removed all openmp stuff

include/compactsufsort/compactsufsort_imp.hpp

@@ -8,6 +8,7 @@
 #include "trsort_imp.hpp"
 #include <mummer/timer.hpp>
 
+#undef _OPENMP
 #ifdef _OPENMP
 # include <omp.h>
 #endif

include/mummer/mgaps.hh

@@ -146,7 +146,7 @@ int ClusterMatches::Cluster_each_long(Match_t * A, int N, Output out) const {
   openmp_qsort(A + 1, A + N + 1, By_Start2);
   N = Filter_Matches (A + 1, N);
 
-#pragma omp parallel for schedule(dynamic)
+//#pragma omp parallel for schedule(dynamic)
   for  (int i = 1;  i < N;  i ++) {
     long int i_end  = A [i] . Start2 + A [i] . Len;
     long int i_diag = A [i] . Start2 - A [i] . Start1;
@@ -163,7 +163,7 @@ int ClusterMatches::Cluster_each_long(Match_t * A, int N, Output out) const {
   }
 
   //  Set the cluster id of each match and reset Good flag
-#pragma omp parallel for
+//#pragma omp parallel for
   for  (int i = 1;  i <= N;  i ++) {
     A [i] . cluster_id = UF.find (i);
     assert(A[i].cluster_id > 0);
@@ -173,15 +173,15 @@ int ClusterMatches::Cluster_each_long(Match_t * A, int N, Output out) const {
 
   // Determine and process clusters
   int cluster_size, print_ct = 0;
-#pragma omp parallel
+//#pragma omp parallel
   {
-#pragma omp single
+//#pragma omp single
     for (int i = 1;  i <= N;  i += cluster_size) {
       int j;
       for  (j = i + 1;  j <= N && A [i] . cluster_id == A [j] . cluster_id;  j ++)
         ;
       cluster_size = j - i;
-#pragma omp task firstprivate(i, cluster_size) shared(out)
+//#pragma omp task firstprivate(i, cluster_size) shared(out)
       print_ct += Process_Cluster (A + i, cluster_size, out);
     }
   }

include/mummer/openmp_qsort.hpp

@@ -18,9 +18,9 @@ void openmp_qsort(Iterator begin, Iterator end, Compare Comp) {
   if(sz < 1024)
     return std::sort(begin, end, Comp);
 
-#pragma omp parallel
+//#pragma omp parallel
   {
-#pragma omp single
+//#pragma omp single
     {
       openmp_qsort_imp::openmp_qsort_(begin, end, sz, Comp);
     }
@@ -52,15 +52,15 @@ void openmp_qsort_(Iterator begin, Iterator end, const size_t sz, Compare Comp)
   assert((size_t)sz1 <= sz);
   assert((size_t)sz1 + (size_t)sz2 + 1 == sz);
   if(sz1 > 1024) {
-#pragma omp task firstprivate(p, sz1)
+//#pragma omp task firstprivate(p, sz1)
     openmp_qsort_(begin, p, sz1, Comp);
     if(sz2 > 1024)
       openmp_qsort_(p + 1, end, sz2, Comp);
     else
       std::sort(p + 1, end, Comp);
   } else {
     if(sz2 > 1024)
-#pragma omp task firstprivate(p, sz2)
+//#pragma omp task firstprivate(p, sz2)
       openmp_qsort_(p + 1, end, sz2, Comp);
     else
       std::sort(p + 1, end, Comp);

include/mummer/postnuc.hh

@@ -355,7 +355,7 @@ void merge_syntenys::processSyntenys_long_each(Container& Syntenys, const FR2& B
   std::atomic<size_t> pos(0);
   const auto end = Syntenys.end();
 
-#pragma omp parallel
+//#pragma omp parallel
   {
     auto CurrSp = Syntenys.begin();
     size_t prev = 0;

include/mummer/sparseSA_imp.hpp

@@ -1,6 +1,7 @@
 #ifndef __SPARSESA_IMP_H__
 #define __SPARSESA_IMP_H__
 
+#undef _OPENMP
 #ifdef _OPENMP
 #include <omp.h>
 #endif

src/essaMEM/sparseSA.cpp

@@ -490,11 +490,11 @@ void sparseSA::construct(bool off48){
       ISA.resize(N, off48);
       if(SA.is_small) {
         compactsufsort::create((const unsigned char*)(S + 0), (int*)SA.small.data(), N);
-#pragma omp parallel for
+//#pragma omp parallel for
         for(long i = 0; i < N; ++i) { ISA.small[SA.small[i]] = i; }
       } else {
         compactsufsort::create((const unsigned char*)(S + 0), SA.large.begin(), N);
-#pragma omp parallel for
+//#pragma omp parallel for
         for(long i = 0; i < N; ++i) { ISA.large[SA.large[i]] = i; }
       }
     }

src/tigr/mgaps.cc

@@ -63,7 +63,7 @@ int ClusterMatches::Filter_Matches(Match_t * A, const int N) {
 //  diagonal.  Pack all remaining matches into the front of  A  and
 //  reduce the value of  N  if any matches are removed.
 //  Matches in  A  *MUST* be sorted by  Start2  value.
-#pragma omp parallel for schedule(dynamic)
+//#pragma omp parallel for schedule(dynamic)
   for  (int i = 0;  i < N - 1;  i ++) {
     if  (! A[i].Good) continue;
 

src/umd/nucmer_main.cc

@@ -8,6 +8,7 @@
 #include <src/umd/nucmer_cmdline.hpp>
 #include <thread_pipe.hpp>
 
+#undef _OPENMP
 #ifdef _OPENMP
 #include <omp.h>
 #endif