Hi,
I installed sonLib as the instructions.
Many apps can run normally, like cPecanLastz, but two of them like sonLib_fastaCTest, sonLib_cigarTest can not and tell me they are core dumped.
I used strace and it prints like this:
[zoum@diggers bin]$ strace ./sonLib_fastaCTest
execve("./sonLib_fastaCTest", ["./sonLib_fastaCTest"], [/* 34 vars */]) = 0
brk(NULL) = 0x1517000
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f3593111000
access("/etc/ld.so.preload", R_OK) = -1 ENOENT (No such file or directory)
open("/home/zoum/srcs/lzo-2.10/zm/lib/tls/x86_64/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/zoum/srcs/lzo-2.10/zm/lib/tls/x86_64", 0x7ffc236c1f10) = -1 ENOENT (No such file or directory)
open("/home/zoum/srcs/lzo-2.10/zm/lib/tls/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/zoum/srcs/lzo-2.10/zm/lib/tls", 0x7ffc236c1f10) = -1 ENOENT (No such file or directory)
open("/home/zoum/srcs/lzo-2.10/zm/lib/x86_64/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/zoum/srcs/lzo-2.10/zm/lib/x86_64", 0x7ffc236c1f10) = -1 ENOENT (No such file or directory)
open("/home/zoum/srcs/lzo-2.10/zm/lib/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/zoum/srcs/lzo-2.10/zm/lib", {st_mode=S_IFDIR|0755, st_size=114, ...}) = 0
open("/usr/lib64/tls/x86_64/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/usr/lib64/tls/x86_64", 0x7ffc236c1f10) = -1 ENOENT (No such file or directory)
open("/usr/lib64/tls/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/usr/lib64/tls", {st_mode=S_IFDIR|0555, st_size=6, ...}) = 0
open("/usr/lib64/x86_64/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/usr/lib64/x86_64", 0x7ffc236c1f10) = -1 ENOENT (No such file or directory)
open("/usr/lib64/libm.so.6", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\3\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\20S\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=1137024, ...}) = 0
mmap(NULL, 3150120, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f3592bef000
mprotect(0x7f3592cf0000, 2093056, PROT_NONE) = 0
mmap(0x7f3592eef000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x100000) = 0x7f3592eef000
close(3) = 0
open("/home/zoum/srcs/lzo-2.10/zm/lib/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
open("/usr/lib64/tls/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
open("/usr/lib64/libc.so.6", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\3\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\240%\2\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=2151672, ...}) = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f3593110000
mmap(NULL, 3981792, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f3592822000
mprotect(0x7f35929e4000, 2097152, PROT_NONE) = 0
mmap(0x7f3592be4000, 24576, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x1c2000) = 0x7f3592be4000
mmap(0x7f3592bea000, 16864, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7f3592bea000
close(3) = 0
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f359310e000
arch_prctl(ARCH_SET_FS, 0x7f359310e740) = 0
mprotect(0x7f3592be4000, 16384, PROT_READ) = 0
mprotect(0x7f3592eef000, 4096, PROT_READ) = 0
mprotect(0x61b000, 4096, PROT_READ) = 0
mprotect(0x7f3593112000, 4096, PROT_READ) = 0
brk(NULL) = 0x1517000
brk(0x1538000) = 0x1538000
brk(NULL) = 0x1538000
open(NULL, O_RDONLY) = -1 EFAULT (Bad address)
--- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_MAPERR, si_addr=0} ---
+++ killed by SIGSEGV (core dumped) +++
段错误(吐核)
How can i fix this? Thank you very much.