|
|
# GenericIO
|
|
|
|
|
|
GenericIO is a write-optimized library for writing self-describing scientific data files on large-scale parallel file systems.
|
|
|
|
|
|
## Reference
|
|
|
|
|
|
Habib, et al., HACC: Simulating Future Sky Surveys on State-of-the-Art Supercomputing Architectures, New Astronomy, 2015
|
|
|
(http://arxiv.org/abs/1410.2805).
|
|
|
|
|
|
## Source Code
|
|
|
|
|
|
A source archive is available here: [genericio-20190417.tar.gz](http://www.mcs.anl.gov/~turam/genericio/genericio-20190417.tar.gz) (previous releases: [genericio-20170925.tar.gz](http://www.alcf.anl.gov/~hfinkel/genericio/genericio-20170925.tar.gz) [genericio-20160829.tar.gz](http://www.alcf.anl.gov/~hfinkel/genericio/genericio-20160829.tar.gz) [genericio-20160412.tar.gz](http://www.alcf.anl.gov/~hfinkel/genericio/genericio-20150608.tar.gz) [genericio-20150608.tar.gz](http://www.alcf.anl.gov/~hfinkel/genericio/genericio-20150608.tar.gz)), or from git:
|
|
|
|
|
|
```bash
|
|
|
git clone http://git.mcs.anl.gov/genericio.git
|
|
|
```
|
|
|
## Output file partitions (subfiles)
|
|
|
|
|
|
If you're running on an IBM BG/Q supercomputer, then the number of subfiles (partitions) chosen is based on the I/O nodes in an automatic way. Otherwise, by default, the GenericIO library picks the number of subfiles based on a fairly-naive hostname-based hashing scheme. This works reasonably-well on small clusters, but not on larger systems. On a larger system, you might want to set these environmental variables:
|
|
|
|
|
|
```bash
|
|
|
GENERICIO_PARTITIONS_USE_NAME=0
|
|
|
GENERICIO_RANK_PARTITIONS=256
|
|
|
```
|
|
|
|
|
|
Where the number of partitions (256 above) determines the number of subfiles used. If you're using a Lustre file system, for example, an optimal number of files is:
|
|
|
|
|
|
```
|
|
|
# of files * stripe count ~ # OSTs
|
|
|
```
|
|
|
|
|
|
On Titan, for example, there are 1008 OSTs, and a default stripe count of 4, so we use approximately 256 files.
|
|
|
|
|
|
## Benchmarks
|
|
|
|
|
|
Once you build the library and associated programs (using make), you can run, for example:
|
|
|
|
|
|
```bash
|
|
|
$ mpirun -np 8 ./mpi/GenericIOBenchmarkWrite /tmp/out.gio 123456 2
|
|
|
Wrote 9 variables to /tmp/out (4691036 bytes) in 0.2361s: 18.9484 MB/s
|
|
|
```
|
|
|
|
|
|
```bash
|
|
|
$ mpirun -np 8 ./mpi/GenericIOBenchmarkRead /tmp/out.gio
|
|
|
Read 9 variables from /tmp/out (4688028 bytes) in 0.223067s: 20.0426 MB/s [excluding header read]
|
|
|
```
|
|
|
|
|
|
The read benchmark always reads all of the input data. The output benchmark takes two numerical parameters, one if the number of data rows to write, and the second is a random seed (which slightly perturbs the per-rank output sizes, but not by much). Each row is 36 bytes for these benchmarks.
|
|
|
|
|
|
The write benchmark can be passed the -c parameter to enable output compression. Both benchmarks take an optional -a parameter to request that homogeneous aggregates (i.e. "float4") be used instead of using separate arrays for each position/velocity component.
|
|
|
|
|
|
## Python module
|
|
|
|
|
|
The repository includes a genericio Python module that can read genericio-formatted files and return numpy arrays. This is included in the standard build. To use it, once you've built genericio, you can read genericio data as follows:
|
|
|
|
|
|
```bash
|
|
|
$ export PYTHONPATH=${GENERICIO_DIR}/python
|
|
|
$ python
|
|
|
>>> import genericio
|
|
|
>>> genericio.gio_inspect('m000-99.fofproperties')
|
|
|
Number of Elements: 1691
|
|
|
[data type] Variable name
|
|
|
---------------------------------------------
|
|
|
[i 32] fof_halo_count
|
|
|
[i 64] fof_halo_tag
|
|
|
[f 32] fof_halo_mass
|
|
|
[f 32] fof_halo_mean_x
|
|
|
[f 32] fof_halo_mean_y
|
|
|
[f 32] fof_halo_mean_z
|
|
|
[f 32] fof_halo_mean_vx
|
|
|
[f 32] fof_halo_mean_vy
|
|
|
[f 32] fof_halo_mean_vz
|
|
|
[f 32] fof_halo_vel_disp
|
|
|
|
|
|
(i=integer,f=floating point, number bits size)
|
|
|
>>> genericio.gio_read('m000-99.fofproperties','fof_halo_mass')
|
|
|
array([[ 4.58575588e+13],
|
|
|
[ 5.00464689e+13],
|
|
|
[ 5.07078771e+12],
|
|
|
...,
|
|
|
[ 1.35221006e+13],
|
|
|
[ 5.29125710e+12],
|
|
|
[ 7.12849857e+12]], dtype=float32)
|
|
|
|
|
|
``` |
|
|
\ No newline at end of file |