Re: [sqlite] Anybody know why mono SQLite uses SqliteConnection but Windows uses SQLiteConnection?

[J Decker]

mono install.exe often works.

On Fri, Nov 18, 2016 at 9:16 PM, Jim Henderson 
wrote:

> Thanks for the suggestion, Bill.
>
> Will this run on a Linux system? The zip file has Install.exe and Test.exe
> inside it.
>
> Jim
>
>
> On 18-Nov-2016 7:44 AM, Drago, William @ CSG - NARDA-MITEQ wrote:
>
>> Do any of you know why the two different versions of SQLite have different
>>> case in the method names?
>>>
>>> Thanks,
>>> Jim
>>>
>>> Is there a reason why you can't use this one which should have the
>> correct case?
>>
>> https://system.data.sqlite.org/index.html/doc/trunk/www/down
>> loads.wiki#sqlite-netFx451-binary-Mono-2013
>>
>> --
>> Bill Drago
>> Staff Engineer
>> L3 Narda-MITEQ
>> 435 Moreland Road
>> Hauppauge, NY 11788
>> 631-272-5947 / william.dr...@l-3com.com
>>
>> CONFIDENTIALITY, EXPORT CONTROL AND DISCLAIMER NOTE:This e-mail and any
>> attachments are solely for the use of the addressee and may contain
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>> event this e-mail contains technical data within the definition of the
>> International Traffic in Arms Regulations or Export Administration
>> Regulations, it is subject to the export control laws of the
>> U.S.Government. The recipient should check this e-mail and any attachments
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Re: [sqlite] Anybody know why mono SQLite uses SqliteConnection but Windows uses SQLiteConnection?

[Jim Henderson]

Thanks for the suggestion, Bill.

Will this run on a Linux system? The zip file has Install.exe and 
Test.exe inside it.


Jim

On 18-Nov-2016 7:44 AM, Drago, William @ CSG - NARDA-MITEQ wrote:

Do any of you know why the two different versions of SQLite have different
case in the method names?

Thanks,
Jim


Is there a reason why you can't use this one which should have the correct case?

https://system.data.sqlite.org/index.html/doc/trunk/www/downloads.wiki#sqlite-netFx451-binary-Mono-2013

--
Bill Drago
Staff Engineer
L3 Narda-MITEQ
435 Moreland Road
Hauppauge, NY 11788
631-272-5947 / william.dr...@l-3com.com

CONFIDENTIALITY, EXPORT CONTROL AND DISCLAIMER NOTE:This e-mail and any 
attachments are solely for the use of the addressee and may contain information 
that is privileged or confidential. Any disclosure, use or distribution of the 
information contained herein is prohibited. In the event this e-mail contains 
technical data within the definition of the International Traffic in Arms 
Regulations or Export Administration Regulations, it is subject to the export 
control laws of the U.S.Government. The recipient should check this e-mail and 
any attachments for the presence of viruses as L-3 does not accept any 
liability associated with the transmission of this e-mail. If you have received 
this communication in error, please notify the sender by reply e-mail and 
immediately delete this message and any attachments.
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Re: [sqlite] Changing ID's to UUID

[James K. Lowden]

On Fri, 18 Nov 2016 10:22:15 -0800
Jens Alfke  wrote:

> You?d have to assign a central ?count server? to hand out consecutive
> numbers

No.  You need only enumerate the sources, and accept that the key is
the unique counter from the source plus the centrally assigned source
identifier.  

> You can assign ?peer IDs?, but then you need a sure-fire-unique way
> to assign them (using the MAC address is not sure-fire-unique) 

The sure-fire way to assign them is simple enumeration when they connect
to the central server to upload their information.  If the "peer" will
ever need to retrieve the information, it will need to store its
assigned id.  Else it's just up to central to keep everything
straight.  

> the system has to keep a persistent counter that can?t ever be rolled
> back, even in the case of something like restoring an OS backup. 

That's just not a problem if each system is in control of its own
counter.  

--jkl
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Re: [sqlite] I keep getting seg faults building my database using python sqlite3

[James K. Lowden]

On Fri, 18 Nov 2016 10:56:37 -0800
Roger Binns  wrote:

> Popen calls fork (it seems like you are doing Unix/Mac, not Windows).
> fork() duplicates the process including all open file descriptors.
> One or more of those descriptors belong to open SQLite databases and
> ancillary files.

Good catch, Roger.  It's a liability, but I slightly disagree with your
characterization.  

> - Running any Python code (destructors can be called which then run in
> the parent and child)

Yes, if those destructors affect shared resources.  The OP did say the
processes on the other side of popen were C programs.  

> - Not having file descriptors closed so the child process trashes them
> (close_fds Popen argument is False in python 2.x but True in python
> 3.x).  

The child process can't "trash" the parent's descriptors.  When the
child exits, the OS will close its descriptors, that's all.  But, yes,
if the child process is making some assumption about open descriptors
it receives at startup, that could be lead to problems.  Especially if
it scribbles on the SQLite database.  

> Also python 2.x subprocess module is broken in many ways.

My foray into Unicode in Python convinced me once and for all that
Python 3 is the only way to go.  But would you care to elaborate on the
problems with 2.x subprocess?  

--jkl
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Re: [sqlite] Hung query question

[Eduardo Morras]

On Fri, 18 Nov 2016 19:20:06 +
David Raymond  wrote:

> I've got a query that I've tried a few times here that seems like
> it's hanging up on something and I'm wondering if it's just some
> brain dead thing I'm forgetting or doing wrong.
> 
> I've got a database with a bunch of records, and am trying to
> populate a table in another database with coordinate extremes for
> each state. Using the CLI I open up the side database, attach the
> main one and run
> 
> insert into coordExtremes select State, min(Latitude), max(Latitude),
> min(Longitude), max(Longitude) from foo.bar group by State;
> 
> Twice I've left that running overnight and it's still been sitting
> there not completed the next day when I came in. I gave up on using
> the CLI to do it and wrote a quick Python script to scan through the
> whole big table once and keep track of the extremes, and it finished
> in all of 15 minutes. So I'm left scratching my head as to what's up.
> If anyone can think of something or sees where I'm being an idiot,
> please let me know.

Is python using bigger cache? Increase cache with pragma in CLI. 

Set it to 100-500MB for foo db, don't need to waste cache on destiny db
(where you insert the data). Change foo with the real origin db name.

pragma foo.cache_size=-50

Why don't use R*Tree virtual table?  http://www.sqlite.org/rtree.html
---   ---
Eduardo Morras 
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Re: [sqlite] Hung query question

[Simon Slavin]

On 18 Nov 2016, at 7:20pm, David Raymond  wrote:

> insert into coordExtremes select State, min(Latitude), max(Latitude), 
> min(Longitude), max(Longitude) from foo.bar group by State;

Apologies.  Correction to my earlier post:


Create indexes on table foo for the State, latitude and longitude columns.

CREATE INDEX idx_foo_lat ON foo (State, Latitude);
CREATE INDEX idx_foo_long ON foo (State, Longitude);
ANALYZE;

Then try the SELECT again.

Simon.
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Re: [sqlite] Hung query question

[Simon Slavin]

On 18 Nov 2016, at 7:20pm, David Raymond  wrote:

> insert into coordExtremes select State, min(Latitude), max(Latitude), 
> min(Longitude), max(Longitude) from foo.bar group by State;

Create indexes on table foo for the latitude and longitude columns.

CREATE INDEX idx_foo_lat ON foo (Latitude);
CREATE INDEX idx_foo_long ON foo (Longitude);
ANALYZE;

Then try the SELECT again.

Simon.
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[sqlite] Hung query question

[David Raymond]

I've got a query that I've tried a few times here that seems like it's hanging 
up on something and I'm wondering if it's just some brain dead thing I'm 
forgetting or doing wrong.

I've got a database with a bunch of records, and am trying to populate a table 
in another database with coordinate extremes for each state. Using the CLI I 
open up the side database, attach the main one and run

insert into coordExtremes select State, min(Latitude), max(Latitude), 
min(Longitude), max(Longitude) from foo.bar group by State;

Twice I've left that running overnight and it's still been sitting there not 
completed the next day when I came in. I gave up on using the CLI to do it and 
wrote a quick Python script to scan through the whole big table once and keep 
track of the extremes, and it finished in all of 15 minutes. So I'm left 
scratching my head as to what's up. If anyone can think of something or sees 
where I'm being an idiot, please let me know.

Below are more details, gonna try it again with the pre-compiled CLI rather 
than my self-compiled version to make sure it's not just something I managed to 
screw up in my compilation process. Of course, if it's the same then it won't 
finish by the time I send this.

pragma quick_check; is running at the moment. File is ~33 gigs with ~110 
million records. If quick_check finishes with nothing before I leave for the 
weekend I'll kick off a full integrity_check.


This is on 64 bit Windows 7 Enterprise. Both databases are in WAL mode.

The main data table is the only table in the main file. (Names have been 
changed to protect the innocent):
create table bar
(
id integer primary key,
State text collate nocase,
Latitude real,
Longitude real,
someOtherID int,
bunch of other fields including between the above
);
create index idx_bar_1 on bar (State, field2, field3, field4);
create index idx_bar_2 on bar (someOtherID);

select * from sqlite_stat1;
tbl|idx|stat
bar|idx_bar_1|109801252 2152966 3766 2887 2
bar|idx_bar_2|109801252 1

In the side database file what I'm trying to populate is:
create table coordExtremes
(
State text not null primary key collate nocase
check (length(State) = 2),
minLat real,
maxLat real,
minLon real,
maxLon real
);

sqlite> select sqlite_version();
sqlite_version()
3.15.1

sqlite> select sqlite_source_id();
sqlite_source_id()
2016-11-04 12:08:49 1136863c76576110e710dd5d69ab6bf347c65e36

sqlite> pragma compile_options;
compile_option
COMPILER=gcc-4.9.3
DEFAULT_MMAP_SIZE=0
ENABLE_COLUMN_METADATA
ENABLE_DBSTAT_VTAB
ENABLE_MEMORY_MANAGEMENT
ENABLE_RTREE
LIKE_DOESNT_MATCH_BLOBS
MAX_MMAP_SIZE=0
OMIT_SHARED_CACHE
SYSTEM_MALLOC
THREADSAFE=0


attach database 'theBigOne.sqlite' as foo;

explain query plan insert into coordExtremes select State, min(Latitude), 
max(Latitude), min(Longitude), max(Longitude) from foo.bar group by State;

selectid|order|from|detail
0|0|0|SCAN TABLE bar USING INDEX idx_bar_1

explain insert into coordExtremes select State, min(Latitude), max(Latitude), 
min(Longitude), max(Longitude) from foo.bar group by State;
addr  opcode p1p2p3p4 p5  comment
  -        -  --  -
0 Init   0 78000  Start at 78
1 InitCoroutine  7 56200
2 Noop   1 3 000
3 Integer0 16000  r[16]=0; clear abort 
flag
4 Integer0 15000  r[15]=0; indicate 
accumulator empty
5 Null   0 1919   00  r[19..19]=NULL
6 Gosub  1853000
7 OpenRead   0 3 2 16 00  root=3 iDb=2; bar
8 OpenRead   2 4 2 k(5,NOCASE,NOCASE,NOCASE,NOCASE,)  00  
root=4 iDb=2; idx_bar_1
9 Rewind 2 38210  00
10  Seek   2 0 000  Move 0 to 2.rowid
11  Column 2 0 20   00  r[20]=bar.State
12  Compare19201 k(1,NOCASE)00  r[19] <-> r[20]
13  Jump   141814   00
14  Move   2019100  r[19]=r[20]
15  Gosub  1744000  output one row
16  IfPos  1655000  if r[16]>0 then 
r[16]-=0, goto 55; check abort flag
17  Gosub  1853000  reset accumulator
18  Column 0 1421   00  r[21]=bar.Latitude
19  RealAffinity   210 000
20  CollSeq220 0 (BINARY)   00
21  AggStep0   0 219 min(1) 01  accum=r[9] 
step(r[21])
22  Column 0 1421   00  r[21]=bar.Latitude
23  RealAffinity   210 0 

Re: [sqlite] I keep getting seg faults building my database using python sqlite3

[Roger Binns]

On 18/11/16 08:55, Kevin O'Gorman wrote:
>> I am not.  All of the python code is a single thread.  The closest I come
> is a few times where I use subprocess.Popen to create what amounts to a
> pipeline, and one place where I start a number of copies of a C program in
> parallel, but each is a separate process with its own input and output
> files.

Ding ding ding.  You didn't mention which version of Python.

Popen calls fork (it seems like you are doing Unix/Mac, not Windows).
fork() duplicates the process including all open file descriptors.  One
or more of those descriptors belong to open SQLite databases and
ancillary files.

If the child process does virtually anything, it will result in crashes.
 Examples of doing things include:

- Running any Python code (destructors can be called which then run in
the parent and child)

- Not having file descriptors closed so the child process trashes them
(close_fds Popen argument is False in python 2.x but True in python
3.x).  Also python 2.x subprocess module is broken in many ways.

There are three methods for addressing this assuming it is the cause.

0: Python 3 is safer if you aren't already using it.  The subprocess32
module for Python 2 backports Python 3 subprocess if you are stuck on
Python 2

1: Make sure that the process that does SQLite work is a "leaf".  ie it
doesn't call subprocess or make any child processes.  Instead a master
process feeds it data on its stdin/out

2: Switch to APSW which has a fork checker built in.  This will catch
the fork problem no matter how it happens, and whatever is going on in
other libraries you may use:


https://rogerbinns.github.io/apsw/apsw.html?highlight=fork#apsw.fork_checker

Disclaimer:  I am the author of APSW

Roger



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Re: [sqlite] Changing ID's to UUID

[Jens Alfke]

> On Nov 16, 2016, at 5:59 AM, Keith Medcalf  wrote:
> 
> What I do not understand is why one would use a UUID (randomly generated 
> bunch of bytes) as a key in a database.  It is long, every use must be 
> checked for collisions, and inherently far less efficient than the simple 
> integer sequence it is replacing.

Distributed databases such as CouchDB and Couchbase do this. (I work on 
Couchbase Mobile.) When a database record is to be replicated between any 
number of peer databases, it obviously becomes infeasible to assign it a simple 
auto-incremented integer. (You’d have to assign a central ‘count server’ to 
hand out consecutive numbers, and then your system becomes bottlenecked on that 
server; it limits the rate at which the entire system can create records, and 
becomes a single point of failure.)

You can assign ‘peer IDs’, but then you need a sure-fire-unique way to assign 
them (using the MAC address is not sure-fire-unique) and the system has to keep 
a persistent counter that can’t ever be rolled back, even in the case of 
something like restoring an OS backup. You can use a timestamp to try to avoid 
rollback problems, but now you’ve added the well-known problems of using clocks 
in a distributed system. Worse, you’ve started leaking a significant amount of 
interesting information about your computer, which in some cases can be a 
privacy problem.

In the face of all that, simply generating a sufficiently long 
cryptographically-random number is very attractive.

> THe problem is an inability to properly determine and assess risk.  When 
> using a sequence the probability of a collision is 0.  When using a random 
> generated number (passing a bunch of random data through a digest function) 
> has a probability of collision of 100%. 

Um. Either you’re trolling me, or you don’t have a good understanding of 
probability.

In any case, this thread is pretty far off-topic and we should stop arguing 
this. I will not respond to any further posts.

—Jens
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Re: [sqlite] I keep getting seg faults building my database using python sqlite3

[Simon Slavin]

On 18 Nov 2016, at 6:18pm, James K. Lowden  wrote:

> The most likely culprit in my mind is RAM.  You're exercising new memory
> pretty hard, running a bunch of processes at it at full tilt.  Any
> defect in the chips or DMA could explain what you're seeing.  An easy
> test, not necessarily cheap, would be to replace the RAM (or, if
> possible, run with some removed).  

Or borrow someone else's computer.

Simon.
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Re: [sqlite] I keep getting seg faults building my database using python sqlite3

[James K. Lowden]

On Fri, 18 Nov 2016 08:55:11 -0800
"Kevin O'Gorman"  wrote:

> All of the python code is a single thread.  The closest I come
> is a few times where I use subprocess.Popen to create what amounts to
> a pipeline, and one place where I start a number of copies of a C
> program in parallel, but each is a separate process with its own
> input and output files.  These C programs have been in use for a
> number of months for earlier stages of this project, and I regard
> them as quite reliable.  None of them uses threads, and they are
> mostly very simple filters.

As you know, a process started with Popen cannot corrupt the Python
process's memory.  If you're not doing anything to defeat the GIL, a
segfault inside the Python interpreter would be considered a bug.  

But is it happening in the interpreter, or in SQLite for that matter?
ISTM that's what you need to know.  To know that, you're going to need
to run a debug version of the interpreter under gdb.  When it faults, a
backtrace will tell you where.  That's not definititive proof; memory
corruption is often detected far from where it was caused.  But if the
fault is at a consistent place in SQLite code, for example, you can
use a hardware watchpoint to discover what's writing to it.  

I don't know what more to suggest.  I would be surprised if you find a
fault in Python, in the Python standard library, or in SQLite.  I'm
sure it won't be in anything on the other side of a popen call.  Are
there non-standard libraries or Python modules in use that you haven't
mentioned?  

The most likely culprit in my mind is RAM.  You're exercising new memory
pretty hard, running a bunch of processes at it at full tilt.  Any
defect in the chips or DMA could explain what you're seeing.  An easy
test, not necessarily cheap, would be to replace the RAM (or, if
possible, run with some removed).  

I have two war stories related to rotten I/O hardware, where the device
appeared to work for all intents and purposes, but was actually a
high-speed bit munger. Those were both over 20 years ago.  It will
be interesting to hear if that turns out to be your issue.  

HTH.  

--jkl

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Re: [sqlite] I keep getting seg faults building my database using python sqlite3

[Kevin O'Gorman]

On Fri, Nov 18, 2016 at 8:38 AM, Roger Binns  wrote:

> On 17/11/16 19:14, Kevin O'Gorman wrote:
> > SO: I need help bifurcating this problem.  For instance, how can I tell
> if
> > the fault lies in SQLite, or in python? Or even in the hardware, given
> that
> > the time to failure is so variable?
>
> Are you using threads, threading related settings etc in any way?  The
> python sqlite3 module (aka pysqlite) is not threadsafe.  That doesn't
> stop people "working around" it, which can lead to crashes.
>
> Roger
>
>
> I am not.  All of the python code is a single thread.  The closest I come
is a few times where I use subprocess.Popen to create what amounts to a
pipeline, and one place where I start a number of copies of a C program in
parallel, but each is a separate process with its own input and output
files.  These C programs have been in use for a number of months for
earlier stages of this project, and I regard them as quite reliable.  None
of them uses threads, and they are mostly very simple filters.

The one that runs in parallel cannot be the culprit, however, because the
code has not reached the point where it would come into play.  That is the
step where the results get "cached" (in flat files) and all of the early
results are in those files.  This thing is dying before reaching unknown
territory where new results are needed.  The reason the results exist is
that they were generated by previous versions of the software that did not
use Python.  I am switching because (a) I want a database instead of flat
files for speed reasons and (b) the C code was getting too hard to maintain.

All of this is a hobby project, and I can share any parts of it that you
care to see.
-- 
#define QUESTION ((bb) || (!bb)) /* Shakespeare */
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Re: [sqlite] I keep getting seg faults building my database using python sqlite3

[Kevin O'Gorman]

On Fri, Nov 18, 2016 at 3:11 AM, Simon Slavin  wrote:

> Forgot to say ...
>
> Most of these problems result from attempting to reuse memory you've
> already released.  Even if the error is happening inside a SQLite routine,
> it will be because you passed it a pointer to an SQLite connection which
> had already been _close()'d or a statement which had already been
> _finalize()'d.
>
>
> Well, the entire process runs under a single connection that is never
closed. Although cursors are opened and closed within some of the Python
functions, the close is always at the end of the function.  And I have no
idea how things get finalized under python, or if that's an issue.  Anyway,
most of the time I use patterns like
  for row in c1.execute(...)
or
  with dbfile.connect() as conn:
and as I understand it, these protect me from most errors of that kind.

Moreover, it seems to me that these would all lead to failure at exactly
the same point, rather than at three points up to an hour different from
each other.

I was thinking it more likely to be one of
a) random hardware malfunction
b) some bug in memory handling that was subject to influence by other
activity in the machine)
c) some bug in hanling pointers to the python structures (it would have to
be a python or sqlite3 bug.)




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Re: [sqlite] I keep getting seg faults building my database using python sqlite3

[Roger Binns]

On 17/11/16 19:14, Kevin O'Gorman wrote:
> SO: I need help bifurcating this problem.  For instance, how can I tell if
> the fault lies in SQLite, or in python? Or even in the hardware, given that
> the time to failure is so variable?

Are you using threads, threading related settings etc in any way?  The
python sqlite3 module (aka pysqlite) is not threadsafe.  That doesn't
stop people "working around" it, which can lead to crashes.

Roger




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Re: [sqlite] I keep getting seg faults building my database using python sqlite3

[Simon Slavin]

Forgot to say ...

Most of these problems result from attempting to reuse memory you've already 
released.  Even if the error is happening inside a SQLite routine, it will be 
because you passed it a pointer to an SQLite connection which had already been 
_close()'d or a statement which had already been _finalize()'d.

Simon.
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Re: [sqlite] I keep getting seg faults building my database using python sqlite3

[Simon Slavin]

On 18 Nov 2016, at 3:14am, Kevin O'Gorman  wrote:

> SO: I need help bifurcating this problem.  For instance, how can I tell if
> the fault lies in SQLite, or in python? Or even in the hardware, given that
> the time to failure is so variable?

Normal recommendation is to use GDB.  You can find several tutorials on how to 
use GDB to spot seg faults on the web.

Some other deveopment environments have shells around GBD or tools which will 
spot misused memory, for example Apple's Xcode environment.

Simon.
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