crash on Ubuntu 16.04 (64bit)

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crash on Ubuntu 16.04 (64bit)

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
--
Dr. Ivo Alxneit
Catalysis for Energy Group
Bioenergy and Catalysis Laboratory        phone: +41 56 310 4092
Paul Scherrer Institute                     fax: +41 56 310 2688
CH-5232 Villigen                      gnupg key: 0x515E30C7
Switzerland
https://www.psi.ch/ceg/


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

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Re: crash on Ubuntu 16.04 (64bit)

Shokishy
I get the same problem on Ubuntu 17.04

Yesterday it was working fine and now I get a segfault when I run ImageJ.

I tried doing a clean install of ImageJ but it didn't solved the problem.
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Re: crash on Ubuntu 16.04 (64bit)

Volker Baecker
In reply to this post by Ivo Alxneit
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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Re: crash on Ubuntu 16.04 (64bit)

Ivo Alxneit
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: +41 56 310 4092
Paul Scherrer Institute                     fax: +41 56 310 2688
CH-5232 Villigen                      gnupg key: 0x515E30C7
Switzerland
https://www.psi.ch/ceg/


--
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Re: crash on Ubuntu 16.04 (64bit)

ctrueden
In reply to this post by Shokishy
Hi FĂ©lix,

Please see this discussion on the ImageJ Forum:
http://forum.imagej.net/t/unable-to-start-imagej-on-
ubuntu-16-04-2-fresh-install/5757

The problem is apparently with the Linux kernel update. From the forum
thread:

> I ran into the exact same problem today in Ubuntu 16.04 after updating
> to 4.4.0-81. After booting with kernel 4.4.0-79 (and presumably any
> earlier kernels) ImageJ / FIJI are working without a problem.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Jun 22, 2017 at 4:12 AM, Shokishy <[hidden email]> wrote:

> I get the same problem on Ubuntu 17.04
>
> Yesterday it was working fine and now I get a segfault when I run ImageJ.
>
> I tried doing a clean install of ImageJ but it didn't solved the problem.
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.c
> om/crash-on-Ubuntu-16-04-64bit-tp5018935p5018937.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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