Hello there,
It has come to our attention that H5DWrite() can cause memory to grow
continuously. I have been reading some discussion with the HDF5 feature
of "free lists", but do not understand why the memory keeps growing
without stop.
I also have tried HDF5 library API H5garbage_collect() without any
success.
The HDF5 version I am using is HDF5-1.6.5 and the platform Linux 2.6.20.
The source code of the test and the test results of Google performance
tool are attached below.
The memory usage can be crucial for my process. Is there a workaround
(without affect the write performance) for the issue? Do I have missed
anything in the test?
Thanks in advance,
Zane
1. Simple Test Code -- modified from HDF5 example code, h5_write.cpp
#include "hdf5.h"
#include <stdlib.h>
#include <stdio.h>
int
main (int argc, char *argv[])
{
hid_t file; /* handles */
hid_t dataspace = -1;
hid_t dataset = -1;
hid_t filespace = -1;
hid_t cparms = -1;
hsize_t dims [1] = {1};
hsize_t maxdims[1] = {H5S_UNLIMITED};
hsize_t chunk_dims[1] ={2048};
hsize_t size[1] = {1};
hsize_t offset[1] = {1};
int data[1] = { 0 };
int fillvalue = 0;
int counter = 1000000;
if (argc > 1)
{
counter = atoi(argv[1]);
}
/*
* Create the data space with unlimited dimensions.
*/
dataspace = H5Screate_simple(1, dims, maxdims);
/*
* Create a new file. If file exists its contents will be
overwritten.
*/
file = H5Fcreate("h5_write_test.h5", H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT);
/*
* Modify dataset creation properties, i.e. enable chunking.
*/
cparms = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk( cparms, 1, chunk_dims);
H5Pset_fill_value (cparms, H5T_NATIVE_INT, &fillvalue );
/*
* Create a new dataset within the file using cparms
* creation properties.
*/
dataset = H5Dcreate(file, "data", H5T_NATIVE_INT, dataspace,
cparms);
/*
* Extend the dataset in a loop
*/
for (int i = 1; i < counter; ++i)
{
offset[0] = size[0];
data [0] = i;
size[0] = offset[0] + dims[0];
/*
* Extend the dataset by 1
*/
H5Dextend (dataset, size);
/*
* Select a hyperslab.
*/
if (filespace > 0)
{
H5Sclose(filespace);
}
filespace = H5Dget_space (dataset);
/*
* Select a hyperslab.
*/
H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, dims,
NULL);
/*
* Write the data to the hyperslab.
*/
H5Dwrite(dataset, H5T_NATIVE_INT, dataspace, filespace,
H5P_DEFAULT, data);
}
/*
* Close/release resources.
*/
H5Dclose(dataset);
H5Sclose(dataspace);
H5Sclose(filespace);
H5Pclose(cparms);
H5Fclose(file);
return 0;
}
2. Test results with Google performance tool:
$ env HEAPPROFILE=/tmp/test_performance.hprof
HEAP_PROFILE_INUSE_INTERVAL=102400
LD_PRELOAD=/software/thirdparty/google-perftools/1.5/lib/libtcmalloc.so
build/exfeed/test/h5_write 10000000000
Starting tracking the heap
Dumping heap profile to /tmp/test_performance.hprof.0001.heap (0 MB
currently in use)
Dumping heap profile to /tmp/test_performance.hprof.0002.heap (0 MB
currently in use)
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currently in use)
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currently in use)
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currently in use)
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currently in use)
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currently in use)
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currently in use)
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currently in use)
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