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fix markdown typesetting
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markcmiller86 authored Oct 2, 2018
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50 changes: 25 additions & 25 deletions INSTALLING.md
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Expand Up @@ -21,44 +21,44 @@ just run the command './macsio', it will do something but probably
not what you want. Here are some example command-lines. . .

- To run with Multiple Independent File (MIF) mode to 8 HDF5 files. . .
```shell
mpirun -np 93 macsio --interface hdf5 --parallel_file_mode MIF 8
```
```shell
mpirun -np 93 macsio --interface hdf5 --parallel_file_mode MIF 8
```
- Same thing to but a Single Shared File (SIF) mode to 1 HDF5 file. . .
```shell
mpirun -np 93 macsio --interface hdf5 --parallel_file_mode SIF 1
```
```shell
mpirun -np 93 macsio --interface hdf5 --parallel_file_mode SIF 1
```
- Default per-proc request size is 80,0000 bytes (10K doubles). To use
a different request size, use --part_size . . .
```shell
mpirun -np 128 macsio --interface hdf5 --parallel_file_mode MIF 8 --part_size 10M
```
'M' means either decimal Megabytes (Mb) or binary Mibibytes (Mi)
depending on setting for --units_prefix_system. Default is binary.
```shell
mpirun -np 128 macsio --interface hdf5 --parallel_file_mode MIF 8 --part_size 10M
```
'M' means either decimal Megabytes (Mb) or binary Mibibytes (Mi)
depending on setting for --units_prefix_system. Default is binary.
- Default #parts/proc is 2, which is common for applications that support
'domain overload' workflows. Change with --avg_num_parts <float> arg
```shell
mpirun -np 128 macsio --interface hdf5 --parallel_file_mode MIF 8 --avg_num_parts 2.5
```
```shell
mpirun -np 128 macsio --interface hdf5 --parallel_file_mode MIF 8 --avg_num_parts 2.5
```
means that 50% of procs have 2 parts and 50 % of procs have 3 parts.
- Default number of dumps is 10, change with --num_dumps argument. . .
```shell
mpirun -np 128 macsio --interface hdf5 --parallel_file_mode MIF 8 --num_dumps 2
```
```shell
mpirun -np 128 macsio --interface hdf5 --parallel_file_mode MIF 8 --num_dumps 2
```
- Set various debugging levels (1,2 or 3, more info in logs with higher numbers)
```shell
mpirun -np 128 macsio --interface hdf5 --parallel_file_mode MIF 8 --debug_level 2
```
```shell
mpirun -np 128 macsio --interface hdf5 --parallel_file_mode MIF 8 --debug_level 2
```
Note: debugging can degrade performance and skew timing results
- Getting more help. . .
```shell
./macsio --help
```
```shell
./macsio --help
```
Will produce a lot of help output including MACSio's main arguments as well as arguments
specific to any enabled plugins.
- To use H5Z-ZFP compression plugin, be sure to have the plugin compiled and available
with the same compiler and version of HDF5 you are using with MACSIO. Then to run it
```shell
```shell
env HDF5_PLUGIN_PATH=<path-to-plugin-dir> mpirun -np 4 ./macsio/macsio --interface hdf5 --parallel_file_mode MIF 2 --avg_num_parts 2.5 --part_size 40000 --part_dim 2 --part_type rectilinear --num_dumps 2 --filebase macsio_mif --fileext h5 --debug_level 1 --plugin_args --compression zfp rate=4
```
```
where `path-to-plugin-dir` is the path to the directory containing `libh5zzfp.{a,so,dylib}`

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