[Monetdb-developers] [Monetdb-checkins]MonetDB/src/gdkgdk_utils.mx, MonetDB_1-22, 1.206, 1.206.2.1

Peter Boncz P.Boncz at cwi.nl
Mon Feb 11 19:05:37 CET 2008


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=56967&atid=482468
> >
> > 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 at 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
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> > >
> > >
> > >
> > >
> > >
> >
> > --
> > | Dr. Stefan Manegold | mailto:Stefan.Manegold at 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 at 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 at 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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