Pathological behaviour when building large hash index

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Will Muldrew

5 Dec 2013 5 Dec '13

2:37 p.m.

Hi I've been investigating very slow queries on my 350M row dataset when selecting for equality on a non-unique string id. e.g. select count(*) from t_order where orderId = 'FOO'; This query takes ~4.5 hours to build a thash index. Subsequent repeats hit the cache and are sub milli. select count(*) from t_order where time > '1970-01-01' and orderId = 'FOO' This second one is consistently finished in a few seconds or less, and doesn't create any indexes. The first query is a bit of a show-stopper. It spends a huge about of time in BAThash (gdk_search.c), and incurs a lot of page faults while reading and writing at random across a multi GB mmaped thash file. Additionally these page faults are hampered by the OS trying to write dirty pages out in the background. I've got plenty of RAM overall (130GB), but the 'active' page proportion for the thash file seems to be stuck at about 25% - giving me a 0.75 probability of a miss. * Is there some way to make my OS less keen to evict pages? (swappiness = 0 already) I should have plenty of room to have the whole thash file resident. Additionally, allowing it to sit on dirty pages longer would reduce the total write IO. * Is there some way to simply prevent large thash creation? For many applications I'd rather have slower consistent queries, then incur a massively slow query following a restart (not great in a prod environment!) * Is there some way to generate the hash index with a more sympathetic algo that doesn't degrade so steeply. e.g some hash + sort. (I have literally no experience with this!) -Will Muldrew

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Stefan Manegold

5 Dec 5 Dec

3:54 p.m.

Hi Will, could you please also share with us which version of MonetDB you are using, and OS you are running? Pleass find more comments & questions inlined below. ----- Original Message -----

...

Hi

I've been investigating very slow queries on my 350M row dataset when selecting for equality on a non-unique string id. e.g.

select count(*) from t_order where orderId = 'FOO';

Is your orderId column unique, or are there duplicate values?

...

This query takes ~4.5 hours to build a thash index. Subsequent repeats hit the cache and are sub milli.

select count(*) from t_order where time > '1970-01-01' and orderId = 'FOO'

This second one is consistently finished in a few seconds or less, and doesn't create any indexes.

The first query is a bit of a show-stopper. It spends a huge about of time in BAThash (gdk_search.c), and incurs a lot of page faults while reading and writing at random across a multi GB mmaped thash file. Additionally these page faults are hampered by the OS trying to write dirty pages out in the background. I've got plenty of RAM overall (130GB), but the 'active' page proportion for the thash file seems to be stuck at about 25% - giving me a 0.75 probability of a miss.

* Is there some way to make my OS less keen to evict pages? (swappiness = 0 already) I should have plenty of room to have the whole thash file resident. Additionally, allowing it to sit on dirty pages longer would reduce the total write IO.

In fact, if there is sufficient memory in total, there would be no need to flush dirty (non-persistent) pages at all, but we have not yet found a good way to hit this to the OS --- madvice() did not have much/any useful efficet for us on Linux. Maybe some of the issues dicsussed here play a role: http://engineering.linkedin.com/performance/optimizing-linux-memory-manageme... ? While we have not yet encountered the NUMA problem reported there, we have encountered the transparent huge page problems, and usually disable them as also suggested in the above posting.

...

* Is there some way to simply prevent large thash creation? For many applications I'd rather have slower consistent queries, then incur a massively slow query following a restart (not great in a prod environment!)

Not easily right now. However, you can either add the "fake" time predicate as you did above, which (in this case) triggers MonetDB's optimizer to push the time predicate (either because it's in timestamp (int) rather then varchar (string), or because the time column happens to be ordered) below the orderId predicate and this avoid the hash build, or change the following line(s) in gdk/gdk_select.c (in case you built MonetDB yourself from source): hash = b->batPersistence == PERSISTENT && (size_t) ATOMsize(b->ttype) > sizeof(BUN) / 4 && BATcount(b) * (ATOMsize(b->ttype) + 2 * sizeof(BUN)) < GDK_mem_maxsize / 2; -> hash = FALSE; We'll consider whether we can provide a better solution in a future release.

...

* Is there some way to generate the hash index with a more sympathetic algo that doesn't degrade so steeply. e.g some hash + sort. (I have literally no experience with this!)

We'll also look into this. However, building a hash index inherently incurs random access, so chances are slim ... Best, Stefan

...

-Will Muldrew

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

Will Muldrew

4:32 p.m.

Hi Stefan Here are my version details: MonetDB-11.15.17 CentOS release 6.3 kernel 3.6.2 I think I might proceed with a patched version with the hash disabled. That's totally fine for me right now, though obviously it'd be nice to be on the trunk! W.r.t. a less random access hash generation. This is all very hand-wavey but how about: 1) generate a sequence of (hash,oid) pairs to some file or mmapped area. 2). use some well-known "external sort" algo to sort these pairs by hash (e.g. split, qsort, merge). 3). build your final hash by iterating through this sorted datastructure. Your memory writing would then be sequential and you'd get good page hit characteristics. You just need to choose a decent sort algo - ideally which works transparently over memmapped data. What do you think? I might even have a crack at it myself :) -Will On 5 December 2013 15:54, Stefan Manegold wrote:

...

Hi Will,

could you please also share with us which version of MonetDB you are using, and OS you are running?

Pleass find more comments & questions inlined below.

----- Original Message -----

...
Hi

I've been investigating very slow queries on my 350M row dataset when selecting for equality on a non-unique string id. e.g.

select count(*) from t_order where orderId = 'FOO';

Is your orderId column unique, or are there duplicate values?

...
This query takes ~4.5 hours to build a thash index. Subsequent repeats hit the cache and are sub milli.

select count(*) from t_order where time > '1970-01-01' and orderId = 'FOO'

This second one is consistently finished in a few seconds or less, and doesn't create any indexes.

The first query is a bit of a show-stopper. It spends a huge about of time in BAThash (gdk_search.c), and incurs a lot of page faults while reading and writing at random across a multi GB mmaped thash file. Additionally these page faults are hampered by the OS trying to write dirty pages out in the background. I've got plenty of RAM overall (130GB), but the 'active' page proportion for the thash file seems to be stuck at about 25% - giving me a 0.75 probability of a miss.

* Is there some way to make my OS less keen to evict pages? (swappiness = 0 already) I should have plenty of room to have the whole thash file resident. Additionally, allowing it to sit on dirty pages longer would reduce the total write IO.

In fact, if there is sufficient memory in total, there would be no need to flush dirty (non-persistent) pages at all, but we have not yet found a good way to hit this to the OS --- madvice() did not have much/any useful efficet for us on Linux.

Maybe some of the issues dicsussed here play a role:

http://engineering.linkedin.com/performance/optimizing-linux-memory-manageme... ?

While we have not yet encountered the NUMA problem reported there, we have encountered the transparent huge page problems, and usually disable them as also suggested in the above posting.

...
* Is there some way to simply prevent large thash creation? For many applications I'd rather have slower consistent queries, then incur a massively slow query following a restart (not great in a prod environment!)

Not easily right now. However, you can either add the "fake" time predicate as you did above, which (in this case) triggers MonetDB's optimizer to push the time predicate (either because it's in timestamp (int) rather then varchar (string), or because the time column happens to be ordered) below the orderId predicate and this avoid the hash build, or change the following line(s) in gdk/gdk_select.c (in case you built MonetDB yourself from source):

hash = b->batPersistence == PERSISTENT && (size_t) ATOMsize(b->ttype) > sizeof(BUN) / 4 && BATcount(b) * (ATOMsize(b->ttype) + 2 * sizeof(BUN)) < GDK_mem_maxsize / 2; -> hash = FALSE;

We'll consider whether we can provide a better solution in a future release.

...
* Is there some way to generate the hash index with a more sympathetic algo that doesn't degrade so steeply. e.g some hash + sort. (I have literally no experience with this!)

We'll also look into this. However, building a hash index inherently incurs random access, so chances are slim ...

Best, Stefan

...
-Will Muldrew

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

Will Muldrew

4:41 p.m.

Hi Stefan I've added that hash = FALSE patch, and now my simple query returns reliably in 6 seconds. It's still a lot slower than the indexed one (obviously), and 12x slower than the one with the time > '1970-01-01' optimiser nudge (which causes parallelism), but it'll do for now. Thanks -Will On 5 December 2013 16:32, Will Muldrew wrote:

...

Hi Stefan

Here are my version details:

MonetDB-11.15.17 CentOS release 6.3 kernel 3.6.2

I think I might proceed with a patched version with the hash disabled. That's totally fine for me right now, though obviously it'd be nice to be on the trunk!

W.r.t. a less random access hash generation. This is all very hand-wavey but how about: 1) generate a sequence of (hash,oid) pairs to some file or mmapped area. 2). use some well-known "external sort" algo to sort these pairs by hash (e.g. split, qsort, merge). 3). build your final hash by iterating through this sorted datastructure.

Your memory writing would then be sequential and you'd get good page hit characteristics. You just need to choose a decent sort algo - ideally which works transparently over memmapped data.

What do you think? I might even have a crack at it myself :)

-Will

On 5 December 2013 15:54, Stefan Manegold wrote:

...
Hi Will,

could you please also share with us which version of MonetDB you are using, and OS you are running?

Pleass find more comments & questions inlined below.

----- Original Message -----

...
Hi

I've been investigating very slow queries on my 350M row dataset when selecting for equality on a non-unique string id. e.g.

select count(*) from t_order where orderId = 'FOO';

Is your orderId column unique, or are there duplicate values?

...
This query takes ~4.5 hours to build a thash index. Subsequent repeats hit the cache and are sub milli.

select count(*) from t_order where time > '1970-01-01' and orderId = 'FOO'

This second one is consistently finished in a few seconds or less, and doesn't create any indexes.

The first query is a bit of a show-stopper. It spends a huge about of time in BAThash (gdk_search.c), and incurs a lot of page faults while reading and writing at random across a multi GB mmaped thash file. Additionally these page faults are hampered by the OS trying to write dirty pages out in the background. I've got plenty of RAM overall (130GB), but the 'active' page proportion for the thash file seems to be stuck at about 25% - giving me a 0.75 probability of a miss.

* Is there some way to make my OS less keen to evict pages? (swappiness = 0 already) I should have plenty of room to have the whole thash file resident. Additionally, allowing it to sit on dirty pages longer would reduce the total write IO.

In fact, if there is sufficient memory in total, there would be no need to flush dirty (non-persistent) pages at all, but we have not yet found a good way to hit this to the OS --- madvice() did not have much/any useful efficet for us on Linux.

Maybe some of the issues dicsussed here play a role:

http://engineering.linkedin.com/performance/optimizing-linux-memory-manageme... ?

While we have not yet encountered the NUMA problem reported there, we have encountered the transparent huge page problems, and usually disable them as also suggested in the above posting.

...
* Is there some way to simply prevent large thash creation? For many applications I'd rather have slower consistent queries, then incur a massively slow query following a restart (not great in a prod environment!)

Not easily right now. However, you can either add the "fake" time predicate as you did above, which (in this case) triggers MonetDB's optimizer to push the time predicate (either because it's in timestamp (int) rather then varchar (string), or because the time column happens to be ordered) below the orderId predicate and this avoid the hash build, or change the following line(s) in gdk/gdk_select.c (in case you built MonetDB yourself from source):

hash = b->batPersistence == PERSISTENT && (size_t) ATOMsize(b->ttype) > sizeof(BUN) / 4 && BATcount(b) * (ATOMsize(b->ttype) + 2 * sizeof(BUN)) < GDK_mem_maxsize / 2; -> hash = FALSE;

We'll consider whether we can provide a better solution in a future release.

...
* Is there some way to generate the hash index with a more sympathetic algo that doesn't degrade so steeply. e.g some hash + sort. (I have literally no experience with this!)

We'll also look into this. However, building a hash index inherently incurs random access, so chances are slim ...

Best, Stefan

...
-Will Muldrew

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

Stefan Manegold

4:49 p.m.

Hi Will, thank for reminding me: the optimizer still sees your query as point query and thus prevents parallelization in order to build/use the hash index. Maybe you can "fool" the optimizer (and I hope noone else is reading what I'm writing now ... ;-)) by "disguising" the point predicate as range predicate, say, "where orderId between 'FOO' and 'FOO'" --- in fact, I rather hope (for us) that is will not work ... Stefan ----- Original Message -----

...

Hi Stefan

I've added that hash = FALSE patch, and now my simple query returns reliably in 6 seconds. It's still a lot slower than the indexed one (obviously), and 12x slower than the one with the time > '1970-01-01' optimiser nudge (which causes parallelism), but it'll do for now.

Thanks

-Will

On 5 December 2013 16:32, Will Muldrew < will.muldrew@gmail.com > wrote:

Hi Stefan

Here are my version details:

MonetDB-11.15.17 CentOS release 6.3 kernel 3.6.2

I think I might proceed with a patched version with the hash disabled. That's totally fine for me right now, though obviously it'd be nice to be on the trunk!

W.r.t. a less random access hash generation. This is all very hand-wavey but how about: 1) generate a sequence of (hash,oid) pairs to some file or mmapped area. 2). use some well-known "external sort" algo to sort these pairs by hash (e.g. split, qsort, merge). 3). build your final hash by iterating through this sorted datastructure.

Your memory writing would then be sequential and you'd get good page hit characteristics. You just need to choose a decent sort algo - ideally which works transparently over memmapped data.

What do you think? I might even have a crack at it myself :)

-Will

On 5 December 2013 15:54, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

could you please also share with us which version of MonetDB you are using, and OS you are running?

Pleass find more comments & questions inlined below.

----- Original Message -----

...
Hi

I've been investigating very slow queries on my 350M row dataset when selecting for equality on a non-unique string id. e.g.

select count(*) from t_order where orderId = 'FOO';

Is your orderId column unique, or are there duplicate values?

...
This query takes ~4.5 hours to build a thash index. Subsequent repeats hit the cache and are sub milli.

select count(*) from t_order where time > '1970-01-01' and orderId = 'FOO'

This second one is consistently finished in a few seconds or less, and doesn't create any indexes.

The first query is a bit of a show-stopper. It spends a huge about of time in BAThash (gdk_search.c), and incurs a lot of page faults while reading and writing at random across a multi GB mmaped thash file. Additionally these page faults are hampered by the OS trying to write dirty pages out in the background. I've got plenty of RAM overall (130GB), but the 'active' page proportion for the thash file seems to be stuck at about 25% - giving me a 0.75 probability of a miss.

* Is there some way to make my OS less keen to evict pages? (swappiness = 0 already) I should have plenty of room to have the whole thash file resident. Additionally, allowing it to sit on dirty pages longer would reduce the total write IO.

In fact, if there is sufficient memory in total, there would be no need to flush dirty (non-persistent) pages at all, but we have not yet found a good way to hit this to the OS --- madvice() did not have much/any useful efficet for us on Linux.

Maybe some of the issues dicsussed here play a role: http://engineering.linkedin.com/performance/optimizing-linux-memory-manageme... ?

While we have not yet encountered the NUMA problem reported there, we have encountered the transparent huge page problems, and usually disable them as also suggested in the above posting.

...
* Is there some way to simply prevent large thash creation? For many applications I'd rather have slower consistent queries, then incur a massively slow query following a restart (not great in a prod environment!)

Not easily right now. However, you can either add the "fake" time predicate as you did above, which (in this case) triggers MonetDB's optimizer to push the time predicate (either because it's in timestamp (int) rather then varchar (string), or because the time column happens to be ordered) below the orderId predicate and this avoid the hash build, or change the following line(s) in gdk/gdk_select.c (in case you built MonetDB yourself from source):

hash = b->batPersistence == PERSISTENT && (size_t) ATOMsize(b->ttype) > sizeof(BUN) / 4 && BATcount(b) * (ATOMsize(b->ttype) + 2 * sizeof(BUN)) < GDK_mem_maxsize / 2; -> hash = FALSE;

We'll consider whether we can provide a better solution in a future release.

...
* Is there some way to generate the hash index with a more sympathetic algo that doesn't degrade so steeply. e.g some hash + sort. (I have literally no experience with this!)

We'll also look into this. However, building a hash index inherently incurs random access, so chances are slim ...

Best, Stefan

...
-Will Muldrew

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

Will Muldrew

4:58 p.m.

Sorry! sql>select count(*) from t_order2 where orderId between 'AAAAAA' and 'AAAAAA'; +------+ | L1 | +======+ | 0 | +------+ 1 tuple (596.202ms) On 5 December 2013 16:49, Stefan Manegold wrote:

...

Hi Will,

thank for reminding me: the optimizer still sees your query as point query and thus prevents parallelization in order to build/use the hash index.

Maybe you can "fool" the optimizer (and I hope noone else is reading what I'm writing now ... ;-)) by "disguising" the point predicate as range predicate, say, "where orderId between 'FOO' and 'FOO'" --- in fact, I rather hope (for us) that is will not work ...

Stefan

...
Hi Stefan

I've added that hash = FALSE patch, and now my simple query returns reliably in 6 seconds. It's still a lot slower than the indexed one (obviously), and 12x slower than the one with the time > '1970-01-01' optimiser nudge (which causes parallelism), but it'll do for now.

Thanks

-Will

On 5 December 2013 16:32, Will Muldrew < will.muldrew@gmail.com > wrote:

Hi Stefan

Here are my version details:

MonetDB-11.15.17 CentOS release 6.3 kernel 3.6.2

I think I might proceed with a patched version with the hash disabled. That's totally fine for me right now, though obviously it'd be nice to be on the trunk!

W.r.t. a less random access hash generation. This is all very hand-wavey but how about: 1) generate a sequence of (hash,oid) pairs to some file or mmapped area. 2). use some well-known "external sort" algo to sort these pairs by hash (e.g. split, qsort, merge). 3). build your final hash by iterating through this sorted datastructure.

Your memory writing would then be sequential and you'd get good page hit characteristics. You just need to choose a decent sort algo - ideally which works transparently over memmapped data.

What do you think? I might even have a crack at it myself :)

-Will

On 5 December 2013 15:54, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

could you please also share with us which version of MonetDB you are using, and OS you are running?

Pleass find more comments & questions inlined below.

----- Original Message -----

...
Hi

I've been investigating very slow queries on my 350M row dataset when selecting for equality on a non-unique string id. e.g.

select count(*) from t_order where orderId = 'FOO';

Is your orderId column unique, or are there duplicate values?

...
This query takes ~4.5 hours to build a thash index. Subsequent repeats hit the cache and are sub milli.

select count(*) from t_order where time > '1970-01-01' and orderId = 'FOO'

This second one is consistently finished in a few seconds or less, and doesn't create any indexes.

The first query is a bit of a show-stopper. It spends a huge about of time in BAThash (gdk_search.c), and incurs a lot of page faults while reading and writing at random across a multi GB mmaped thash file. Additionally

...
...
page faults are hampered by the OS trying to write dirty pages out in

...
...
background. I've got plenty of RAM overall (130GB), but the 'active'

----- Original Message ----- these the page

...
...
proportion for the thash file seems to be stuck at about 25% - giving me a 0.75 probability of a miss.

* Is there some way to make my OS less keen to evict pages? (swappiness = 0 already) I should have plenty of room to have the whole thash file resident. Additionally, allowing it to sit on dirty pages longer would reduce the total write IO.

In fact, if there is sufficient memory in total, there would be no need to flush dirty (non-persistent) pages at all, but we have not yet found a good way to hit this to the OS --- madvice() did not have much/any useful efficet for us on Linux.

Maybe some of the issues dicsussed here play a role:

...
?

While we have not yet encountered the NUMA problem reported there, we have encountered the transparent huge page problems, and usually disable them as also suggested in the above posting.

...
* Is there some way to simply prevent large thash creation? For many applications I'd rather have slower consistent queries, then incur a massively slow query following a restart (not great in a prod environment!)

Not easily right now. However, you can either add the "fake" time predicate as you did above, which (in this case) triggers MonetDB's optimizer to push the time

...
(either because it's in timestamp (int) rather then varchar (string), or because the time column happens to be ordered) below the orderId

...
and this avoid the hash build, or change the following line(s) in gdk/gdk_select.c (in case you built MonetDB yourself from source):

hash = b->batPersistence == PERSISTENT && (size_t) ATOMsize(b->ttype) > sizeof(BUN) / 4 && BATcount(b) * (ATOMsize(b->ttype) + 2 * sizeof(BUN)) < GDK_mem_maxsize / 2; -> hash = FALSE;

We'll consider whether we can provide a better solution in a future release.

...
* Is there some way to generate the hash index with a more sympathetic algo that doesn't degrade so steeply. e.g some hash + sort. (I have

http://engineering.linkedin.com/performance/optimizing-linux-memory-manageme... predicate predicate literally no

...
...
experience with this!)

We'll also look into this. However, building a hash index inherently incurs random access, so chances are slim ...

Best, Stefan

...
-Will Muldrew

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

Stefan Manegold

5:04 p.m.

hm, that's with the index in place? If so: good for our optimizer, but unfortunately not so good for you ... If not: - good for you! - impressive for our "execution engine" (scan) (- "embarrassing" for our optimizer ... well, it's a minor detail ...) ;-) Stefan ----- Original Message -----

...

Sorry!

sql>select count(*) from t_order2 where orderId between 'AAAAAA' and 'AAAAAA'; +------+ | L1 | +======+ | 0 | +------+ 1 tuple (596.202ms)

On 5 December 2013 16:49, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

thank for reminding me: the optimizer still sees your query as point query and thus prevents parallelization in order to build/use the hash index.

Maybe you can "fool" the optimizer (and I hope noone else is reading what I'm writing now ... ;-)) by "disguising" the point predicate as range predicate, say, "where orderId between 'FOO' and 'FOO'" --- in fact, I rather hope (for us) that is will not work ...

Stefan

----- Original Message -----

...
Hi Stefan

I've added that hash = FALSE patch, and now my simple query returns reliably in 6 seconds. It's still a lot slower than the indexed one (obviously), and 12x slower than the one with the time > '1970-01-01' optimiser nudge (which causes parallelism), but it'll do for now.

Thanks

-Will

On 5 December 2013 16:32, Will Muldrew < will.muldrew@gmail.com > wrote:

Hi Stefan

Here are my version details:

MonetDB-11.15.17 CentOS release 6.3 kernel 3.6.2

I think I might proceed with a patched version with the hash disabled. That's totally fine for me right now, though obviously it'd be nice to be on the trunk!

W.r.t. a less random access hash generation. This is all very hand-wavey but how about: 1) generate a sequence of (hash,oid) pairs to some file or mmapped area. 2). use some well-known "external sort" algo to sort these pairs by hash (e.g. split, qsort, merge). 3). build your final hash by iterating through this sorted datastructure.

Your memory writing would then be sequential and you'd get good page hit characteristics. You just need to choose a decent sort algo - ideally which works transparently over memmapped data.

What do you think? I might even have a crack at it myself :)

-Will

On 5 December 2013 15:54, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

could you please also share with us which version of MonetDB you are using, and OS you are running?

Pleass find more comments & questions inlined below.

----- Original Message -----

...
Hi

I've been investigating very slow queries on my 350M row dataset when selecting for equality on a non-unique string id. e.g.

select count(*) from t_order where orderId = 'FOO';

Is your orderId column unique, or are there duplicate values?

...
This query takes ~4.5 hours to build a thash index. Subsequent repeats hit the cache and are sub milli.

select count(*) from t_order where time > '1970-01-01' and orderId = 'FOO'

This second one is consistently finished in a few seconds or less, and doesn't create any indexes.

The first query is a bit of a show-stopper. It spends a huge about of time in BAThash (gdk_search.c), and incurs a lot of page faults while reading and writing at random across a multi GB mmaped thash file. Additionally these page faults are hampered by the OS trying to write dirty pages out in the background. I've got plenty of RAM overall (130GB), but the 'active' page proportion for the thash file seems to be stuck at about 25% - giving me a 0.75 probability of a miss.

* Is there some way to make my OS less keen to evict pages? (swappiness = 0 already) I should have plenty of room to have the whole thash file resident. Additionally, allowing it to sit on dirty pages longer would reduce the total write IO.

In fact, if there is sufficient memory in total, there would be no need to flush dirty (non-persistent) pages at all, but we have not yet found a good way to hit this to the OS --- madvice() did not have much/any useful efficet for us on Linux.

Maybe some of the issues dicsussed here play a role: http://engineering.linkedin.com/performance/optimizing-linux-memory-manageme... ?

While we have not yet encountered the NUMA problem reported there, we have encountered the transparent huge page problems, and usually disable them as also suggested in the above posting.

...
* Is there some way to simply prevent large thash creation? For many applications I'd rather have slower consistent queries, then incur a massively slow query following a restart (not great in a prod environment!)

Not easily right now. However, you can either add the "fake" time predicate as you did above, which (in this case) triggers MonetDB's optimizer to push the time predicate (either because it's in timestamp (int) rather then varchar (string), or because the time column happens to be ordered) below the orderId predicate and this avoid the hash build, or change the following line(s) in gdk/gdk_select.c (in case you built MonetDB yourself from source):

hash = b->batPersistence == PERSISTENT && (size_t) ATOMsize(b->ttype) > sizeof(BUN) / 4 && BATcount(b) * (ATOMsize(b->ttype) + 2 * sizeof(BUN)) < GDK_mem_maxsize / 2; -> hash = FALSE;

We'll consider whether we can provide a better solution in a future release.

...
* Is there some way to generate the hash index with a more sympathetic algo that doesn't degrade so steeply. e.g some hash + sort. (I have literally no experience with this!)

We'll also look into this. However, building a hash index inherently incurs random access, so chances are slim ...

Best, Stefan

...
-Will Muldrew

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

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-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

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Will Muldrew

7:57 p.m.

No index! On 5 Dec 2013 17:05, "Stefan Manegold" wrote:

...

hm, that's with the index in place?

If so: good for our optimizer, but unfortunately not so good for you ...

If not: - good for you! - impressive for our "execution engine" (scan) (- "embarrassing" for our optimizer ... well, it's a minor detail ...)

;-)

Stefan

...
Sorry!

sql>select count(*) from t_order2 where orderId between 'AAAAAA' and 'AAAAAA'; +------+ | L1 | +======+ | 0 | +------+ 1 tuple (596.202ms)

On 5 December 2013 16:49, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

thank for reminding me: the optimizer still sees your query as point query and thus prevents parallelization in order to build/use the hash index.

Maybe you can "fool" the optimizer (and I hope noone else is reading what I'm writing now ... ;-)) by "disguising" the point predicate as range

...
say, "where orderId between 'FOO' and 'FOO'" --- in fact, I rather hope (for us) that is will not work ...

Stefan

----- Original Message -----

...
Hi Stefan

I've added that hash = FALSE patch, and now my simple query returns reliably in 6 seconds. It's still a lot slower than the indexed one (obviously), and 12x slower than the one with the time > '1970-01-01' optimiser nudge (which causes parallelism), but it'll do for now.

Thanks

-Will

On 5 December 2013 16:32, Will Muldrew < will.muldrew@gmail.com > wrote:

Hi Stefan

Here are my version details:

MonetDB-11.15.17 CentOS release 6.3 kernel 3.6.2

I think I might proceed with a patched version with the hash disabled. That's totally fine for me right now, though obviously it'd be nice to be on

...
...
trunk!

W.r.t. a less random access hash generation. This is all very hand-wavey but how about: 1) generate a sequence of (hash,oid) pairs to some file or mmapped area. 2). use some well-known "external sort" algo to sort

...
...
pairs by hash (e.g. split, qsort, merge). 3). build your final hash by iterating through this sorted datastructure.

Your memory writing would then be sequential and you'd get good page hit characteristics. You just need to choose a decent sort algo - ideally which works transparently over memmapped data.

What do you think? I might even have a crack at it myself :)

-Will

On 5 December 2013 15:54, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

could you please also share with us which version of MonetDB you are using, and OS you are running?

Pleass find more comments & questions inlined below.

----- Original Message -----

...
Hi

I've been investigating very slow queries on my 350M row dataset when selecting for equality on a non-unique string id. e.g.

select count(*) from t_order where orderId = 'FOO';

Is your orderId column unique, or are there duplicate values?

...
This query takes ~4.5 hours to build a thash index. Subsequent repeats hit the cache and are sub milli.

select count(*) from t_order where time > '1970-01-01' and orderId = 'FOO'

This second one is consistently finished in a few seconds or less, and doesn't create any indexes.

The first query is a bit of a show-stopper. It spends a huge about of time in BAThash (gdk_search.c), and incurs a lot of page faults while reading and writing at random across a multi GB mmaped thash file. Additionally

...
...
...
page faults are hampered by the OS trying to write dirty pages out in the background. I've got plenty of RAM overall (130GB), but the 'active'

...
...
...
proportion for the thash file seems to be stuck at about 25% - giving me a 0.75 probability of a miss.

* Is there some way to make my OS less keen to evict pages? (swappiness = 0 already) I should have plenty of room to have the whole thash file resident. Additionally, allowing it to sit on dirty pages longer would reduce

...
...
...
total write IO.

In fact, if there is sufficient memory in total, there would be no need to flush dirty (non-persistent) pages at all, but we have not yet found a good way to hit this to the OS --- madvice() did not have much/any useful efficet for us on Linux.

Maybe some of the issues dicsussed here play a role:

http://engineering.linkedin.com/performance/optimizing-linux-memory-manageme...

...
?

While we have not yet encountered the NUMA problem reported there, we have encountered the transparent huge page problems, and usually disable them as also suggested in the above posting.

...
* Is there some way to simply prevent large thash creation? For many applications I'd rather have slower consistent queries, then incur a massively slow query following a restart (not great in a prod environment!)

Not easily right now. However, you can either add the "fake" time predicate as you did above, which (in this case) triggers MonetDB's optimizer to push the time predicate (either because it's in timestamp (int) rather then varchar (string), or because the time column happens to be ordered) below the orderId

...
...
and this avoid the hash build, or change the following line(s) in gdk/gdk_select.c (in case you built MonetDB yourself from source):

hash = b->batPersistence == PERSISTENT && (size_t) ATOMsize(b->ttype) > sizeof(BUN) / 4 && BATcount(b) * (ATOMsize(b->ttype) + 2 * sizeof(BUN)) < GDK_mem_maxsize / 2; -> hash = FALSE;

We'll consider whether we can provide a better solution in a future release.

...
* Is there some way to generate the hash index with a more sympathetic algo that doesn't degrade so steeply. e.g some hash + sort. (I have

----- Original Message ----- predicate, the these these page the predicate literally

...
...
...
no experience with this!)

We'll also look into this. However, building a hash index inherently incurs random access, so chances are slim ...

Best, Stefan

...
-Will Muldrew

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

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-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

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Will Muldrew

6 Dec 6 Dec

11:28 a.m.

w.r.t. the slow hash index creation, I did find an OS setting that improved things dramatically - first hash building query is now ~3 minutes rather than 4.5 hrs. I found that my /proc/sys/vm/dirty_background_ratio setting was 0, and so the OS kicked in and started writing as soon as pages were dirty. This gets in the way of the page fault servicing. I set it to 20, which now means that the OS doesn't start flushing for a while and so mserver gets to max out CPU dirtying up pages during the thash creation. A little bit later, the flusher kicks in and mserver slows down to 0.1 CPU. Flushing completes, mserver picks up to 100%, etc... We make a lot quicker progress. I'm still confused by why my OS doesn't seem to want to keep all the pages of thash in memory. If I look in /proc/{pid}/numa_maps I can see that during the thash creation, for the thash mem mapped file the 'active' page count (which I believe is the memory resident portion) seems to not want to increase to more than ~0.25 of the total 'mapped' page count. My assumption is that if this proportion was closer to 1.0, then my memory access wouldn't be causing page faults in the first place. I've got lots of RAM spare, and am using interleaved numa settings, so I don't understand what's preventing active growing. Does anyone have an idea, or know how I can diagnose this? -Will On 5 December 2013 19:57, Will Muldrew wrote:

...

No index! On 5 Dec 2013 17:05, "Stefan Manegold" wrote:

...
hm, that's with the index in place?

If so: good for our optimizer, but unfortunately not so good for you ...

If not: - good for you! - impressive for our "execution engine" (scan) (- "embarrassing" for our optimizer ... well, it's a minor detail ...)

;-)

Stefan

...
Sorry!

sql>select count(*) from t_order2 where orderId between 'AAAAAA' and 'AAAAAA'; +------+ | L1 | +======+ | 0 | +------+ 1 tuple (596.202ms)

On 5 December 2013 16:49, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

thank for reminding me: the optimizer still sees your query as point query and thus prevents parallelization in order to build/use the hash index.

Maybe you can "fool" the optimizer (and I hope noone else is reading what I'm writing now ... ;-)) by "disguising" the point predicate as range

...
say, "where orderId between 'FOO' and 'FOO'" --- in fact, I rather hope (for us) that is will not work ...

Stefan

----- Original Message -----

...
Hi Stefan

I've added that hash = FALSE patch, and now my simple query returns reliably in 6 seconds. It's still a lot slower than the indexed one (obviously), and 12x slower than the one with the time > '1970-01-01' optimiser nudge (which causes parallelism), but it'll do for now.

Thanks

-Will

On 5 December 2013 16:32, Will Muldrew < will.muldrew@gmail.com > wrote:

Hi Stefan

Here are my version details:

MonetDB-11.15.17 CentOS release 6.3 kernel 3.6.2

I think I might proceed with a patched version with the hash disabled. That's totally fine for me right now, though obviously it'd be nice to be on

...
...
trunk!

W.r.t. a less random access hash generation. This is all very hand-wavey but how about: 1) generate a sequence of (hash,oid) pairs to some file or mmapped area. 2). use some well-known "external sort" algo to sort

...
...
pairs by hash (e.g. split, qsort, merge). 3). build your final hash by iterating through this sorted datastructure.

Your memory writing would then be sequential and you'd get good page hit characteristics. You just need to choose a decent sort algo - ideally which works transparently over memmapped data.

What do you think? I might even have a crack at it myself :)

-Will

On 5 December 2013 15:54, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

could you please also share with us which version of MonetDB you are using, and OS you are running?

Pleass find more comments & questions inlined below.

----- Original Message -----

...
Hi

I've been investigating very slow queries on my 350M row dataset when selecting for equality on a non-unique string id. e.g.

select count(*) from t_order where orderId = 'FOO';

Is your orderId column unique, or are there duplicate values?

...
This query takes ~4.5 hours to build a thash index. Subsequent repeats hit the cache and are sub milli.

select count(*) from t_order where time > '1970-01-01' and orderId = 'FOO'

This second one is consistently finished in a few seconds or less, and doesn't create any indexes.

The first query is a bit of a show-stopper. It spends a huge about of time in BAThash (gdk_search.c), and incurs a lot of page faults while reading and writing at random across a multi GB mmaped thash file. Additionally

...
...
...
page faults are hampered by the OS trying to write dirty pages out in the background. I've got plenty of RAM overall (130GB), but the 'active' page proportion for the thash file seems to be stuck at about 25% - giving me a 0.75 probability of a miss.

* Is there some way to make my OS less keen to evict pages? (swappiness = 0 already) I should have plenty of room to have the whole thash file resident. Additionally, allowing it to sit on dirty pages longer would reduce

...
...
...
total write IO.

In fact, if there is sufficient memory in total, there would be no need to flush dirty (non-persistent) pages at all, but we have not yet found a good way to hit this to the OS --- madvice() did not have much/any useful efficet for us on Linux.

Maybe some of the issues dicsussed here play a role:

http://engineering.linkedin.com/performance/optimizing-linux-memory-manageme...

...
?

While we have not yet encountered the NUMA problem reported there, we have encountered the transparent huge page problems, and usually disable them as also suggested in the above posting.

...
* Is there some way to simply prevent large thash creation? For many applications I'd rather have slower consistent queries, then incur a massively slow query following a restart (not great in a prod environment!)

Not easily right now. However, you can either add the "fake" time predicate as you did above, which (in this case) triggers MonetDB's optimizer to push the time predicate (either because it's in timestamp (int) rather then varchar (string), or because the time column happens to be ordered) below the orderId

...
...
and this avoid the hash build, or change the following line(s) in gdk/gdk_select.c (in case you built MonetDB yourself from source):

hash = b->batPersistence == PERSISTENT && (size_t) ATOMsize(b->ttype) > sizeof(BUN) / 4 && BATcount(b) * (ATOMsize(b->ttype) + 2 * sizeof(BUN)) < GDK_mem_maxsize / 2; -> hash = FALSE;

We'll consider whether we can provide a better solution in a future release.

...
* Is there some way to generate the hash index with a more sympathetic algo that doesn't degrade so steeply. e.g some hash + sort. (I have

----- Original Message ----- predicate, the these these the predicate literally

...
...
...
no experience with this!)

We'll also look into this. However, building a hash index inherently incurs random access, so chances are slim ...

Best, Stefan

...
-Will Muldrew

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

Stefan Manegold

11:37 a.m.

----- Original Message -----

...

w.r.t. the slow hash index creation, I did find an OS setting that improved things dramatically - first hash building query is now ~3 minutes rather than 4.5 hrs.

I found that my /proc/sys/vm/dirty_background_ratio setting was 0, and so the OS kicked in and started writing as soon as pages were dirty. This gets in the way of the page fault servicing. I set it to 20, which now means that the OS doesn't start flushing for a while and so mserver gets to max out CPU dirtying up pages during the thash creation. A little bit later, the flusher kicks in and mserver slows down to 0.1 CPU. Flushing completes, mserver picks up to 100%, etc... We make a lot quicker progress.

This is great news. Thank you very much for sharing! On our Fedora 18 machines, the default dirty_background_ratio appears to be 10.

...

I'm still confused by why my OS doesn't seem to want to keep all the pages of thash in memory. If I look in /proc/{pid}/numa_maps I can see that during the thash creation, for the thash mem mapped file the 'active' page count (which I believe is the memory resident portion) seems to not want to increase to more than ~0.25 of the total 'mapped' page count. My assumption is that if this proportion was closer to 1.0, then my memory access wouldn't be causing page faults in the first place. I've got lots of RAM spare, and am using interleaved numa settings, so I don't understand what's preventing active growing. Does anyone have an idea, or know how I can diagnose this?

I don't right now, we I hope we can collect all related experiences and knowledge in this thread and turn it into general advice. Thanks, again, for your patience and willingness to experiment and share your experiences! Stefan

...

-Will

On 5 December 2013 19:57, Will Muldrew < will.muldrew@gmail.com > wrote:

No index! On 5 Dec 2013 17:05, "Stefan Manegold" < Stefan.Manegold@cwi.nl > wrote:

hm, that's with the index in place?

If so: good for our optimizer, but unfortunately not so good for you ...

If not: - good for you! - impressive for our "execution engine" (scan) (- "embarrassing" for our optimizer ... well, it's a minor detail ...)

;-)

Stefan

----- Original Message -----

...
Sorry!

sql>select count(*) from t_order2 where orderId between 'AAAAAA' and 'AAAAAA'; +------+ | L1 | +======+ | 0 | +------+ 1 tuple (596.202ms)

On 5 December 2013 16:49, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

thank for reminding me: the optimizer still sees your query as point query and thus prevents parallelization in order to build/use the hash index.

Maybe you can "fool" the optimizer (and I hope noone else is reading what I'm writing now ... ;-)) by "disguising" the point predicate as range predicate, say, "where orderId between 'FOO' and 'FOO'" --- in fact, I rather hope (for us) that is will not work ...

Stefan

----- Original Message -----

...
Hi Stefan

I've added that hash = FALSE patch, and now my simple query returns reliably in 6 seconds. It's still a lot slower than the indexed one (obviously), and 12x slower than the one with the time > '1970-01-01' optimiser nudge (which causes parallelism), but it'll do for now.

Thanks

-Will

On 5 December 2013 16:32, Will Muldrew < will.muldrew@gmail.com > wrote:

Hi Stefan

Here are my version details:

MonetDB-11.15.17 CentOS release 6.3 kernel 3.6.2

I think I might proceed with a patched version with the hash disabled. That's totally fine for me right now, though obviously it'd be nice to be on the trunk!

W.r.t. a less random access hash generation. This is all very hand-wavey but how about: 1) generate a sequence of (hash,oid) pairs to some file or mmapped area. 2). use some well-known "external sort" algo to sort these pairs by hash (e.g. split, qsort, merge). 3). build your final hash by iterating through this sorted datastructure.

Your memory writing would then be sequential and you'd get good page hit characteristics. You just need to choose a decent sort algo - ideally which works transparently over memmapped data.

What do you think? I might even have a crack at it myself :)

-Will

On 5 December 2013 15:54, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

could you please also share with us which version of MonetDB you are using, and OS you are running?

Pleass find more comments & questions inlined below.

----- Original Message -----

...
Hi

I've been investigating very slow queries on my 350M row dataset when selecting for equality on a non-unique string id. e.g.

select count(*) from t_order where orderId = 'FOO';

Is your orderId column unique, or are there duplicate values?

...
This query takes ~4.5 hours to build a thash index. Subsequent repeats hit the cache and are sub milli.

select count(*) from t_order where time > '1970-01-01' and orderId = 'FOO'

This second one is consistently finished in a few seconds or less, and doesn't create any indexes.

The first query is a bit of a show-stopper. It spends a huge about of time in BAThash (gdk_search.c), and incurs a lot of page faults while reading and writing at random across a multi GB mmaped thash file. Additionally these page faults are hampered by the OS trying to write dirty pages out in the background. I've got plenty of RAM overall (130GB), but the 'active' page proportion for the thash file seems to be stuck at about 25% - giving me a 0.75 probability of a miss.

* Is there some way to make my OS less keen to evict pages? (swappiness = 0 already) I should have plenty of room to have the whole thash file resident. Additionally, allowing it to sit on dirty pages longer would reduce the total write IO.

In fact, if there is sufficient memory in total, there would be no need to flush dirty (non-persistent) pages at all, but we have not yet found a good way to hit this to the OS --- madvice() did not have much/any useful efficet for us on Linux.

Maybe some of the issues dicsussed here play a role: http://engineering.linkedin.com/performance/optimizing-linux-memory-manageme... ?

While we have not yet encountered the NUMA problem reported there, we have encountered the transparent huge page problems, and usually disable them as also suggested in the above posting.

...
* Is there some way to simply prevent large thash creation? For many applications I'd rather have slower consistent queries, then incur a massively slow query following a restart (not great in a prod environment!)

Not easily right now. However, you can either add the "fake" time predicate as you did above, which (in this case) triggers MonetDB's optimizer to push the time predicate (either because it's in timestamp (int) rather then varchar (string), or because the time column happens to be ordered) below the orderId predicate and this avoid the hash build, or change the following line(s) in gdk/gdk_select.c (in case you built MonetDB yourself from source):

hash = b->batPersistence == PERSISTENT && (size_t) ATOMsize(b->ttype) > sizeof(BUN) / 4 && BATcount(b) * (ATOMsize(b->ttype) + 2 * sizeof(BUN)) < GDK_mem_maxsize / 2; -> hash = FALSE;

We'll consider whether we can provide a better solution in a future release.

...
* Is there some way to generate the hash index with a more sympathetic algo that doesn't degrade so steeply. e.g some hash + sort. (I have literally no experience with this!)

We'll also look into this. However, building a hash index inherently incurs random access, so chances are slim ...

Best, Stefan

...
-Will Muldrew

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

Will Muldrew

11:40 a.m.

No problem - monetdb is an exciting project! On 6 December 2013 11:37, Stefan Manegold wrote:

...

----- Original Message -----

...
w.r.t. the slow hash index creation, I did find an OS setting that improved things dramatically - first hash building query is now ~3 minutes rather than 4.5 hrs.

I found that my /proc/sys/vm/dirty_background_ratio setting was 0, and so the OS kicked in and started writing as soon as pages were dirty. This gets in the way of the page fault servicing. I set it to 20, which now means that the OS doesn't start flushing for a while and so mserver gets to max out CPU dirtying up pages during the thash creation. A little bit later, the flusher kicks in and mserver slows down to 0.1 CPU. Flushing completes, mserver picks up to 100%, etc... We make a lot quicker progress.

This is great news. Thank you very much for sharing!

On our Fedora 18 machines, the default dirty_background_ratio appears to be 10.

...
I'm still confused by why my OS doesn't seem to want to keep all the pages of thash in memory. If I look in /proc/{pid}/numa_maps I can see that during the thash creation, for the thash mem mapped file the 'active' page count (which I believe is the memory resident portion) seems to not want to increase to more than ~0.25 of the total 'mapped' page count. My assumption is that if this proportion was closer to 1.0, then my memory access wouldn't be causing page faults in the first place. I've got lots of RAM spare, and am using interleaved numa settings, so I don't understand what's preventing active growing. Does anyone have an idea, or know how I can diagnose this?

I don't right now, we I hope we can collect all related experiences and knowledge in this thread and turn it into general advice.

Thanks, again, for your patience and willingness to experiment and share your experiences!

Stefan

...
-Will

On 5 December 2013 19:57, Will Muldrew < will.muldrew@gmail.com > wrote:

No index! On 5 Dec 2013 17:05, "Stefan Manegold" < Stefan.Manegold@cwi.nl > wrote:

hm, that's with the index in place?

If so: good for our optimizer, but unfortunately not so good for you ...

If not: - good for you! - impressive for our "execution engine" (scan) (- "embarrassing" for our optimizer ... well, it's a minor detail ...)

;-)

Stefan

...
Sorry!

sql>select count(*) from t_order2 where orderId between 'AAAAAA' and 'AAAAAA'; +------+ | L1 | +======+ | 0 | +------+ 1 tuple (596.202ms)

On 5 December 2013 16:49, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

thank for reminding me: the optimizer still sees your query as point query and thus prevents parallelization in order to build/use the hash index.

Maybe you can "fool" the optimizer (and I hope noone else is reading what I'm writing now ... ;-)) by "disguising" the point predicate as range predicate, say, "where orderId between 'FOO' and 'FOO'" --- in fact, I rather hope (for us) that is will not work ...

Stefan

----- Original Message -----

...
Hi Stefan

I've added that hash = FALSE patch, and now my simple query returns reliably in 6 seconds. It's still a lot slower than the indexed one (obviously), and 12x slower than the one with the time > '1970-01-01' optimiser nudge (which causes parallelism), but it'll do for now.

Thanks

-Will

On 5 December 2013 16:32, Will Muldrew < will.muldrew@gmail.com > wrote:

Hi Stefan

Here are my version details:

MonetDB-11.15.17 CentOS release 6.3 kernel 3.6.2

I think I might proceed with a patched version with the hash disabled. That's totally fine for me right now, though obviously it'd be nice to be on the trunk!

W.r.t. a less random access hash generation. This is all very hand-wavey but how about: 1) generate a sequence of (hash,oid) pairs to some file or mmapped area. 2). use some well-known "external sort" algo to sort

----- Original Message ----- these

...
...
pairs by hash (e.g. split, qsort, merge). 3). build your final hash by iterating through this sorted datastructure.

Your memory writing would then be sequential and you'd get good page hit characteristics. You just need to choose a decent sort algo - ideally which works transparently over memmapped data.

What do you think? I might even have a crack at it myself :)

-Will

On 5 December 2013 15:54, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

could you please also share with us which version of MonetDB you are using, and OS you are running?

Pleass find more comments & questions inlined below.

----- Original Message -----

...
Hi

I've been investigating very slow queries on my 350M row dataset when selecting for equality on a non-unique string id. e.g.

select count(*) from t_order where orderId = 'FOO';

Is your orderId column unique, or are there duplicate values?

...
This query takes ~4.5 hours to build a thash index. Subsequent repeats hit the cache and are sub milli.

select count(*) from t_order where time > '1970-01-01' and orderId = 'FOO'

This second one is consistently finished in a few seconds or less, and doesn't create any indexes.

The first query is a bit of a show-stopper. It spends a huge about of time in BAThash (gdk_search.c), and incurs a lot of page faults while reading and writing at random across a multi GB mmaped thash file. Additionally these page faults are hampered by the OS trying to write dirty pages out in the background. I've got plenty of RAM overall (130GB), but the 'active' page proportion for the thash file seems to be stuck at about 25% - giving me a 0.75 probability of a miss.

* Is there some way to make my OS less keen to evict pages? (swappiness = 0 already) I should have plenty of room to have the whole thash file resident. Additionally, allowing it to sit on dirty pages longer would reduce the total write IO.

In fact, if there is sufficient memory in total, there would be no need to flush dirty (non-persistent) pages at all, but we have not yet found a good way to hit this to the OS --- madvice() did not have much/any useful efficet for us on Linux.

Maybe some of the issues dicsussed here play a role:

http://engineering.linkedin.com/performance/optimizing-linux-memory-manageme...

...
?

While we have not yet encountered the NUMA problem reported there, we have encountered the transparent huge page problems, and usually disable them as also suggested in the above posting.

...
* Is there some way to simply prevent large thash creation? For many applications I'd rather have slower consistent queries, then incur a massively slow query following a restart (not great in a prod environment!)

Not easily right now. However, you can either add the "fake" time predicate as you did above, which (in this case) triggers MonetDB's optimizer to push the time predicate (either because it's in timestamp (int) rather then varchar (string), or because the time column happens to be ordered) below the orderId predicate and this avoid the hash build, or change the following line(s) in gdk/gdk_select.c (in case you built MonetDB yourself from source):

hash = b->batPersistence == PERSISTENT && (size_t) ATOMsize(b->ttype) > sizeof(BUN) / 4 && BATcount(b) * (ATOMsize(b->ttype) + 2 * sizeof(BUN)) < GDK_mem_maxsize / 2; -> hash = FALSE;

We'll consider whether we can provide a better solution in a future release.

...
* Is there some way to generate the hash index with a more sympathetic algo that doesn't degrade so steeply. e.g some hash + sort. (I have literally no experience with this!)

We'll also look into this. However, building a hash index inherently incurs random access, so chances are slim ...

Best, Stefan

...
-Will Muldrew

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

Stefan Manegold

12:08 p.m.

Will et al., a value "0" for /proc/sys/vm/dirty_background_ratio could also meant that /proc/sys/vm/dirty_background_bytes was set to a non-0 value; cf., https://www.kernel.org/doc/Documentation/sysctl/vm.txt Did you try whether setting /proc/sys/vm/dirty_background_ratio to a value

...

20 would result in /proc/{pid}/numa_maps growing beyond 25% ?

Stefan ----- Original Message -----

...

No problem - monetdb is an exciting project!

On 6 December 2013 11:37, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

----- Original Message -----

...
w.r.t. the slow hash index creation, I did find an OS setting that improved things dramatically - first hash building query is now ~3 minutes rather than 4.5 hrs.

I found that my /proc/sys/vm/dirty_background_ratio setting was 0, and so the OS kicked in and started writing as soon as pages were dirty. This gets in the way of the page fault servicing. I set it to 20, which now means that the OS doesn't start flushing for a while and so mserver gets to max out CPU dirtying up pages during the thash creation. A little bit later, the flusher kicks in and mserver slows down to 0.1 CPU. Flushing completes, mserver picks up to 100%, etc... We make a lot quicker progress.

This is great news. Thank you very much for sharing!

On our Fedora 18 machines, the default dirty_background_ratio appears to be 10.

...
I'm still confused by why my OS doesn't seem to want to keep all the pages of thash in memory. If I look in /proc/{pid}/numa_maps I can see that during the thash creation, for the thash mem mapped file the 'active' page count (which I believe is the memory resident portion) seems to not want to increase to more than ~0.25 of the total 'mapped' page count. My assumption is that if this proportion was closer to 1.0, then my memory access wouldn't be causing page faults in the first place. I've got lots of RAM spare, and am using interleaved numa settings, so I don't understand what's preventing active growing. Does anyone have an idea, or know how I can diagnose this?

I don't right now, we I hope we can collect all related experiences and knowledge in this thread and turn it into general advice.

Thanks, again, for your patience and willingness to experiment and share your experiences!

Stefan

...
-Will

On 5 December 2013 19:57, Will Muldrew < will.muldrew@gmail.com > wrote:

No index! On 5 Dec 2013 17:05, "Stefan Manegold" < Stefan.Manegold@cwi.nl > wrote:

hm, that's with the index in place?

If so: good for our optimizer, but unfortunately not so good for you ...

If not: - good for you! - impressive for our "execution engine" (scan) (- "embarrassing" for our optimizer ... well, it's a minor detail ...)

;-)

Stefan

----- Original Message -----

...
Sorry!

sql>select count(*) from t_order2 where orderId between 'AAAAAA' and 'AAAAAA'; +------+ | L1 | +======+ | 0 | +------+ 1 tuple (596.202ms)

On 5 December 2013 16:49, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

thank for reminding me: the optimizer still sees your query as point query and thus prevents parallelization in order to build/use the hash index.

Maybe you can "fool" the optimizer (and I hope noone else is reading what I'm writing now ... ;-)) by "disguising" the point predicate as range predicate, say, "where orderId between 'FOO' and 'FOO'" --- in fact, I rather hope (for us) that is will not work ...

Stefan

----- Original Message -----

...
Hi Stefan

I've added that hash = FALSE patch, and now my simple query returns reliably in 6 seconds. It's still a lot slower than the indexed one (obviously), and 12x slower than the one with the time > '1970-01-01' optimiser nudge (which causes parallelism), but it'll do for now.

Thanks

-Will

On 5 December 2013 16:32, Will Muldrew < will.muldrew@gmail.com > wrote:

Hi Stefan

Here are my version details:

MonetDB-11.15.17 CentOS release 6.3 kernel 3.6.2

I think I might proceed with a patched version with the hash disabled. That's totally fine for me right now, though obviously it'd be nice to be on the trunk!

W.r.t. a less random access hash generation. This is all very hand-wavey but how about: 1) generate a sequence of (hash,oid) pairs to some file or mmapped area. 2). use some well-known "external sort" algo to sort these pairs by hash (e.g. split, qsort, merge). 3). build your final hash by iterating through this sorted datastructure.

Your memory writing would then be sequential and you'd get good page hit characteristics. You just need to choose a decent sort algo - ideally which works transparently over memmapped data.

What do you think? I might even have a crack at it myself :)

-Will

On 5 December 2013 15:54, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

could you please also share with us which version of MonetDB you are using, and OS you are running?

Pleass find more comments & questions inlined below.

----- Original Message -----

...
Hi

I've been investigating very slow queries on my 350M row dataset when selecting for equality on a non-unique string id. e.g.

select count(*) from t_order where orderId = 'FOO';

Is your orderId column unique, or are there duplicate values?

...
This query takes ~4.5 hours to build a thash index. Subsequent repeats hit the cache and are sub milli.

select count(*) from t_order where time > '1970-01-01' and orderId = 'FOO'

This second one is consistently finished in a few seconds or less, and doesn't create any indexes.

The first query is a bit of a show-stopper. It spends a huge about of time in BAThash (gdk_search.c), and incurs a lot of page faults while reading and writing at random across a multi GB mmaped thash file. Additionally these page faults are hampered by the OS trying to write dirty pages out in the background. I've got plenty of RAM overall (130GB), but the 'active' page proportion for the thash file seems to be stuck at about 25% - giving me a 0.75 probability of a miss.

* Is there some way to make my OS less keen to evict pages? (swappiness = 0 already) I should have plenty of room to have the whole thash file resident. Additionally, allowing it to sit on dirty pages longer would reduce the total write IO.

In fact, if there is sufficient memory in total, there would be no need to flush dirty (non-persistent) pages at all, but we have not yet found a good way to hit this to the OS --- madvice() did not have much/any useful efficet for us on Linux.

Maybe some of the issues dicsussed here play a role: http://engineering.linkedin.com/performance/optimizing-linux-memory-manageme... ?

While we have not yet encountered the NUMA problem reported there, we have encountered the transparent huge page problems, and usually disable them as also suggested in the above posting.

...
* Is there some way to simply prevent large thash creation? For many applications I'd rather have slower consistent queries, then incur a massively slow query following a restart (not great in a prod environment!)

Not easily right now. However, you can either add the "fake" time predicate as you did above, which (in this case) triggers MonetDB's optimizer to push the time predicate (either because it's in timestamp (int) rather then varchar (string), or because the time column happens to be ordered) below the orderId predicate and this avoid the hash build, or change the following line(s) in gdk/gdk_select.c (in case you built MonetDB yourself from source):

hash = b->batPersistence == PERSISTENT && (size_t) ATOMsize(b->ttype) > sizeof(BUN) / 4 && BATcount(b) * (ATOMsize(b->ttype) + 2 * sizeof(BUN)) < GDK_mem_maxsize / 2; -> hash = FALSE;

We'll consider whether we can provide a better solution in a future release.

...
* Is there some way to generate the hash index with a more sympathetic algo that doesn't degrade so steeply. e.g some hash + sort. (I have literally no experience with this!)

We'll also look into this. However, building a hash index inherently incurs random access, so chances are slim ...

Best, Stefan

...
-Will Muldrew

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

Will Muldrew

1:26 p.m.

Hi Stefan [13:24:23] $ cat /proc/sys/vm/dirty_background_bytes 0 Think it was that way before (I know it's mutually exclusive with the ratio) The new setting didn't appear to have any effect on the active ratio. -Will On 6 December 2013 12:08, Stefan Manegold wrote:

...

Will et al.,

a value "0" for /proc/sys/vm/dirty_background_ratio could also meant that /proc/sys/vm/dirty_background_bytes was set to a non-0 value; cf., https://www.kernel.org/doc/Documentation/sysctl/vm.txt

Did you try whether setting /proc/sys/vm/dirty_background_ratio to a value

...
20 would result in /proc/{pid}/numa_maps growing beyond 25% ?

Stefan

...
No problem - monetdb is an exciting project!

On 6 December 2013 11:37, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

----- Original Message -----

...
w.r.t. the slow hash index creation, I did find an OS setting that improved things dramatically - first hash building query is now ~3 minutes rather than 4.5 hrs.

I found that my /proc/sys/vm/dirty_background_ratio setting was 0, and so the OS kicked in and started writing as soon as pages were dirty. This gets in the way of the page fault servicing. I set it to 20, which now means

...
...
the OS doesn't start flushing for a while and so mserver gets to max out CPU dirtying up pages during the thash creation. A little bit later, the flusher kicks in and mserver slows down to 0.1 CPU. Flushing completes, mserver picks up to 100%, etc... We make a lot quicker progress.

This is great news. Thank you very much for sharing!

On our Fedora 18 machines, the default dirty_background_ratio appears to be 10.

...
I'm still confused by why my OS doesn't seem to want to keep all the

...
...
of thash in memory. If I look in /proc/{pid}/numa_maps I can see that during the thash creation, for the thash mem mapped file the 'active' page count (which I believe is the memory resident portion) seems to not want to increase to more than ~0.25 of the total 'mapped' page count. My assumption is that if this proportion was closer to 1.0, then my memory access wouldn't be causing page faults in the first place. I've got lots of RAM spare, and am using interleaved numa settings, so I don't understand what's

...
...
active growing. Does anyone have an idea, or know how I can diagnose

----- Original Message ----- that pages preventing this?

...
I don't right now, we I hope we can collect all related experiences and knowledge in this thread and turn it into general advice.

Thanks, again, for your patience and willingness to experiment and share

...
experiences!

Stefan

...
-Will

On 5 December 2013 19:57, Will Muldrew < will.muldrew@gmail.com > wrote:

No index! On 5 Dec 2013 17:05, "Stefan Manegold" < Stefan.Manegold@cwi.nl > wrote:

hm, that's with the index in place?

If so: good for our optimizer, but unfortunately not so good for you ...

If not: - good for you! - impressive for our "execution engine" (scan) (- "embarrassing" for our optimizer ... well, it's a minor detail ...)

;-)

Stefan

----- Original Message -----

...
Sorry!

sql>select count(*) from t_order2 where orderId between 'AAAAAA' and 'AAAAAA'; +------+ | L1 | +======+ | 0 | +------+ 1 tuple (596.202ms)

On 5 December 2013 16:49, Stefan Manegold < Stefan.Manegold@cwi.nl > wrote:

Hi Will,

thank for reminding me: the optimizer still sees your query as point query and thus prevents parallelization in order to build/use the hash index.

Maybe you can "fool" the optimizer (and I hope noone else is reading what I'm writing now ... ;-)) by "disguising" the point predicate as range predicate, say, "where orderId between 'FOO' and 'FOO'" --- in fact, I rather hope (for us) that is will not work ...

Stefan

----- Original Message -----

...
Hi Stefan

I've added that hash = FALSE patch, and now my simple query returns reliably in 6 seconds. It's still a lot slower than the indexed one (obviously), and 12x slower than the one with the time > '1970-01-01' optimiser nudge (which causes parallelism), but it'll do for now.

Thanks

-Will

On 5 December 2013 16:32, Will Muldrew < will.muldrew@gmail.com > wrote:

Hi Stefan

Here are my version details:

MonetDB-11.15.17 CentOS release 6.3 kernel 3.6.2

I think I might proceed with a patched version with the hash disabled. That's totally fine for me right now, though obviously it'd be nice to be on the trunk!

W.r.t. a less random access hash generation. This is all very hand-wavey but how about: 1) generate a sequence of (hash,oid) pairs to some file or mmapped area. 2). use some well-known "external sort" algo to sort these pairs by hash (e.g. split, qsort, merge). 3). build your final hash by iterating through this sorted datastructure.

Your memory writing would then be sequential and you'd get good

your page

...
...
...
...
hit characteristics. You just need to choose a decent sort algo - ideally which works transparently over memmapped data.

What do you think? I might even have a crack at it myself :)

-Will

On 5 December 2013 15:54, Stefan Manegold < Stefan.Manegold@cwi.nl> wrote:

Hi Will,

could you please also share with us which version of MonetDB you are using, and OS you are running?

Pleass find more comments & questions inlined below.

----- Original Message -----

...
Hi

I've been investigating very slow queries on my 350M row dataset when selecting for equality on a non-unique string id. e.g.

select count(*) from t_order where orderId = 'FOO';

Is your orderId column unique, or are there duplicate values?

...
This query takes ~4.5 hours to build a thash index. Subsequent repeats hit the cache and are sub milli.

select count(*) from t_order where time > '1970-01-01' and orderId = 'FOO'

This second one is consistently finished in a few seconds or less, and doesn't create any indexes.

The first query is a bit of a show-stopper. It spends a huge about of time in BAThash (gdk_search.c), and incurs a lot of page faults while reading and writing at random across a multi GB mmaped thash file. Additionally these page faults are hampered by the OS trying to write dirty pages out in the background. I've got plenty of RAM overall (130GB), but the 'active' page proportion for the thash file seems to be stuck at about 25% - giving me a 0.75 probability of a miss.

* Is there some way to make my OS less keen to evict pages? (swappiness = 0 already) I should have plenty of room to have the whole thash file resident. Additionally, allowing it to sit on dirty pages longer would reduce the total write IO.

In fact, if there is sufficient memory in total, there would be no need to flush dirty (non-persistent) pages at all, but we have not yet found a good way to hit this to the OS --- madvice() did not have much/any useful efficet for us on Linux.

Maybe some of the issues dicsussed here play a role:

http://engineering.linkedin.com/performance/optimizing-linux-memory-manageme...

...
?

While we have not yet encountered the NUMA problem reported there, we have encountered the transparent huge page problems, and usually disable them as also suggested in the above posting.

...
* Is there some way to simply prevent large thash creation? For many applications I'd rather have slower consistent queries, then incur a massively slow query following a restart (not great in a prod environment!)

Not easily right now. However, you can either add the "fake" time predicate as you did above, which (in this case) triggers MonetDB's optimizer to push the time predicate (either because it's in timestamp (int) rather then varchar (string), or because the time column happens to be ordered) below the orderId predicate and this avoid the hash build, or change the following line(s) in gdk/gdk_select.c (in case you built MonetDB yourself from source):

hash = b->batPersistence == PERSISTENT && (size_t) ATOMsize(b->ttype) > sizeof(BUN) / 4 && BATcount(b) * (ATOMsize(b->ttype) + 2 * sizeof(BUN)) < GDK_mem_maxsize / 2; -> hash = FALSE;

We'll consider whether we can provide a better solution in a future release.

...
* Is there some way to generate the hash index with a more sympathetic algo that doesn't degrade so steeply. e.g some hash + sort. (I have literally no experience with this!)

We'll also look into this. However, building a hash index inherently incurs random access, so chances are slim ...

Best, Stefan

...
-Will Muldrew

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

-- | Stefan.Manegold@CWI.nl | DB Architectures (DA) | | www.CWI.nl/~manegold/ | Science Park 123 (L321) | | +31 (0)20 592-4212 | 1098 XG Amsterdam (NL) |

_______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list

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Stefan Manegold
Will Muldrew