Closed michelwandermaas closed 8 years ago
Update on the issue:
The files are now being closed, although there are now memory errors/double free`s, possibly some bugs regarding the files, and some bugs regarding the name/directory of the files.
Valgrind:
==8155== Command: ./Ninja -m extmem --alph_type d --in_type a --out_type t -i /home/michel/Desktop/round_of_tests_1/DF0000001.fasta -o /home/michel/Desktop/round_of_tests_1/DF0000001_NJ_J_EX.tree ==8155== Reading... Using External Memory... Calculating distances.... Generating tree.... ==8155== Stack overflow in thread #1: can't grow stack to 0xffe801000
Normal execution: michel@michel-Lenovo-Y50-70-Touch:~/NINJA_git_develop/NINJA/NINJA$ ./Ninja_debug -m extmem --alph_type d --in_type a --out_type t -i /home/michel/Desktop/round_of_tests_1/DF0000001.fasta -o /home/michel/Desktop/round_of_tests_1/DF0000001_NJ_J_EX.tree Reading... Using External Memory... Calculating distances.... Generating tree.... Segmentation fault (core dumped)
GDB:
Stackoverflow
The bug is related to CandidateHeap::clear() and TreeBuilderExtMem::~TreeBuilderExtMem().
File problems are solved along with the directory/name bug.
The bug is now back again:
Reading... Using External Memory... created temporary directory for this run of NINJA : treeBuilderManager Calculating distances.... Generating tree.... File deleted: ArrayHeapExtMem delete. File deleted: ArrayHeapExtMem delete. File deleted: ArrayHeapExtMem delete. File deleted: ArrayHeapExtMem delete. File deleted: ArrayHeapExtMem delete. File deleted: ArrayHeapExtMem delete. File deleted: ArrayHeapExtMem delete. File deleted: ArrayHeapExtMem delete. File deleted: ArrayHeapExtMem delete. File deleted: ArrayHeapExtMem delete. File deleted: ArrayHeapExtMem delete. File deleted: ArrayHeapExtMem delete. File deleted: ArrayHeapExtMem delete. File deleted: ArrayHeapExtMem delete. treeBuilderManager/arrayHeapExtMemarrayHeapExtMemarrayHeapExtMem: Too many open files Critical Error, aborting.
Fixed by opening/closing file in every read/write operation in the ArrayHeapExtMem.
~/NINJA_git_develop/NINJA/NINJA$ ./Ninja_debug -m extmem --alph_type d --in_type a --out_type t -i /home/michel/Desktop/round_of_tests_1/DF0000001.fasta -o /home/michel/Desktop/round_of_tests_1/DF0000001_NJ_J_EX.tree Reading... Using External Memory... Calculating distances.... Generating tree.... treeBuilderManagerarrayHeapExtMemarrayHeapExtMemarrayHeapExtMem: Too many open files Critical Error, aborting. Aborted (core dumped)