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README with AVX2 compilation

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Saurabh
2021-07-19 08:46:23 -07:00
committed by Heng Li
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README.md
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## mm2-fast
### Introduction
mm2-fast is an accelerated implementation of minimap2 on modern CPUs. mm2-fast accelerates all three major modules of minimap2: Seeding, Chaining, and Alignment, achieving upto 3.5x speedup over minimap2.
mm2-fast is an accelerated implementation of minimap2 on modern CPUs. mm2-fast accelerates all three major modules of minimap2: Seeding, Chaining, and Alignment, achieving up to 3.5x speedup over minimap2.
mm2-fast is a drop-in replacement of minimap2, providing the same functionality with the exact same output.
In the current version, all the modules are optimized using **AVX2** and **AVX-512** vectorization. For non-AVX-512 machines, mm2-fast runs as minimap2 code.
In the current version, all the modules are optimized using **AVX-512** vectorization. For **AVX2** systems, mm2-fast can be run with optimized seeding and AVX2 based vectorized alignment. The chaining module is not optimized for AVX2. The following table shows AVX2/AVX512 compatibility for three modules along with their default settings.
+------------+------------+-----------------------------------+
| AVX512 | AVX2 | Default settings |
+-----------+------------+------------+-----------------------------------+
| Seeding | Yes | Yes | AVX512/AVX2: Disabled |
+-----------+------------+------------+-----------------------------------+
| Chaining | Yes | No | AVX512: Enabled, AVX2: NA |
+-----------+------------+------------+-----------------------------------+
| Alignment | Yes | Yes | AVX512: Enabled, AVX2: Disabled |
+-------------------------------------+-----------------------------------+
### Usage
```sh
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# Compile with all optimizations disabled (runs as minimap2)
make clean && make no_opt=1
# Enable optimized seeding and AVX2 based alignment for AVX2 systems (By default, all optimizations are disabled for AVX2 systems)
make clean && make lhash=1 use_avx2=1
```
The original README content of minimap2 follows.