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Created February 19, 2015 10:20
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-
diff -ENwbu ./bkb_merger.h KMC/kmer_counter/bkb_merger.h
--- ./bkb_merger.h 2015-01-29 22:37:50.000000000 +0100
+++ KMC/kmer_counter/bkb_merger.h 2015-02-19 11:14:42.806689539 +0100
@@ -133,8 +133,7 @@
template<typename KMER_T, unsigned SIZE>
void CBigKmerBinMerger<KMER_T, SIZE>::Process()
{
- // BLESS
- int32 bin_id(0);
+ int32 bin_id;
uint32 size = 0;
uint32 counter_size = min(BYTE_LOG(cutoff_max), BYTE_LOG(counter_max));
uint32 lut_recs = 1 << 2 * lut_prefix_len;
diff -ENwbu ./defs.h KMC/kmer_counter/defs.h
--- ./defs.h 2015-01-29 22:37:50.000000000 +0100
+++ KMC/kmer_counter/defs.h 2015-02-19 11:14:42.806689539 +0100
@@ -83,10 +83,6 @@
#define MIN_SR 1
#define MAX_SR 16
-// BLESS
-#define MIN_NODES 1
-#define MIN_RANK 0
-
typedef float count_t;
diff -ENwbu ./kb_reader.h KMC/kmer_counter/kb_reader.h
--- ./kb_reader.h 2015-01-29 22:37:50.000000000 +0100
+++ KMC/kmer_counter/kb_reader.h 2015-02-19 11:14:42.806689539 +0100
@@ -44,10 +44,6 @@
int32 lut_prefix_len;
uint32 max_x;
- // BLESS
- int num_nodes;
- int rank;
-
bool both_strands;
bool use_quake;
@@ -86,10 +82,6 @@
max_x = Params.max_x;
s_mapper = Queues.s_mapper;
lut_prefix_len = Params.lut_prefix_len;
-
- // BLESS
- num_nodes = Params.num_nodes;
- rank = Params.rank;
}
//----------------------------------------------------------------------------------
@@ -117,8 +109,6 @@
bd->init_random();
while((bin_id = bd->get_next_random_bin()) >= 0) // Get id of the next bin to read
{
- // BLESS
- if ((bin_id % num_nodes) == rank) {
bd->read(bin_id, file, name, size, n_rec, n_plus_x_recs, buffer_size, kmer_len);
fflush(stdout);
@@ -198,11 +188,9 @@
//Remove temporary file
#ifndef DEVELOP_MODE
-// DEBUG
-// file->Remove();
+ file->Remove();
#endif
disk_logger->log_remove(size);
- } // BLESS
}
diff -ENwbu ./kb_storer.cpp KMC/kmer_counter/kb_storer.cpp
--- ./kb_storer.cpp 2015-01-29 22:37:49.000000000 +0100
+++ KMC/kmer_counter/kb_storer.cpp 2015-02-19 11:14:42.806689539 +0100
@@ -32,10 +32,6 @@
bd = Queues.bd;
working_directory = Params.working_directory;
- // BLESS
- num_nodes = Params.num_nodes;
- rank = Params.rank;
-
mem_mode = Params.mem_mode;
s_mapper = Queues.s_mapper;
@@ -194,15 +190,12 @@
for(int i = 0; i < n_bins; ++i)
{
- // BLESS
- if ((i % num_nodes) == rank) {
f_name = GetName(i);
buf_sizes[i] = 0;
files[i]->Open(f_name);
bd->insert(i, files[i], f_name, 0, 0, 0, 0);
- } // BLESS
}
return true;
diff -ENwbu ./kb_storer.h KMC/kmer_counter/kb_storer.h
--- ./kb_storer.h 2015-01-29 22:37:50.000000000 +0100
+++ KMC/kmer_counter/kb_storer.h 2015-02-19 11:14:42.806689539 +0100
@@ -40,10 +40,6 @@
uint64 max_mem_buffer;
uint64 max_mem_single_package;
- // BLESS
- int num_nodes;
- int rank;
-
CSignatureMapper *s_mapper;
CDiskLogger *disk_logger;
uchar* tmp_buff;
Common subdirectories: ./KMC and KMC/kmer_counter/KMC
diff -ENwbu ./kmer_counter.cpp KMC/kmer_counter/kmer_counter.cpp
--- ./kmer_counter.cpp 2015-01-29 22:37:50.000000000 +0100
+++ KMC/kmer_counter/kmer_counter.cpp 2015-02-19 11:14:42.806689539 +0100
@@ -153,11 +153,6 @@
cout << " -sp<value> - number of splitting threads\n";
cout << " -sr<value> - number of sorter threads\n";
cout << " -so<value> - number of threads per single sorter\n";
-
- // BLESS
- cout << " -d<value> - number of nodes\n";
- cout << " -a<value> - rank of a current node\n";
-
cout << "Example:\n";
cout << "kmc -k27 -m24 NA19238.fastq NA.res \\data\\kmc_tmp_dir\\\n";
cout << "kmc -k27 -q -m24 @files.lst NA.res \\data\\kmc_tmp_dir\\\n";
@@ -173,10 +168,6 @@
if(argc < 4)
return false;
- // BLESS
- Params.num_nodes = -1;
- Params.rank = -1;
-
for(i = 1 ; i < argc; ++i)
{
if(argv[i][0] != '-')
@@ -253,31 +244,6 @@
Params.p_mem_mode = true;
else if(strncmp(argv[i], "-b", 2) == 0)
Params.p_both_strands = false;
- // BLESS
- // number of nodes
- else if(strncmp(argv[i], "-d", 2) == 0)
- {
- tmp = atoi(&argv[i][2]);
- if(tmp < MIN_NODES)
- {
- cout << "Wrong parameter: the number of nodes " << tmp << " should be >= " << MIN_NODES << "\n";
- return false;
- }
- else
- Params.num_nodes = tmp;
- }
- // rank
- else if(strncmp(argv[i], "-a", 2) == 0)
- {
- tmp = atoi(&argv[i][2]);
- if(tmp < MIN_RANK)
- {
- cout << "Wrong parameter: the rank of nodes should be >= " << MIN_RANK << "\n";
- return false;
- }
- else
- Params.rank = tmp;
- }
// Number of reading threads
else if(strncmp(argv[i], "-sf", 3) == 0)
{
@@ -373,20 +339,6 @@
}
}
- // BLESS
- if (Params.num_nodes == -1) {
- cout << "No parameter: the option -n is mandatory" << "\n";
- return false;
- }
- else if (Params.rank == -1) {
- cout << "No parameter: the option -rank is mandatory" << "\n";
- return false;
- }
- else if (Params.rank >= Params.num_nodes) {
- cout << "Wrong parameter: the rank " << Params.rank << " should be smaller than the number of nodes " << Params.num_nodes << "\n";
- return false;
- }
-
if(argc - i < 3)
return false;
Common subdirectories: ./libs and KMC/kmer_counter/libs
diff -ENwbu ./params.h KMC/kmer_counter/params.h
--- ./params.h 2015-01-29 22:37:50.000000000 +0100
+++ KMC/kmer_counter/params.h 2015-02-19 11:14:42.814689539 +0100
@@ -105,10 +105,6 @@
vector<int> n_omp_threads;// number of OMP threads per sorters
uint32 max_x; //k+x-mers will be counted
- // BLESS
- int num_nodes;
- int rank;
-
uint32 gzip_buffer_size;
uint32 bzip2_buffer_size;
diff -ENwbu ./splitter.h KMC/kmer_counter/splitter.h
--- ./splitter.h 2015-01-29 22:37:50.000000000 +0100
+++ KMC/kmer_counter/splitter.h 2015-02-19 11:14:42.814689539 +0100
@@ -77,8 +77,7 @@
void InitBins(CKMCParams &Params, CKMCQueues &Queues);
~CSplitter();
- // BLESS
- bool ProcessReads(uchar *_part, uint64 _part_size, int num_nodes, int rank);
+ bool ProcessReads(uchar *_part, uint64 _part_size);
void Complete();
void GetTotal(uint64 &_n_reads);
@@ -97,14 +96,12 @@
template <> class CSplitter_Impl<false> {
public:
- // BLESS
- static bool ProcessReads(CSplitter<false> &ptr, uchar *_part, uint64 _part_size, int num_nodes, int rank);
+ static bool ProcessReads(CSplitter<false> &ptr, uchar *_part, uint64 _part_size);
};
template <> class CSplitter_Impl<true> {
public:
- // BLESS
- static bool ProcessReads(CSplitter<true> &ptr, uchar *_part, uint64 _part_size, int num_nodes, int rank);
+ static bool ProcessReads(CSplitter<true> &ptr, uchar *_part, uint64 _part_size);
};
//----------------------------------------------------------------------------------
@@ -524,11 +521,9 @@
//----------------------------------------------------------------------------------
// Process the reads from the given FASTQ file part
-// BLESS
-template <bool QUAKE_MODE> bool CSplitter<QUAKE_MODE>::ProcessReads(uchar *_part, uint64 _part_size, int num_nodes, int rank)
+template <bool QUAKE_MODE> bool CSplitter<QUAKE_MODE>::ProcessReads(uchar *_part, uint64 _part_size)
{
- // BLESS
- return CSplitter_Impl<QUAKE_MODE>::ProcessReads(*this, _part, _part_size, num_nodes, rank);
+ return CSplitter_Impl<QUAKE_MODE>::ProcessReads(*this, _part, _part_size);
}
//----------------------------------------------------------------------------------
@@ -545,8 +540,7 @@
//----------------------------------------------------------------------------------
// Process the reads from the given FASTQ file part
-// BLESS
-bool CSplitter_Impl<false>::ProcessReads(CSplitter<false> &ptr, uchar *_part, uint64 _part_size, int num_nodes, int rank)
+bool CSplitter_Impl<false>::ProcessReads(CSplitter<false> &ptr, uchar *_part, uint64 _part_size)
{
ptr.part = _part;
ptr.part_size = _part_size;
@@ -596,11 +590,8 @@
if (len >= ptr.kmer_len)
{
bin_no = ptr.s_mapper->get_bin_id(current_signature.get());
- // BLESS
- if ((bin_no % num_nodes) == (unsigned int)rank) {
ptr.bins[bin_no]->PutExtendedKmer(seq + i - len, len);
}
- }
len = 0;
++i;
break;
@@ -611,10 +602,7 @@
if (len >= ptr.kmer_len)
{
bin_no = ptr.s_mapper->get_bin_id(current_signature.get());
- // BLESS
- if ((bin_no % num_nodes) == (unsigned int)rank) {
ptr.bins[bin_no]->PutExtendedKmer(seq + i - len, len);
- }
len = ptr.kmer_len - 1;
}
current_signature.set(end_mmer);
@@ -628,10 +616,7 @@
else if (signature_start_pos + ptr.kmer_len - 1 < i)//need to find new signature
{
bin_no = ptr.s_mapper->get_bin_id(current_signature.get());
- // BLESS
- if ((bin_no % num_nodes) == (unsigned int)rank) {
ptr.bins[bin_no]->PutExtendedKmer(seq + i - len, len);
- }
len = ptr.kmer_len - 1;
//looking for new signature
++signature_start_pos;
@@ -652,10 +637,7 @@
if (len == ptr.kmer_len + 255) //one byte is used to store counter of additional symbols in extended k-mer
{
bin_no = ptr.s_mapper->get_bin_id(current_signature.get());
- // BLESS
- if ((bin_no % num_nodes) == (unsigned int)rank) {
ptr.bins[bin_no]->PutExtendedKmer(seq + i + 1 - len, len);
- }
i -= ptr.kmer_len - 2;
len = 0;
break;
@@ -666,12 +648,9 @@
if (len >= ptr.kmer_len)//last one in read
{
bin_no = ptr.s_mapper->get_bin_id(current_signature.get());
- // BLESS
- if ((bin_no % num_nodes) == (unsigned int)rank) {
ptr.bins[bin_no]->PutExtendedKmer(seq + i - len, len);
}
}
- }
putchar('*');
fflush(stdout);
@@ -684,8 +663,7 @@
//----------------------------------------------------------------------------------
// Process the reads from the given FASTQ file part
-// BLESS: the quake mode is true: no modification
-bool CSplitter_Impl<true>::ProcessReads(CSplitter<true> &ptr, uchar *_part, uint64 _part_size, int num_nodes, int rank)
+bool CSplitter_Impl<true>::ProcessReads(CSplitter<true> &ptr, uchar *_part, uint64 _part_size)
{
ptr.part = _part;
ptr.part_size = _part_size;
@@ -827,10 +805,6 @@
CSplitter<QUAKE_MODE> *spl;
uint64 n_reads;
- // BLESS
- int num_nodes;
- int rank;
-
public:
CWSplitter(CKMCParams &Params, CKMCQueues &Queues);
~CWSplitter();
@@ -848,10 +822,6 @@
pmm_fastq = Queues.pmm_fastq;
spl = new CSplitter<QUAKE_MODE>(Params, Queues);
spl->InitBins(Params, Queues);
-
- // BLESS
- num_nodes = Params.num_nodes;
- rank = Params.rank;
}
//----------------------------------------------------------------------------------
@@ -871,8 +841,7 @@
uint64 size;
if(pq->pop(part, size))
{
- // BLESS
- spl->ProcessReads(part, size, num_nodes, rank);
+ spl->ProcessReads(part, size);
pmm_fastq->free(part);
}
}
Common subdirectories: ./x64 and KMC/kmer_counter/x64
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