Plug memory leak #7

ms609 · 2021-06-16T16:26:49Z

p0 seems never to be freed.
This PR adds a record of its unincremented address to the tr object, and frees it in freeTree().
valgrind suggests that this plugs the leak.

free(p0) Need also to change legacy.h

Unmatched CALLOC

ms609 · 2023-07-24T08:51:40Z

I couldn't pick this thread up on GitHub so assume you got to the bottom of it – but let me know if not.

…

On Tue, 18 Jul 2023 at 09:38, JGLAHE ***@***.***> wrote: common.h includes R.h but this header isn't among the source files? How should this be compiled? Cheers — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAM56G5X4SSD5AULBHCQBN3XQZDOHANCNFSM46ZZ43GA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

JGLAHE · 2023-07-25T15:30:14Z

Yes sorry I got confused: aberer/RogueNaRok lists two public forks (the most recent of which is yours), but accessing it from that ms609/RogueNaRok link goes to the ms609:master branch, which is what I cloned, and thus got an error about common.h requiring R.h.

I commented about it here before I found the ms609:patch-1 branch through somewhere, maybe one of the CRAN pages (I can't recall exactly? obviously I wasn't thinking clearly). But that worked well, so hopefully this eventually gets merged...

JGLAHE · 2023-08-23T08:53:58Z

Hi, sorry just getting back to this:

RogueNaRok $make
gcc  -c -o common.o common.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
gcc  -c -o RogueNaRok.o RogueNaRok.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
gcc  -c -o Tree.o Tree.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
gcc  -c -o BitVector.o BitVector.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
gcc  -c -o HashTable.o HashTable.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
gcc  -c -o List.o List.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
gcc  -c -o Array.o Array.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
gcc  -c -o Dropset.o Dropset.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
gcc  -c -o ProfileElem.o ProfileElem.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
gcc  -c -o legacy.o legacy.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
gcc  -c -o newFunctions.o newFunctions.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
gcc  -c -o parallel.o parallel.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
gcc  -c -o Node.o Node.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
gcc  -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -o RogueNaRok common.o RogueNaRok.o Tree.o BitVector.o HashTable.o List.o Array.o Dropset.o ProfileElem.o legacy.o newFunctions.o parallel.o Node.o -lm
/usr/bin/ld: RogueNaRok.o:(.bss+0x10080): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: Tree.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here
/usr/bin/ld: Tree.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: BitVector.o:(.bss+0x20): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here
/usr/bin/ld: BitVector.o:(.bss+0x10020): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: HashTable.o:(.bss+0x0): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: List.o:(.bss+0x0): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: Dropset.o:(.bss+0x20): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here
/usr/bin/ld: Dropset.o:(.bss+0x10020): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: ProfileElem.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here
/usr/bin/ld: ProfileElem.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: legacy.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here
/usr/bin/ld: legacy.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: newFunctions.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here
/usr/bin/ld: newFunctions.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: Node.o:(.bss+0x0): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:49: RogueNaRok] Error 1

and,

RogueNaRok $make mode=parallel
gcc  -c -o common.o common.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS
gcc  -c -o RogueNaRok.o RogueNaRok.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS
gcc  -c -o Tree.o Tree.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS
gcc  -c -o BitVector.o BitVector.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS
gcc  -c -o HashTable.o HashTable.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS
gcc  -c -o List.o List.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS
gcc  -c -o Array.o Array.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS
gcc  -c -o Dropset.o Dropset.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS
gcc  -c -o ProfileElem.o ProfileElem.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS
gcc  -c -o legacy.o legacy.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS
gcc  -c -o newFunctions.o newFunctions.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS
gcc  -c -o parallel.o parallel.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS
gcc  -c -o Node.o Node.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS
gcc  -Wall -D_GNU_SOURCE -O3 -DNDEBUG  -DPARALLEL -DPORTABLE_PTHREADS  -o RogueNaRok-parallel common.o RogueNaRok.o Tree.o BitVector.o HashTable.o List.o Array.o Dropset.o ProfileElem.o legacy.o newFunctions.o parallel.o Node.o -lm -pthread
/usr/bin/ld: RogueNaRok.o:(.bss+0x100c0): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: Tree.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0xc0): first defined here
/usr/bin/ld: Tree.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: BitVector.o:(.bss+0x20): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0xc0): first defined here
/usr/bin/ld: BitVector.o:(.bss+0x10020): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: HashTable.o:(.bss+0x0): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: List.o:(.bss+0x0): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: Dropset.o:(.bss+0x20): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0xc0): first defined here
/usr/bin/ld: Dropset.o:(.bss+0x10020): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: ProfileElem.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0xc0): first defined here
/usr/bin/ld: ProfileElem.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: legacy.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0xc0): first defined here
/usr/bin/ld: legacy.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: newFunctions.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0xc0): first defined here
/usr/bin/ld: newFunctions.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: parallel.o:(.bss+0x0): multiple definition of `globalPArgs'; RogueNaRok.o:(.bss+0x68): first defined here
/usr/bin/ld: parallel.o:(.bss+0x20): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0xc0): first defined here
/usr/bin/ld: parallel.o:(.bss+0x10020): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
/usr/bin/ld: Node.o:(.bss+0x0): multiple definition of `processID'; common.o:(.bss+0x480): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:46: RogueNaRok] Error 1

This was via git clone -b patch-1 https://github.com/ms609/RogueNaRok.git
GNU Make 4.3 Built for x86_64-pc-linux-gnu
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0

I tried moving some definitions around (processID; bits_in_16bits) and it also complained about globalPArgs in debug and it got rid of the warning but aborted as soon as it started on the examples (I don't know C at all)

Cheers

ms609 · 2023-08-23T10:28:09Z

From the logs, this doesn't look related to the changes introduced in the patch; do you encounter the same issues make-ing the master branch, or do they only occur on the patch? From: lLLHMM ***@***.***> Sent: 23 August 2023 16:54 To: aberer/RogueNaRok ***@***.***> Cc: SMITH, MARTIN R. ***@***.***>; Author ***@***.***> Subject: Re: [aberer/RogueNaRok] Plug memory leak (#7) [EXTERNAL EMAIL] Hi, sorry just getting back to this: RogueNaRok $make gcc -c -o common.o common.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o RogueNaRok.o RogueNaRok.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o Tree.o Tree.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o BitVector.o BitVector.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o HashTable.o HashTable.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o List.o List.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o Array.o Array.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o Dropset.o Dropset.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o ProfileElem.o ProfileElem.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o legacy.o legacy.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o newFunctions.o newFunctions.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o parallel.o parallel.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o Node.o Node.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -Wall -D_GNU_SOURCE -O3 -DNDEBUG -o RogueNaRok common.o RogueNaRok.o Tree.o BitVector.o HashTable.o List.o Array.o Dropset.o ProfileElem.o legacy.o newFunctions.o parallel.o Node.o -lm /usr/bin/ld: RogueNaRok.o:(.bss+0x10080): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: Tree.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here /usr/bin/ld: Tree.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: BitVector.o:(.bss+0x20): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here /usr/bin/ld: BitVector.o:(.bss+0x10020): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: HashTable.o:(.bss+0x0): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: List.o:(.bss+0x0): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: Dropset.o:(.bss+0x20): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here /usr/bin/ld: Dropset.o:(.bss+0x10020): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: ProfileElem.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here /usr/bin/ld: ProfileElem.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: legacy.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here /usr/bin/ld: legacy.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: newFunctions.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here /usr/bin/ld: newFunctions.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: Node.o:(.bss+0x0): multiple definition of `processID'; common.o:(.bss+0x480): first defined here collect2: error: ld returned 1 exit status make: *** [Makefile:49: RogueNaRok] Error 1 and, RogueNaRok $make gcc -c -o common.o common.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o RogueNaRok.o RogueNaRok.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o Tree.o Tree.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o BitVector.o BitVector.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o HashTable.o HashTable.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o List.o List.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o Array.o Array.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o Dropset.o Dropset.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o ProfileElem.o ProfileElem.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o legacy.o legacy.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o newFunctions.o newFunctions.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o parallel.o parallel.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -c -o Node.o Node.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG gcc -Wall -D_GNU_SOURCE -O3 -DNDEBUG -o RogueNaRok common.o RogueNaRok.o Tree.o BitVector.o HashTable.o List.o Array.o Dropset.o ProfileElem.o legacy.o newFunctions.o parallel.o Node.o -lm /usr/bin/ld: RogueNaRok.o:(.bss+0x10080): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: Tree.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here /usr/bin/ld: Tree.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: BitVector.o:(.bss+0x20): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here /usr/bin/ld: BitVector.o:(.bss+0x10020): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: HashTable.o:(.bss+0x0): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: List.o:(.bss+0x0): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: Dropset.o:(.bss+0x20): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here /usr/bin/ld: Dropset.o:(.bss+0x10020): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: ProfileElem.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here /usr/bin/ld: ProfileElem.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: legacy.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here /usr/bin/ld: legacy.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: newFunctions.o:(.bss+0x0): multiple definition of `bits_in_16bits'; RogueNaRok.o:(.bss+0x80): first defined here /usr/bin/ld: newFunctions.o:(.bss+0x10000): multiple definition of `processID'; common.o:(.bss+0x480): first defined here /usr/bin/ld: Node.o:(.bss+0x0): multiple definition of `processID'; common.o:(.bss+0x480): first defined here collect2: error: ld returned 1 exit status make: *** [Makefile:49: RogueNaRok] Error 1 ? - Reply to this email directly, view it on GitHub<#7 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAM56G2JB2JBPK35ORV7RBLXWXALDANCNFSM46ZZ43GA>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

JGLAHE · 2023-08-23T11:01:14Z

Thank you for the quick response!

I assume I can just use the patch-1 makefile for the master branch (there's no makefile)?

Anyway, make just gave me the same error as last time:

RogueNaRok $make
gcc  -c -o common.o common.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG
In file included from common.c:31:
common.h:43:10: fatal error: R.h: No such file or directory
   43 | #include <R.h>
      |          ^~~~~
compilation terminated.
make: *** [Makefile:53: common.o] Error 1

ms609 · 2023-08-23T11:05:04Z

I meant for the RogueNaRok master branch, rather than the ms609 repo (which is modified to be called from inside R, rather than as a standalone app, and thus lacks a makefile). If it is simpler you could manually copy the modifications to your own branch of the main repo? From: lLLHMM ***@***.***> Sent: 23 August 2023 19:01 To: aberer/RogueNaRok ***@***.***> Cc: SMITH, MARTIN R. ***@***.***>; Author ***@***.***> Subject: Re: [aberer/RogueNaRok] Plug memory leak (#7) [EXTERNAL EMAIL] Thank you for the quick response! I assume I can just use the patch-1 makefile for the master branch (there's no makefile)? Anyway, make just gave me the same error as last time: RogueNaRok $make gcc -c -o common.o common.c -Wall -D_GNU_SOURCE -O3 -DNDEBUG In file included from common.c:31: common.h:43:10: fatal error: R.h: No such file or directory 43 | #include <R.h> | ^~~~~ compilation terminated. make: *** [Makefile:53: common.o] Error 1 - Reply to this email directly, view it on GitHub<#7 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAM56G7LSRZRCTJBYDXAIBTXWXPILANCNFSM46ZZ43GA>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

JGLAHE · 2023-08-23T11:47:59Z

Yes, sorry I misunderstood; yes I'll fork it cheers

ms609 and others added 3 commits June 16, 2021 17:02

Plug memory leak

fbe7db0

free(p0) Need also to change legacy.h

nodeptr p0;

639242e

free(taxaDroppedHere);

562f448

Unmatched CALLOC

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Plug memory leak #7

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ms609 commented Jun 16, 2021

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Plug memory leak #7

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