HI Stefan, Martin –
We are open to any suggestions.
Stephan, I understand your reasons for making the change from “steal” to “copy”. Is it possible to have both options? Before loading the new tables I do a “copy *.bin” from the “saved” directory to the “loading” directory. This takes less than an hour. Are there multiple steps involved in the monetdb copy that results in it not finishing overnight?
From the perspective of a user that deals with very large data, a big selling point of monetdb is the ability to create data a column at a time and load using the COPY BINARY command. I have often bragged on monetdb’s ability to reload the entire table of 2 billion rows, 100+ columns in 3-4 minutes. I would still brag if it took an hour.
Our data base contains a row for each of the 2 billion positions on the maize genome. Each row has a chromosome and position column as well as many other traits scored for this position. We expect to continue to add columns as more data is curated. The data is then used for genomic analysis. While I’m not presented with new data every week, I generally gather data once a month that needs to be added. Having the db down for several days to reload can be problematic.
Let me know if there is other data I can collect to help analyze this problem.
Thanks - Lynn
On 3/9/17, 7:49 AM, "users-list on behalf of Martin Kersten" wrote:
Hi Stefan, Lynn
One way to move forward is to move the old functionality into the DataVault.
There a directory of MonetDB compliant binary data can potentially be
handled without the overhead incurred by copying.
On 09/03/2017 13:41, Stefan Manegold wrote:
> Hi Lynn,
>
> I understood and understand that your machine exclusively used by MonetDB.
>
> My question was more to investigate (using iostat & top) what CPU and/or IO
> load MonetDB creates while loading the data, in other words trying to understand
> whether the experienced performace degradiation can be realted to either increased
> I/O or CPU activity.
> Afterall, copying 726 GB does cost some time, expecially since this does not
> fit into RAM (and thus into file system caches) ...
>
> I also understood and understand that you're loading into empty tables.
> The resaons for us to discontinue the "move feature" include that
> (a) it only worked if both to be loaded data and dbfarm are on the same filesystem,
> (b) and it only worked when loading into empty tables.
> While both seem yo (must) hold for you to get the fast performance, they do not
> hold in many other cases. Moreover, people ded not like the fact the (some of)
> the files they loaded from "were gone" after the load, even if the load did not
> succeed ...
>
> You could consider downgrading (well, most probabaly you'd then first have to dump
> your entire DB(s) and then re-load them after the downgrade),
> but it's very unlikely, that we revive the move feature.
> hence, you'd never be able to upgrade again.
>
> I'd prefer that we could understand where the significant degrading comes from,
> and whether it's something we could fix ...
>
> Best,
> Stefan
>
> ps: you dbfarm is not necesarily where your monetdb installation (program) is,
> but rather where you find the merovingian.log
>
> ----- On Mar 9, 2017, at 1:26 PM, Lynn Carol Johnson lcj34@cornell.edu wrote:
>
>> HI Stephen -
>>
>> Copying the machine administrators on this email.
>>
>> The machine on which monetdb lives has 256GB RAM, 24 fast cores, 16TB of RAID10
>> storage and 1TB of SSD scratch space. This machine is used mostly for monetdb.
>> When I run “top” I see nothing little else running on it. No other IO going
>> on. The access to this machine is limited and I generally know who other than
>> myself is on it.
>>
>> Before loading new columns I ALWAYs do a “drop table”. Then I run “create table
>> …” with the new columns added to the list. Follow this with a “COPY BINARY
>> INTO …” . So I monetdb is always loading into an empty table.
>>
>> On disk, the binary files take up 726G of space.
>>
>> Jarek – I load from a directory in /workdir/lcj34/monetdbFiles. Monetdb lives
>> in /local/monetdb. Are these the same file system?
>>
>> Stephen: I the last load command around 3:30 yesterday afternoon and it was
>> still not complete this morning. We’ve been very happy with monetdb, but this
>> is quite troubling. Is it a problem to downgrade the monetdb load from
>> dec2016-SP2 back to jun2016-sp2?
>>
>> Thanks - Lynn
>>
>> On 3/9/17, 2:00 AM, "users-list on behalf of Stefan Manegold"
>> > Stefan.Manegold@cwi.nl> wrote:
>>
>> Hi Lynn Carol,
>>
>> COPY BINARY INTO now indeed copies the data,
>> and that can add some cost to it,
>> in particular in case your data is large
>> and your dbfarm is on the same I/O system,
>> or even the same (single) disk.
>>
>> To better understand your situation,
>> could you possibly share how big your (binary) data
>> is that you load (i.e., how much diskspace do the 135 files
>> with 2 billions values each occupy),
>> and whether you I/O system is a single hard disk, or a RAID system,
>> or an SSD?
>> Also, how much RAM does you machine have?
>>
>> Given that you used to exploit the old COPY BINARY INTO's "move feature",
>> I assume your data and your dbfarm are on the same filesystem.
>>
>> (NB. in the old version, we could do the "move trick" only when bulk-loading
>> into an empty table; when loading more data into a non-empty table, we also
>> had to copy the data ...)
>>
>> In case your machine has more than one filesystem, each on a different
>> hard disk / SSD / RAID, you coudl try to have your to-be-loaded data on one
>> and your dbfarm on the other, spreading the I/O load over both
>> (one mostly reading, the other mostly writing).
>>
>> You can also inspect you systems I/O activity during the load, e.g.,
>> using iostat.
>>
>> Best,
>> Stefan
>>
>> ----- On Mar 8, 2017, at 10:12 PM, Lynn Carol Johnson lcj34@cornell.edu wrote:
>>
>> > BTW, my 135 binary files together are 726G. I note the dec2016 release says:
>> >
>> >
>> >
>> > BATattach now copies the input file instead of "stealing" it.
>> >
>> >
>> >
>> > Could this be why it’s gone from 3 minutes to over 3 hours to load this data? My
>> > files and monetdb are on the same machine – no network access. And “top” shows
>> > nothing of significance running on the machine except mserver5.
>> >
>> >
>> >
>> > I loved the speed with which I could add new columns to my table by dropping it,
>> > re-create the table, COPY BINARY INTO table. Hoping you have ideas to get this
>> > back, or an idea on what could be wrong.
>> >
>> >
>> >
>> > Thanks - Lynn
>> >
>> >
>> >
>> >
>> > From: users-list on behalf of
>> > Lynn Carol Johnson
>> > Reply-To: Communication channel for MonetDB users
>> > Date: Wednesday, March 8, 2017 at 3:19 PM
>> > To: Communication channel for MonetDB users
>> > Subject: DEC2016-SP2 and BINARY bulk load
>> >
>> >
>> >
>> >
>> >
>> > Hi all –
>> >
>> >
>> >
>> > I have always used the COPY BINARY INTO … commands to load my 2.0 Billion row
>> > genetic data into a monetdb table. With 135 columns, it has been blindingly
>> > fast.
>> >
>> >
>> >
>> > Last week I moved from the June2016-SP2 release to dec2016-SP2. My binary loads
>> > are taking WAY longer. I killed one after 3 hours (via “call sys.stop(pid)” so
>> > it could clean up properly). I then started the load again, thinking perhaps
>> > the problem was related to the new columns I was adding.
>> >
>> > I have since dropped the table and remade it using the same data and scripts
>> > that worked in just over 3 minutes in February on the jun2016-SP2 load. It is
>> > really chugging along – I’m up to 30 minutes and counting. I don’t have access
>> > to the sql log files, but the Merovingian.log shows nothing.
>> >
>> >
>> >
>> > I do notice that previously the binary files, once loaded, were removed from the
>> > loading directly. This does not happen now. Were these files previously “moved”
>> > and now they are copied?
>> >
>> >
>> >
>> > Has anyone see this performance issue with Dec2016-SP2 COPY BINARY INTO ….
>> > Commands?
>> >
>> >
>> >
>> > Thanks - Lynn
>> >
>> > _______________________________________________
>> > 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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