Hi all,
I recently noticed few such issues, related to different speeds when
writing once with references and once with separate datasets. It turns
out it is a windows specific problem. I attach the test code (replace
the time measurement macros with your own) and an excel file with my
results and the THG results. This is the response of THG:
"I spent some more time debugging and benchmarking, and I have been
unable to find any problems with the windows file driver. I suspect
the anomalous performance is probably due to some sort of buffering
the operating system does, as the total wall time is typically about
the same. Even though the windows driver (by default) uses
"unbuffered" I/O functions, the use of these functions does not
prevent buffering by the underlying filesystem driver. For what it's
worth, defining WINDOWS_USE_STDIO in h5pubconf.h seems to make the
performance more consistent, albeit with much higher CPU usage.
Here are my results (on an old P4 laptop, XP 32 bit, VS2008 Express).
I measured the wall time, as well as the kernel and user time. I also
metered the windows file driver to keep track of the total number of
reads, writes, and truncates, as well as the total number of bytes
read and written. All of these meaurements are totals for the 30 runs
(not averaged). The first 4 benchmarks do not use STDIO, while the
last 4 do."
HTH
-- dimitris
#include <string.h>
#include "hdf5.h"
#define INSTRUMENTWITHTIMEPROFILER
const char* filename="test_layer_performance.h5";
int *data=0;
int *rdata=0;
int datasize = 0;
//Create
void createHyperslab1()
{
hid_t fid, gid, sid, did; /* file ID */
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gcreate(fid,"hyperslab1",H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
hsize_t dims[]={6,datasize};
sid = H5Screate_simple(2,dims,dims);
did =
H5Dcreate(gid,"hyperslab1",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Sclose(sid);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
}
void createHyperslab2()
{
hid_t fid, gid, sid, did; /* file ID */
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gcreate(fid,"hyperslab2",H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
hsize_t dims[]={datasize,6};
sid = H5Screate_simple(2,dims,dims);
did =
H5Dcreate(gid,"hyperslab2",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Sclose(sid);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
}
void createSeparate()
{
hid_t fid, gid, sid, did; /* file ID */
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gcreate(fid,"Separate",H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
hsize_t dims[]={datasize};
sid = H5Screate_simple(1,dims,dims);
did =
H5Dcreate(gid,"Separate1",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Dclose(did);
did =
H5Dcreate(gid,"Separate2",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Dclose(did);
did =
H5Dcreate(gid,"Separate3",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Dclose(did);
did =
H5Dcreate(gid,"Separate4",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Dclose(did);
did =
H5Dcreate(gid,"Separate5",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Dclose(did);
did =
H5Dcreate(gid,"Separate6",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Sclose(sid);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
}
void createReferences()
{
hid_t fid, gid, sid, did; /* file ID */
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gcreate(fid,"References",H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
hsize_t dims[]={6};
sid = H5Screate_simple(1,dims,dims);
did =
H5Dcreate(gid,"References",H5T_STD_REF_OBJ,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Sclose(sid);
H5Dclose(did);
hobj_ref_t ref[6];
dims[0]=datasize;
sid = H5Screate_simple(1,dims,dims);
did =
H5Dcreate(gid,"Separate1",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Dclose(did);
did =
H5Dcreate(gid,"Separate2",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Dclose(did);
did =
H5Dcreate(gid,"Separate3",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Dclose(did);
did =
H5Dcreate(gid,"Separate4",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Dclose(did);
did =
H5Dcreate(gid,"Separate5",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Dclose(did);
did =
H5Dcreate(gid,"Separate6",H5T_NATIVE_INT,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Sclose(sid);
H5Dclose(did);
H5Rcreate(&ref[0], gid,"Separate1", H5R_OBJECT,-1);
H5Rcreate(&ref[1], gid,"Separate2", H5R_OBJECT,-1);
H5Rcreate(&ref[2], gid,"Separate3", H5R_OBJECT,-1);
H5Rcreate(&ref[3], gid,"Separate4", H5R_OBJECT,-1);
H5Rcreate(&ref[4], gid,"Separate5", H5R_OBJECT,-1);
H5Rcreate(&ref[5], gid,"Separate6", H5R_OBJECT,-1);
did = H5Dopen(gid,"References",H5P_DEFAULT);
H5Dwrite(did,H5T_STD_REF_OBJ,H5S_ALL,H5S_ALL,H5P_DEFAULT,ref);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
}
void createComposite()
{
hid_t fid, gid, sid, did; /* file ID */
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gcreate(fid,"Composite",H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
hsize_t dims[]={6};
sid = H5Screate_simple(1,dims,dims);
dims[0]=datasize;
hid_t tid = H5Tarray_create2( H5T_NATIVE_INT, 1, dims );
did =
H5Dcreate(gid,"Composite",tid,sid,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
H5Sclose(sid);
H5Dclose(did);
H5Gclose(gid);
H5Tclose(tid);
H5Fclose(fid);
}
//Write
void writeHyperslab1()
{
hid_t fid, gid, sid, did; /* file ID */
hsize_t dims[3];
hsize_t start[3];
hsize_t count[3];
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gopen(fid,"hyperslab1",H5P_DEFAULT);
did = H5Dopen(gid,"hyperslab1",H5P_DEFAULT);
sid=H5Dget_space(did);
H5Sget_simple_extent_dims(sid,dims,NULL);
memcpy(count,dims,sizeof(count));
memset(start,0,sizeof(start));
start[0]=3;
count[0]=1;
H5Sselect_hyperslab(sid,H5S_SELECT_SET,start,NULL,count,NULL);
hsize_t nels = datasize;
hid_t mid = H5Screate_simple(1, &nels, &nels);
H5Dwrite(did,H5T_NATIVE_INT,mid,sid,H5P_DEFAULT,data);
H5Sclose(mid);
H5Sclose(sid);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
}
void writeHyperslab2()
{
hid_t fid, gid, sid, did; /* file ID */
hsize_t dims[3];
hsize_t start[3];
hsize_t count[3];
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gopen(fid,"hyperslab2",H5P_DEFAULT);
did = H5Dopen(gid,"hyperslab2",H5P_DEFAULT);
sid=H5Dget_space(did);
H5Sget_simple_extent_dims(sid,dims,NULL);// returns [6][datasize]?!?!?
memcpy(count,dims,sizeof(count));
memset(start,0,sizeof(start));
start[1]=3;
count[1]=1;
H5Sselect_hyperslab(sid,H5S_SELECT_SET,start,NULL,count,NULL);
hsize_t nels = datasize;
hid_t mid = H5Screate_simple(1, &nels, &nels);
H5Dwrite(did,H5T_NATIVE_INT,mid,sid,H5P_DEFAULT,data);
H5Sclose(mid);
H5Sclose(sid);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
}
void writeSeparate()
{
hid_t fid, gid, did; /* file ID */
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gopen(fid,"Separate",H5P_DEFAULT);
did = H5Dopen(gid,"Separate3",H5P_DEFAULT);
H5Dwrite(did,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,data);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
}
void writeReferences()
{
hid_t fid, gid, sid, did; /* file ID */
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gopen(fid,"References",H5P_DEFAULT);
did = H5Dopen(gid,"References",H5P_DEFAULT);
hobj_ref_t ref[6];
H5Dread(did,H5T_STD_REF_OBJ,H5S_ALL,H5S_ALL,H5P_DEFAULT,ref);
hid_t rid = H5Rdereference(gid,H5R_OBJECT,&(ref[2]));
H5Dwrite(rid,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,data);
H5Dclose(rid);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
}
void writeComposite()
{
hid_t fid, gid, sid, did; /* file ID */
hsize_t start[1];
hsize_t count[1];
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gopen(fid,"Composite",H5P_DEFAULT);
did = H5Dopen(gid,"Composite",H5P_DEFAULT);
sid=H5Dget_space(did);
start[0]=3;
count[0]=1;
H5Sselect_hyperslab(sid,H5S_SELECT_SET,start,NULL,count,NULL);
hid_t tid = H5Dget_type(did);
hsize_t nels = 1;
hid_t mid = H5Screate_simple(1, &nels, &nels);
H5Dwrite(did,tid,mid,sid,H5P_DEFAULT,data);
H5Sclose(mid);
H5Tclose(tid);
H5Sclose(sid);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
}
//read
void readHyperslab1()
{
hid_t fid, gid, sid, did; /* file ID */
hsize_t dims[3];
hsize_t start[3];
hsize_t count[3];
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gopen(fid,"hyperslab1",H5P_DEFAULT);
did = H5Dopen(gid,"hyperslab1",H5P_DEFAULT);
sid=H5Dget_space(did);
H5Sget_simple_extent_dims(sid,dims,NULL);
memcpy(count,dims,sizeof(count));
memset(start,0,sizeof(start));
start[0]=3;
count[0]=1;
H5Sselect_hyperslab(sid,H5S_SELECT_SET,start,NULL,count,NULL);
hsize_t nels = datasize;
hid_t mid = H5Screate_simple(1, &nels, &nels);
H5Dread(did,H5T_NATIVE_INT,mid,sid,H5P_DEFAULT,rdata);
H5Sclose(mid);
H5Sclose(sid);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
if (rdata[datasize-1]!=datasize-1)
{
throw "Wrong Size";
}
}
void readHyperslab2()
{
hid_t fid, gid, sid, did; /* file ID */
hsize_t dims[3];
hsize_t start[3];
hsize_t count[3];
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gopen(fid,"hyperslab2",H5P_DEFAULT);
did = H5Dopen(gid,"hyperslab2",H5P_DEFAULT);
sid=H5Dget_space(did);
H5Sget_simple_extent_dims(sid,dims,NULL);// returns [6][datasize]?!?!?
memcpy(count,dims,sizeof(count));
memset(start,0,sizeof(start));
start[1]=3;
count[1]=1;
H5Sselect_hyperslab(sid,H5S_SELECT_SET,start,NULL,count,NULL);
hsize_t nels = datasize;
hid_t mid = H5Screate_simple(1, &nels, &nels);
H5Dread(did,H5T_NATIVE_INT,mid,sid,H5P_DEFAULT,rdata);
H5Sclose(mid);
H5Sclose(sid);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
if (rdata[datasize-1]!=datasize-1)
{
throw "Wrong Size";
}
}
void readSeparate()
{
hid_t fid, gid, did; /* file ID */
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gopen(fid,"Separate",H5P_DEFAULT);
did = H5Dopen(gid,"Separate3",H5P_DEFAULT);
H5Dread(did,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,rdata);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
if (rdata[datasize-1]!=datasize-1)
{
throw "Wrong Size";
}
}
void readReferences()
{
hid_t fid, gid, sid, did; /* file ID */
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gopen(fid,"References",H5P_DEFAULT);
did = H5Dopen(gid,"References",H5P_DEFAULT);
hobj_ref_t ref[6];
H5Dread(did,H5T_STD_REF_OBJ,H5S_ALL,H5S_ALL,H5P_DEFAULT,ref);
hid_t rid = H5Rdereference(gid,H5R_OBJECT,&(ref[2]));
H5Dread(rid,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,rdata);
H5Dclose(rid);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
if (rdata[datasize-1]!=datasize-1)
{
throw "Wrong Size";
}
}
void readComposite()
{
hid_t fid, gid, sid, did; /* file ID */
hsize_t start[1];
hsize_t count[1];
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
gid = H5Gopen(fid,"Composite",H5P_DEFAULT);
did = H5Dopen(gid,"Composite",H5P_DEFAULT);
sid=H5Dget_space(did);
start[0]=3;
count[0]=1;
H5Sselect_hyperslab(sid,H5S_SELECT_SET,start,NULL,count,NULL);
hid_t tid = H5Dget_type(did);
hsize_t nels = 1;
hid_t mid = H5Screate_simple(1, &nels, &nels);
H5Dread(did,tid,mid,sid,H5P_DEFAULT,rdata);
H5Sclose(mid);
H5Tclose(tid);
H5Sclose(sid);
H5Dclose(did);
H5Gclose(gid);
H5Fclose(fid);
if (rdata[datasize-1]!=datasize-1)
{
throw "Wrong Size";
}
}
int main (void)
{
hid_t fid; /* file ID */
datasize=1000000;
data=new int[datasize];
rdata=new int[datasize];
int i;
for(i=0;i<datasize;i++)
{
data[i]=i;
}
std::string name;
BEGINPROFILER
for(i=0;i<30;i++)
{
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
H5Fclose(fid);
name = "createHyperslab1";
BEGINPROFILERBLOCK(name)
createHyperslab1();
ENDPROFILERBLOCK(name);
/* name = "createHyperslab2";
BEGINPROFILERBLOCK(name)
createHyperslab2();
ENDPROFILERBLOCK(name);*/
name = "createSeparate";
BEGINPROFILERBLOCK(name)
createSeparate();
ENDPROFILERBLOCK(name);
name = "createReferences";
BEGINPROFILERBLOCK(name)
createReferences();
ENDPROFILERBLOCK(name);
name = "createComposite";
BEGINPROFILERBLOCK(name)
createComposite();
ENDPROFILERBLOCK(name);
// write
name = "writeHyperslab1";
BEGINPROFILERBLOCK(name)
writeHyperslab1();
ENDPROFILERBLOCK(name);
/*name = "writeHyperslab2";
BEGINPROFILERBLOCK(name)
writeHyperslab2();
ENDPROFILERBLOCK(name);*/
name = "writeSeparate";
BEGINPROFILERBLOCK(name)
writeSeparate();
ENDPROFILERBLOCK(name);
name = "writeReferences";
BEGINPROFILERBLOCK(name)
writeReferences();
ENDPROFILERBLOCK(name);
name = "writeComposite";
BEGINPROFILERBLOCK(name)
writeComposite();
ENDPROFILERBLOCK(name);
//read
name = "readHyperslab1";
BEGINPROFILERBLOCK(name)
readHyperslab1();
ENDPROFILERBLOCK(name);
/*name = "readHyperslab2";
BEGINPROFILERBLOCK(name)
readHyperslab2();
ENDPROFILERBLOCK(name);*/
name = "readSeparate";
BEGINPROFILERBLOCK(name)
readSeparate();
ENDPROFILERBLOCK(name);
name = "readReferences";
BEGINPROFILERBLOCK(name)
readReferences();
ENDPROFILERBLOCK(name);
name = "readComposite";
BEGINPROFILERBLOCK(name)
readComposite();
ENDPROFILERBLOCK(name);
ENDPROFILERCYCLE
}
ENDPROFILER
delete [] data;
delete [] rdata;
}
HDF5_performance_layers.xls (77 KB)
