Thread: fast read of binary data
Dear All I am currently implementing using a compressed binary storage scheme genotyping data. These are basically vectors of binary data which may be megabytes in size. Our current implementation uses the data type bit varying. What we want to do is very simple: we want to retrieve such records from the database and transfer it unaltered to the client which will do something (uncompressing) with it. As massive amounts of data are to be moved, speed is of great importance, precluding any to and fro conversions. Our current implementation uses Perl DBI; we can retrieve the data ok, but apparently there is some converting going on. Further, we would like to use ODBC from Fortran90 (wrapping the C-library) for such transfers. However, all sorts funny things happen here which look like conversion issues. In old fashioned network database some decade ago (in pre SQL times) this was no problem. Maybe there is someone here who knows the PG internals sufficiently well to give advice on how big blocks of memory (i.e. bit varying records) can between transferred UNALTERED between backend and clients. looking forward to you response. greetings Eildert -- Eildert Groeneveld =================================================== Institute of Farm Animal Genetics (FLI) Mariensee 31535 Neustadt Germany Tel : (+49)(0)5034 871155 Fax : (+49)(0)5034 871143 e-mail: eildert.groeneveld@fli.bund.de web: http://vce.tzv.fal.de ==================================================
Eildert Groeneveld wrote: > I am currently implementing using a compressed binary storage scheme > genotyping data. These are basically vectors of binary data which may be > megabytes in size. > > Our current implementation uses the data type bit varying. > > What we want to do is very simple: we want to retrieve such records from > the database and transfer it unaltered to the client which will do > something (uncompressing) with it. As massive amounts of data are to be > moved, speed is of great importance, precluding any to and fro > conversions. > > Our current implementation uses Perl DBI; we can retrieve the data ok, > but apparently there is some converting going on. > > Further, we would like to use ODBC from Fortran90 (wrapping the > C-library) for such transfers. However, all sorts funny things happen > here which look like conversion issues. > > In old fashioned network database some decade ago (in pre SQL times) > this was no problem. Maybe there is someone here who knows the PG > internals sufficiently well to give advice on how big blocks of memory > (i.e. bit varying records) can between transferred UNALTERED between > backend and clients. Using the C API you can specify binary mode for your data, which meand that they won't be converted. I don't think you will be able to use this with DBI or ODBC, but maybe binary corsors can help (http://www.postgresql.org/docs/current/static/sql-declare.html), but I don't know if DBI or ODBC handles them well. If you can avoid DBI or ODBC, that would be best. Yours, Laurenz Albe
On 12-11-2012 11:45, Eildert Groeneveld wrote: > Dear All > > I am currently implementing using a compressed binary storage scheme > genotyping data. These are basically vectors of binary data which may be > megabytes in size. > > Our current implementation uses the data type bit varying. Wouldn't 'bytea' be a more logical choice for binary data? http://www.postgresql.org/docs/9.2/interactive/datatype-binary.html > What we want to do is very simple: we want to retrieve such records from > the database and transfer it unaltered to the client which will do > something (uncompressing) with it. As massive amounts of data are to be > moved, speed is of great importance, precluding any to and fro > conversions. > > Our current implementation uses Perl DBI; we can retrieve the data ok, > but apparently there is some converting going on. > > Further, we would like to use ODBC from Fortran90 (wrapping the > C-library) for such transfers. However, all sorts funny things happen > here which look like conversion issues. > > In old fashioned network database some decade ago (in pre SQL times) > this was no problem. Maybe there is someone here who knows the PG > internals sufficiently well to give advice on how big blocks of memory > (i.e. bit varying records) can between transferred UNALTERED between > backend and clients. Although I have no idea whether bytea is treated differently in this context. Bit varying should be about as simple as possible (given that it only has 0's and 1's) Best regards, Arjen
On Mon, Nov 12, 2012 at 4:45 AM, Eildert Groeneveld <eildert.groeneveld@fli.bund.de> wrote: > Dear All > > I am currently implementing using a compressed binary storage scheme > genotyping data. These are basically vectors of binary data which may be > megabytes in size. > > Our current implementation uses the data type bit varying. > > What we want to do is very simple: we want to retrieve such records from > the database and transfer it unaltered to the client which will do > something (uncompressing) with it. As massive amounts of data are to be > moved, speed is of great importance, precluding any to and fro > conversions. > > Our current implementation uses Perl DBI; we can retrieve the data ok, > but apparently there is some converting going on. > > Further, we would like to use ODBC from Fortran90 (wrapping the > C-library) for such transfers. However, all sorts funny things happen > here which look like conversion issues. > > In old fashioned network database some decade ago (in pre SQL times) > this was no problem. Maybe there is someone here who knows the PG > internals sufficiently well to give advice on how big blocks of memory > (i.e. bit varying records) can between transferred UNALTERED between > backend and clients. > > looking forward to you response. Fastest/best way to transfer binary data to/from postgres is going to mean direct coding against libpq since most drivers wall you off from the binary protocol (this may or may not be the case with ODBC). If I were you I'd be writing C code to manage the database and linking the C compiled object to the Fortran application. Assuming the conversion doesn't go the way you want (briefly looking, there is a 'bytea as LO' option you may want to explore), ODBC brings nothing but complication in this regard unless your application has to support multiple database vendors or you have zero C chops in-house. merlin
On Mo, 2012-11-12 at 12:18 +0100, Albe Laurenz wrote: > Eildert Groeneveld wrote: > > I am currently implementing using a compressed binary storage scheme > > genotyping data. These are basically vectors of binary data which may be > > megabytes in size. > > > > Our current implementation uses the data type bit varying. > > > > What we want to do is very simple: we want to retrieve such records from > > the database and transfer it unaltered to the client which will do > > something (uncompressing) with it. As massive amounts of data are to be > > moved, speed is of great importance, precluding any to and fro > > conversions. > > > > Our current implementation uses Perl DBI; we can retrieve the data ok, > > but apparently there is some converting going on. > > > > Further, we would like to use ODBC from Fortran90 (wrapping the > > C-library) for such transfers. However, all sorts funny things happen > > here which look like conversion issues. > > > > In old fashioned network database some decade ago (in pre SQL times) > > this was no problem. Maybe there is someone here who knows the PG > > internals sufficiently well to give advice on how big blocks of memory > > (i.e. bit varying records) can between transferred UNALTERED between > > backend and clients. > > Using the C API you can specify binary mode for your data, which > meand that they won't be converted. > > I don't think you will be able to use this with DBI or ODBC, > but maybe binary corsors can help > (http://www.postgresql.org/docs/current/static/sql-declare.html), > but I don't know if DBI or ODBC handles them well. > > If you can avoid DBI or ODBC, that would be best. ok, I did have a look at the libpq librar, and you are right, there is a way to obtain binary data from the backend through the PQexecParams res = PQexecParams(conn, "DECLARE myportal CURSOR FOR select genotype_bits from v_genotype_data", 0, /* zero param */ NULL, /* let the backend deduce param type */ paramValues, NULL, /* don't need param lengths since text*/ NULL, /* default to all text params */ 1); /* ask for binary results */ genotype_bits is defined as bit varying in the backend. When writing the results: for (i = 0; i < PQntuples(res); i++) { for (j = 0; j < nFields; j++) fwrite(PQgetvalue(res, i, j),100000,1,f); } it is clear that the results are NOT in binary format: eg(eno,snp): od -b junk |head 0000000 061 060 061 060 061 060 061 060 061 060 061 060 061 060 061 060 clearly, these are nice 0 and 1 in ASCII and not as I need it as a bit stream. Also, (and in line with this) PQgetvalue(res, i, j) seems to be of type text. What am I missing?
On 22.11.2012 09:54, Eildert Groeneveld wrote:
> ok, I did have a look at the libpq librar, and you are right, there is a
> way to obtain binary data from the backend through the PQexecParams
>
> res = PQexecParams(conn,
> "DECLARE myportal CURSOR FOR select genotype_bits
> from v_genotype_data",
> 0, /* zero param */
> NULL, /* let the backend deduce param type */
> paramValues,
> NULL, /* don't need param lengths since text*/
> NULL, /* default to all text params */
> 1); /* ask for binary results */
>
> genotype_bits is defined as bit varying in the backend. When writing the
> results:
> for (i = 0; i< PQntuples(res); i++)
> {
> for (j = 0; j< nFields; j++)
> fwrite(PQgetvalue(res, i, j),100000,1,f);
> }
>
> it is clear that the results are NOT in binary format:
> eg(eno,snp): od -b junk |head
> 0000000 061 060 061 060 061 060 061 060 061 060 061 060 061 060 061 060
You need to ask for binary results when you execute the FETCH
statements. Asking for binary results on the DECLARE CURSOR statement
has no effect, as DECLARE CURSOR doesn't return any results; it's the
FETCH that follows that returns the result set.
- Heikki