Re: crash on Ubuntu 16.04 (64bit)

Posted by Ivo Alxneit on Jun 22, 2017; 10:40am
URL: http://imagej.273.s1.nabble.com/crash-on-Ubuntu-16-04-64bit-tp5018935p5018940.html

Hi Volker

thanks, the ImageJ.sh script works like a charm!



On 22.06.2017 11:52, Volker Baecker wrote:

> 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
>>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Dr. Ivo Alxneit
Catalysis for Energy Group
Bioenergy and Catalysis Laboratory        phone: [phone]
Paul Scherrer Institute                     fax: [phone]
CH-5232 Villigen                      gnupg key: 0x515E30C7
Switzerland
https://www.psi.ch/ceg/


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