[Monetdb-developers] mem_bigsize

11 Feb 2008

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=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) {
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--
| 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       |

    

Peter Boncz

Stefan Manegold

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