Hey Peter,
Thanks for the response. I'm pretty sure its not a memory leak (one that's
noticeable in the process) that is causing the problem. The windows process
seems to be fine. I'm not sure, but I think it has something to do with the
gzip compression. If I turn compression off I can write a very very large
file 166GB but of course it has a lot less data than with compression.
However, it seems when I set compression to anything between 1 and 9, there
is a problem.
I'll try compiling the latest code and try again.
Thanks, Aaron
-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org]
On Behalf Of Peter Cao
Sent: Friday, November 06, 2009 12:38 PM
To: hdf-forum@hdfgroup.org
Subject: Re: [Hdf-forum] Exception when writing to large files on windows
Aaron,
I don't know exact the cause of the problem. We fixed some other
potential memory leaks.
If you are building hdf-java from the source, you can try our latest
source code to see if it fix
your problem (run svn co
http://svn.hdfgroup.uiuc.edu/hdf-java/branches/hdf-java-2.6/\).
There is a small memory leak, which we are still trying to figure out.
You have to run over night
to see the noticeable memory builds-up.
Thanks
--pc
Aaron Kagawa wrote:
Greetings,
In earlier emails I asked about a memory leak with our code. That has
been resolved; thanks for your responses. My next email asked about
File Families. The reason behind that was because we are seeing an
exception when running a test in windows that writes to a file that
eventually becomes very large without file families.
Here is the error:
...
********************************
time: 37610000
9949259.0 values a second
currentDims: 376100010000, ensuring dataset size: 376100010000,
startDims: 376100000000
usedMemory: 2.6641311645507812, totalMemory: 32.75, freeMemory:
30.08586883544922, maxMemory: 493.0625
37610000, CommittedVirtualMemorySize: 99.8828125,
getTotalPhysicalMemorySize: 2047.9999990463257,
getFreePhysicalMemorySize1477.40625
2 objects still open:
id: 16777216, null, H5I_FILE
id: 87941649, null, H5I_DATASET
ncsa.hdf.hdf5lib.exceptions.HDF5InternalErrorException: System error
message
HDF5-DIAG: Error detected in HDF5 (1.8.2) thread 0:
#000: ..\..\..\src\H5Dio.c line 267 in H5Dwrite(): can't write data
major: Dataset
minor: Write failed
#001: ..\..\..\src\H5Dio.c line 582 in H5D_write(): can't write data
major: Dataset
minor: Write failed
#002: ..\..\..\src\H5Dchunk.c line 1641 in H5D_chunk_write(): unable to
read raw data chunk
major: Low-level I/O
minor: Read failed
#003: ..\..\..\src\H5Dchunk.c line 2508 in H5D_chunk_lock(): unable to
preempt chunk(s) from cache
major: Low-level I/O
minor: Unable to initialize object
#004: ..\..\..\src\H5Dchunk.c line 2317 in H5D_chunk_cache_prune():
unable to preempt one or more raw data cache entry
major: Low-level I/O
minor: Unable to flush data from cache
#005: ..\..\..\src\H5Dchunk.c line 2183 in H5D_chunk_cache_evict():
cannot flush indexed storage buffer
major: Low-level I/O
minor: Write failed
#006: ..\..\..\src\H5Dchunk.c line 2111 in H5D_chunk_flush_entry():
unable to write raw data to file
major: Low-level I/O
minor: Write failed
#007: ..\..\..\src\H5Fio.c line 159 in H5F_block_write(): file write
failed
major: Low-level I/O
minor: Write failed
#008: ..\..\..\src\H5FDint.c line 185 in H5FD_write(): driver write
request failed
major: Virtual File Layer
minor: Write failed
#009: ..\..\..\src\H5FDwindows.c line 921 in H5FD_windows_write(): file
write failed
major: Low-level I/O
minor: Write failed
#010: ..\..\..\src\H5FDwindows.c line 921 in H5FD_windows_write():
Invalid argument
major: Internal error (too specific to document in detail)
minor: System error message
ncsa.hdf.hdf5lib.exceptions.HDF5InternalErrorException: System error
message
at ncsa.hdf.hdf5lib.H5.H5Dwrite_long(Native Method)
at ncsa.hdf.hdf5lib.H5.H5Dwrite(H5.java:1031)
at h5.TestHDF5WriteLowLevel.main(TestHDF5WriteLowLevel.java:123)
The error occurs under these conditions:
* run TestHDF5WriteLowLevel (see the complete code below) test
with an NUMBER_OF_LOOPS set to 100000000000
* run the test on Windows XP 32 bit, Windows XP 64 bit, or Windows
Vista 64 bit. (in all cases we use 32 bit java since the java
hdf5 release was only for 32 bit)
* when the file size of the hdf5 file gets to be over 22 GB. This
number varies over about 6 runs, but its always over 20GB and
under about 26GB. (getting to a file size of 22+ GB takes a
while. the test usually runs for over 5 hours).
* when the "startDims" print out is around 376100000000 (376
billion). This number varies but is usually around 350billion to
under 400 billion values.
Some additional notes:
* we have never seen this fail when running on linux. On linux
we've reached numbers like 80+ gigs and over a trillion values.
* we've created another TestHDF5WriteLowLevel test to use file
families. With File Family (setting the limit to 1GB) running on
windows we are currently on over 1 trillion values and 64GB. So
the file families seems to work for windows. It appears that the
object layer does not support file families. Therefore, at this
point in time we cannot integrate this into our application,
because we rely too heavily on the Object layer. Is there a plan
to support file family in the upcoming release?
We are targeting Windows as our primarily OS, so this problem is a
major problem for us. A couple of questions that I'm hoping that the
community can help us with:
* Is this a know problem for windows? Or are we doing something wrong?
* Do others see this problem occurring?
* Can others duplicate our problem?
thanks, Aaron Kagawa
package h5;
import java.io.File;
import java.util.Arrays;
import sun.management.ManagementFactory;
import com.sun.management.OperatingSystemMXBean;
import ncsa.hdf.hdf5lib.H5;
import ncsa.hdf.hdf5lib.HDF5Constants;
/**
* Implements a simple test writes to a dataset in a loop. This test is
meant to test the memory
* used in a windows process. it seems that the windows process continues
to grow, while the
* java heap space stays constant.
*/
public class TestHDF5WriteLowLevel {
private static final int INSERT_SIZE = 10000;
private static final long NUMBER_OF_LOOPS = 200;
private static final int PRINTLN_INTERVAL = 10000;
private static final double MB = 1024.0 * 1024.0;
public static void main(String args) {
long numberOfLoops = NUMBER_OF_LOOPS;
int printlnInterval = PRINTLN_INTERVAL;
if (args.length == 1) {
numberOfLoops = Long.parseLong(args[0]);
}
if (args.length == 2) {
printlnInterval = Integer.parseInt(args[0]);
}
System.out.println("INSERT_SIZE: " + INSERT_SIZE);
System.out.println("TIMES: " + numberOfLoops);
try {
// create a new file
File javaFile = new File("TestHDF5Write-" +
System.currentTimeMillis() + ".h5");
int fapl = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS);
H5.H5Pset_fclose_degree(fapl, HDF5Constants.H5F_CLOSE_STRONG);
int fileId = H5.H5Fcreate (javaFile.getAbsolutePath(),
HDF5Constants.H5F_ACC_TRUNC,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
// create group (there is no good reason for us to have a group
here)
int groupId = H5.H5Gcreate (fileId, "/group", 0);
// create data set
long chunkSize = new long { 3000 };
int gzipCompressionLevel = 2;
int dataspaceId = H5.H5Screate_simple(1, new long { INSERT_SIZE },
new long { HDF5Constants.H5S_UNLIMITED });
int pid = H5.H5Pcreate(HDF5Constants.H5P_DATASET_CREATE);
H5.H5Pset_layout(pid, HDF5Constants.H5D_CHUNKED);
H5.H5Pset_chunk(pid, 1, chunkSize);
H5.H5Pset_deflate(pid, gzipCompressionLevel);
int dataSetId = H5.H5Dcreate(groupId, "/group/Dataset1",
HDF5Constants.H5T_NATIVE_LLONG, dataspaceId, pid);
long newDataArray = new long[INSERT_SIZE];
Arrays.fill(newDataArray, System.currentTimeMillis());
H5.H5Dwrite(dataSetId, HDF5Constants.H5T_NATIVE_LLONG,
HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT,
newDataArray);
H5.H5Dclose(dataSetId);
H5.H5Gclose(groupId);
long startTime = 0;
long endTime;
long duration;
OperatingSystemMXBean osm;
for (long loopIndex = 0; loopIndex < numberOfLoops; loopIndex++) {
if (startTime == 0) {
startTime = System.currentTimeMillis();
}
// figure out how big the current dims are
dataSetId = H5.H5Dopen(fileId, "/group/Dataset1");
int datasetDataspace = H5.H5Dget_space(dataSetId); //aka
file_space_id
long currentDims = new long[1];
H5.H5Sget_simple_extent_dims(datasetDataspace, currentDims, null);
H5.H5Sclose(datasetDataspace);
// extend the data set
H5.H5Dextend(dataSetId, new long { currentDims[0] +
INSERT_SIZE});
// select the file space
int filespace = H5.H5Dget_space(dataSetId); //aka file_space_id
H5.H5Sselect_hyperslab(filespace, HDF5Constants.H5S_SELECT_SET,
new long { currentDims[0] },
new long {1}, new long { INSERT_SIZE }, null);
// make the data to add
newDataArray = new long[INSERT_SIZE];
Arrays.fill(newDataArray, System.currentTimeMillis());
if (loopIndex % printlnInterval == 0) {
System.out.println("********************************");
System.out.println("time: " + loopIndex);
endTime = System.currentTimeMillis();
duration = endTime - startTime;
if (duration == 0) {
duration = 1;
}
System.out.println("\t" + (printlnInterval * INSERT_SIZE /
((float) duration / 1000)) + " values a second");
startTime = endTime;
System.out.println("\tcurrentDims: " + currentDims[0]
+ ", ensuring dataset size: " + ((loopIndex +1) *
INSERT_SIZE)
+ ", startDims: " + (loopIndex * INSERT_SIZE));
System.out.println("\t"
+ "usedMemory: " + ((Runtime.getRuntime().totalMemory() -
Runtime.getRuntime().freeMemory()) / MB)
+ ", totalMemory: " + (Runtime.getRuntime().totalMemory() /
MB)
+ ", freeMemory: " + (Runtime.getRuntime().freeMemory() /
MB)
+ ", maxMemory: " + (Runtime.getRuntime().maxMemory() /
MB));
osm = (OperatingSystemMXBean)
ManagementFactory.getOperatingSystemMXBean();
System.out.println("\t" + loopIndex
+ ", CommittedVirtualMemorySize: " +
(osm.getCommittedVirtualMemorySize()) / MB
+ ", getTotalPhysicalMemorySize: " +
osm.getTotalPhysicalMemorySize() / MB
+ ", getFreePhysicalMemorySize" +
osm.getFreePhysicalMemorySize() / MB);
printOpenHDF5Objects(fileId);
}
// write the data
int memoryDataspace = H5.H5Screate_simple(1, new long {
INSERT_SIZE }, null); //aka mem_space_id
H5.H5Dwrite(dataSetId, HDF5Constants.H5T_NATIVE_LLONG,
memoryDataspace, filespace, HDF5Constants.H5P_DEFAULT, newDataArray);
H5.H5Sclose(memoryDataspace);
H5.H5Sclose(filespace);
H5.H5Fflush(dataSetId, HDF5Constants.H5F_SCOPE_LOCAL);
H5.H5Dclose(dataSetId);
}
H5.H5Fflush(fileId, HDF5Constants.H5F_SCOPE_GLOBAL);
H5.H5Fclose(fileId);
}
catch (Exception e) {
e.printStackTrace();
}
System.exit(0);
}
/** print the open hdf5 objects associated with the hdf5 file */
public static void printOpenHDF5Objects(int fid) {
try {
int count;
count = H5.H5Fget_obj_count(fid, HDF5Constants.H5F_OBJ_ALL);
int objs = new int[count];
H5.H5Fget_obj_ids(fid, HDF5Constants.H5F_OBJ_ALL, count, objs);
String name = new String[1];
System.out.println("\t" + count + " objects still open:");
for (int i = 0; i < count; i++) {
int type = H5.H5Iget_type(objs[i]);
System.out.print("\t\tid: " + objs[i] + ", " + name[0]);
if (HDF5Constants.H5I_DATASET == type) {
System.out.println(", H5I_DATASET");
}
else if (HDF5Constants.H5I_FILE == type) {
System.out.println(", H5I_FILE");
}
else if (HDF5Constants.H5I_GROUP == type) {
System.out.println(", H5I_GROUP");
}
else if (HDF5Constants.H5I_DATATYPE == type) {
System.out.println(", H5I_DATATYPE");
}
else if (HDF5Constants.H5I_ATTR == type) {
System.out.println(", H5I_ATTR");
}
else {
System.out.println(", UNKNOWN " + type);
}
}
}
catch (Exception e) {
e.printStackTrace();
}
}
}
------------------------------------------------------------------------
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
