I'm running a data preparation script with Sparklyr on Rstudio (running in EMR). The code exuction crashes and I got this error report I don't understand properly:
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x00007f99b77fb968, pid=12298, tid=0x00007f99b8167940
#
# JRE version: OpenJDK Runtime Environment (8.0_171-b10) (build 1.8.0_171-b10)
# Java VM: OpenJDK 64-Bit Server VM (25.171-b10 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C [libR.so+0xbe968]
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# If you would like to submit a bug report, please visit:
# http://bugreport.java.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
/proc/meminfo:
MemTotal: 32949048 kB
MemFree: 11480880 kB
MemAvailable: 19345760 kB
Buffers: 455776 kB
Cached: 5598268 kB
SwapCached: 0 kB
Active: 14572612 kB
Inactive: 3704688 kB
Active(anon): 12223280 kB
Inactive(anon): 48 kB
Active(file): 2349332 kB
Inactive(file): 3704640 kB
Unevictable: 0 kB
Mlocked: 0 kB
SwapTotal: 0 kB
SwapFree: 0 kB
Dirty: 748 kB
Writeback: 0 kB
AnonPages: 12223264 kB
Mapped: 198336 kB
...
I want to know how to fix the problem so my code could run entirely ?
Thanks in advance !
Related
I've started working with Puppeteer and for some reason I cannot get it to work on my box. This error seems to be a common problem (SO1, SO2) but all of the solutions do not solve this error for me. I have tested it with a clean node package (see reproduction) and I have taken the example from the official Puppeteer 'Getting started' webpage.
How can I resolve this error?
Versions and hardware
/tmp/so_example » uname -a
Linux tom.arch 5.15.2-arch1-1 #1 SMP PREEMPT Fri, 12 Nov 2021 19:22:10 +0000 x86_64 GNU/Linux
/tmp/so_example » node --version
v17.1.0
/tmp/so_example » npm list
so_example#1.0.0 /tmp/so_example
└── puppeteer#11.0.0
/tmp/so_example » cat /proc/meminfo
MemTotal: 32492764 kB
MemFree: 600032 kB
MemAvailable: 24446556 kB
Buffers: 7149964 kB
Cached: 9549048 kB
SwapCached: 0 kB
Active: 9843552 kB
Inactive: 10980476 kB
Active(anon): 462692 kB
Inactive(anon): 5481100 kB
Active(file): 9380860 kB
Inactive(file): 5499376 kB
Unevictable: 723108 kB
Mlocked: 17336 kB
SwapTotal: 0 kB
SwapFree: 0 kB
Dirty: 4 kB
Writeback: 0 kB
AnonPages: 4848276 kB
Mapped: 625156 kB
Shmem: 1816292 kB
KReclaimable: 9438608 kB
Slab: 10007568 kB
SReclaimable: 9438608 kB
SUnreclaim: 568960 kB
KernelStack: 26240 kB
PageTables: 63012 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
WritebackTmp: 0 kB
CommitLimit: 16246380 kB
Committed_AS: 16256172 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 103964 kB
VmallocChunk: 0 kB
Percpu: 14592 kB
HardwareCorrupted: 0 kB
AnonHugePages: 0 kB
ShmemHugePages: 0 kB
ShmemPmdMapped: 0 kB
FileHugePages: 0 kB
FilePmdMapped: 0 kB
CmaTotal: 0 kB
CmaFree: 0 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
HugePages_Surp: 0
Hugepagesize: 2048 kB
Hugetlb: 0 kB
DirectMap4k: 5072608 kB
DirectMap2M: 20758528 kB
DirectMap1G: 7340032 kB
/tmp/so_example » lscpu
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Address sizes: 39 bits physical, 48 bits virtual
Byte Order: Little Endian
CPU(s): 16
On-line CPU(s) list: 0-15
Vendor ID: GenuineIntel
Model name: Intel(R) Core(TM) i7-10875H CPU # 2.30GHz
CPU family: 6
Model: 165
Thread(s) per core: 2
Core(s) per socket: 8
Socket(s): 1
Stepping: 2
CPU max MHz: 5100.0000
CPU min MHz: 800.0000
BogoMIPS: 4601.60
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology
nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnow
prefetch cpuid_fault epb invpcid_single ssbd ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust sgx bmi1 avx2 smep bmi2 erms invpcid mpx rdseed adx smap clflushopt inte
l_pt xsaveopt xsavec xgetbv1 xsaves dtherm ida arat pln pts hwp hwp_notify hwp_act_window hwp_epp pku ospke sgx_lc md_clear flush_l1d arch_capabilities
Virtualization features:
Virtualization: VT-x
Caches (sum of all):
L1d: 256 KiB (8 instances)
L1i: 256 KiB (8 instances)
L2: 2 MiB (8 instances)
L3: 16 MiB (1 instance)
NUMA:
NUMA node(s): 1
NUMA node0 CPU(s): 0-15
Vulnerabilities:
Itlb multihit: KVM: Mitigation: VMX disabled
L1tf: Not affected
Mds: Not affected
Meltdown: Not affected
Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp
Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Spectre v2: Mitigation; Enhanced IBRS, IBPB conditional, RSB filling
Srbds: Not affected
Tsx async abort: Not affected
Reproduction
/tmp/so_example » npm init -y
Wrote to /tmp/so_example/package.json:
{
"name": "so_example",
"version": "1.0.0",
"description": "",
"main": "index.js",
"scripts": {
"test": "echo \"Error: no test specified\" && exit 1"
},
"keywords": [],
"author": "",
"license": "ISC"
}
/tmp/so_example » npm i puppeteer
added 57 packages, and audited 58 packages in 11s
8 packages are looking for funding
run `npm fund` for details
found 0 vulnerabilities
/tmp/so_example » npm list
so_example#1.0.0 /tmp/so_example
└── puppeteer#11.0.0
/tmp/so_example » echo "const puppeteer = require('puppeteer');
(async () => {
const browser = await puppeteer.launch();
const page = await browser.newPage();
await page.goto('https://google.com');
await browser.close();
})();" > example.js
/tmp/so_example » nvm use 17
Now using node v17.1.0 (npm v8.1.2)
/tmp/so_example » node example.js
/tmp/so_example/node_modules/puppeteer/lib/cjs/puppeteer/common/Connection.js:226
error: new Errors_js_1.ProtocolError(),
^
ProtocolError: Protocol error (Page.navigate): Target closed.
at /tmp/so_example/node_modules/puppeteer/lib/cjs/puppeteer/common/Connection.js:226:24
at new Promise (<anonymous>)
at CDPSession.send (/tmp/so_example/node_modules/puppeteer/lib/cjs/puppeteer/common/Connection.js:222:16)
at navigate (/tmp/so_example/node_modules/puppeteer/lib/cjs/puppeteer/common/FrameManager.js:148:47)
at FrameManager.navigateFrame (/tmp/so_example/node_modules/puppeteer/lib/cjs/puppeteer/common/FrameManager.js:131:13)
at Frame.goto (/tmp/so_example/node_modules/puppeteer/lib/cjs/puppeteer/common/FrameManager.js:500:41)
at Page.goto (/tmp/so_example/node_modules/puppeteer/lib/cjs/puppeteer/common/Page.js:1167:53)
at /tmp/so_example/example.js:6:14
at processTicksAndRejections (node:internal/process/task_queues:96:5) {
originalMessage: undefined
}
Node.js v17.1.0
I get the same error with the following versions:
/tmp/so_example » nvm use 16
Now using node v16.13.0 (npm v8.1.0)
/tmp/so_example » nvm use 15
Now using node v15.14.0 (npm v7.7.6)
/tmp/so_example » nvm use 14
Now using node v14.18.1 (npm v6.14.15)
Update: Docker
I've also tried the same installation on Docker following this guide. With this setup it seems to work. This suggests it is an OS/package related issue.
/tmp/so_example » echo "const puppeteer = require('puppeteer');
(async () => {
const browser = await puppeteer.launch({
headless: true,
args: [
'--disable-gpu',
'--disable-dev-shm-usage',
'--disable-setuid-sandbox',
'--no-sandbox',
]
});
const page = await browser.newPage();
await page.goto('https://google.com');
await browser.close();
console.log('If I made it here there is no error');
})();" > example.js
/tmp/so_example » echo "FROM node:17-slim
# Chrome dependencies
RUN apt-get update && apt-get -f install -y \\
fonts-liberation \\
gconf-service \\
#libappindicator1 \\
libasound2 \\
libatk1.0-0 \\
libcairo2 \\
libcups2 \\
libfontconfig1 \\
libgbm-dev \\
libgdk-pixbuf2.0-0 \\
libgtk-3-0 \\
libicu-dev \\
libjpeg-dev \\
libnspr4 \\
libnss3 \\
libpango-1.0-0 \\
libpangocairo-1.0-0 \\
libpng-dev \\
libx11-6 \\
libx11-xcb1 \\
libxcb1 \\
libxcomposite1 \\
libxcursor1 \\
libxdamage1 \\
libxext6 \\
libxfixes3 \\
libxi6 \\
libxrandr2 \\
libxrender1 \\
libxss1 \\
libxtst6 \\
xdg-utils
COPY . ./
RUN npm install
# Make browser executable for puppeteer
RUN chmod -R o+rwx node_modules/puppeteer/.local-chromium
CMD [\"node\", \"example.js\"]" > Dockerfile
/tmp/so_example » docker run -it $(docker build -q .)
If I made it here there is no error
Edit: static chromium path
As commented on this question, adding
executablePath: 'path/to/local/chromium'
to the puppeteer configuration makes the reproduction run on the system. I would still like to know why the chromium packaged with puppeteer does not work as using a static path to a local executable is a really bad practice in a multi-dev environment.
Surprisingly, after updating to Puppeteer version 12.0.0, everything seems to work. As of yet I do not know what caused the issue and what made it go away, but it works now.
EDIT: The changelog can be found here, and presumably the update to Chromium 97.0.4692.0 is what resolved the issue.
There's too much for me to put this in a comment, so I will summarize here. Maybe it will help you, or someone else. I should also mention this is for RHEL EC2 instances behind a corporate proxy (not Arch Linux), but I still feel like it may help. I had to do the following to get puppeteer working. This is straight from my docs, but I had to hand-jam the contents because my docs are on an intranet.
I had to install all of these libraries manually. I also don't know what the Arch Linux equivalents are. Some are duplicates from your question, but I don't think they all are:
pango libXcomposite libXcursor libXdamage libXext libXi libXtst cups-libs libXScrnSaver libXrandr GConf2 alsa-lib atk gtk3 ipa-gothic-fonts xorg-x11-fonts-100dpi xorg-x11-fonts-75dpi xorg-x11-utils xorg-x11-fonts-cyrillic xorg-x11-fonts-Type1 xorg-x11-fonts-misc liberation-mono-fonts liberation-narrow-fonts liberation-narrow-fonts liberation-sans-fonts liberation-serif-fonts glib2
If Arch Linux uses SELinux, you may also have to run this:
setsebool -P unconfirmed_chrome_sandbox_transition 0
It is also worth adding dumpio: true to your options to debug. Should give you a more detailed output from puppeteer, instead of the generic error. As I mentioned in my comment. I have this option ignoreDefaultArgs: ['--disable-extensions']. I can't tell you why because I don't remember. I think it is related to this issue, but also could be related to my corporate proxy.
I'd like to run a basic Angular 2 app on an Ubuntu EC2 instance.
In my case, I installed Angular CLI, and created a new site in /var/www
ng new test
then
ng serve --port 8080
It looks like my basic Angular2 app is running fine
** NG Live Development Server is listening on localhost:8080, open your browser on http://localhost:8080 **
Hash: e0094cf33de0e6b8f264
Time: 9090ms
chunk {0} polyfills.bundle.js, polyfills.bundle.js.map (polyfills) 171 kB {4} [initial] [rendered]
chunk {1} main.bundle.js, main.bundle.js.map (main) 5.28 kB {3} [initial] [rendered]
chunk {2} styles.bundle.js, styles.bundle.js.map (styles) 10.5 kB {4} [initial] [rendered]
chunk {3} vendor.bundle.js, vendor.bundle.js.map (vendor) 2.18 MB [initial] [rendered]
chunk {4} inline.bundle.js, inline.bundle.js.map (inline) 0 bytes [entry] [rendered]
webpack: Compiled successfully.
I know port 8080 is open in my security groups, because I just ran a basic Node JS app a few minutes ago in /var/www. When I try to go to http://[Public DNS]:8080, Safari says it can't connect. There's also nothing in my apache logs.
Turns out the real issue is this:
https://github.com/angular/angular-cli/issues/6070
I've tried editing the server.js file and running with the --publicHost option, but those aren't working. I'm using non CLI Angular with the default port 3000 and that's working on EC2 (after adding the security group settings).
i am having a centos vps. i have installed erlang
by the command
rpm -Uvh erlang-17.4-1.el6.x86_64.rpm
Now whenever i try to run my rabbitmq-server. or i just issue erl command
then i get this error.
Failed to create main carrier for ll_alloc Aborted
is it some memory issue erlang is unable to get free memory or what?
here are memory stats of the machine
sudo cat /proc/meminfo
MemTotal: 4194304 kB
MemFree: 104520 kB
Cached: 2718800 kB
Buffers: 0 kB
Active: 1729508 kB
Inactive: 2170684 kB
Active(anon): 559168 kB
Inactive(anon): 627436 kB
Active(file): 1170340 kB
Inactive(file): 1543248 kB
Unevictable: 0 kB
Mlocked: 0 kB
SwapTotal: 0 kB
SwapFree: 0 kB
Dirty: 44 kB
Writeback: 0 kB
AnonPages: 1186604 kB
Shmem: 5212 kB
Slab: 189472 kB
SReclaimable: 155768 kB
SUnreclaim: 33704 kB
what should i do?
i figured out it was a memory issue when i shutdown tomcat to make available few more mbs of memory than the erl started.
has anyone ever seen the following Java segmentation fault at libglib g_list_last? The stack shows nothing more than the g_list_last and it says that "Current thread is native thread".
The Java 6 VM was running JBOSS 6 and there was no custom native code.
The server runs normally for some hours and then breaks... always with the exactly same error. I'm posting the most interesting excerpts from the hs_err file.
Thanks in advance for any clue!
Regards,
Doug
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGSEGV (0xb) at pc=0x0000003e5022a5e3, pid=14845, tid=1196464448
#
# JRE version: 6.0_23-b05
# Java VM: Java HotSpot(TM) 64-Bit Server VM (19.0-b09 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C [libglib-2.0.so.0+0x2a5e3] g_list_last+0x13
#
# If you would like to submit a bug report, please visit:
# http://java.sun.com/webapps/bugreport/crash.jsp
#
--------------- T H R E A D ---------------
Current thread is native thread
siginfo:si_signo=SIGSEGV: si_errno=0, si_code=1 (SEGV_MAPERR), si_addr=0x0000010068f06abb
Registers:
RAX=0x0000010068f06ab3, RBX=0x000000004d59ee10, RCX=0x000000004e60aeb0, RDX=0x0000000000000000
RSP=0x0000000047508e18, RBP=0x00002aaab9afcca0, RSI=0x00002aaab9afcca0, RDI=0x0000010068f06ab3
R8 =0x0000000000000001, R9 =0x0000000000003a93, R10=0x0000000000000000, R11=0x0000003e5022abb0
R12=0x000000047c6556b8, R13=0x00002aaab8c7a3f0, R14=0x000000004d698e40, R15=0x000000004da3c4b0
RIP=0x0000003e5022a5e3, EFL=0x0000000000010202, CSGSFS=0x0000000000000033, ERR=0x0000000000000004
TRAPNO=0x000000000000000e
...
R11=0x0000003e5022abb0
0x0000003e5022abb0: g_list_append+0 in /lib64/libglib-2.0.so.0 at 0x0000003e50200000
R12=0x000000047c6556b8
[error occurred during error reporting (printing registers, top of stack, instructions near pc), id 0xb]
Stack: [0x00000000474c9000,0x000000004750a000], sp=0x0000000047508e18, free space=255k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C [libglib-2.0.so.0+0x2a5e3] g_list_last+0x13
--------------- P R O C E S S ---------------
VM state:not at safepoint (normal execution)
VM Mutex/Monitor currently owned by a thread: None
Heap
PSYoungGen total 4767296K, used 4345622K [0x00000006c2800000, 0x0000000800000000, 0x0000000800000000)
eden space 4368704K, 99% used [0x00000006c2800000,0x00000007caaac208,0x00000007cd250000)
from space 398592K, 4% used [0x00000007cd250000,0x00000007ce369990,0x00000007e5790000)
to space 373184K, 0% used [0x00000007e9390000,0x00000007e9390000,0x0000000800000000)
PSOldGen total 10403840K, used 1828930K [0x0000000447800000, 0x00000006c2800000, 0x00000006c2800000)
object space 10403840K, 17% used [0x0000000447800000,0x00000004b7210910,0x00000006c2800000)
PSPermGen total 288448K, used 288427K [0x0000000347800000, 0x00000003591b0000, 0x0000000447800000)
object space 288448K, 99% used [0x0000000347800000,0x00000003591aaf10,0x00000003591b0000)
...
--------------- S Y S T E M ---------------
OS:Red Hat Enterprise Linux Server release 5.5 (Tikanga)
uname:Linux 2.6.18-194.el5 #1 SMP Tue Mar 16 21:52:39 EDT 2010 x86_64
libc:glibc 2.5 NPTL 2.5
rlimit: STACK 10240k, CORE 0k, NPROC 1056767, NOFILE 16384, AS infinity
load average:1.01 0.58 0.40
/proc/meminfo:
MemTotal: 132086452 kB
MemFree: 12656648 kB
Buffers: 1441372 kB
Cached: 107627992 kB
SwapCached: 0 kB
Active: 77778444 kB
Inactive: 39851400 kB
HighTotal: 0 kB
HighFree: 0 kB
LowTotal: 132086452 kB
LowFree: 12656648 kB
SwapTotal: 61440552 kB
SwapFree: 61440552 kB
Dirty: 864 kB
Writeback: 0 kB
AnonPages: 8560164 kB
Mapped: 84312 kB
Slab: 1645472 kB
PageTables: 31956 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
CommitLimit: 127483776 kB
Committed_AS: 20373196 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 297932 kB
VmallocChunk: 34359436991 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
Hugepagesize: 2048 kB
CPU:total 32 (8 cores per cpu, 2 threads per core) family 6 model 47 stepping 2, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, ht
Memory: 4k page, physical 132086452k(12656648k free), swap 61440552k(61440552k free)
vm_info: Java HotSpot(TM) 64-Bit Server VM (19.0-b09) for linux-amd64 JRE (1.6.0_23-b05), built on Nov 12 2010 14:12:21 by "java_re" with gcc 3.2.2 (SuSE Linux)
I am using a NFS mounted File system for Linux based embedded system box. I have few shared libraries, sizes of which varies from 1MB to 20MB. I am running the application which is dependent on these libraries.
While running the application, i checked the /proc/TaskPID/smap.
Size: 4692 kB
Rss: 1880 kB
Pss: 1880 kB
Shared_Clean: 0 kB
Shared_Dirty: 0 kB
Private_Clean: 1880 kB
Private_Dirty: 0 kB
Referenced: 1880 kB
Anonymous: 0 kB
Swap: 0 kB
KernelPageSize: 4 kB
MMUPageSize: 4 kB
Now as per my understanding, it means that Library is partially loaded (Since RSS says lesser value to Size)? If so, on a reference to other portion, trying to get that part into memory (Hope my understanding is correct) will be more costlier in case of NFS mounted system.So can we make it load every thing before running?