Re: crash on Ubuntu 16.04 (64bit)

Posted by Volker Baecker on Jun 22, 2017; 9:52am
URL: http://imagej.273.s1.nabble.com/crash-on-Ubuntu-16-04-64bit-tp5018935p5018938.html

Hi,
we have the same here since yesterday, on different versions of ubuntu,
following an update of ubuntu. It applies to FIJI and to ImageJ. The
problem is the binary ImageJ launcher (ImageJ-linux64 for FIJI and
ImageJ for ImageJ). Running ImageJ without the launcher, i.e. using
something like:

./jre/bin/java -Xmx6000m -cp ij.jar:. ij.ImageJ

and running FIJI with the script ImageJ.sh from:

https://github.com/imagej/imagej/blob/master/bin/ImageJ.sh

works fine.

Best regards,
Volker Baecker






Ivo Alxneit:

> Dear all
>
> After a few updates to my Ubuntu system (I cannot pin down to last
> working state) ImageJ (pretty much up-to-date as I update automatically)
> now segfaults right away.
>
> $ uname -a
> Linux foobar 4.4.0-81-generic #104-Ubuntu SMP Wed Jun 14 08:17:06 UTC
> 2017 x86_64 x86_64 x86_64 GNU/Linux
>
> $ java -version
> openjdk version "1.8.0_131"
> OpenJDK Runtime Environment (build 1.8.0_131-8u131-b11-0ubuntu1.16.04.2-b11)
> OpenJDK 64-Bit Server VM (build 25.131-b11, mixed mode)
>
> $strace ImageJ
> (lots left out)
> lstat("/fast_home", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
> lstat("/fast_home/alxneit", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
> lstat("/fast_home/alxneit/Fiji.app", {st_mode=S_IFDIR|0775,
> st_size=4096, ...}) = 0
> lstat("/fast_home/alxneit/Fiji.app/java", {st_mode=S_IFDIR|0775,
> st_size=4096, ...}) = 0
> lstat("/fast_home/alxneit/Fiji.app/java/linux-amd64",
> {st_mode=S_IFDIR|0775, st_size=4096, ...}) = 0
> lstat("/fast_home/alxneit/Fiji.app/java/linux-amd64/jdk1.8.0_66",
> {st_mode=S_IFDIR|0775, st_size=4096, ...}) = 0
> lstat("/fast_home/alxneit/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre",
> {st_mode=S_IFDIR|0775, st_size=4096, ...}) = 0
> lstat("/fast_home/alxneit/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib",
> {st_mode=S_IFDIR|0775, st_size=4096, ...}) = 0
> lstat("/fast_home/alxneit/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/rt.jar",
> {st_mode=S_IFREG|0755, st_size=66027660, ...}) = 0
> open("/fast_home/alxneit/Fiji.app/java/linux-amd64/jdk1.8.0_66/jre/lib/rt.jar",
> O_RDONLY) = 4
> fstat(4, {st_mode=S_IFREG|0755, st_size=66027660, ...}) = 0
> fcntl(4, F_GETFD)                       = 0
> fcntl(4, F_SETFD, FD_CLOEXEC)           = 0
> read(4, "PK\3\4", 4)                    = 4
> lseek(4, 0, SEEK_END)                   = 66027660
> lseek(4, 66027532, SEEK_SET)            = 66027532
> read(4, "\0\0\0\0\0\0\0\0\0\0\0\0\345\276\321\3java/lang/String"...,
> 128) = 128
> mmap(NULL, 1933452, PROT_READ, MAP_SHARED, 4, 0x3d20000) = 0x7fadc542a000
> mmap(NULL, 323584, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1,
> 0) = 0x7fadc53db000
> brk(0x1c70000)                          = 0x1c70000
> lseek(4, 64096521, SEEK_SET)            = 64096521
> read(4,
> "PK\3\4\n\0\0\10\0\0\335\213FG\355;\266\206\331\5\0\0\331\5\0\0\26\0\0\0",
> 30) = 30
> lseek(4, 64096573, SEEK_SET)            = 64096573
> read(4,
> "\312\376\272\276\0\0\0004\0N\7\0001\n\0\1\0002\n\0\21\0003\n\0004\0005\n\0\1\0"...,
> 1497) = 1497
> .
> . many lseek / read
> .
> lseek(4, 63549712, SEEK_SET)            = 63549712
> read(4,
> "\312\376\272\276\0\0\0004\0\25\n\0\4\0\21\n\0\4\0\22\7\0\23\7\0\24\1\0\20ser"...,
> 382) = 382
> mmap(NULL, 1052672, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_ANONYMOUS|MAP_STACK, -1, 0) = 0x7fadc52da000
> mprotect(0x7fadc52da000, 4096, PROT_NONE) = 0
> clone(child_stack=0x7fadc53d9ff0,
> flags=CLONE_VM|CLONE_FS|CLONE_FILES|CLONE_SIGHAND|CLONE_THREAD|CLONE_SYSVSEM|CLONE_SETTLS|CLONE_PARENT_SETTID|CLONE_CHILD_CLEARTID,
> parent_tidptr=0x7fadc53da9d0, tls=0x7fadc53da700,
> child_tidptr=0x7fadc53da9d0) = 8620
> futex(0x1c7f054, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x1c7f050, {FUTEX_OP_SET,
> 0, FUTEX_OP_CMP_GT, 1}) = 1
> futex(0x1c7f028, FUTEX_WAKE_PRIVATE, 1) = 1
> futex(0x1b76754, FUTEX_WAIT_PRIVATE, 3, NULL) = 0
> futex(0x1b76728, FUTEX_WAKE_PRIVATE, 1) = 0
> --- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_MAPERR,
> si_addr=0x7ffe18b1f230} ---
> rt_sigprocmask(SIG_SETMASK, ~[RTMIN RT_1], ~[KILL STOP RTMIN RT_1], 8) = 0
> --- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_MAPERR,
> si_addr=0x7ffe18b1ffe0} ---
> +++ killed by SIGSEGV (core dumped) +++
>
>
> Any help / suggestions appreciated
>

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