Chromium debug build no TCMalloc symbols - google-chrome

I compiled Chromium as debug build
# Set build arguments here. See `gn help buildargs`.
enable_nacl=false
symbol_level=2
is_asan = true
is_lsan = false
is_debug = true
but somehow I cannot see TCMalloc symbols when using TCMalloc inspection script:
https://github.com/marcinguy/tcmalloc-inspector
With sample program compiled against TCMalloc it works.
In Chromium it cannot find these symbols:
# tcmalloc
pageheap_ = gdb.parse_and_eval('\'tcmalloc::Static::pageheap_\'')
central_cache_ = gdb.parse_and_eval('\'tcmalloc::Static::central_cache_\'')
thread_heaps_ = gdb.parse_and_eval('\'tcmalloc::ThreadCache::thread_heaps_\'')
sizemap_ = gdb.parse_and_eval('\'tcmalloc::Static::sizemap_\'') # XXX cache
spantype = gdb.lookup_type('tcmalloc::Span').pointer()
knumclasses = gdb.parse_and_eval('kNumClasses') # XXX skip 0?
kmaxpages = gdb.parse_and_eval('kMaxPages')
pagesize = 1 << int(gdb.parse_and_eval('kPageShift'))
How can I compile Chromium, TCMalloc used by Chromium with debug symbols, those symbols?
Thanks,

Related

Not saving html interactive file with R

I am trying to design a circos plot using BioCircos R package. BioCircos allows to save the plots as .html interactive files. However, when I run the package using RScript the saved .html file is empty. To save the .html file I used saveWidget option from htmlwidgets package. Is it something wrong with saveWidget option? The code I used follows:
#!/usr/bin/Rscript
######R script for BioCircos test
library(htmlwidgets)
library(BioCircos)
genomes <- list("chra1" = 217471166, "chra2" = 181034961, "chra3" = 153873357, "chra4" = 153961319, "chra5" = 164033575,
"chra6" = 154486312, "chra7" = 133565930, "chra8" = 147241510, "chra9" = 91218944, "chra10" = 52432566, "chrb1" = 843366180, "chrb2" = 842558404, "chrb3" = 707956555, "chrb4" = 635713434, "chrb5" = 567300182,
"chrb6" = 439630435, "chrb7" = 236595445, "chrb8" = 231667822, "chrb9" = 230778867, "chrb10" = 151572763, "chrb11" = 103205957) # custom genome
links_chromosomes_01 <- c("chra1", "chra2", "chra3", "chra4", "chra4", "chra5", "chra6", "chra7", "chra7", "chra8", "chra8", "chra9", "chra10") # Chromosomes on which the links should start
links_chromosomes_02 <- c("chrb2", "chrb3", "chrb1", "chrb9", "chrb10", "chrb4", "chrb5", "chrb6", "chrb1", "chrb8", "chrb3", "chrb7", "chrb6") # Chromosomes on which the links should end
links_pos_01 <- c(115060347, 102611974, 14761160, 128700431, 128681496, 42116205, 58890582, 40356090,
146935315, 136481944, 157464876, 39323393, 84752508, 136164354,
99573657, 102580613,
111139346, 120764772, 90748238, 122164776,
44933176, 18823342,
48771409, 128288229, 150613881, 18509106, 123913217, 51237349,
34237851, 53357604, 78270031,
25306417, 25320614,
94266153,
41447919, 28810876, 2802465,
45583472,
81968637, 27858237, 17263637,
30569409) ### links chra chromosomes
links_pos_02 <- c(410543481, 463189512, 825903588, 353914638, 354135472, 717707494, 643107332, 724899652,
583713545, 558756961, 642015290, 154999098, 340216235, 557731577,
643350872, 655077847,
85356666, 157889318, 226411560, 161566470,
109857786, 25338955,
473876792, 124495704, 46258030, 572314729, 141584107, 426419779,
531245660, 220131772, 353941099,
62422773, 62387030,
116923325,
76544045, 33452274, 7942164,
642047816,
215981114, 39278129, 23302654,
418922633) ### links chrb chromosomes
links_labels <- c("aldh1a3", "amh", "cyp26b1", "dmrt1", "dmrt3", "fgf20", "hhip", "srd5a3",
"amhr2", "dhh", "fgf9", "nr0b1", "rspo1", "wnt1",
"aldh1a2", "cyp19a1",
"lhx9", "pdgfb", "ptch2", "sox10",
"cbln1", "wt1",
"esr1", "foxl2", "gata4", "lrpprc", "serpine2", "srd5a2",
"asns", "ctnnb1", "srd5a1",
"cyp26a1", "cyp26c1",
"wnt4",
"ar", "nr5a1", "ptgds",
"fgf16",
"cxcr4", "pdgfa", "sox8",
"sox9")
tracklist <- BioCircosLinkTrack('myLinkTrack', links_chromosomes_01, links_pos_01,
links_pos_01, links_chromosomes_02, links_pos_02, links_pos_02,
maxRadius = 0.55, labels = links_labels)
#plotting results
plot_chra_chrb <- BioCircos(tracklist, genome = chra_chrb_genomes, genomeFillColor = "RdBu", chrPad = 0.02, displayGenomeBorder = FALSE, genomeLabelTextSize = "10pt", genomeTicksScale = 4e+3,
elementId = "chra_chrb_comp_plot_test.html")
saveWidget(plot_chra_chrb, "chra_chrb_comp_plot_test.html", selfcontained = F, libdir = "lib")
The command line to run this script:
Rscript /path_to/Circle_plot_test.r
I tried to use this script in RStudio (without saveWidget() command), however it took too long to run in my personnel computer and the results was not displayed. However, this could be due to memory usage setup because when I took off some data, the script easily generates the plot in RStudio and I am able to save it. Is there other way to save the .hmtl interactive files in R or am I doing something wrong using htmlwidgets package in my script?
Thanks all in advance for any help and comments.

When you said it took too long to run, that was a sign that something was wrong! You weren't getting anything when you used saveWidget, because there is nothing returned from BioCiros.
I found two things that are a problem. The first one will result in a blank output—you can't use a '.' in the element ID. This ID will be used in the HTML coding.
You were getting huge delays due to the scale you set for genomeTickScale. That scaling value is for a tick mark attribute. I'm not sure why you set it to .004. However, when I comment out that line, it renders immediately. I have no issues with saving the widget, either.
--One other thing, you had chra_chrb_genomes as the object name assigned to the parameter genome in the function BioCircos. I assumed it was the object genome from your question since it was the only unused object.
The only things I changed were in the BioCircos function:
(plot_chra_chrb <- BioCircos(tracklist, genome = genomes, #chra_chrb_genomes,
genomeFillColor = "RdBu",
chrPad = 0.02,
displayGenomeBorder = FALSE,
genomeLabelTextSize = "10pt",
# genomeTicksScale = 4e+3, # problematic
elementId = "chra_chrb_comp_plot_test" # no periods
))

Data block not supported with packer version 1.6.1 in hcl2 templates

I created a packer json template on my local system with packer 1.7.7 installed.
Then I upgraded to hcl2 template. However, when I run the packer pipeline over the jenkins node having packer version 1.6.1. It throws this error:
Blocks of type "data" are not expected here.
Error: Unsupported block type
After researching, I realized that packer version 1.6.1 doesn't support data blocks in its templates, but it supports hcl2 templates.
Can anyone explain how I can replace the data block (ref template below) with something supported in packer version 1?
data "amazon-ami" "autogenerated_1"{
access_key = "${var.aws_access_key}"
filters = {
root-device-type = "ebs"
virtualization-type = "hvm"
name = "**** Linux *"
}
most_recent = true
region = "${var.aws_region}"
owners = ["${var.owner_id}"]
secret_key = "${var.aws_secret_key}"
}
when I am trying to consume this ami id in the source block It gives me error.
ami_name = "${var.ami_name}"
associate_public_ip_address = false
force_deregister = true
iam_instance_profile = "abc"
instance_type = "****"
region = "${var.aws_region}"
source_ami = data.amazon-ami.autogenerated_1.id
ssh_interface = "private_ip"
ssh_username = "user"
subnet_id = "subnet-********"
vpc_id = "vpc-***********"
}

The packer pipeline over the jenkins node having packer version 1.6.1.
Its not supported in such an old version. From docs:
Note: Data Sources is a feature included in Packer 1.7 and later

Prevent double compilation of c files in cython

I am writing a wrapper over c libriary and this lib has file with almost all functions, let say, all_funcs.c. This file in turn requires compilation of lots of another c files
I have created all_funcs.pyx, where I wraped all functions, but I also want to create a submodule, that has access to functions from all_funcs.c. What works for now is adding all c-files to both Extensions in setup.py, however each c-file compiles twice: first for all_funcs.pyx and second for submodule extension.
Are there any ways to provide common sourse files to each Extension?
Example of current setup.py:
ext_helpers = Extension(name=SRC_DIR + '.wrapper.utils.helpers',
sources=[SRC_DIR + '/wrapper/utils/helpers.pyx'] + source_files_paths,
include_dirs=[SRC_DIR + '/include/'])
ext_all_funcs = Extension(name=SRC_DIR + '.wrapper.all_funcs',
sources=[SRC_DIR + '/wrapper/all_funcs.pyx'] + source_files_paths,
include_dirs=[SRC_DIR + '/include/'])
EXTENSIONS = [
ext_helpers,
ext_all_funcs,
]
if __name__ == "__main__":
setup(
packages=PACKAGES,
zip_safe=False,
name='some_name',
ext_modules=cythonize(EXTENSIONS, language_level=3)
)
source_files_paths - the list with common c source files

Note: this answer only explains how to avoid multiple compilation of c/cpp-files using libraries-argument of setup-function. It doesn't however explain how to avoid possible problems due to ODR-violation - for that see this SO-post.
Adding libraries-argument to setup will trigger build_clib prior to building of ext_modules (when running setup.py build or setup.py install commands), the resulting static library will also be automatically passed to the linker, when extensions are linked.
For your setup.py, this means:
from setuptools import setup, find_packages, Extension
...
#common c files compiled to a static library:
mylib = ('mylib', {'sources': source_files_paths}) # possible further settings
# no common c-files (taken care of in mylib):
ext_helpers = Extension(name=SRC_DIR + '.wrapper.utils.helpers',
sources=[SRC_DIR + '/wrapper/utils/helpers.pyx'],
include_dirs=[SRC_DIR + '/include/'])
# no common c-files (taken care of in mylib):
ext_all_funcs = Extension(name=SRC_DIR + '.wrapper.all_funcs',
sources=[SRC_DIR + '/wrapper/all_funcs.pyx'],
include_dirs=[SRC_DIR + '/include/'])
EXTENSIONS = [
ext_helpers,
ext_all_funcs,
]
if __name__ == "__main__":
setup(
packages=find_packages(where=SRC_DIR),
zip_safe=False,
name='some_name',
ext_modules=cythonize(EXTENSIONS, language_level=3),
# will be build as static libraries and automatically passed to linker:
libraries = [mylib]
)
To build the extensions inplace one should invoke:
python setupy.py build_clib build_ext --inplace
as build_ext alone is not enough: we need the static libraries to build before they can be used in extensions.

How to configure Tomcat Catalina logs in json using default jar(tomact-juli.jar)

I have updated the logging.properties file of tomcat to print the logs in json format.
But, the issue is value of "message " has some escape characters, which makes my log invalid json.
Please let me know how to escape these characters(:,[,],/) in json using default tomcat-juli.jar and used as a string.
Below is my updated logging.properties file:
handlers = 1catalina.org.apache.juli.AsyncFileHandler, 2localhost.org.apache.juli.AsyncFileHandler, 3manager.org.apache.juli.AsyncFileHandler, 4host-manager.org.apache.juli.AsyncFileHandler, java.util.logging.ConsoleHandler
.handlers = 1catalina.org.apache.juli.AsyncFileHandler, java.util.logging.ConsoleHandler
############################################################
# Handler specific properties.
# Describes specific configuration info for Handlers.
############################################################
java.util.logging.SimpleFormatter.format = {"date" :"%1$tF", "timestamp": "%1$tT" , "loggerlevel": "%4$s", "loggersource": "%3$s" , "message": "%5$s%6$s"}%n
1catalina.org.apache.juli.AsyncFileHandler.level = FINE
1catalina.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs
1catalina.org.apache.juli.AsyncFileHandler.prefix = catalina.
1catalina.org.apache.juli.AsyncFileHandler.formatter = java.util.logging.SimpleFormatter
2localhost.org.apache.juli.AsyncFileHandler.level = FINE
2localhost.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs
2localhost.org.apache.juli.AsyncFileHandler.prefix = localhost.
2localhost.org.apache.juli.AsyncFileHandler.formatter = java.util.logging.SimpleFormatter
3manager.org.apache.juli.AsyncFileHandler.level = FINE
3manager.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs
3manager.org.apache.juli.AsyncFileHandler.prefix = manager.
3manager.org.apache.juli.AsyncFileHandler.formatter = java.util.logging.SimpleFormatter
4host-manager.org.apache.juli.AsyncFileHandler.level = FINE
4host-manager.org.apache.juli.AsyncFileHandler.directory = ${catalina.base}/logs
4host-manager.org.apache.juli.AsyncFileHandler.prefix = host-manager.
4host-manager.org.apache.juli.AsyncFileHandler.formatter = java.util.logging.SimpleFormatter
java.util.logging.ConsoleHandler.level = FINE
java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
############################################################
# Facility specific properties.
# Provides extra control for each logger.
############################################################
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = INFO
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].handlers = 2localhost.org.apache.juli.AsyncFileHandler
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].level = INFO
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].handlers = 3manager.org.apache.juli.AsyncFileHandler
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/host-manager].level = INFO
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/host-manager].handlers = 4host-manager.org.apache.juli.AsyncFileHandler

I would suggest you official way (without using middleware):
Download Elastic JUL formatter and logging core libraries:
https://mvnrepository.com/artifact/co.elastic.logging/jul-ecs-formatter
https://mvnrepository.com/artifact/co.elastic.logging/ecs-logging-core
Put them into tomcat/bin folder
List them in CLASSPATH system property in tomcat/bin/setenv.sh(bat).
If no such file - create it with the next content: on Unix -
export CLASSPATH="$CLASSPATH:ecs-logging-core.jar:jul-ecs-formatter.jar"
on Windows - set CLASSPATH=%CLASSPATH%;ecs-logging-core.jar;jul-ecs-formatter.jar
Edit tomcat/conf/logging.properties in such way:
handlers = java.util.logging.ConsoleHandler
.handlers = java.util.logging.ConsoleHandler
...
java.util.logging.ConsoleHandler.formatter = co.elastic.logging.jul.EcsFormatter
Such configuration will make tomcat to write all events in appropriate Elastic (Logstash) JSON format into console (stdout) which is very suitable when you running in docker or other container.
Documentation https://www.elastic.co/guide/en/ecs-logging/java/1.x/setup.html

I would do the following:
Download and build devatherock's jul json formatter
Download json-simple
Add both to your tomcat startup classpath in the $CATALINA_BASE/bin/setenv.sh script
In $CATALINA_BASE/conf/logging.properties, add or change the formatters for your log handlers to io.github.devatherock.json.formatter.JSONFormatter

VIM Syntastic error for HTML5

I'm a newcomer to VIM and installed GVIM successfully on my Windows 8.1 laptop. I uploaded the Syntastics plugin using Pathogen and, as I'm planning to write an ionic project, I also copied the tidy5 for html5 binary (from http://www.htacg.org/tidy-html5/) and referred to the binary in my VIMRC as follows:
" SYNTASTIC
set statusline+=%#warningmsg#
set statusline+=%{SyntasticStatuslineFlag()}
set statusline+=%*
" automatically load errors in the location list:
let g:syntastic_always_populate_loc_list = 1
let g:syntastic_auto_loc_list = 1
" check on errors when a file is loaded:
let g:syntastic_check_on_open = 1
" check on errors when saving the file:
let g:syntastic_check_on_wq = 0
let g:syntastic_html_tidy_execute = 'C:\Program Files (x86)\tidy-5.1.25-win32\bin\tidy'
let g:syntastic_shell='C:\Windows\System32\cmd'
" check debugging messages in vim with :mes:
let g:syntastic_debug = 1
let g:syntastic_mode_map = {"mode": "active",
\"active_filetypes" : ["html","javascript","json"],
\"passive_filetypes" : ["html", "javascript","json"] }
When I run
:SyntasticInfo
I get the following output
Syntastic version: 3.7.0-76 (Vim 704, Windows)
Info for filetype: html
Global mode: active
Filetype html is active
The current file will be checked automatically
Available checkers: -
Currently enabled checkers: -
For some reason, my default checkers aren't loading, and when I run
echo syntastic#util#system('echo %PATH%')
I get a E484 error
Error detected while processing function syntastic#util#system:
line 9:
E484: Can't open file C:\Users\Dirk\AppData\Local\Temp\VIo8366.tmp
-1
I suspect there are multiple issues here, so I assume the first one I need to solve is the E484 error. Any help appreciated.