Update, Bug Fix, and Feature Add
Description:
- Updated how AC_{ENABLE,WITH} help messages were being generated.
Autoconf now gives you an AC_HELP_STRING macro to use to create
them.
- Fixed the problem with Linux LFS on RedHat 7.3 machines. It wasn't
finding getdents64(), so we can't rely on that being present
anymore...
- Added GPFS detection and setting.
- Updated how compression is specified. It's no longer necessary to
test for HAVE_ZLIB_H, HAVE_LIBZ, and HAVE_COMPRESS2. The one macro
{H5_}HAVE_COMPRESSION takes care of all of these.
Solution:
Changed the check for Linux LFS from looking for getdents() to
looking at the version number of the kernel (using the uname -r
command). You can still override with the --enable-linux-lfs switch
if you really believe that your <2.4 kernel has LFS support.
Platforms tested:
Linux (2.2 and 2.4)
New Feature
Description:
Added interleaved block pattern to MPI and HDF5 access methods. Also,
changed the blocks to just use the same size as the regular blocks for I/O,
instead of a separate block size.
Platforms tested:
IRIX64 6.5 (modi4) w/parallel
Feature Add
Description:
Added support for testing only the "write" operations. Use the "-w"
or "--write-only" flags for this.
Platforms tested:
Linux (parallel) & Modi4 (parallel)
Code cleanup and new feature.
Description:
Cleaned out some old debug print statments.
Added option -B for interleaved I/O block size.
(Just parsing and sanity check is done. Real I/O implementation
is not done yet.)
Platforms tested:
eirene(pp)
Feature Addition
Description:
Added feature which prints out the parameters and the MPI_Info object
for a run for each process.
Added some functions for the GPFS system. They are ifdef'ed out right
now (well, they need to ahve the non-existant H5_HAVE_GPFS macro set)
and aren't in use just yet. But the stub functions are there.
Platforms tested:
Linux
Folded the changes made in v1.4 into v1.5.
print library version information in help page too.
Specify the nofill feature supported in v1.5 only.
Print the values of the KB, MB and GB in case a user wants to see them.
Setup a macro, H5_HAVE_NOFILL, to indicate if Dataset no fill feature
is supported. If not, --no-fill is an invalid option.
Platforms tested:
modi4
Update
Description:
Updating the source for the PIO performance tests with the current
code that's in the V1.4 branch. It includes the newest command-line
parameters.
Platforms tested:
Linux-pp
Feature
Description:
moved the routines of setting up and dumping MPI-info object to
test library so that it is avaiable for all tests too.
Platforms tested:
modi4(pp), eirene (serial)
Bug fix
Description:
Was not able to handle data size (file size) larger than 32bits.
Was using long, which is only 4 bytes big in SP, thus overflowing
into negative when trying to address 2GB or larger.
Solution:
Changed those variables involved in file size/offset calculation
to type off_t. (If a certain system/compiler has off_t defined
as 4 bytes, it can't write to file size larger than 2GB anyway.)
Note that the lseek of SP with -D_LARGE_FILE still fails for
offset larger than 2GB (works for 2GB). That has to be fixed
soon.
Platforms tested:
burrwhite (linux 2.4) and modi4 parallel.
Bug fix, feature
Description:
Added code to time pure MPI_File_write_xxx and read_xxx routines.
Moved the setting of the timer_g to when timer is created (new)
and destroyed.
Platforms tested:
modi4pp
Modification
Description:
Put some of the variables into the global space so that random
functions can access them. (The output and timer variables which
point to the output file and timer resp.)
Placed the debug level 4 prints into the timer module so that it's
easier to automatically put timer start/stop printfs for new timers
which are created.
Added timers for MPI Time calls (called HDF5_MPI_WRITE and
HDF5_MPI_READ).
Platforms tested:
Linux
Bug Fix
Description:
There was a duplicate declaration of print_indent() in the header and
in the source files.
Solution:
Removed the public declaration and made the function static again.
Platforms tested:
Arabica
Bug fix
Description:
The symbol "RAW" is already defined in some ioctl.h files.
Changed it to RAWIO.
Platforms tested:
Tflops.
(I am commiting this from TFLOPS. Will check it out immediate
to test on local machines.)
Code cleanup
Description:
Platform dependent code related to the struct stat and fstat
calls polluted source codes. Hard to maintain.
Solution:
Platform dependent code are moved to H5private.h and then internal
code can #include H5private.h. Repeat those macro definition for
the stdio and multi drivers since they area examples for writing
a virtual file driver. They must not use any internal code.
Platforms tested:
eirene (parallel), modi4 (serial including gass driver.)
Bug Fix
Description:
So, for Raw I/O in parallel, if you open a file with truncation by
multiple processes, it looks as if one process could open the file
and start writing to it while another process also opens the file
with truncation, thus wiping out all of the stuff the first process
wrote to the file.
This is bad.
Also added some garbage collection to the pio_perf routine to reclaim
the space taken by some of the tables.
Solution:
Placed an MPI_Barrier() statement after the Raw open()/create() call
so that all processes are synced up before they start writing to the
file.
Added free() calls to the tables which weren't being free'd.
Platforms tested:
Linux-pp (eirene)
Purpose:
Feature Fix
Description:
Added timer from open to close for write. Changed reporting of time
for write and read to only measure the actual read/write instead of
the open/close as well...
Platforms tested:
Linux(pp)
Purpose:
Feature Fix
Description:
Changed so the "pio_perf" module handles creating and destroying the
MPI Comm. Worked it so we get the minimum, maximum, and average times
over a set of iterations.
Solution:
Lots. Had to pull the MPI Comm code from the "pio_engine" module and
place it in the "pio_perf" module. Then worked on a way to have all
processes send their time output to process 0, who collects it and
gives back the min, max, and avg times for the iterations.
Platforms tested:
Linux. Doesn't work if you use more than 1 processor...*hrmph*
Purpose:
Feature Changes
Description:
Okay, I needed to add in more parameters so that the user can modify
how things are supposed to work with the PIO programs. Also needed
to change the algorithm a bit to make these work. And needed to add
in timing for the READ option.
Solution:
Added the above things. The parameters took a major rewrite of the
command-line parsing stuff. Here's the usage statement:
usage: pio_perf [OPTIONS]
OPTIONS
-h, --help Print a usage message and exit
-d N, --num-dsets=N Number of datasets per file [default:1]
-f S, --file-size=S Size of a single file [default: 64M]
-F N, --num-files=N Number of files [default: 1]
-H, --hdf5 Run HDF5 performance test
-i, --num-iterations Number of iterations to perform [default: 1]
-m, --mpiio Run MPI/IO performance test
-o F, --output=F Output raw data into file F [default: none]
-P N, --max-num-processes=N Maximum number of processes to use [default: 1]
-p N, --min-num-processes=N Minimum number of processes to use [default: 1]
-r, --raw Run raw (UNIX) performance test
-X S, --max-xfer-size=S Maximum transfer buffer size [default: 1M]
-x S, --min-xfer-size=S Minimum transfer buffer size [default: 1K]
F - is a filename.
N - is an integer >=0.
S - is a size specifier, an integer >=0 followed by a size indicator:
K - Kilobyte
M - Megabyte
G - Gigabyte
Example: 37M = 37 Megabytes
Platforms tested:
Linux, but not fully finished...
Added nfiles and ndsets parameters checking.
Removed iteration variable since iterations would be done
in Control routine.
Platforms tested:
Eirene(pp) and modi4(pp)
Bug fix (or more like feature)
Description:
MPI_File_open does not truncate the filesize if file already exists.
This created confusion during debugging as what the real file size
is. It also interfere the real write bandwidth since the times
required to allocate new disk-space vanishes for subsequent writes
that are for offset shorter than previous file sizes.
Added a MPI_File_set_size to reset the file size to 0 for every new
file.
Another bug is that the 'remove()' call may not work for MPIO/PHDF5
files. (e.g., filename may have some MPI prefix like "pfs:filename").
Replaced "remove" with MPI_File_delete for those cases.
Platforms tested:
modi4(pp) and eirene (pp)
bug fix, new feature
Description:
Added HDF5 write in do_write.
Added a complete do_read.
Still need timing code for the read part.
Platforms tested:
eirene (pp), modi4(pp).
Did not test serial since all changes were done in parallel area.
Bug fixes, new features
Description:
There was a coding error in handling file open flags. Changed it
to use &.
Added do_cleanup to cleanup temporary test files but only if
$HDF5_NOCLEANUP is not set. This is consistent with other test programs.
Added logic so that each process is writing its own slabs of data only.
Moved the number of process, rank of process and the communicator used
for PIO run to be global variables. Makes the coding easier. (but this
is not thread-safe.)
Platforms tested:
modi4(pp) and eirene(pp).
Purpose:
Bug Fix
Description:
Fixed so that it will display the correct timing data. It will also
write to the correct file (which it wasn't before).
Solution:
Put the code in for displaying the time. Had to change the way I was
passing an object to the pio_fopen() function from just being a
structure to being a pointer so that the changes could be propagated
back.
Platforms tested:
Linux
Purpose:
Small Fixes
Description:
After conversation with Albert, here are some small fixes for the
performance stuff. Not too significant. Though, we did add the
"buffer size" as a parameter I pass to the engine.
Purpose:
Feature Fix
Description:
Added code so that it measures the time it takes to do I/O and return
that to the calling function.
This code doesn't quite work yet. There is something wrong with the
MPI code in the "pio_engine.c" file...I don't know what's up with
it...
Platforms tested:
Linux
Bug fix
Description:
Cleaned up obvious syntax errors to make it to compile.
Changed unnecessarily unsigned variables to signed to avoid
messy compiler warnings.
Platforms tested:
eirene (parallel)
Purpose:
Code Cleanup and Feature Add
Description:
Finally checking in the changes I made to the performance code. It
just modularizes it a bit more and performs some more checks, etc. I
also renamed the timer functions to be more inline with how other
things are named here...
Platforms tested:
Linux
Purpose:
bug Fix
Description:
Changed the code so that if parallel stuff isn't enabled, then we
don't compile the parallel code.
Solution:
Cleaned up the code and put #ifdef's around it checking for parallel
flags.
Platforms tested:
Linux
New addition
Description:
Initial version of the Parallel I/O performance measurement program.
Not fully implemented yet but checking them in before I may destroy
them by accident.
Don't run this in small file system (like AFS or eirene) since it
generates gigabytes test files.
Platforms tested:
modi4 64bits. It compiled and ran but took a long time because
the current test parametes are too "wild".
