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TravisWheelerLab / NINJA

Nearly Infinite Neighbor Joining Application
MIT License
5 stars 7 forks source link

File bug #4

Closed michelwandermaas closed 8 years ago

michelwandermaas commented 8 years ago

~/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)

michelwandermaas commented 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().

michelwandermaas commented 8 years ago

File problems are solved along with the directory/name bug.

michelwandermaas commented 8 years ago

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.

michelwandermaas commented 8 years ago

Fixed by opening/closing file in every read/write operation in the ArrayHeapExtMem.