[gmx-users] very strange directory dependent segmentation faults please HELP!
Claudio J. Margulis
claudio-margulis at uiowa.edu
Fri Dec 26 18:00:01 CET 2003
This is the output that i get after running "strace mdrun" (it doesn't
mean much to me I will compare it to the one i get in a directory in
which the program runs fine. Please let me know if you see anything
obviously strange.
The only thing i can see is that the program is looking for files at
different possible locations until it finds them, first some library,
then some other input file under the share directory, etc.
Perhaps my PATH environment is too long? I don't know what to think.
Any help is appreciated!
Thanks and happy holidays!
--------------------------------------------------------------------
node1-claudiom 150 % strace mdrun
execve("/usr/local/gromacs/serial/i686-pc-linux-gnu/bin/mdrun",
["mdrun"], [/* 39 vars */]) = 0
uname({sys="Linux", node="node1.chem.uiowa.edu", ...}) = 0
brk(0) = 0x826ac08
old_mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS,
-1, 0) = 0x40013000
open("/etc/ld.so.preload", O_RDONLY) = -1 ENOENT (No such file or
directory)
open("/opt/intel/compiler70/ia32/lib/mmx/libnsl.so.1", O_RDONLY) = -1
ENOENT (No such file or directory)
stat64("/opt/intel/compiler70/ia32/lib/mmx", 0xbfffd060) = -1 ENOENT (No
such file or directory)
open("/opt/intel/compiler70/ia32/lib/libnsl.so.1", O_RDONLY) = -1 ENOENT
(No such file or directory)
stat64("/opt/intel/compiler70/ia32/lib", {st_mode=S_IFDIR|0777,
st_size=1360, ...}) = 0
open("/etc/ld.so.cache", O_RDONLY) = 3
fstat64(3, {st_mode=S_IFREG|0644, st_size=88914, ...}) = 0
old_mmap(NULL, 88914, PROT_READ, MAP_PRIVATE, 3, 0) = 0x40014000
close(3) = 0
open("/lib/libnsl.so.1", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0008<\0\000"...,
512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=86872, ...}) = 0
old_mmap(NULL, 76416, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) =
0x4002a000
old_mmap(0x4003a000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED,
3, 0x10000) = 0x4003a000
old_mmap(0x4003b000, 6784, PROT_READ|PROT_WRITE,
MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x4003b000
close(3) = 0
open("/opt/intel/compiler70/ia32/lib/libm.so.6", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/lib/libm.so.6", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0P5\0\000"...,
512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=208984, ...}) = 0
old_mmap(NULL, 131520, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) =
0x4003d000
old_mmap(0x4005d000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED,
3, 0x20000) = 0x4005d000
close(3) = 0
open("/opt/intel/compiler70/ia32/lib/libXm.so.3", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/usr/X11R6/lib/libXm.so.3", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0pn\4\000"...,
512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=2386852, ...}) = 0
old_mmap(NULL, 2393640, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) =
0x4005e000
old_mmap(0x4028c000, 106496, PROT_READ|PROT_WRITE,
MAP_PRIVATE|MAP_FIXED, 3, 0x22d000) = 0x4028c000
old_mmap(0x402a6000, 1576, PROT_READ|PROT_WRITE,
MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x402a6000
close(3) = 0
open("/opt/intel/compiler70/ia32/lib/libXt.so.6", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/usr/X11R6/lib/libXt.so.6", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\220\277"...,
512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=329232, ...}) = 0
old_mmap(NULL, 334020, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) =
0x402a7000
old_mmap(0x402f5000, 16384, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED,
3, 0x4d000) = 0x402f5000
close(3) = 0
open("/opt/intel/compiler70/ia32/lib/libSM.so.6", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/usr/X11R6/lib/libSM.so.6", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\0\"\0\000"...,
512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=32184, ...}) = 0
old_mmap(NULL, 35252, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) =
0x402f9000
old_mmap(0x40301000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED,
3, 0x7000) = 0x40301000
close(3) = 0
open("/opt/intel/compiler70/ia32/lib/libICE.so.6", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/usr/X11R6/lib/libICE.so.6", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0 at 5\0\000"...,
512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=82320, ...}) = 0
old_mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS,
-1, 0) = 0x40302000
old_mmap(NULL, 92688, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) =
0x40303000
old_mmap(0x40317000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED,
3, 0x13000) = 0x40317000
old_mmap(0x40318000, 6672, PROT_READ|PROT_WRITE,
MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x40318000
close(3) = 0
open("/opt/intel/compiler70/ia32/lib/libXext.so.6", O_RDONLY) = -1
ENOENT (No such file or directory)
open("/usr/X11R6/lib/libXext.so.6", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\20)\0\000"...,
512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=53520, ...}) = 0
old_mmap(NULL, 56796, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) =
0x4031a000
old_mmap(0x40327000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED,
3, 0xc000) = 0x40327000
close(3) = 0
open("/opt/intel/compiler70/ia32/lib/libXp.so.6", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/usr/X11R6/lib/libXp.so.6", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0P\36\0\000"...,
512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=26956, ...}) = 0
old_mmap(NULL, 30028, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) =
0x40328000
old_mmap(0x4032f000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED,
3, 0x6000) = 0x4032f000
close(3) = 0
open("/opt/intel/compiler70/ia32/lib/libX11.so.6", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/usr/X11R6/lib/libX11.so.6", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\200\23"...,
512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=908016, ...}) = 0
old_mmap(NULL, 912092, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) =
0x40330000
old_mmap(0x4040c000, 12288, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED,
3, 0xdb000) = 0x4040c000
close(3) = 0
open("/opt/intel/compiler70/ia32/lib/libcxa.so.3", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0 }\0\000"...,
512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=241125, ...}) = 0
old_mmap(NULL, 206996, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) =
0x4040f000
old_mmap(0x40431000, 69632, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED,
3, 0x21000) = 0x40431000
close(3) = 0
open("/opt/intel/compiler70/ia32/lib/libc.so.6", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/lib/libc.so.6", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0hV\1\000"...,
512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=1474056, ...}) = 0
old_mmap(NULL, 1201892, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) =
0x40442000
old_mmap(0x40562000, 12288, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED,
3, 0x120000) = 0x40562000
old_mmap(0x40565000, 9956, PROT_READ|PROT_WRITE,
MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x40565000
close(3) = 0
open("/opt/intel/compiler70/ia32/lib/libXmu.so.6", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/opt/intel/compiler70/ia32/lib/libXmu.so.6", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/usr/X11R6/lib/libXmu.so.6", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\360J\0"...,
512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=89456, ...}) = 0
old_mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS,
-1, 0) = 0x40568000
old_mmap(NULL, 89352, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) =
0x40569000
old_mmap(0x4057e000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED,
3, 0x15000) = 0x4057e000
close(3) = 0
open("/opt/intel/compiler70/ia32/lib/libdl.so.2", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/opt/intel/compiler70/ia32/lib/libdl.so.2", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/lib/libdl.so.2", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\214\27"...,
512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=15372, ...}) = 0
old_mmap(NULL, 8624, PROT_READ|PROT_EXEC, MAP_PRIVATE, 3, 0) =
0x4057f000
old_mmap(0x40581000, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED,
3, 0x2000) = 0x40581000
close(3) = 0
munmap(0x40014000, 88914) = 0
rt_sigaction(SIGILL, {0x8210d40, ~[], SA_RESTORER, 0x40468d48},
{SIG_DFL}, 8) = 0
rt_sigprocmask(SIG_BLOCK, NULL, [], 8) = 0
rt_sigaction(SIGILL, {SIG_DFL}, NULL, 8) = 0
brk(0) = 0x826ac08
brk(0x826bc08) = 0x826bc08
brk(0) = 0x826bc08
brk(0x826c000) = 0x826c000
write(2, " ", 25 ) = 25
write(2, ":-) G R O M A C S (-:\n", 30:-) G R O M A C S
(-:
) = 30
write(2, "\n", 1
) = 1
getcwd("/scratch/claudiom/111", 511) = 22
open("/scratch/claudiom/111/mdrun", O_RDONLY) = -1 ENOENT (No such file
or directory)
open("/usr/local/bin/mdrun", O_RDONLY) = -1 ENOENT (No such file or
directory)
open("/usr/local/j2sdk_nb/j2sdk1.4.2/bin/mdrun", O_RDONLY) = -1 ENOENT
(No such file or directory)
open("/bin/mdrun", O_RDONLY) = -1 ENOENT (No such file or
directory)
open("/usr/bin/mdrun", O_RDONLY) = -1 ENOENT (No such file or
directory)
open("/usr/X11R6/bin/mdrun", O_RDONLY) = -1 ENOENT (No such file or
directory)
open("/usr/sbin/mdrun", O_RDONLY) = -1 ENOENT (No such file or
directory)
open("/sbin/mdrun", O_RDONLY) = -1 ENOENT (No such file or
directory)
open("/etc/mdrun", O_RDONLY) = -1 ENOENT (No such file or
directory)
open("/usr/etc/mdrun", O_RDONLY) = -1 ENOENT (No such file or
directory)
open("/usr/local/gromacs/i686-pc-linux-gnu/bin/mdrun", O_RDONLY) = -1
ENOENT (No such file or directory)
open("/usr/local/gromacs/serial/i686-pc-linux-gnu/bin/mdrun", O_RDONLY)
= 3
close(3) = 0
readlink("/usr/local/gromacs/serial/i686-pc-linux-gnu/bin/mdrun",
0xbfffc2b0, 511) = -1 EINVAL (Invalid argument)
open("/usr/local/gromacs/serial/i686-pc-linux-gnu/bin/share/top/gurgle.dat", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/local/gromacs/serial/i686-pc-linux-gnu/bin/share/gromacs/top/gurgle.dat", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/local/gromacs/serial/i686-pc-linux-gnu/bin/share/gromacs-3.1.4/top/gurgle.dat", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/local/gromacs/serial/i686-pc-linux-gnu/bin/share/gromacs/gromacs-3.1.4/top/gurgle.dat", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/local/gromacs/serial/i686-pc-linux-gnu/share/top/gurgle.dat",
O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/local/gromacs/serial/i686-pc-linux-gnu/share/gromacs/top/gurgle.dat", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/local/gromacs/serial/i686-pc-linux-gnu/share/gromacs-3.1.4/top/gurgle.dat", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/local/gromacs/serial/i686-pc-linux-gnu/share/gromacs/gromacs-3.1.4/top/gurgle.dat", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/local/gromacs/serial/share/top/gurgle.dat", O_RDONLY) = 3
close(3) = 0
--- SIGSEGV (Segmentation fault) @ 0 (0) ---
+++ killed by SIGSEGV +++
On Fri, 2003-12-26 at 02:35, Lieven Buts wrote:
> On Wednesday 24 December 2003 19:00, Claudio J. Margulis wrote:
> > Does anybody understand this behavior:
> >
> > node1-claudiom 63 % pwd
> > /scratch/claudiom/111
> > node1-claudiom 64 % ls
> > topol.tpr
> > node1-claudiom 65 % mdrun
> >
> > :-) G R O M A C S (-:
> >
> > Segmentation fault
>
> You could try running mdrun through strace, if the latter is available on your
> system. (It should be present on most Linux systems.)
>
> To do this, use "strace mdrun", which will print a list of the system calls
> mdrun uses up to the point of the segmentation fault. This might provide a
> clue as to what it is trying to do. Since it crashes pretty quickly, there
> shouldn't be too many calls to sort through.
>
>
> Happy holidays to all,
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