jan 2008 10:48:58 -0000 1.206 > +++ gdk_utils.mx 9 Feb 2008 15:38:11 -0000 1.206.2.1 > @@ -1050,6 +1050,7 @@ > #endif > } > size = (size + 7) & ~7; /* round up to a multiple of eight */ > +#if 0 > if (size > GDK_mem_bigsize) { > size_t newsize = size + sizeof(size_t) + sizeof(size_t); > size_t newmax = MAX(*maxsize, newsize); > @@ -1064,6 +1065,7 @@ > *maxsize = newmax - (sizeof(size_t) + sizeof(size_t)); > return (void *) s; > } > +#endif > CHKMEM(size, 0); > GDKmalloc_prefixsize(s, size); > if (s == NULL) { > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Monetdb-checkins mailing list > Monetdb-checkins(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/monetdb-checkins >

1 0

Re: [Monetdb-developers] [Monetdb-checkins] MonetDB/src/gdk gdk_utils.mx, MonetDB_1-22, 1.206, 1.206.2.1
by Martin Kersten 10 Feb '08

10 Feb '08

Shouldn't then also monetdb.conf be adjusted Peter Boncz wrote: > Update of /cvsroot/monetdb/MonetDB/src/gdk > In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv29651 > > Modified Files: > Tag: MonetDB_1-22 > gdk_utils.mx > Log Message: > disable use of vmalloc() > > > > Index: gdk_utils.mx > =================================================================== > RCS file: /cvsroot/monetdb/MonetDB/src/gdk/gdk_utils.mx,v > retrieving revision 1.206 > retrieving revision 1.206.2.1 > diff -u -d -r1.206 -r1.206.2.1 > --- gdk_utils.mx 14 Jan 2008 10:48:58 -0000 1.206 > +++ gdk_utils.mx 9 Feb 2008 15:38:11 -0000 1.206.2.1 > @@ -1050,6 +1050,7 @@ > #endif > } > size = (size + 7) & ~7; /* round up to a multiple of eight */ > +#if 0 > if (size > GDK_mem_bigsize) { > size_t newsize = size + sizeof(size_t) + sizeof(size_t); > size_t newmax = MAX(*maxsize, newsize); > @@ -1064,6 +1065,7 @@ > *maxsize = newmax - (sizeof(size_t) + sizeof(size_t)); > return (void *) s; > } > +#endif > CHKMEM(size, 0); > GDKmalloc_prefixsize(s, size); > if (s == NULL) { > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Monetdb-checkins mailing list > Monetdb-checkins(a)lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/monetdb-checkins >

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Re: [Monetdb-developers] [Monetdb-checkins] MonetDB5/src/optimizer opt_replicator.mx, , 1.10, 1.11
by Stefan Manegold 09 Feb '08

09 Feb '08

On Sat, Feb 09, 2008 at 03:49:10PM +0000, Milena Ivanova wrote: > Update of /cvsroot/monetdb/MonetDB5/src/optimizer > In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv450 > > Modified Files: > opt_replicator.mx > Log Message: > Fix make warning. Why didn't it show with my flags set to > CONFIGURE_OPTIONS="--enable-debug --disable-optimize --enable-strict"? `man gcc` says ======== [...] -Wuninitialized Warn if an automatic variable is used without first being initialized or if a variable may be clobbered by a "setjmp" call. These warnings are possible only in optimizing compilation, because they require data flow information that is computed only when optimizing. If you don’t specify -O, you simply won’t get these warnings. [...] ======== hence, these warnings (=> error) only occur with optimization enabled. Stefan > > Index: opt_replicator.mx > =================================================================== > RCS file: /cvsroot/monetdb/MonetDB5/src/optimizer/opt_replicator.mx,v > retrieving revision 1.10 > retrieving revision 1.11 > diff -u -d -r1.10 -r1.11 > --- opt_replicator.mx 8 Feb 2008 16:44:33 -0000 1.10 > +++ opt_replicator.mx 9 Feb 2008 15:49:08 -0000 1.11 > @@ -242,7 +242,7 @@ > Replica r; > int (*cmp) (ptr, ptr); > ptr nilptr; > - int i, minr; > + int i, minr = -1; > size_t minc = (size_t) GDK_lng_max; > bit leq, lsub, heq, hsub; > int rs[replnr], ri=0; /* subset replicas */ > -- | 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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