Hi, sorry to not get back sooner, I've found a couple of other interesting
things. The speed issue doesn't seem to exist running in linux, the same
code runs in a blink. In windows, the really, really slow runs (several
minutes) only seem to happen when running from within visual studios. When
run from command line it's slow, e.g. 15 seconds for 4000 vectors, but not
minutes slow, and the time doesn't seem to grow as I saw before with visual
studios.
#ifdef __cplusplus
extern "C" {
#endif
#include <hdf5.h>
#ifdef __cplusplus
}
#endif
#include <vector>
#include <iostream>
#include <stdlib.h>
#include <math.h>
using namespace std;
int main() {
unsigned long long totalNumVecs = 500000;
unsigned long long vecLength = 128;
hid_t baseType = H5T_NATIVE_FLOAT;
unsigned long long roughNumVecsToGet = 4000;
unsigned long long skipRate = (unsigned long
long)ceilf((float)totalNumVecs / (float)roughNumVecsToGet);
vector<unsigned long long> vecInds;
for( int rowInd = 0; rowInd < totalNumVecs; rowInd += skipRate) {
vecInds.push_back(rowInd);
}
int rank = 2;
hsize_t dims[2];
dims[0] = totalNumVecs;
dims[1] = vecLength;
hid_t fileSpaceId = H5Screate_simple(rank, dims, NULL);
hsize_t fileBlockCount[2];
hsize_t fileOffset[2];
hsize_t selectionDims[2];
selectionDims[0] = 1;
fileBlockCount[0] = 1;
fileOffset[0] = vecInds[0];
for(int ir = 1; ir < rank; ++ir) {
selectionDims[ir] = dims[ir];
fileBlockCount[ir] = 1;
fileOffset[ir] = 0;
}
cout << "begin hyperslab building" << endl;
H5Sselect_hyperslab(fileSpaceId, H5S_SELECT_SET, (const hsize_t*)
fileOffset, NULL, (const hsize_t*) fileBlockCount, selectionDims);
unsigned long long numVecsToRead = vecInds.size();
for (hsize_t id=1; id < numVecsToRead; ++id) {
if ( (id % 50) == 0) {
cout << id << "/" << numVecsToRead << endl;
}
fileOffset[0] = vecInds[id];
H5Sselect_hyperslab(fileSpaceId, H5S_SELECT_OR, (const hsize_t*)
fileOffset, NULL, (const hsize_t*) fileBlockCount, selectionDims);
}
cout << "end hyperslab building" << endl;
return 0;
}
Thanks,
Ken
On Wed, May 26, 2010 at 8:17 AM, Quincey Koziol <[email protected]> wrote:
> Hi Ken,
>
> On May 25, 2010, at 5:36 PM, Ken Sullivan wrote:
>
> > Hi, I'm running into slow performance when selecting several (>1000)
> non-consecutive rows from a 2-dimensional matrix, typically ~500,000 X 100.
> The bottleneck is the for loop where each row vector index is OR'ed into
> the hyperslab, i.e.:
> >
> > LOG4CXX_INFO(logger,"TIME begin hyperslab building"); //print out with
> time stamp
> > //select file buffer hyperslabs
> > H5Sselect_hyperslab(fileSpaceId, H5S_SELECT_SET, (const hsize_t*)
> fileOffset, NULL, (const hsize_t*) fileBlockCount, selectionDims);
> > for (hsize_t id = 1; id < numVecsToRead; ++id) {
> > LOG4CXX_INFO(logger, id << "/" << numVecsToRead);
> > fileOffset[0] = fileLocs1Dim[id];
> > H5Sselect_hyperslab(fileSpaceId, H5S_SELECT_OR, (const hsize_t*)
> fileOffset, NULL, (const hsize_t*) fileBlockCount, selectionDims);
> > }
> > LOG4CXX_INFO(logger,"TIME end hyperslab building");
> >
> > One interesting thing is the time between each loop increases between
> each iteration, e.g. no time at all between 1-2-3-4-5, but seconds between
> 1000-1001-1002. So, the time to select the hyperslab is worse than linear,
> and can become amazingly time consuming, e.g. >10 minutes (!) for a few
> thousand. The read itself is very quick.
>
> Drat! Sounds like we've got an O(n^2) algorithm (or worse)
> somewhere in the code that combines two selections. Can you send us a
> standalone program that demonstrates the problem, so we can file an issue
> for this, and get it fixed?
>
> > My current workaround is to check if the number of vectors to select is
> greater than a heuristically determined number where it seems the time to
> read the entire file (half a million row vectors) and copy the requested
> vectors is less than the time to run the hyperslab selection. Generally the
> number works out to ~500 vecs/0.5 seconds.
> >
> > While poking around the code, I found a similar function,
> H5Scombine_hyperslab() that is only compiled if NEW_HYPERSLAB_API is
> defined. Using this significantly reduced the time of selection, in
> particular the time for each OR-ing seemed constant, so 2000 vectors took
> twice as long as 1000, not many times as with H5Sselect_hyperslab().
> However, it's still 10s of seconds for few thousand vector selection, and
> so it's still much quicker to read all and copy (~1/2 second).
> > Reading all and copying is not an ideal solution, as it requires
> malloc/free ~250MB unnecessarily, and if I use H5Scombine_hyperslab() the
> crossover number goes up, i.e. more than 500, and it's less likely to be
> needed. I'm a bit nervous however about using this undocumented code.
> >
> > So...am I doing something wrong? Is there a speedy way to select a
> hyperslab consisting of 100s or 1000s of non-consecutive vectors? Is
> NEW_HYPERSLAB_API safe?
>
> Currently, the NEW_HYPERSLAB_API is not tested or supported, so I
> wouldn't use it.
>
> Quincey
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [email protected]
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
