22 May 2001
Dear Sir;
First, thank you for PostGres. It is great!
Second, I am puzzled by repeated, apparently pointless calls to memmove() in
the function pqReadData, which is in `src/interfaces/libpq/fe-misc.c'.
I am running and looking at PostGres version 7.1.1 built on a Alpha running
Digital UNIX. I use the Digital compilers to build PostGres.
I created a table using the `script'
-- Create genome_seq table
--
-- genome_seq contains information extracted from NCBI H sapiens genome contigs
--
-- table label
-- -----------
-- accession
-- version
-- organism
-- chromosome
-- comments
-- sequence
-- length
--
CREATE TABLE genome_seq (
accession text,
version text,
organism text,
chromosome text,
comments text,
sequence text,
length int4
)
--
GENOME_SEQ.TABLE (END)
The `sequence' can be a long string. I have sequence strings of tens of millions
of characters.
I create a file of the rows and load the data using the `COPY FROM' SQL command
for performance as suggested in the documents. (I believe this is irrelevant.)
I am using PostGres and the libpq library calls to get the sequence quickly. It
worked well for sequences of 150k characters but bogged down for the 10M
character strings, taking a minute or so, which seemed excessive to me.
I used top to watch system activity and noticed that the the client was getting
essentially all the CPU cycles, and the backend was getting essentially nothing.
I did not understand why the client needs to spend a lot of time with long text
strings so I repeated this with the `psql' interface and found the same
phenomenon, which makes sense because it uses libpq too.
I ran both my program and psql under dbx and interrupted it repeatedly while
it ate up CPU cycles and found the function stack looked like
genbank_db=# select sequence from genome_seq where version = 'NT_009151.3';
Interrupt
signal Interrupt at >*[memmove, 0x3ff81499998] subq r5, 0x8, r5
(dbx) where
> 0 memmove(0x0, 0x0, 0x0, 0x0, 0x0) [0x3ff81499998]
1 pqReadData(0x0, 0x0, 0x3ffbffe8880, 0x14000c400, 0x0) [0x3ffbffeb16c]
2 PQgetResult(0x3ffbffe8880, 0x14000c400, 0x0, 0x100400000, 0x3ffbffe8aa0) [0x3ffbffe887c]
3 PQexec(0x14000a4c0, 0x0, 0x140000a00, 0x14000e3c0, 0x0) [0x3ffbffe8a9c]
4 SendQuery(0x0, 0x14000eb40, 0x12000b410, 0x14000eb40, 0x3b) [0x120009024]
5 MainLoop(0x14000d320, 0x3e00000000, 0x14000eb40, 0x100000000, 0x1) [0x12000b42c]
6 main(0x0, 0x0, 0x0, 0x0, 0x100000002) [0x12000d364]
(dbx)
which puzzled me.
I added diagnostics to pqReadData() so the function looks like
.
.
.
int
pqReadData(PGconn *conn)
{
int someread = 0;
int nread;
static int mncount = 0;
static long onumbyte = 0;
fprintf( stderr,
"pqReadData: start\n" );
if (conn->sock < 0)
{
printfPQExpBuffer(&conn->errorMessage,
"pqReadData() -- connection not open\n");
return -1;
}
/* Left-justify any data in the buffer to make room */
if (conn->inStart < conn->inEnd)
{
/*
if( conn->inStart != 0 )
{
*/
memmove(conn->inBuffer, conn->inBuffer + conn->inStart,
conn->inEnd - conn->inStart);
++mncount;
fprintf( stderr,
"pqReadData: count: %d memmove( dst: %ld src: %ld numbyt: %ld ) del_numbyt: %ld inStart: %ld\n",
mncount,
(long)conn->inBuffer,
(long)( conn->inBuffer + conn->inStart ),
(long)( conn->inEnd - conn->inStart ),
(long)( conn->inEnd - conn->inStart ) - onumbyte,
(long)( conn->inStart ) );
onumbyte = conn->inEnd - conn->inStart;
/*
}
*/
conn->inEnd -= conn->inStart;
conn->inCursor -= conn->inStart;
conn->inStart = 0;
}
.
.
.
.
I start up psql and make a query
select sequence from genome_seq where version = 'NT_009151.3';
and the resulting stderr looks like
startup: begin: stderr
pqReadData: start
pqReadData: start
pqReadData: start
pqReadData: start
pqReadData: start
pqReadData: count: 1 memmove( dst: 5368891392 src: 5368891421 numbyt: 8163 ) del_numbyt: 8163 inStart: 29
pqReadData: start
pqReadData: count: 2 memmove( dst: 5368891392 src: 5368891392 numbyt: 16355 ) del_numbyt: 8192 inStart: 0
src/interfaces/libpq/fe-misc.c: realloc mem
pqReadData: start
pqReadData: count: 3 memmove( dst: 5381845472 src: 5381845472 numbyt: 24547 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 4 memmove( dst: 5381845472 src: 5381845472 numbyt: 32739 ) del_numbyt: 8192 inStart: 0
src/interfaces/libpq/fe-misc.c: realloc mem
pqReadData: start
pqReadData: count: 5 memmove( dst: 5381878272 src: 5381878272 numbyt: 40931 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 6 memmove( dst: 5381878272 src: 5381878272 numbyt: 49123 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 7 memmove( dst: 5381878272 src: 5381878272 numbyt: 57315 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 8 memmove( dst: 5381878272 src: 5381878272 numbyt: 65507 ) del_numbyt: 8192 inStart: 0
src/interfaces/libpq/fe-misc.c: realloc mem
pqReadData: start
pqReadData: count: 9 memmove( dst: 5381943840 src: 5381943840 numbyt: 73699 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 10 memmove( dst: 5381943840 src: 5381943840 numbyt: 81891 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 11 memmove( dst: 5381943840 src: 5381943840 numbyt: 90083 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 12 memmove( dst: 5381943840 src: 5381943840 numbyt: 98275 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 13 memmove( dst: 5381943840 src: 5381943840 numbyt: 106467 ) del_numbyt: 8192 inStart: 0
.
.
. (many lines omitted)
.
pqReadData: start
pqReadData: count: 1562 memmove( dst: 5398590208 src: 5398590208 numbyt: 12804067 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 1563 memmove( dst: 5398590208 src: 5398590208 numbyt: 12812259 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 1564 memmove( dst: 5398590208 src: 5398590208 numbyt: 12820451 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 1565 memmove( dst: 5398590208 src: 5398590208 numbyt: 12828643 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 1566 memmove( dst: 5398590208 src: 5398590208 numbyt: 12836835 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 1567 memmove( dst: 5398590208 src: 5398590208 numbyt: 12845027 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 1568 memmove( dst: 5398590208 src: 5398590208 numbyt: 12853219 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 1569 memmove( dst: 5398590208 src: 5398590208 numbyt: 12861411 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 1570 memmove( dst: 5398590208 src: 5398590208 numbyt: 12869603 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 1571 memmove( dst: 5398590208 src: 5398590208 numbyt: 12877795 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 1572 memmove( dst: 5398590208 src: 5398590208 numbyt: 12885987 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 1573 memmove( dst: 5398590208 src: 5398590208 numbyt: 12894179 ) del_numbyt: 8192 inStart: 0
pqReadData: start
pqReadData: count: 1574 memmove( dst: 5398590208 src: 5398590208 numbyt: 12902371 ) del_numbyt: 8192 inStart: 0
Incidentally, the length of sequence is 12908986 characters.
It appears to me that the memmove is moving data from and to the
same memory locations ~1500 times incrementing the number of bytes
moved by 8K each time.
I tried skipping the memmove when the conn->inStart == 0
and found that the output sequence is identical to when it is not
skipped, as I expected.
I appreciate your consideration.
Best Wishes,
Brent Ewing
--
--------------------------------
Brent Ewing
bge@u.washington.edu
[206] 616 6040
University of Washington
Box 352145
Seattle, Washington 98195-2145
--------------------------------
