martin-steinegger

/////////////////////////////////////////////////////////////////////////////////////
// Compare HMMs with one another and look for sub-optimal alignments that share no pair with previous ones
// The function is called with q and t
// If q and t are equal (self==1), only the upper right part of the matrix is calculated: j>=i+3
/////////////////////////////////////////////////////////////////////////////////////
void Hit::Viterbi(HMM* q, HMM* t, float** Sstruc)
{
  
  // Linear topology of query (and template) HMM:
  // 1. The HMM HMM has L+2 columns. Columns 1 to L contain 

martin-steinegger

#!/bin/bash -e

export CC=gcc
export CXX=g++

cat <<'CPUDOC' | $CC -std=gnu99 -o "testcpu" -xc -
#include <stdio.h>
#define D(x) __builtin_cpu_supports((x))?(x)
int main(){puts(D("avx2"):D("sse4.1"):"fail");}
CPUDOC

martin-steinegger

{% set version = "2-23394" %}
{% set sha256 = "4734846e6fcc78a80058f1c699b2deb7f2a6b5c0cf1c1f1dd75a20403b81f387" %}

package:
  name: mmseqs2
  version: {{ version }}

source:
  fn: mmseqs2-{{ version }}.tar.gz
  url: https://github.com/soedinglab/mmseqs2/archive/{{ version }}.tar.gz

martin-steinegger

Index: src/alignment/MsaFilter.cpp
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
--- src/alignment/MsaFilter.cpp	(revision 2339462c06eab0bee64e4fc0ebebf7707f6e53fd)
+++ src/alignment/MsaFilter.cpp	(date 1520402320000)
@@ -245,6 +245,13 @@
             << ": " << __func__ << ":" << "\n";
             Debug(Debug::WARNING)

martin-steinegger

template <unsigned int N> __m256i _mm256_shift_left2(__m256i a) { 
    __m256i mask = _mm256_srli_si256( 
                        _mm256_permute2x128_si256(a, a, _MM_SHUFFLE(0,0,3,0)) , 16-N); 
    return _mm256_or_si256(_mm256_slli_si256(a,N),mask); 
}

martin-steinegger

inline float get_first( const __m128 vec){return _mm_cvtss_f32(_mm_shuffle_ps(vec,vec, _MM_SHUFFLE2(0,0)));}
inline float get_second(const __m128 vec){return _mm_cvtss_f32(_mm_shuffle_ps(vec,vec, _MM_SHUFFLE2(0,1)));}
inline float get_third( const __m128 vec){return _mm_cvtss_f32(_mm_shuffle_ps(vec,vec, _MM_SHUFFLE2(1,0)));}
inline float get_fourth(const __m128 vec){return _mm_cvtss_f32(_mm_shuffle_ps(vec,vec, _MM_SHUFFLE2(1,1)));}