Hi Quincey,
I have tried the same code against HDF5-1.8.2 and got the same results.
Thanks,
Zane
Hi Zane,
On May 10, 2010, at 3:24 AM, Zhengying Wang wrote:
> 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?
That is a very old release, could you update to the latest 1.8.x
release? Your code looks reasonable...
Quincey
> 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)
> Dumping heap profile to /tmp/test_performance.hprof.0003.heap (0 MB
> currently in use)
> Dumping heap profile to /tmp/test_performance.hprof.0004.heap (0 MB
> currently in use)
> Dumping heap profile to /tmp/test_performance.hprof.0005.heap (0 MB
> currently in use)
> Dumping heap profile to /tmp/test_performance.hprof.0006.heap (0 MB
> currently in use)
> Dumping heap profile to /tmp/test_performance.hprof.0007.heap (0 MB
> currently in use)
> Dumping heap profile to /tmp/test_performance.hprof.0008.heap (0 MB
> currently in use)
> Dumping heap profile to /tmp/test_performance.hprof.0009.heap (0 MB
> currently in use)
> Dumping heap profile to /tmp/test_performance.hprof.0010.heap (1 MB
> currently in use)
> Dumping heap profile to /tmp/test_performance.hprof.0011.heap (1 MB
> currently in use)
> Dumping heap profile to /tmp/test_performance.hprof.0012.heap (1 MB
> currently in use)
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> currently in use)
> Dumping heap profile to /tmp/test_performance.hprof.0014.heap (1 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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> 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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> 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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> currently in use)
> Dumping heap profile to /tmp/test_performance.hprof.0461.heap (48 MB
> currently in use)
>
> _______________________________________________
> 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
End of Hdf-forum Digest, Vol 11, Issue 8
****************************************
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
