Compiling and Installing MEGAHIT

Procedure

Use PuTTY to log in to the server as the root user.
Run the following command to go to the source code installation directory:
```
cd /path/to/MEGAHIT
```
Run the following command to decompress the source code package:
```
tar -xvf v1.2.9.tar.gz
```
Run the following command to switch to the folder of the decompressed files:
```
cd megahit-1.2.9
```

Run the following command to modify the CMakeLists.txt file:

Open CMakeLists.txt.
```
vi CMakeLists.txt
```

Press i to enter the insert mode and modify the file as follows:

Before the modification:

6     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
...
76 set_target_properties(megahit_core PROPERTIES COMPILE_FLAGS "-mbmi2 -DUSE_BMI2 -mpopcnt")
77 set_target_properties(megahit_core_popcnt PROPERTIES COMPILE_FLAGS "-mpopcnt")

After the modification:

6     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -march=armv8.2-a")
...
76 set_target_properties(megahit_core PROPERTIES COMPILE_FLAGS "")
77 set_target_properties(megahit_core_popcnt PROPERTIES COMPILE_FLAGS "")

Press Esc, type :wq!, and press Enter to save the file and exit.

Run the following command to switch the directory:
```
cd ./src/utils/
```
Run the following command to copy the header file of the Kunpeng Porting Advisor to the current directory:
```
cp /path/to/PORT_ADVISOR/portadv/tools/inline_asm/config/KunpengTrans.h ./
```

Run the following command to modify cpu_dispatch.h:

vi cpu_dispatch.h

The new code content has been marked:

#if defined(__aarch64__)       // New code
  #include "KunpengTrans.h"     // New code
#endif      // New code
 
#ifndef MEGAHIT_CPU_DISPATCH_H
#define MEGAHIT_CPU_DISPATCH_H
 
inline bool HasPopcnt() {
  unsigned eax, ebx, ecx, edx;
#ifdef _MSC_VER
  int cpuid[4];
  __cpuid(cpuid, 1);
  eax = cpuid[0], ebx = cpuid[1], ecx = cpuid[2], edx = cpuid[3];
#else
#if defined(__x86_64__)    // New code
  asm volatile("cpuid\n\t"
               : "=a"(eax), "=b"(ebx), "=c"(ecx), "=d"(edx)
               : "0"(1));
#elif defined(__aarch64__)    // New code
  {
    eax = 1;      // New code
    GetSupportedCPUID(&eax,&ebx,&ecx,&edx);     // New code
  }
#endif  // New code
#endif
  return ecx >> 23U & 1U;
}
 
inline bool HasBmi2() {
  unsigned eax, ebx, ecx, edx;
#ifdef _MSC_VER
  int cpuid[4];
  __cpuidex(cpuid, 7, 0);
  eax = cpuid[0], ebx = cpuid[1], ecx = cpuid[2], edx = cpuid[3];
#else
#if defined(__x86_64__)    // New code
  asm volatile("cpuid\n\t"
               : "=a"(eax), "=b"(ebx), "=c"(ecx), "=d"(edx)
               : "0"(7), "2"(0));
#elif defined(__aarch64__)        // New code
  {
    eax = 7;    // New code
    ecx = 0;    // New code
    GetSupportedCPUID(&eax,&ebx,&ecx,&edx);    // New code
  }
#endif    // New code
#endif
  return ebx >> 8U & 1U;
}
 
#endif  // MEGAHIT_CPU_DISPATCH_H

Run the following command to switch the directory:
```
cd ../kmlib/
```
Run the following command to modify the kmrns.h file and replace the header file:
```
vi kmrns.h
```
Before the modification:
```
#include <x86intrin.h>
```
After the modification:
```
#include <sse2neon.h>
```
Run the following command to copy the sse2neon.h header file to the current directory:
```
cp /path/to/SSE2NEON/sse2neon-1.5.0/sse2neon.h ./
```
Run the following command to create a build folder and go to the folder:
```
mkdir /path/to/MEGAHIT/build && cd /path/to/MEGAHIT/build
```

Run the following commands to perform the compilation and installation:

CC=`which gcc` CXX=`which g++` cmake -DCMAKE_INSTALL_PREFIX=/path/to/MEGAHIT -DCMAKE_BUILD_TYPE=Release ../
make -j 16
make install

Run the following command to load the environment variable:
```
export PATH=/path/to/MEGAHIT/bin:$PATH
```

Parent topic: megahit 1.2.9 Porting Guide (CentOS 7.6)