There are several UNDONEs in generate_fjalar_entries.c, typedata.c and ?(other 
files)? relating to a problem caused by a change in the DWARF info for global 
static members.  I've gotten it to work, but had to comment out a couple of 
data integrety asserts - that is not a good thing.  See generate_fjalar_entries 
lines 918, 1043, 2107 and typedata.c line 2200

(don't remember if any time the options is used or certains test case(s))
seems to be around line 222 in kvasir_main.c.  I have a note that says when I 
fixed that is then got an assert in decls-output.c (around 484)

compiler changes or platform changes may require clean-output.pl to be 
modified. This file is located in daikon/tests/kvasir-tests.  (Also in 
dyncomp-tests, but while I have not used it, I think it is different.)  It 
contains address ranges that map into STATIC, HEAP, and STACK.  This is done to 
simplify comparing to goal files.

How can I instrument local variables in functions? The documentation states 
that fjalar doesnt provide support for it yet, but it can be extended easily. 
Can anyone suggest how can this be done?

I want to put a random value into some variables during runtime by 
instrumentation. Can that be done with fjalar?

// test.c
// gcc -gdwarf-2 -no-pie -O0 -fno-stack-clash-protection test.c -o test

struct struct_b {};
struct struct_c {};

struct test_struct {
  int a;
  struct struct_b b;
  struct struct_c c;
};

int func(struct test_struct *test) { return 0; }
int main(int argc, char *argv[]) { return 0; }

kvasir-dtrace ./test
==855701== kvasir-5.8.19, C/C++ Language Front-End for Daikon with DynComp comparability analysis tool.
==855701== Copyright (C) 2007-2022, University of Washington CSE PLSE Group
==855701== Using Valgrind-3.19.0.Fjalar and LibVEX; rerun with -h for copyright info
==855701== Command: ./test
==855701== 

kvasir: generate_fjalar_entries.c:774 (repCheckAllEntries): Assertion 'curMember->memberVar->data_member_location > prev_data_member_location' failed.
Segmentation fault (core dumped)

$ uname -a
Linux xxx 3.19.0-58-generic #64~14.04.1-Ubuntu SMP Fri Mar 18 19:05:43 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

../coregrind/link_tool_exe_linux 0x38000000 gcc  -Wno-cast-qual   -o fjalar-x86-linux -m32 -mpreferred-stack-boundary=2 -O2 -g -std=gnu99 -Wall -Wmissing-prototypes -Wshadow -Wpointer-arith -Wstrict-prototypes -Wmissing-declarations -Wcast-align -Wcast-qual -Wwrite-strings -Wempty-body -Wformat -Wformat-security -Wignored-qualifiers -Wmissing-parameter-type -Wold-style-declaration -fno-stack-protector -fno-strict-aliasing -fno-builtin -fomit-frame-pointer -Iinclude -I../VEX/pub -I../include -I.. -O0 -static -nodefaultlibs -nostartfiles -u _start  -m32 fjalar_x86_linux-mc_leakcheck.o fjalar_x86_linux-mc_malloc_wrappers.o fjalar_x86_linux-mc_main.o fjalar_x86_linux-mc_translate.o fjalar_x86_linux-mc_machine.o fjalar_x86_linux-mc_errors.o fjalar_x86_linux-fjalar_dwarf.o fjalar_x86_linux-fjalar_main.o fjalar_x86_linux-fjalar_runtime.o fjalar_x86_linux-fjalar_select.o fjalar_x86_linux-generate_fjalar_entries.o fjalar_x86_linux-GenericHashtable.o fjalar_x86_linux-fjalar_traversal.o fjalar_x86_linux-readelf.o fjalar_x86_linux-dwarf.o libiberty/fjalar_x86_linux-dwarfnames.o fjalar_x86_linux-elfcomm.o fjalar_x86_linux-typedata.o fjalar_x86_linux-disambig.o fjalar_x86_linux-my_libc.o fjalar_x86_linux-my_libc_float.o fjalar_x86_linux-tsearch.o kvasir/fjalar_x86_linux-kvasir_main.o kvasir/fjalar_x86_linux-decls-output.o kvasir/fjalar_x86_linux-dtrace-output.o kvasir/fjalar_x86_linux-union_find.o kvasir/fjalar_x86_linux-dyncomp_main.o kvasir/fjalar_x86_linux-dyncomp_runtime.o kvasir/fjalar_x86_linux-dyncomp_translate.o ../coregrind/libcoregrind-x86-linux.a ../VEX/libvex-x86-linux.a -lgcc 
fjalar_x86_linux-readelf.o: In function `dump_relocations':
/bat0/stac/fjalar/valgrind/fjalar/readelf.c:1272: undefined reference to `_bfd_int64_low'
/bat0/stac/fjalar/valgrind/fjalar/readelf.c:1272: undefined reference to `_bfd_int64_high'
/bat0/stac/fjalar/valgrind/fjalar/readelf.c:1272: undefined reference to `_bfd_int64_low'
/bat0/stac/fjalar/valgrind/fjalar/readelf.c:1272: undefined reference to `_bfd_int64_high'
collect2: error: ld returned 1 exit status
make[3]: *** [fjalar-x86-linux] Error 1
make[3]: Leaving directory `/bat0/stac/fjalar/valgrind/fjalar'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/bat0/stac/fjalar/valgrind/fjalar'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/bat0/stac/fjalar/valgrind'
make: *** [all] Error 2

git clone https://github.com/codespecs/fjalar.git
cd fjalar
sudo apt-get install binutils-dev
./auto-everything.sh

I got an error about zconf.h not found, so as suggested here: https://bugs.launchpad.net/ubuntu/+source/zlib/+bug/1155307 I create following symbolic link:
sudo ln -s /usr/include/x86_64-linux-gnu/zconf.h /usr/include

executed ./auto-everything.sh again
Got above error.

The 'how to update' doc needs to be updated to talk about porting changes from 
stand alone bintuils/readelf to our readelf.c/dwarf.c.

Fjalar and Kvasir use a mixture of printf, fprintf, puts, fputs, and others.  
Some of these are handled by my_libc.c and some are handled by Valgrind (via 
the VG_ prefix).  This leads to different output (due to different 
implementations of format chars) and some mixed up buffering.

This is the exact same implementation problem as issue #7 - passing structs in 
registers.  On AMD64 gcc optimizes properly aligned struct copys by doing a REP 
MOVSQ.  Valgrind changes this into a series of register loads and stores and we 
have the same comparability set problem.

                 -Mike

cd daikonparent
wget http://plse.cs.washington.edu/daikon/download/daikon-5.8.6.tar.gz
tar zxf daikon-5.8.6.tar.gz

#The absolute pathname of the directory that contains Daikon
export DAIKONDIR=daikonparent/daikon-5.8.6
source $DAIKONDIR/scripts/daikon.bashrc

cd $DAIKONDIR
cd ..
git clone https://github.com/codespecs/fjalar.git

cd $DAIKONDIR
make kvasir

cd $DAIKONDIR/scripts/
gcc -g -no-pie total.c
kvasir-dtrace ./a.out

==16605== kvasir-5.8.6, C/C++ Language Front-End for Daikon with DynComp comparability analysis tool.
==16605== Copyright (C) 2007-2020, University of Washington CSE PLSE Group
==16605== Using Valgrind-3.16.1.Fjalar and LibVEX; rerun with -h for copyright info
==16605== Command: ./a.out
==16605==

kvasir: generate_fjalar_entries.c:647 (repCheckAllEntries): Assertion 'f->endPC' failed.
Segmentation fault (core dumped)

gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)

#include <stdio.h>
#include <stdlib.h>
int main()
{
        int n = 10, i, total = 0;
        int *arr;
        arr = (int *) malloc(n * sizeof(int));
        for (i = 0; i < n; i++) {
                arr[i] = i * i;
                total += arr[i];
        }
        printf("Total = %d\n", total);
        free(arr);
        return 0;
}

In file included from fjalar_dwarf.h:27,
                 from fjalar_include.h:32,
                 from fjalar_main.h:42,
                 from readelf.c:106:
dwarf.h:23:27: error: conflicting types for 'uintptr_t'
   23 | typedef unsigned long int uintptr_t;
      |                           ^~~~~~~~~
In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/stdint.h:9,
                 from /usr/include/bfd_stdint.h:7,
                 from /usr/include/bfd.h:44,
                 from readelf.c:99:
/usr/include/stdint.h:96:23: note: previous declaration of 'uintptr_t' was here
   96 | typedef unsigned int  uintptr_t;
      |                       ^~~~~~~~~
In file included from fjalar_dwarf.h:27,
                 from fjalar_include.h:32,
                 from fjalar_main.h:42,
                 from readelf.c:106:
dwarf.h:24:27: error: conflicting types for 'uint64_t'
   24 | typedef unsigned long int uint64_t;
      |                           ^~~~~~~~
In file included from /usr/include/stdint.h:37,
                 from /usr/lib/gcc/x86_64-pc-linux-gnu/9.1.0/include/stdint.h:9,
                 from /usr/include/bfd_stdint.h:7,
                 from /usr/include/bfd.h:44,
                 from readelf.c:99:
/usr/include/bits/stdint-uintn.h:27:20: note: previous declaration of 'uint64_t' was here
   27 | typedef __uint64_t uint64_t;
      |                    ^~~~~~~~

Currently, to get a dump of the internal IR, you need to edit mc_translate.c 
and recompile.  This should be changed to a runtime option. 

What steps will reproduce the problem?
1. FJALAR_DPRINT at generate_fjalar_entries.c:3107 is currently commented out; 
need to turn back on 
2. run with --fjalar-debug
3. test case needs to be c++ with a class with member funcstions

basic-tool/../dwarf.h:232:34: error: unknown type name ‘size_t’
extern void * xcrealloc (void *, size_t, size_t);

/usr/include/stdio.h:48:25: error: conflicting types for ‘FILE’
typedef struct _IO_FILE FILE;

compare output of running daikon/tests/kvasir/tests/TypedefTest on x86 vs. 
amd64.  The later passes small structs in registers.  Current implementation of 
kvasir only assigns a single value tag field to an entire register.  Hence, 
when the struct is loaded into the register to pass as argument we mark all 
struct fields that happen to map to the same register as having an interaction 
when in fact they do not.  Test case needs to be modifed back to have first 
struct element (a) being an int instead of a long.  decls output will then show 
a and b in same compare set on amd64 but in separate sets on x86 (correctly).

This is a serious problem, but is part of the current design.  Fix will be a 
major work item.

What steps will reproduce the problem?
1.sudo make kvasir

What is the expected output? What do you see instead?
The make fails with the following output:
readelf.c:53:17: fatal error: bfd.h: No such file or directory
compilation terminated.
make[4]: *** [fjalar_x86_linux-readelf.o] Error 1
make[4]: Leaving directory 
`/home/saikat/Downloads/daikon/kvasir/valgrind/fjalar'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory 
`/home/saikat/Downloads/daikon/kvasir/valgrind/fjalar'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/saikat/Downloads/daikon/kvasir/valgrind'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/saikat/Downloads/daikon/kvasir/valgrind'
make: *** [kvasir] Error 2

What version of the product are you using? On what operating system?
I am using Daikon 5.0 on Ubuntu 12.04LTS 32 bit OS

Am i missing any step?

tag_is_collection_type, definition at typedata.c:188.  According to DWARF, sets 
are collection types, but I suspect our meaning is more restrictive and this 
may not be the right thing to do.

pgbovine@bovine-linode ~/fjalar
$ git diff
diff --git a/valgrind/Makefile.all.am b/valgrind/Makefile.all.am
index 68f8fe5..04a04bd 100644
--- a/valgrind/Makefile.all.am
+++ b/valgrind/Makefile.all.am
@@ -110,6 +110,12 @@ AM_CFLAGS_BASE = \
        -fno-strict-aliasing \
        -fno-builtin

+# If have latest gcc then default inlining
+# has been changed, use std=gnu89 to get old style
+if COMPILER_IS_V5
+AM_CFLAGS_BASE += -std=gnu89
+endif
+
 # These flags are used for building the preload shared objects (PSOs).
 # The aim is to give reasonable performance but also to have good
 # stack traces, since users often see stack traces extending