Compiling error with newest mpi and gcc on PACE

[jianshu93]

Hello Team,

I have the following error:

[jzhao399@login-phoenix-slurm-1 build]$ make -j 4
Consolidate compiler generated dependencies of target bliss-utils
Consolidate compiler generated dependencies of target statAndCompare
Consolidate compiler generated dependencies of target metaG
[ 16%] Built target bliss-utils
[ 16%] Built target statAndCompare
Consolidate compiler generated dependencies of target log-sort
Consolidate compiler generated dependencies of target log-sort-graph500
Consolidate compiler generated dependencies of target GraphGenlib
[ 25%] Linking CXX executable ../bin/log-sort-graph500
[ 25%] Building CXX object src/CMakeFiles/log-sort.dir/logSort.cpp.o
[ 37%] Building CXX object src/CMakeFiles/metaG.dir/assembly.cpp.o
[ 70%] Built target GraphGenlib
Consolidate compiler generated dependencies of target sys_probe
[ 79%] Built target sys_probe
Consolidate compiler generated dependencies of target TextInspector
[ 83%] Building CXX object ext/bliss/utils/CMakeFiles/TextInspector.dir/text_inspector.cpp.o
[ 87%] Built target log-sort-graph500
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/data_block.hpp:72,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:41,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/utils/text_inspector.cpp:26:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:41:12: error: too many template-parameter-lists
41 | struct container_mem_traits<::std::vector<T, A> > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:45:12: error: too many template-parameter-lists
45 | struct container_mem_traits<::std::array<T, N> > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:49:12: error: too many template-parameter-lists
49 | struct container_mem_traits<::std::basic_string<CharT, Traits, Allocator>> { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/data_block.hpp:72,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:41,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/utils/text_inspector.cpp:26:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:53:12: error: too many template-parameter-lists
53 | struct container_mem_traits<::std::valarray > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:57:12: error: too many template-parameter-lists
57 | struct container_mem_traits<::std::initializer_list > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:62:12: error: too many template-parameter-lists
62 | struct container_mem_traits< T* > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/utils/text_inspector.cpp:26:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:155:149: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
155 | void handleError(const std::string& errType, const Iterator &start, const Iterator &end, const size_t& startOffset, const size_t& endOffset) throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:173:151: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
173 | void handleWarning(const std::string& errType, const Iterator &start, const Iterator &end, const size_t& startOffset, const size_t& endOffset) throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:206:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
206 | throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:220:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
220 | throw (bliss::io::IOException) {};
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:225:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
225 | throw (bliss::io::IOException) {};
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:242:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
242 | size_t increment(Iterator &iter, const Iterator &end, size_t &offset, size_t & seq_offset, SequenceType& output) throw (bliss::io::IOException)
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:267:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
267 | size_t increment(Iterator &iter, const Iterator &end, size_t &offset, SequenceType& output) throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:572:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
572 | const size_t _L2BlockSize = 0, const size_t _L1BlockSize = 0) throw (bliss::io::IOException)
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:637:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
637 | const size_t _L2BlockSize = 0, const size_t _L1BlockSize = 0 ) throw (bliss::io::IOException)
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:979:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
979 | L1BlockType& loadL1DataForRange(const RangeType &range) throw (bliss::io::IOException)
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:1386:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
1386 | int openFile(const std::string& fn) throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:1418:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
1418 | size_t getFileSize(const int& fd) throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:1462:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
1462 | PointerType map(const RangeType &r) throw (IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/utils/text_inspector.cpp: In function 'int main(int, char**)':
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/utils/text_inspector.cpp:53:9: warning: unused variable 'myerr' [-Wunused-variable]
53 | int myerr = errno;
| ^~~~~
make[2]: *** [ext/bliss/utils/CMakeFiles/TextInspector.dir/text_inspector.cpp.o] Error 1
make[1]: *** [ext/bliss/utils/CMakeFiles/TextInspector.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:15:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:166:22: error: '__m128i' does not name a type
166 | static constexpr __m128i const simd_mask = reinterpret_cast<const __m128i>(simd_mask_b);
| ^~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:171:22: error: '__m128i' does not name a type
171 | static constexpr __m128i const simd_rev_mask = reinterpret_cast<const __m128i>(simd_rev_mask_b);
| ^~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:175:22: error: '__m128i' does not name a type
175 | static constexpr __m128i const simd_lut1_lo = reinterpret_cast<const __m128i>(simd_lut1_lo_b);
| ^~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:177:22: error: '__m128i' does not name a type
177 | static constexpr __m128i const simd_lut1_hi = reinterpret_cast<const __m128i>(simd_lut1_hi_b);
| ^~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:180:22: error: '__m128i' does not name a type
180 | static constexpr __m128i const simd_lut2_lo = reinterpret_cast<const __m128i>(simd_lut2_lo_b);
| ^~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:182:22: error: '__m128i' does not name a type
182 | static constexpr __m128i const simd_lut2_hi = reinterpret_cast<const __m128i>(simd_lut2_hi_b);
| ^~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:188:22: error: '__m128i' does not name a type
188 | static constexpr __m128i const simd_true_mask = reinterpret_cast<const __m128i>(simd_true_mask_b);
| ^~~~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/logSort.cpp:20:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:166:22: error: '__m128i' does not name a type
166 | static constexpr __m128i const simd_mask = reinterpret_cast<const __m128i>(simd_mask_b);
| ^~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:171:22: error: '__m128i' does not name a type
171 | static constexpr __m128i const simd_rev_mask = reinterpret_cast<const __m128i>(simd_rev_mask_b);
| ^~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:175:22: error: '__m128i' does not name a type
175 | static constexpr __m128i const simd_lut1_lo = reinterpret_cast<const __m128i>(simd_lut1_lo_b);
| ^~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:177:22: error: '__m128i' does not name a type
177 | static constexpr __m128i const simd_lut1_hi = reinterpret_cast<const __m128i>(simd_lut1_hi_b);
| ^~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:180:22: error: '__m128i' does not name a type
180 | static constexpr __m128i const simd_lut2_lo = reinterpret_cast<const __m128i>(simd_lut2_lo_b);
| ^~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:182:22: error: '__m128i' does not name a type
182 | static constexpr __m128i const simd_lut2_hi = reinterpret_cast<const __m128i>(simd_lut2_hi_b);
| ^~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:188:22: error: '__m128i' does not name a type
188 | static constexpr __m128i const simd_true_mask = reinterpret_cast<const __m128i>(simd_true_mask_b);
| ^~~~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/data_block.hpp:72,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:41,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/fastq_loader.hpp:23,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:9,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/logSort.cpp:24:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:41:12: error: too many template-parameter-lists
41 | struct container_mem_traits<::std::vector<T, A> > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:45:12: error: too many template-parameter-lists
45 | struct container_mem_traits<::std::array<T, N> > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:49:12: error: too many template-parameter-lists
49 | struct container_mem_traits<::std::basic_string<CharT, Traits, Allocator>> { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/data_block.hpp:72,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:41,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/fastq_loader.hpp:23,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:9,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/logSort.cpp:24:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:53:12: error: too many template-parameter-lists
53 | struct container_mem_traits<::std::valarray > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:57:12: error: too many template-parameter-lists
57 | struct container_mem_traits<::std::initializer_list > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:62:12: error: too many template-parameter-lists
62 | struct container_mem_traits< T* > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/fastq_loader.hpp:23,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:9,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/logSort.cpp:24:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:155:149: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
155 | r &end, const size_t& startOffset, const size_t& endOffset) throw (bliss::io::IOException) {
| ^~~~~

/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:173:151: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
173 | r &end, const size_t& startOffset, const size_t& endOffset) throw (bliss::io::IOException) {
| ^~~~~

/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:206:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
206 | throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:220:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
220 | throw (bliss::io::IOException) {};
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:225:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
225 | throw (bliss::io::IOException) {};
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:242:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
242 | size_t &offset, size_t & seq_offset, SequenceType& output) throw (bliss::io::IOException)
| ^~~~~

/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:267:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
267 | const Iterator &end, size_t &offset, SequenceType& output) throw (bliss::io::IOException) {
| ^~~~~

/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:572:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
572 | nst size_t _L2BlockSize = 0, const size_t _L1BlockSize = 0) throw (bliss::io::IOException)
| ^~~~~

/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:637:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
637 | st size_t _L2BlockSize = 0, const size_t _L1BlockSize = 0 ) throw (bliss::io::IOException)
| ^~~~~

/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:979:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
979 | L1BlockType& loadL1DataForRange(const RangeType &range) throw (bliss::io::IOException)
| ^~~~~

/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:1386:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
1386 | int openFile(const std::string& fn) throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:1418:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
1418 | size_t getFileSize(const int& fd) throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:1462:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
1462 | PointerType map(const RangeType &r) throw (IOException) {
| ^~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:9,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/logSort.cpp:24:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/fastq_loader.hpp:212:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
212 | throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/fastq_loader.hpp:319:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
319 | , size_t &offset, size_t &seq_offset, SequenceType& output) throw (bliss::io::IOException)
| ^~~~~

/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/fastq_loader.hpp:404:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
404 | const Iterator &end, size_t &offset, SequenceType& output) throw (bliss::io::IOException) {
| ^~~~~

In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/data_block.hpp:72,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:41,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/fastq_loader.hpp:23,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:9,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:21:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:41:12: error: too many template-parameter-lists
41 | struct container_mem_traits<::std::vector<T, A> > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:45:12: error: too many template-parameter-lists
45 | struct container_mem_traits<::std::array<T, N> > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:49:12: error: too many template-parameter-lists
49 | struct container_mem_traits<::std::basic_string<CharT, Traits, Allocator>> { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/data_block.hpp:72,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:41,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/fastq_loader.hpp:23,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:9,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:21:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:53:12: error: too many template-parameter-lists
53 | struct container_mem_traits<::std::valarray > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:57:12: error: too many template-parameter-lists
57 | struct container_mem_traits<::std::initializer_list > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/utils/container_traits.hpp:62:12: error: too many template-parameter-lists
62 | struct container_mem_traits< T* > { static constexpr bool is_contiguous = true; };
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/fastq_loader.hpp:23,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:9,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:21:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:155:149: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
155 | void handleError(const std::string& errType, const Iterator &start, const Iterator &end, const size_t& startOffset, const size_t& endOffset) throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:173:151: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
173 | void handleWarning(const std::string& errType, const Iterator &start, const Iterator &end, const size_t& startOffset, const size_t& endOffset) throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:206:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
206 | throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:220:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
220 | throw (bliss::io::IOException) {};
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:225:8: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
225 | throw (bliss::io::IOException) {};
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:242:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
242 | size_t increment(Iterator &iter, const Iterator &end, size_t &offset, size_t & seq_offset, SequenceType& output) throw (bliss::io::IOException)
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:267:100: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
267 | size_t increment(Iterator &iter, const Iterator &end, size_t &offset, SequenceType& output) throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:572:91: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
572 | const size_t _L2BlockSize = 0, const size_t _L1BlockSize = 0) throw (bliss::io::IOException)
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:637:83: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
637 | const size_t _L2BlockSize = 0, const size_t _L1BlockSize = 0 ) throw (bliss::io::IOException)
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:979:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
979 | L1BlockType& loadL1DataForRange(const RangeType &range) throw (bliss::io::IOException)
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:1386:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
1386 | int openFile(const std::string& fn) throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:1418:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
1418 | size_t getFileSize(const int& fd) throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/file_loader.hpp:1462:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
1462 | PointerType map(const RangeType &r) throw (IOException) {
| ^~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:9,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:21:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/fastq_loader.hpp:212:9: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
212 | throw (bliss::io::IOException) {
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/fastq_loader.hpp:319:121: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
319 | size_t increment(Iterator &iter, const Iterator &end, size_t &offset, size_t &seq_offset, SequenceType& output) throw (bliss::io::IOException)
| ^~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/io/fastq_loader.hpp:404:101: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
404 | size_t increment(Iterator &iter, const Iterator &end, size_t &offset, SequenceType& output) throw (bliss::io::IOException) {
| ^~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:24:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/postProcess.hpp: In function 'void generateReadToPartitionMapping(cmdLineParams&, std::vector<count_t>&, std::vector&, std::vector&, std::vector&, MPI_Comm)':
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/postProcess.hpp:92:81: warning: lambda capture initializers only available with '-std=c++14' or '-std=gnu++14'
92 | [&localVector = localVector](const T& x){
| ^~~~~~~~~~~
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/postProcess.hpp:96:81: warning: lambda capture initializers only available with '-std=c++14' or '-std=gnu++14'
96 | [&localVector = localVector](const T& x){
| ^~~~~~~~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/ext/mxx/samplesort.hpp:32,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/ext/mxx/sort.hpp:14,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/sortTuples.hpp:8,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/ccl.hpp:18,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/logSort.cpp:25:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/ext/mxx/distribution.hpp: In instantiation of '_Iterator mxx::block_decompose_partitions(_Iterator, _Iterator, _Iterator, MPI_Comm) [with _Iterator = __gnu_cxx::__normal_iterator<std::tuple<long unsigned int, unsigned int, unsigned int>, std::vector<std::tuple<long unsigned int, unsigned int, unsigned int> > >; MPI_Comm = int]':
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/ccl.hpp:761:45: required from 'void cluster_reads_par_inactive(bool, std::vector<_Tp>&, MPI_Comm) [with tuple_t = std::tuple<long unsigned int, unsigned int, unsigned int>; MPI_Comm = int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/logSort.cpp:107:66: required from here
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/ext/mxx/distribution.hpp:349:27: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__normal_iterator<std::tuple<long unsigned int, unsigned int, unsigned int>, std::vector<std::tuple<long unsigned int, unsigned int, unsigned int> > >::difference_type' {aka 'long int'} and 'long unsigned int' [-Wsign-compare]
349 | bool fits = end-begin >= left_part.local_size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/ext/mxx/samplesort.hpp:32,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/ext/mxx/sort.hpp:14,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/sortTuples.hpp:8,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:20:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/ext/mxx/distribution.hpp: In instantiation of '_Iterator mxx::block_decompose_partitions(_Iterator, _Iterator, _Iterator, MPI_Comm) [with _Iterator = __gnu_cxx::__normal_iterator<std::tuple<long unsigned int, unsigned int, unsigned int>, std::vector<std::tuple<long unsigned int, unsigned int, unsigned int> > >; MPI_Comm = int]':
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:181:62: required from here
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/ext/mxx/distribution.hpp:349:27: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__normal_iterator<std::tuple<long unsigned int, unsigned int, unsigned int>, std::vector<std::tuple<long unsigned int, unsigned int, unsigned int> > >::difference_type' {aka 'long int'} and 'long unsigned int' [-Wsign-compare]
349 | bool fits = end-begin >= left_part.local_size();
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/logSort.cpp:25:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/ccl.hpp: In instantiation of 'void unique(std::vector<_Tp>&, const Comparator&, const Equal&, MPI_Comm) [with T = std::tuple<long unsigned int, unsigned int, unsigned int>; Comparator = unique<std::tuple<long unsigned int, unsigned int, unsigned int> >::<lambda(const std::tuple<long unsigned int, unsigned int, unsigned int>&, const std::tuple<long unsigned int, unsigned int, unsigned int>&)>; Equal = unique<std::tuple<long unsigned int, unsigned int, unsigned int> >::<lambda(const std::tuple<long unsigned int, unsigned int, unsigned int>&, const std::tuple<long unsigned int, unsigned int, unsigned int>&)>; MPI_Comm = int]':
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/ccl.hpp:289:9: required from 'void unique(std::vector<_Tp>&, MPI_Comm) [with T = std::tuple<long unsigned int, unsigned int, unsigned int>; MPI_Comm = int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/ccl.hpp:333:9: required from 'void cluster_reads_par(std::vector<_Tp>&, MPI_Comm) [with tuple_t = std::tuple<long unsigned int, unsigned int, unsigned int>; MPI_Comm = int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/logSort.cpp:105:50: required from here
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/ccl.hpp:156:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::tuple<long unsigned int, unsigned int, unsigned int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
156 | for (int i = 0; i < splitters.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/logSort.cpp:20:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp: In instantiation of 'bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE> bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE>::do_reverse_complement_swar(const bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE>&) const [with A = bliss::common::alphabet::DNA_T<>; typename std::enable_if<((std::is_same<A, bliss::common::alphabet::DNA_T<> >::value || std::is_same<A, bliss::common::alphabet::RNA_T<> >::value) || std::is_same<A, bliss::common::alphabet::DNA16_T<> >::value), int>::type = 0; unsigned int KMER_SIZE = 31; ALPHABET = bliss::common::alphabet::DNA_T<>; WORD_TYPE = long unsigned int]':
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:906:62: required from 'bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE> bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE>::reverse_complement() const [with unsigned int KMER_SIZE = 31; ALPHABET = bliss::common::alphabet::DNA_T<>; WORD_TYPE = long unsigned int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:362:54: required from 'void includeAllKmersinAllReads::fillValuesfromReads(std::vector&, BaseCharIterator, BaseCharIterator, std::vector&, std::vector&, ReadIdType) [with T = std::tuple<long unsigned int, unsigned int, unsigned int>; BaseCharIterator = bliss::iterator::transform_iterator<__gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char, std::allocator > >, bliss::common::ASCII2<bliss::common::alphabet::DNA_T<>, unsigned char> >; KmerType = bliss::common::Kmer<31, bliss::common::alphabet::DNA_T<>, long unsigned int>; ReadIdType = unsigned int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:120:30: required from 'void readFASTQFile(cmdLineParams&, std::vector&, std::vector&, std::vector&, MPI_Comm) [with KmerType = bliss::common::Kmer<31, bliss::common::alphabet::DNA_T<>, long unsigned int>; typeOfReadingOperation = includeAllKmersinAllReads<bliss::common::Kmer<31, bliss::common::alphabet::DNA_T<>, long unsigned int> >; T = std::tuple<long unsigned int, unsigned int, unsigned int>; MPI_Comm = int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/logSort.cpp:96:141: required from here
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:1823:32: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
1823 | return ::std::move(result);
| ^
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:1823:32: note: remove 'std::move' call
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:20,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:21:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/packedRead.hpp: In instantiation of 'void getUnPackedRead(std::array<_Tp, _Nm>&, ReadIdType, std::string&) [with ReadInf = readStorageInfo<bliss::common::alphabet::DNA_T<>, long unsigned int>; T = long unsigned int; long unsigned int N = 4; ReadIdType = unsigned int; std::string = std::__cxx11::basic_string]':
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/postProcess.hpp:453:31: required from 'void runParallelAssembly(std::vector<count_t>&, cmdLineParams&, MPI_Comm) [with ReadInf = readStorageInfo<bliss::common::alphabet::DNA_T<>, long unsigned int>; Q = std::tuple<std::array<long unsigned int, 4>, unsigned int, unsigned int, unsigned int>; MPI_Comm = int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/postProcess.hpp:614:39: required from 'void finalPostProcessing(std::vector<count_t>&, std::vector&, std::vector&, cmdLineParams&, MPI_Comm) [with KmerType = bliss::common::Kmer<31, bliss::common::alphabet::DNA_T<>, long unsigned int>; T = std::tuple<long unsigned int, unsigned int, unsigned int>; MPI_Comm = int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:208:93: required from here
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/packedRead.hpp:129:21: warning: comparison of integer expressions of different signedness: 'int' and 'ReadIdType' {aka 'unsigned int'} [-Wsign-compare]
129 | for (int i = 0; i < readLength; i++)
| ~~^~~~~~~~~~~~
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:15:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp: In instantiation of 'bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE> bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE>::do_reverse_complement_swar(const bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE>&) const [with A = bliss::common::alphabet::DNA_T<>; typename std::enable_if<((std::is_same<A, bliss::common::alphabet::DNA_T<> >::value || std::is_same<A, bliss::common::alphabet::RNA_T<> >::value) || std::is_same<A, bliss::common::alphabet::DNA16_T<> >::value), int>::type = 0; unsigned int KMER_SIZE = 20; ALPHABET = bliss::common::alphabet::DNA_T<>; WORD_TYPE = long unsigned int]':
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:906:62: required from 'bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE> bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE>::reverse_complement() const [with unsigned int KMER_SIZE = 20; ALPHABET = bliss::common::alphabet::DNA_T<>; WORD_TYPE = long unsigned int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:186:54: required from 'void includeAllKmers::fillValuesfromReads(std::vector&, BaseCharIterator, BaseCharIterator, std::vector&, std::vector&, ReadIdType) [with T = std::tuple<long unsigned int, unsigned int, short unsigned int, short unsigned int>; BaseCharIterator = bliss::iterator::transform_iterator<__gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char, std::allocator > >, bliss::common::ASCII2<bliss::common::alphabet::DNA_T<>, unsigned char> >; KmerType = bliss::common::Kmer<20, bliss::common::alphabet::DNA_T<>, long unsigned int>; ReadIdType = unsigned int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:120:30: required from 'void readFASTQFile(cmdLineParams&, std::vector&, std::vector&, std::vector&, MPI_Comm) [with KmerType = bliss::common::Kmer<20, bliss::common::alphabet::DNA_T<>, long unsigned int>; typeOfReadingOperation = includeAllKmers<bliss::common::Kmer<20, bliss::common::alphabet::DNA_T<>, long unsigned int> >; T = std::tuple<long unsigned int, unsigned int, short unsigned int, short unsigned int>; MPI_Comm = int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:112:127: required from here
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:1823:32: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
1823 | return ::std::move(result);
| ^
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:1823:32: note: remove 'std::move' call
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp: In instantiation of 'bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE> bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE>::do_reverse_complement_swar(const bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE>&) const [with A = bliss::common::alphabet::DNA_T<>; typename std::enable_if<((std::is_same<A, bliss::common::alphabet::DNA_T<> >::value || std::is_same<A, bliss::common::alphabet::RNA_T<> >::value) || std::is_same<A, bliss::common::alphabet::DNA16_T<> >::value), int>::type = 0; unsigned int KMER_SIZE = 31; ALPHABET = bliss::common::alphabet::DNA_T<>; WORD_TYPE = long unsigned int]':
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:906:62: required from 'bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE> bliss::common::Kmer<KMER_SIZE, ALPHABET, WORD_TYPE>::reverse_complement() const [with unsigned int KMER_SIZE = 31; ALPHABET = bliss::common::alphabet::DNA_T<>; WORD_TYPE = long unsigned int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:283:54: required from 'void includeAllKmersinFilteredReads::fillValuesfromReads(std::vector&, BaseCharIterator, BaseCharIterator, std::vector&, std::vector&, ReadIdType) [with T = std::tuple<long unsigned int, unsigned int, unsigned int>; BaseCharIterator = bliss::iterator::transform_iterator<__gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char, std::allocator > >, bliss::common::ASCII2<bliss::common::alphabet::DNA_T<>, unsigned char> >; KmerType = bliss::common::Kmer<31, bliss::common::alphabet::DNA_T<>, long unsigned int>; ReadIdType = unsigned int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:120:30: required from 'void readFASTQFile(cmdLineParams&, std::vector&, std::vector&, std::vector&, MPI_Comm) [with KmerType = bliss::common::Kmer<31, bliss::common::alphabet::DNA_T<>, long unsigned int>; typeOfReadingOperation = includeAllKmersinFilteredReads<bliss::common::Kmer<31, bliss::common::alphabet::DNA_T<>, long unsigned int> >; T = std::tuple<long unsigned int, unsigned int, unsigned int>; MPI_Comm = int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:146:130: required from here
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:1823:32: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/ext/bliss/src/common/kmer.hpp:1823:32: note: remove 'std::move' call
In file included from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:20,
from /storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:21:
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/packedRead.hpp: In instantiation of 'void getBitsAtPos(std::array<_Tp, _Nm>&, WType&, int, int) [with ReadInf = readStorageInfo<bliss::common::alphabet::DNA_T<>, long unsigned int>; T = long unsigned int; long unsigned int N = 4; WType = long unsigned int]':
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/packedRead.hpp:133:26: required from 'void getUnPackedRead(std::array<_Tp, _Nm>&, ReadIdType, std::string&) [with ReadInf = readStorageInfo<bliss::common::alphabet::DNA_T<>, long unsigned int>; T = long unsigned int; long unsigned int N = 4; ReadIdType = unsigned int; std::string = std::__cxx11::basic_string]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/postProcess.hpp:453:31: required from 'void runParallelAssembly(std::vector<count_t>&, cmdLineParams&, MPI_Comm) [with ReadInf = readStorageInfo<bliss::common::alphabet::DNA_T<>, long unsigned int>; Q = std::tuple<std::array<long unsigned int, 4>, unsigned int, unsigned int, unsigned int>; MPI_Comm = int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/postProcess.hpp:614:39: required from 'void finalPostProcessing(std::vector<count_t>&, std::vector&, std::vector&, cmdLineParams&, MPI_Comm) [with KmerType = bliss::common::Kmer<31, bliss::common::alphabet::DNA_T<>, long unsigned int>; T = std::tuple<long unsigned int, unsigned int, unsigned int>; MPI_Comm = int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:208:93: required from here
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/packedRead.hpp:87:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
87 | if (wordId < ReadInf::nWords - 1) charVal |= readPacked[wordId + 1] << (bitsPerWord - offsetInWord);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
make[2]: *** [src/CMakeFiles/log-sort.dir/logSort.cpp.o] Error 1
make[1]: *** [src/CMakeFiles/log-sort.dir/all] Error 2
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/packedRead.hpp: In instantiation of 'void setBitsAtPos(std::array<_Tp, _Nm>&, WType, int, int) [with ReadInf = readStorageInfo<bliss::common::alphabet::DNA_T<>, long unsigned int>; T = long unsigned int; long unsigned int N = 4; WType = unsigned char]':
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/packedRead.hpp:117:26: required from 'void getPackedRead(std::array<T, N>&, InputIterator, InputIterator) [with ReadInf = readStorageInfo<bliss::common::alphabet::DNA_T<>, long unsigned int>; InputIterator = bliss::iterator::transform_iterator<__gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char, std::allocator > >, bliss::common::ASCII2<bliss::common::alphabet::DNA_T<>, unsigned char> >; T = long unsigned int; long unsigned int N = 4]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:536:29: required from 'void includeWholeReadinFilteredReads::fillValuesfromReads(std::vector&, BaseCharIterator, BaseCharIterator, std::vector&, std::vector&, ReadIdType) [with Q = std::tuple<std::array<long unsigned int, 4>, unsigned int, unsigned int, unsigned int>; BaseCharIterator = bliss::iterator::transform_iterator<__gnu_cxx::__normal_iterator<unsigned char*, std::vector<unsigned char, std::allocator > >, bliss::common::ASCII2<bliss::common::alphabet::DNA_T<>, unsigned char> >; KmerType = bliss::common::Kmer<31, bliss::common::alphabet::DNA_T<>, long unsigned int>; ReadIdType = unsigned int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/parallel_fastq_iterate.hpp:120:30: required from 'void readFASTQFile(cmdLineParams&, std::vector&, std::vector&, std::vector&, MPI_Comm) [with KmerType = bliss::common::Kmer<31, bliss::common::alphabet::DNA_T<>, long unsigned int>; typeOfReadingOperation = includeWholeReadinFilteredReads<bliss::common::Kmer<31, bliss::common::alphabet::DNA_T<>, long unsigned int> >; T = std::tuple<std::array<long unsigned int, 4>, unsigned int, unsigned int, unsigned int>; MPI_Comm = int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/postProcess.hpp:199:72: required from 'void generateSequencesVector(cmdLineParams&, std::vector<count_t>&, std::vector&, std::vector&, MPI_Comm) [with KmerType = bliss::common::Kmer<31, bliss::common::alphabet::DNA_T<>, long unsigned int>; Q = std::tuple<std::array<long unsigned int, 4>, unsigned int, unsigned int, unsigned int>; MPI_Comm = int'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/postProcess.hpp:601:36: required from 'void finalPostProcessing(std::vector<count_t>&, std::vector&, std::vector&, cmdLineParams&, MPI_Comm) [with KmerType = bliss::common::Kmer<31, bliss::common::alphabet::DNA_T<>, long unsigned int>; T = std::tuple<long unsigned int, unsigned int, unsigned int>; MPI_Comm = int]'
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/src/assembly.cpp:208:93: required from here
/storage/home/hcoda1/4/jzhao399/p-ktk3-0/rich_project_bio-konstantinidis/apps/metag_partitioning/include/packedRead.hpp:58:16: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
58 | if (wordId < ReadInf::nWords - 1) readPacked[wordId + 1] |= charVal >> (bitsPerWord - offsetInWord);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
make[2]: *** [src/CMakeFiles/metaG.dir/assembly.cpp.o] Error 1
make[1]: *** [src/CMakeFiles/metaG.dir/all] Error 2
make: *** [all] Error 2