result

The train result is bottom,but I can't know what is issue?
------------- Epoch 1/100 --------------
Learning rate: 0.0001
train: 100%|###########################################################################################| 8128/8128 [1:33:07<00:00,  1.49it/s, loss=nan]
Best epoch: 1
Best score: 0.00000
------------- Epoch 2/100 --------------
Learning rate: 0.0001
train: 100%|###########################################################################################| 8128/8128 [1:31:55<00:00,  1.48it/s, loss=nan]
Best epoch: 1
Best score: 0.00000
------------- Epoch 3/100 --------------
Learning rate: 0.0001
train: 100%|###########################################################################################| 8128/8128 [1:32:11<00:00,  1.46it/s, loss=nan]
Best epoch: 1
Best score: 0.00000
------------- Epoch 4/100 --------------
Learning rate: 0.0001
train: 100%|###########################################################################################| 8128/8128 [1:32:33<00:00,  1.47it/s, loss=nan]
Best epoch: 1
Best score: 0.00000
------------- Epoch 5/100 --------------
Learning rate: 0.0001
train: 100%|###########################################################################################| 8128/8128 [1:32:54<00:00,  1.46it/s, loss=nan]
eval/train: 100%|####################################################################################################| 147/147 [56:08<00:00, 13.30s/it]
train/dc_global_0: 0.99566
train/dc_global_1: 0.00000
train/dc_per_case_0: 0.99520
train/dc_per_case_1: 0.00000
eval/valid: 100%|######################################################################################################| 63/63 [22:02<00:00, 16.13s/it]
valid/dc_global_0: 0.99598
valid/dc_global_1: 0.00000
valid/dc_per_case_0: 0.99486
valid/dc_per_case_1: 0.00000
Train data score: 0.00000
Valid data score: 0.00000
Best epoch: 1
Best score: 0.00000

I see your loss is "nan".
Try decrease learning rate, like 0.00001.
What's the batch size and num of gpu you setting?

I sets the batch_size=4 and the GPU(num_work=2)
------------------ 原始邮件 ------------------
发件人: "Nick<EMAIL_ADDRESS>发送时间: 2019年9月16日(星期一) 下午2:49
收件人<EMAIL_ADDRESS>抄送<EMAIL_ADDRESS><EMAIL_ADDRESS>主题: Re: [nitsaick/kits19-challenge] result  (#2)
I see your loss is "nan".
Try decrease learning rate, like 0.00001.
What's the batch size and num of gpu you setting?
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They seem fine.
Just try decrease learning rate. Make sure loss value is not nan.

ok, thank you!!
------------------ 原始邮件 ------------------
发件人: "Nick<EMAIL_ADDRESS>发送时间: 2019年9月16日(星期一) 下午3:17
收件人<EMAIL_ADDRESS>抄送<EMAIL_ADDRESS><EMAIL_ADDRESS>主题: Re: [nitsaick/kits19-challenge] result  (#2)
They seem fine.
Just try decrease learning rate. Make sure loss value is not nan.
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I try decrease learning rate, but I find the loss value is nan yet.
------------------ 原始邮件 ------------------
发件人: "Nick<EMAIL_ADDRESS>发送时间: 2019年9月16日(星期一) 下午3:17
收件人<EMAIL_ADDRESS>抄送<EMAIL_ADDRESS><EMAIL_ADDRESS>主题: Re: [nitsaick/kits19-challenge] result  (#2)
They seem fine.
Just try decrease learning rate. Make sure loss value is not nan.
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Is the loss nan at the first iteration or first epoch?
Or the loss has normal value at the beginning?
Can you give me your environment detail like Pytorch, Python version, argument, OS, and which GPU you use?
I will try to reproduce your problem.

Thank you for reply!! I set the relevant parameters, python == 3.6 Pytorch == 1.1.0, when starting training loss = Nan
Running command:
Python train_res_unet.py -e 100 -b 4 -l 0.00001 -g 2 -s 512 512 --data "data" --logdir "run/ResUNet" --eval_intvl 5 --vis_intvl 0 --num_workers 2.
Thank you!!
------------------ 原始邮件 ------------------
发件人: "Nick<EMAIL_ADDRESS>发送时间: 2019年9月19日(星期四) 凌晨0:24
收件人<EMAIL_ADDRESS>抄送<EMAIL_ADDRESS><EMAIL_ADDRESS>主题: Re: [nitsaick/kits19-challenge] result  (#2)
Is the loss nan at the first iteration or first epoch?
Or the loss has normal value at the beginning?
Can you give me your environment detail like Pytorch, Python version, argument, OS, and which GPU you use?
I will try to reproduce your problem.
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I try to reproduce your problem.
I test the code on my lab's 3 servers (GTX 1060, GTX 1080Ti, RTX 2080Ti) with different CUDA (9.0, 9.1, 10.0) and PyTorch version (1.1, 1.2).
But I get the correct result on all environment.
I cannot find the problem.

Thank, my lab's servers (GTX 1080) with CUDA(8.0), I re-tested and found that after being sent to the network, the data will become Nan value. I think there is a problem with the network reading data. Thank your for reply.
------------------ 原始邮件 ------------------
发件人: "Nick<EMAIL_ADDRESS>发送时间: 2019年10月18日(星期五) 下午4:57
收件人<EMAIL_ADDRESS>抄送<EMAIL_ADDRESS><EMAIL_ADDRESS>主题: Re: [nitsaick/kits19-challenge] result  (#2)
I try to reproduce your problem.
I test the code on my lab's 3 servers (GTX 1060, GTX 1080Ti, RTX 2080Ti) with different CUDA (9.0, 9.1, 10.0) and PyTorch version (1.1, 1.2).
But I get the correct result on all environment.
I cannot find the problem.
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wrong EC on GO:0004601

The definition of GO:0004601 and the Rhea link make this EC 1.11.1.- instead of <IP_ADDRESS>. Excerpt:
name: peroxidase activity
def: "Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O." [EC:<IP_ADDRESS>]
synonym: "lactoperoxidase activity" NARROW []
synonym: "myeloperoxidase activity" NARROW []
xref: EC:<IP_ADDRESS>
xref: KEGG_REACTION:R03532
xref: MetaCyc:PEROXID-RXN
xref: MIPS_funcat:<IP_ADDRESS>
xref: RHEA:23637

Using RHEA's xref to the EC
RHEA:56136 appears to be more appropriate
2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O; I will change the rhea to this.
And RHEA:23637 is marked obsolete at RHEA anyways.

Replaced RHEA with correct RHEA:56136;


Make hostname in tests overridable

The original form effectively forbade any NixOS configuration that is under
test to explicitly set the hostname.

Motivation for this change
Things done

[ ] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
Built on platform(s)

[ ] NixOS
[ ] macOS
[ ] other Linux distributions

[ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all pkgs that depend on this change using nix-shell -p nix-review --run "nix-review wip"
[ ] Tested execution of all binary files (usually in ./result/bin/)
[ ] Determined the impact on package closure size (by running nix path-info -S before and after)
[ ] Ensured that relevant documentation is up to date
[ ] Fits CONTRIBUTING.md.

Notify maintainers
cc @

LGTM.
Just executing one test that uses networking.hostName to make sure this doesn't break anything:
@GrahamcOfBorg test mysqlReplication

Unfortunately mysqlReplication fails because of an unrelated error (it also fails on master). Trying another test:
@GrahamcOfBorg test proxy


What's the best way to get the POCO model mapped table name?

Dear all,
What's the best way to get the POCO model mapped table name from metadata if the POCO model had been configured use Fluent API ToTable("xxx")?

var table = context.Model.FindEntityType(typeof(Blog)).Relational().TableName;

@rowanmiller
thanks


Move off of cvxopt and quadprog

cvxopt and quadprog use GPLV2/3 licenses, which should be fine per our discussions.
The main issue with using these libraries in critical sections of SMARTS is the GPL requirements it places on users of SMARTS to also keep their projects open-source permissive.

I will create my own simple solver instead of the above mentioned ones.


Support for invertAffineTransform

There's no support for invertAffineTransform in the library currently, src/imgproc/imgproc.dart just needs:
void invertAffineTransform(cv.InputArray M, cv.OutputArray iM) {
  using((arena) {
    bindings.InvertAffineTransform(M.ptr, iM.ptr);
  });
}

👌,will add soon.
BTW, would you mind to provide a test case?

Added in v0.6.6, I am going to close this issue.


Resolve a promise to an empty string instead of rejecting it on local theme in settings.json

I don't think title is representing what changed in code. Maybe, you didn't push some changes?

This should fix #147.
@nuno-silva18 Can you please squash your commits? Sample instruction just in case you need one. If you can't or don't want to do that, I can do it myself.

@sudodoki I tried to squash the commits but I'm not sure if this is how it's supposed to look like, I'd really appreciate some help here!

Closing this in favor of https://github.com/jdan/cleaver/pull/165


Synapse Dedicated Pool:  sys.allocation_units;

select * from sys.allocation_units;
Msg 104385, Level 16, State 1, Line 1
Catalog view 'allocation_units' is not supported in this version.
Can anyone please suggest solution to this
i have searched, but cant able to find right solution
@WilliamAntonRohm
@Vabby547
@LuisGonzalezLT
Originally posted by @ajithkumar-22 in https://github.com/MicrosoftDocs/sql-docs/issues/3749#issuecomment-1057664833
We need this exposed so we can join to sys.dm_pdw_nodes_os_buffer_descriptors.allocation_unit_id for tuning our workloads.

Duplicate of #3749.


analytics: record events for compare and explore

 [Analytics] Add click events to CAN Compare and CAN Explore


Code can't display completely when clicking edit on Bresenham Circles

Describe the bug
Code can't display completely when I click edit on Bresenham Circles
Steps to reproduce the behavior

Navigate to https://arcade.makecode.com/
Click "Bresenham Circles" on "Graphics and Math" -> "Show Instructions"
Click "Edit"

Expect behavior
Code display completely
Actual behavior
Code can't display completely

Additional context

OS: Windows(rs6)
arcade version: 0.15.11
Microsoft MakeCode version: 5.30.38

Good bug @Sheila111


add my list?

https://github.com/RustoMCSpit/awesome-linux-clap-list

Added in 9e80e2d27edf9db27cd24cf8e83e8d61bc9bd17b. Thanks!


MM Great Fairy reward issues

Sometimes the alt-form reward cannot be collected.
Seems to affect Deku Link, unsure about other forms.
Might be related to magic.

Fixed by 87c34dae0d9938612709ad18299a202fe00856ce


Fix vovember typo to november in Norwegian translation

Q
A

Bug fix?
yes

New feature?
no

BC breaks?
no

Related tickets
no

License
MIT

@acrobat @vsn4ik ping? This will be a breaking bug next month as all norwegian users will see "vovember" and think "what the hell?". Bug was introduced 9 months ago: https://github.com/uxsolutions/bootstrap-datepicker/blame/master/js/locales/bootstrap-datepicker.no.js#L10

Could we please merge this?

@Necklaces Thanks! Merged (#2443).


Fix aborting before recording started

If status was .listening when abort was called, it would not actually abort or call the delegate method.

Very nice, thank you


iPhone 6s Plus (8,2) 14.8 Sileo/Zebra Pogo Jailbreak not signing to repos stores

Sign window in Sileo/Zebra to the store is not popuping when pressed on the repo name no matter what tweaks are installed. Tested also on Sileo Nightly for XinaA15 https://github.com/Sileo/Sileo but with no result.
https://user-images.githubusercontent.com/74194283/221408742-6efdc06a-a22b-4e4e-b347-ddaaffc47c8a.MP4

Sign window in Sileo/Zebra to the store is not popuping when pressed on the repo name no matter what tweaks are installed. Tested also on Sileo Nightly for XinaA15 https://github.com/Sileo/Sileo but with no result.

what ios did you dualboot?, thats the jailbreak pogo right ?

Sign window in Sileo/Zebra to the store is not popuping when pressed on the repo name no matter what tweaks are installed. Tested also on Sileo Nightly for XinaA15 https://github.com/Sileo/Sileo but with no result.

what ios did you dualboot?, thats the jailbreak pogo right ?

Dualbooting iOS 14.8, Pogo, yes. Is this fixed?

Sign window in Sileo/Zebra to the store is not popuping when pressed on the repo name no matter what tweaks are installed. Tested also on Sileo Nightly for XinaA15 https://github.com/Sileo/Sileo but with no result.

what ios did you dualboot?, thats the jailbreak pogo right ?

Dualbooting iOS 14.8, Pogo, yes. Is this fixed?

ahhhh i have never seen that error so i think nop


Server responded with 0 code

Hello,
I'm using latest version from github. On Chrome and Chromium everything works fine, but if I use firefox, I got "server responded with 0 code" when uploading json key file.

Closing due to lack of follow up

see: https://github.com/rainlab/googleanalytics-plugin/issues/63


more than 2 replicates can not be used for chips_pipeline

Hi, I am trying to run chipseq_pipeline using more than 2 replicates using the command as below.  But it seems that the program can not take more than 2 replicates.  I also attached part of the log file to show the files the program took.  Is there any parameter I should set to using more replicates?  Thanks.
$ bds /home/ysun/TF_chipseq_pipeline/chipseq.bds -trimmed_fastq TRUE -species hg38 -nth 12 -out_dir CTCF -se -fastq1 CTCF_islet6-1.fastq.gz -fastq2 CTCF_islet6-2.fastq.gz -ctl_fastq1 ctrl_islet2.fastq.gz -ctl_fastq2 ctrl_islet3.fastq.gz -ctl_fastq3 ctrl_islet4.fastq.gz -ctl_fastq4 ctrl_islet5.fastq.gz -ctl_fastq5 ctrl_islet6.fastq.gz
========================================================================
== git info
Latest git commit		: eb3e2369b0397856d616369acdd06f114bf75ff3 (Thu Aug 3 20:12:41 2017)
Reading parameters from section (default) in file(/home/ysun/TF_chipseq_pipeline/default.env)...
== configuration file info
Hostname			: gatsby.ucsd.edu
Configuration file		:
Environment file		: /home/ysun/TF_chipseq_pipeline/default.env
== parallelization info
No parallel jobs		: false
Maximum # threads 		: 12
== cluster/system info
Walltime (general)		: 5h50m
Max. memory (general)		: 7G
Force to use a system		: local
Process priority (niceness)	: 0
Retiral for failed tasks	: 0
Submit tasks to a cluster queue	:
Unlimited cluster mem./walltime	: false
== shell environment info
Conda env. 			: aquas_chipseq
Conda env. for python3		: aquas_chipseq_py3
Conda bin. directory		:
Shell cmd. for init.		: if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/home/ysun/TF_chipseq_pipeline/.:/home/ysun/TF_chipseq_pipeline/modules:/home/ysun/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for init.(py3)	: if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq_py3 | wc -l) != "0" ]]; then source activate aquas_chipseq_py3; sleep 5; fi;  export PATH=/home/ysun/TF_chipseq_pipeline/.:/home/ysun/TF_chipseq_pipeline/modules:/home/ysun/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
Shell cmd. for fin.		: TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0
Cluster task min. len.		: 60
Cluster task delay			: 0
== output directory/title info
Output dir.			: /home/ysun/published/GEO/GSE23784_Stitzel_CellMetab/CTCF
Title (prefix)			: CTCF
Reading parameters from section (default) in file(/home/ysun/TF_chipseq_pipeline/default.env)...
Reading parameters from section (hg38) in file(/home/ysun/bds_pipeline_genome_data/aquas_chipseq_species.conf)...
== species settings
Species				: hg38
Species file			: /home/ysun/bds_pipeline_genome_data/aquas_chipseq_species.conf
Species name (WashU browser)	: hg38
Ref. genome seq. fasta		: /home/ysun/bds_pipeline_genome_data/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta
Chr. sizes file			: /home/ysun/bds_pipeline_genome_data/hg38/hg38.chrom.sizes
Black list bed			: /home/ysun/bds_pipeline_genome_data/hg38/hg38.blacklist.bed.gz
Ref. genome seq. dir.		:
== ENCODE accession settings
ENCODE experiment accession	:
ENCODE award RFA			:
ENCODE assay category		:
ENCODE assay title		:
ENCODE award				:
ENCODE lab				:
ENCODE assembly genome		:
ENCODE alias prefix		: KLAB_PIPELINE
== report settings
URL root for output directory	:
Genome coord. for browser tracks	:
== align bwa settings
Param. for bwa			: -q 5 -l 32 -k 2
BWA index			: /home/ysun/bds_pipeline_genome_data/hg38/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta
Walltime (bwa)			: 47h
Max. memory (bwa)		: 12G
== align multimapping settings
alignments reported for multimapping	: 0
== postalign bam settings
MAPQ reads rm thresh.		: 30
Rm. tag reads with str.		:
No dupe removal in filtering raw bam	: false
Walltime (bam filter)		: 23h
Max. memory (bam filter)	: 12G
Dup marker				: picard
Use sambamba markdup (instead of picard)	: false
== postalign bed/tagalign settings
Max. memory for UNIX shuf			: 12G
== postalign cross-corr. analysis settings
Max. memory for UNIX shuf			: 12G
User-defined cross-corr. peak strandshift	: -1
Extra parameters for cross-corr. analysis	:
== callpeak spp settings
Threshold for # peak		: 300000
Walltime (spp)			: 47h
Max. memory (spp)		: 12G
Stack size for run_spp.R		:
Use-defined cross-corr. peak strandshift; if -1, use frag. len.	:-1
Extra parameters for run_spp.R	:
== callpeak gem settings
Threshold for # peak in GEM		: 300000
Min. length of k-mers in GEM		: 6
Max. length of k-mers in GEM		: 13
Q-value threshold for GEM		: 0.0
Read distribution txt for GEM		: /home/ysun/TF_chipseq_pipeline/etc/Read_Distribution_default.txt
Extra parameters for GEM	:
Walltime (GEM)			: 47h
Max. memory (GEM)		: 15G
== callpeak PeakSeq settings
Target FDR for PeakSeq			:0.05
Number of simulations for PeakSeq	:10
Enrichment mapped frag. len. for PeakSeq	:-1
Minimum interpeak distance for PeakSeq	:-1
Mappability map file for PeakSeq	:
Maximum Q-value for PeakSeq		:0.1
Background model for PeakSeq		:Simulated
Extra parameters for PeakSeq		:
Walltime (PeakSeq)			: 47h
Max. memory (PeakSeq)		: 12G
== callpeak macs2 settings
Genome size (hs,mm)			: hs
Walltime (macs2)			: 23h
Max. memory (macs2)			: 15G
P-value cutoff (macs2 callpeak)		: 0.01
--keep-dup (macs2 callpeak)			: all
--extsize (macs2 callpeak); if -1 then use frag. len.	: -1
--shift (macs2 callpeak)			: 0
Extra parameters for macs2 callpeak		:
== callpeak naiver overlap settings
Bedtools intersect -nonamecheck	: false
== IDR settings
Append IDR threshold to IDR out_dir	: false
== chipseq pipeline settings
replicates 				: 2
Type of ChIP-Seq pipeline		: TF
Final stage for ChIP-Seq		:
Signal tracks for pooled rep. only	: false
Aligner to map raw reads			: bwa
reads to subsample for cross-corr. analysis		: 15000000
reads to subsample exp. replicates (0: no subsampling): 0
reads to subsample controls (0: no subsampling)	: 0
Generate anonymized filt. bam		: false
Peak caller for IDR analysis		: spp
Control rep. depth ratio		: 1.2
Scoring column for IDR			: signal.value
IDR threshold				: 0.05
Force to use pooled ctl			: false
Peak calling for true reps only		: false
No peak calling for self pseudo reps	: false
Disable cross-correlation analysis	: false
Disable g. peak filt. thru. n. peak	: false
Disable genome browser tracks	: false
== checking chipseq parameters ...
== checking input files ...
Rep1 fastq (SE) :
/home/ysun/published/GEO/GSE23784_Stitzel_CellMetab/CTCF_islet6-1.fastq.gz
Rep2 fastq (SE) :
/home/ysun/published/GEO/GSE23784_Stitzel_CellMetab/CTCF_islet6-2.fastq.gz
Control Rep1 fastq (SE) :
/home/ysun/published/GEO/GSE23784_Stitzel_CellMetab/ctrl_islet2.fastq.gz
Control Rep2 fastq (SE) :
/home/ysun/published/GEO/GSE23784_Stitzel_CellMetab/ctrl_islet3.fastq.gz
Distributing 12 to ...
{rep2=1, rep1=4, ctl1=6, ctl2=1}

Or is there any way to using more than 2 replicates?  Thanks.

Please remove -trimmed_fastq TRUE first. That flag is for the ATAC-Seq pipeline, not for ChiP-Seq.
The pipeline can take more than two ChiP replicates but number of controls cannot exceed that of ChiP replicates. You can reduce number of controls by merging control fastqs.
For example, first two controls will be merged and then used for ChiP replicate-1, the rest will be merged and used for ChiP replicate-2. Use parameter syntax -ctl_fastq[REP_ID]:[MERGE_ID].
-ctl_fastq1:1 ctrl_islet2.fastq.gz -ctl_fastq1:2 ctrl_islet3.fastq.gz -ctl_fastq2:1 ctrl_islet4.fastq.gz -ctl_fastq2:2 ctrl_islet5.fastq.gz -ctl_fastq2:3 ctrl_islet6.fastq.gz

Thanks.  I will try and keep you posted.
Also, atac_dnase_pipelines will generate a json file has a very detailed information.  But for chipseq_pipeline the json file does not have as much information as atac_dnase_pipelines does.  I am wondering is that because I did not use "python chipseq.py" but "bds chipseq.bds"?  Or if I can set any parameters to get a more informative json file too?  Thanks.


missing 1 required positional argument: 'outputName'

Hi,
I'm trying to use brats-segment to segment my dataset. I used the command:
brats-segment -t1 $t1_path -t1c $t1c_path -t2 $t2_path -fla $flair_path -d all -o /Volumes/Dati/tmp/BratS_prove/xxx/scan_directory/file.nii.gz -v
where obviously the file "file.nii.gz" does not exist.
This is the output:
DIRNAME is: /Volumes/Dati/tmp/BratS_prove/xxx/scan_directory
FILENAME is: file.nii.gz
Now running a new set of segmentations on input: /Volumes/Dati/tmp/BratS_prove/xxx/scan_directory
/Volumes/Dati/Download/BraTS-Toolkit-master/src/brats-toolkit/brats_toolkit/tmph7gy5dq4
/Volumes/Dati/Download/BraTS-Toolkit-master/src/brats-toolkit/brats_toolkit/tmph7gy5dq4/results
Called singleSegment with method: all
CALLED MULTISEGMENT
[Orchestra] Segmenting with econib
[Weborchestra][Success]Loaded fileformat: {'t1': 't1.nii.gz', 't1c': 't1c.nii.gz', 't2': 't2.nii.gz', 'fla': 'flair.nii.gz'}
[Weborchestra][Info] Writing to path /Volumes/Dati/Download/BraTS-Toolkit-master/src/brats-toolkit/brats_toolkit/tmph7gy5dq4/t1.nii.gz
[Weborchestra][Info] Writing to path /Volumes/Dati/Download/BraTS-Toolkit-master/src/brats-toolkit/brats_toolkit/tmph7gy5dq4/t2.nii.gz
[Weborchestra][Info] Writing to path /Volumes/Dati/Download/BraTS-Toolkit-master/src/brats-toolkit/brats_toolkit/tmph7gy5dq4/t1c.nii.gz
[Weborchestra][Info] Writing to path /Volumes/Dati/Download/BraTS-Toolkit-master/src/brats-toolkit/brats_toolkit/tmph7gy5dq4/flair.nii.gz
[Weborchestra][Info] Images saved correctly
[Weborchestra][Info] Starting the Segmentation with container econib now
ERROR DETAIL:  runContainer() missing 1 required positional argument: 'outputName'
Which could be the problem?
Thanks a lot,
Domenico

I believe we fixed this in BTK the continuation of this repo? @christophbrgr ?
https://github.com/neuronflow/BraTS-Toolkit

Thanks a lot,
I installed the last version.
Please, let me know if I have to do something
Domenico
Il giorno mar 14 set 2021 alle ore 21:02 neuronflow <
@.***> ha scritto:

I believe we fixed this in BTK the continuation of this repo?
@christophbrgr https://github.com/christophbrgr ?
https://github.com/neuronflow/BraTS-Toolkit
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Dear all,
As I told you in the previous email I installed the last version but I
can't resolve the issue (missing 1 required positional argument:
'outputName').
Could you please suggest how to resolve it?
Thank you
Domenico
Il giorno mar 14 set 2021 alle ore 21:02 neuronflow <
@.***> ha scritto:

I believe we fixed this in BTK the continuation of this repo?
@christophbrgr https://github.com/christophbrgr ?
https://github.com/neuronflow/BraTS-Toolkit
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Issue when using Nullable SQL type

Having issues using Nullable field type
https://clickhouse.com/docs/en/sql-reference/data-types/nullable
CREATE TABLE IF NOT EXISTS blocks
(
    `id` String,
    `difficulty` Int64
)
ENGINE = ReplacingMergeTree
PRIMARY KEY id
ORDER BY id

Substreams test code logic
match header.difficulty {
    Some(difficulty) => row.change("difficulty", ("", "123")),
    None => row,
};

❌ Errors

when difficulty=123

2024-07-26T23:47:02.098+0200 ERRO (sink-sql) handle BlockScopedData message at block #10 (4ff4a38b278ab49f7739d3a4ed4e12714386a9fdf72192f2e8f7da7822f10b4d): failed to flush at block #10 (4ff4a38b278ab49f7739d3a4ed4e12714386a9fdf72192f2e8f7da7822f10b4d): dialect flush: failed to get values: converting value "123" to type "*int64" in column "difficulty": unsupported pointer type *int64

when difficulty=null (empty)

2024-07-26T23:47:51.667+0200 ERRO (sink-sql) handle BlockScopedData message at block #10 (4ff4a38b278ab49f7739d3a4ed4e12714386a9fdf72192f2e8f7da7822f10b4d): failed to flush at block #10 (4ff4a38b278ab49f7739d3a4ed4e12714386a9fdf72192f2e8f7da7822f10b4d): dialect flush: executing for entry ["0x476574682f76312e302e302f6c696e75782f676f312e342e32" '\x00' 'ᎈ' '\x00' "0x88e96d4537bea4d9c05d12549907b32561d3bf31f45aae734cdc119f13406cb6" "0x00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000" "0x05a56e2d52c817161883f50c441c3228cfe54d9f" "0x969b900de27b6ac6a67742365dd65f55a0526c41fd18e1b16f1a1215c2e66f59" '�' '\x01' "0x1dcc4de8dec75d7aab85b567b6ccd41ad312451b948a7413f0a142fd40d49347" "0xd4e56740f876aef8c010b86a40d5f56745a118d0906a34e69aec8c0db1cb8fa3" "0x56e81f171bcc55a6ff8345e692c0f86e5b48e01b996cadc001622fb5e363b421" "537" "0xd67e4d450343046425ae4271474353857ab860dbc0a1dde64b41b5cd3a532bf3" '\x00' '�' '\x00' "0x56e81f171bcc55a6ff8345e692c0f86e5b48e01b996cadc001622fb5e363b421"]: clickhouse [Append]:  clickhouse: expected 20 arguments, got 19

✅ work around solution
Set null values as 0

Same issue with Nullable(String)
CREATE TABLE IF NOT EXISTS logs
(
    topic0              String,
    topic1              Nullable(String),
    topic2              Nullable(String),
    topic3              Nullable(String),

❌ Error unsupported pointer type *string

2024-07-28T11:28:39.418+0200 ERRO (sink-sql) handle BlockScopedData message at block #1598910 (f83b4bd9b91d157f2f6d8c3ad90dd69c1b7c050f3a372dc0af792a2533c6b5fe): failed to flush at block #1598910 (f83b4bd9b91d157f2f6d8c3ad90dd69c1b7c050f3a372dc0af792a2533c6b5fe): dialect flush: failed to get values: converting value "0x00000000000000000000000012dbd4c669e3e860a6432dcb69c8ded6b77be616" to type "*string" in column "topic1": unsupported pointer type *string

❌  Error invalid memory address or nil pointer dereference
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x2 addr=0x30 pc=0x1058b7224]

goroutine 94 [running]:
github.com/streamingfast/substreams-sink-sql/db.convertOpToClickhouseValues(0x14001034f90)
        /Users/denis/Github/substreams-sink-sql/db/dialect_clickhouse.go:174 +0x1d4
github.com/streamingfast/substreams-sink-sql/db.clickhouseDialect.Flush({}, {0x1?, 0x0?}, {0x1066e34b0, 0x140001eab10}, 0x140000e4780, {0x1066e34b0?, 0x1065c4820?}, 0x1400088e540?)
        /Users/denis/Github/substreams-sink-sql/db/dialect_clickhouse.go:64 +0x78c
github.com/streamingfast/substreams-sink-sql/db.(*Loader).Flush(0x140000e4780, {0x105a3bda2?, 0x18584e?}, {0x14000512030, 0x28}, 0x1400009a8d8, 0x18584e)
        /Users/denis/Github/substreams-sink-sql/db/flush.go:29 +0x1a0
github.com/streamingfast/substreams-sink-sql/sinker.(*SQLSinker).HandleBlockScopedData(0x14000825c00, {0x1066e34e8, 0x14000516050}, 0x14000715180, 0x10789046a, 0x1400009a8d8)
        /Users/denis/Github/substreams-sink-sql/sinker/sinker.go:125 +0x5d0
github.com/streamingfast/substreams-sink.(*Sinker).doRequest(0x140002bc160, {0x1066e34e8, 0x14000516050}, 0x14000d3a038, 0x14000b34b80, {0x1066c1860, 0x14000883840}, {0x14000883830, 0x1, 0x1}, ...)
        /Users/denis/go/pkg/mod/github.com/streamingfast/substreams-sink@v0.3.4/sinker.go:485 +0x14ec
github.com/streamingfast/substreams-sink.(*Sinker).run(0x140002bc160, {0x1066e34e8, 0x14000516050}, 0x14000d3a038, {0x1066d9ce8, 0x14000825c00})
        /Users/denis/go/pkg/mod/github.com/streamingfast/substreams-sink@v0.3.4/sinker.go:280 +0x624
github.com/streamingfast/substreams-sink.(*Sinker).Run(0x140002bc160, {0x1066e34e8, 0x14000516050}, 0x14000d3a038, {0x1066d9ce8, 0x14000825c00})
        /Users/denis/go/pkg/mod/github.com/streamingfast/substreams-sink@v0.3.4/sinker.go:199 +0x38c
github.com/streamingfast/substreams-sink-sql/sinker.(*SQLSinker).Run(0x14000825c00, {0x1066e34e8, 0x14000516050})
        /Users/denis/Github/substreams-sink-sql/sinker/sinker.go:89 +0x658
created by github.com/streamingfast/cli.(*Application).SuperviseAndStart in goroutine 1
        /Users/denis/go/pkg/mod/github.com/streamingfast/cli@v0.0.4-0.20230825151644-8cc84512cd80/application.go:102 +0x370
make: *** [sql-run] Error 2

Clickhouse best practices recommend avoiding using Nullable fields
https://clickhouse.com/docs/en/cloud/bestpractices/avoid-nullable-columns
This issue isn't fixed in the substreams sink sql, however Nullable types shouldn't be used
Alternative setting integer values to 0 and String values to "" empty string


Path token expansion does not works on Windows

Python and libraries installed into $project_path/env, here excerpt from sublime linter settings file:
        "paths": {
            "linux": [],
            "osx": [],
            "windows": [
                "${project}/env/Scripts",
                "${project}"
            ]
        },
        "python_paths": {
            "linux": [],
            "osx": [],
            "windows": [
                "${project}/env/Scripts",
                "${project}"
            ]
        },

and it looks like SL3 does not runs replace_settings_tokens at all. Here what I could see in console with debug mode turned on:
SublimeLinter: computed PATH from system:
C:\Program Files\Sublime Text 3\${project}\env\Scripts
C:\Program Files\Sublime Text 3\${project}
C:\Program Files\Sublime Text 3\${env:HOME}

I performed small research (like put raise Exception in method replace_settings_tokens) and found that this method never called, i.e. tokens not expanded correctly.

Same here. Stopped working from 3.10.0. 3.9 works fine.

do you know if this issue was fixed in 3.10.1?

Does not work in 3.10.1.


Restricting https protocol does not forbid http

Summary
I would like to allow only https for a certain route, but when configuring the route to do so, http is still available
Steps To Reproduce

Create a route with only HTTPS

curl -X POST http://localhost:8001/services/admin-api/routes \
   --data paths[]=/admin-api \
   --data protocols[]=https

Answer from Kong is
{"id":"64f17672-1fd4-4389-8328-2822be69693d","tags":null,"updated_at":1571932820,"destinations":null,"headers":null,"protocols":["https"],"created_at":1571932820,"snis":null,"service":{"id":"69da34d8-4512-4163-afff-663e25cd5be1"},"name":null,"preserve_host":false,"regex_priority":0,"strip_path":true,"sources":null,"paths":["\/admin-api"],"https_redirect_status_code":426,"hosts":null,"methods":null}

Requesting the route using HTTP

curl -X GET http://MYDOMAIN/admin-api

Kong is responding
{"plugins":{"enabled_in_cluster":["key-auth","acl"], ...

Expected behavior
Accessing route from HTTP should not work
Additional Details & Logs

Kong version 1.3
Using kong ingress kubernetes on Google Cloud
Operating system containerOS

I actually had multiple routes to the same service, some routes with http enabled, so I guess that's not a bug


Deserializing a boolean string is throwing exception

When deserializing a json string with a boolean value like:
{"active": "true"}
I am getting the following error:
Utf8Json.JsonParsingException: expected:'true | false', actual:'"true"'
which I believe is due to the fact that "true" is enclosed in quotes, instead of just being
{"active": true }
Since this is information I am obtaining froma  REST API from a particular website, I have no control of the data that is coming in.
Is there anyway I can work around this? I have attempted to extend the BooleanFormatter class so I can provide a custom BooleanFormatter, but since the class is sealed, I can't seem to do much.
Any help would be quite appreciated!
Thanks.

Closing due to inactivity


Create all-in-one client

The server should be dropped.
If you are beyond that part, you should consider throwing this application into the App Store. Instant fans since NPO doesn't do anything with it yet on the Apple TV 4.
Drop the remote JS files, and parse these directly in Swift 2.x within Xcode, that way everything will be done by the Apple TV 4, which does have way too much power for the current situation.

Users of this project need to side load it onto their devices, which is quite cumbersome. Instead of having everybody go through that again whenever something changes, the app is now automatically updated whenever something changes because the biggest part of the app is hosted on S3.
As long as there's no plan to put this app in the app store, I think keeping the TVML templates and javascript files separate is the best idea. I'm closing this for now, please reopen if I'm missing something.


style: :rocket: Added a simple loader with text

Added a simple loader with text.
please do review and approve

#Hactoberfest2022

Your contribution is greatly appreciated @gopal1996
Don't forget to star the repo and follow me on Github.
Thanks!

can you please add hacktoberfest-accepted label @rohit8020

Sure.
Thanks for reminding @gopal1996 .


[Core Rulebook] Unable to Place Soulfire

Cast Soulfie with Prayer Granted.  Press Place Soulfire nothing happens.  I am seeing console error
Uncaught (in promise) ReferenceError: undefined. effectData is not defined
[Detected 1 package: system:wfrp4e(8.0.2)]
at ChatWFRP._onPlaceAreaEffect (wfrp4e.js:5349:101)
_onPlaceAreaEffect @ wfrp4e.js:5349
await in _onPlaceAreaEffect (async)
dispatch @ jquery.min.js:2
v.handle @ jquery.min.js:2
From: steven.evansfoundry: 12.331wfrp4e: 8.0.2wfrp4e-core: 6.0.0Active Modules: filepicker-plus, lib-wrapper, module-credits, socketlib, warhammer-lib, wfrp4e-gm-toolkit

can now place template after update to game system 8.0.3 but now get
VM828:6 Uncaught (in promise) TypeError: undefined. Cannot read properties of undefined (reading 'result')
[Detected 1 package: warhammer-lib(1.0.1)]
at Object.eval (eval at execute (warhammer.js:319:21), :6:60)
at WarhammerScript.execute (warhammer.js:319:121)
at warhammer.js:957:73
at Array.map ()
at ActiveEffectWFRP4e.handleImmediateScripts (warhammer.js:957:62)
at ActiveEffectWFRP4e._preCreate (warhammer.js:864:27)
at async #preCreateDocumentArray (foundry-esm.js:56392:31)
at async ClientDatabaseBackend._createDocuments (foundry-esm.js:56347:7)
at async ActiveEffectWFRP4e.createDocuments (foundry-esm.js:11423:23)
at async ActiveEffectWFRP4e.create (foundry-esm.js:11567:23)
at async ActorWFRP4e.applyEffect (warhammer.js:4332:13)
at async AreaHelpers.checkTokenAreaEffects (warhammer.js:3542:13)
at async Semaphore._try (foundry-esm.js:6645:19)

This I cannot reproduce, please make sure you're using an updated Soulfire item

The error appears to be with applying the effect to the target.  If I place the template with no (enemy) tokens within it there is no error.  When I test using an orc (from Core rules) with in the template the error appears


[BEAM-11377] Disable mvn http keepalive.

Snapshot quickstart tasks are failing due to a connection reset error from the mvn command. Disable keep alive in mvn to see if that helps resolve the remaining issues. The first solution of adding retry attempts reduced flakiness but not enough to make this task consistently pass.

Thank you for your contribution! Follow this checklist to help us incorporate your contribution quickly and easily:

[ ] Choose reviewer(s) and mention them in a comment (R: @username).
[ ] Format the pull request title like [BEAM-XXX] Fixes bug in ApproximateQuantiles, where you replace BEAM-XXX with the appropriate JIRA issue, if applicable. This will automatically link the pull request to the issue.
[ ] Update CHANGES.md with noteworthy changes.
[ ] If this contribution is large, please file an Apache Individual Contributor License Agreement.

See the Contributor Guide for more tips on how to make review process smoother.

GitHub Actions Tests Status (on master branch)

See CI.md for more information about GitHub Actions CI.

R: @boyuanzz

Run Python PreCommit

Run Python PreCommit


The term 'filter' in documentation contradicts the common usage of the term

m-w.com defines the verb filter
1:  to subject to the action of a filter
2:  to remove by means of a filter
From https://relishapp.com/rspec/rspec-core/v/3-3/docs/command-line/tag-option
"The tag can be a simple name or a name:value pair. In the first case,
examples with :name => true will be filtered."
So I expect examples with :name => true to be removed or subjected to a filter. What actually happens is that examples with :name => true are run and no other examples are run.
So the documentation would make sense to say something like "the examples will be subject to a filter which includes only :name => true."
This usage is also repeated throughout the linked document. It's very confusing on the first read, and even after that, I have to continually remind myself whenever I see it.

I think "filter" can still be used, but we should phrase it as:

The tag can be a simple name or a name:value pair. In the first case,
the examples will be filtered to those with :name => true."

...but obviously there are other ways to phrase it.  We'd gladly accept a PR to improve our docs.  Want to take a stab at it?

Sure. I'll give it shot this weekend.

:+1: Thanks in advance!

@ian-kelling do you still have some time to do this? It'd be great if you could open a PR ^_^

Addressed by #2090.

Thanks to creature for fixing this. Unfortunately I did not get time to do it.

Thanks to creature for fixing this. Unfortunately I did not get time to do it.

No problem! Glad I could help out. :)


Inconsistent information

Risk is labeled as "Niedriges Risiko". But the paragraph below says "Die Infektionswahrscheinlichkeit wird daher als erhöht für Sie eingestuft..." which are in my opinion two contradictory statements.

Is this supposed to happen? And more importantly: What's the actual risk level?
Samsung Galaxy A8
Android-Version 9
App-Version 1.2.0

Hi @XTrandi , this is a duplicate of https://github.com/corona-warn-app/cwa-documentation/issues/405#issue-677662490 and was obviuosly addressed with https://github.com/corona-warn-app/cwa-app-android/pull/1004


DRILL-1457: Push Limit past through UnionExchange.

Aman, could you please review this pull request?

Revise the code based on comments.

+1  LGTM.


Server overview reformat

Align similar  style charts on same row and add x and y axes to the chart for better context.

Merged #783


[IA-1446] Jc docker documentation

This leverages the new build scripts in the terra-docker repo, which automatically produce json documentation, along with a file that contains the current versions. This removes the need to PR changes for leo docker versions.
my linter went a little crazy. I reapplied and fixed some issues, but I think the rest of its changes are arguably improvements.
https://broadworkbench.atlassian.net/browse/IA-1446

Thanks for the PR. The extraneous formatting changes make it hard to focus on the actual changes. Can you please back out any formatting changes that aren't specifically enforced by the eslint rules? Thanks.

I reverted several (it was a lot worse, vscode is currently bugged as far as I can tell and there is no way to stop/configure it from mangling entire javascript files on save. I had to switch to intellij...). I would like to keep the remaining. I think it's arguably more readable in those cases, and not worth the time to manually revert unless there are strong feelings about the original formatting.

Note: I made some updates to get this toward completion:

Removed extraneous state
Initialized form with current cluster values when present
Simplified packages loading
Fixed whitespace and stylistic issues


Added android:fitsSystemWindows="true" to NestedScrollView to allow animations to work

The android:fitsSystemWindows="true" parameter should be propagated down to the inner most container which in this case is a NestedScrollView. Failing do do so will cause any shared element animations to miscalculate the location of the target element in the target activity.

This doesn't work on Galaxy Tab 3 8"
Only the image/toolbar scrolls, the cards remain in position


spliterator is not supported with Apache POI 5.2.0 (Unsupported operation getPhysicalNumberOfRows)

After updating to the latest version of the streaming reader (3.4.0) and Apache POI (5.2.0) the spliterator is no longer usable as it depends on the unsupported operation getPhysicalNumberOfRows. As a workaround I have changed my stream (I was using StreamSupport to make a stream from the spliterator) by a for loop with the row iterator but I would like to use spliterator again if possible. Let me know if you need further clarifications
Apache POI 5.2.0 spliterator implementation:
    /**
     *  Returns a spliterator of the physical rows
     *
     * @return a spliterator of the PHYSICAL rows.  Meaning the 3rd element may not
     * be the third row if say for instance the second row is undefined.
     *
     * @since POI 5.2.0
     */
    @Override
    default Spliterator<Row> spliterator() {
        return Spliterators.spliterator(rowIterator(), getPhysicalNumberOfRows(), 0);
    }

@borjapenman I don't know what the plans for this repo are but I have applied a fix on my fork - https://github.com/pjfanning/excel-streaming-reader/pull/96


feat: updated pg and mysql TransactionManager execute

added for options
isLoggerEnabled
logger
transactionId
timeToRollback

:tada: This PR is included in version 3.41.0 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


Use jest-extended again

Reverts #84, now that we dropped development support for Node v12 in #137.

Interestingly, the number of lines didn't change :sweat_smile:


Reduce backoff durations and log slow API requests

We have seen situations where the agent will appear offline because it has not reported status for more than 5 minutes while the agent appears to be working correctly.  One theory is if the service is not responding the agent will retry for up to an hour due to the backoff config. This would block status updates during that time. The updated backoff maxes out under 3 minutes, and log requests which take over a minute.
This PR also removed unneeded locks from status while debugging

Have you been able to reproduce the issue?  Does this fix it?  Is that why it's a draft?

QE is validating

After 24h of testing the PR with a device created with make agent-vm, the longest sync duration that I see is 447.481481ms.

We want to merge for further testing but this has looked promising in my local testing as well as QE.


Multistage Graph

Is your feature request related to a problem? Please describe.
I would like mention about multistage graph along with it's code.

Please elaborate

Will elaborate about what is multistage graph problem + along  it's code implementation


Lowered six dependency version to 1.5.2

Addresses
https://github.com/GoogleCloudPlatform/gcloud-python/issues/1928
Note that sphinx is the offending library that caused us to abandon https://github.com/grpc/grpc/pull/5284
Sphinx is only a setup dependency, so I was able to work around it.

The driving factor is supporting the 14.04 LTS Ubuntu release, and their debian six package is 1.5.2
http://packages.ubuntu.com/trusty/python-six

LGTM


util: bump gogoproto, protobuf, libcircllhist

Signed-off-by: Daniel Hochman<EMAIL_ADDRESS>Description:
Bump a few deps to the latest release. Eliminates some compiler warnings for me.
Risk Level: Low
Testing:
CI
Docs Changes:
N/A
Release Notes:
N/A

You need to merge master in order to fix tests (see: https://github.com/envoyproxy/envoy/pull/3317).

Thanks!  I'd meant to update circlhist today but you beat me to it :-)


Page Loading-Time Tracker Extension

I've added the Page Loading-Time Tracker Extension.
Related issue: #210

@alisha-kamat there is some error in the code kindly solve them
Also, the video is incomplete, make the video where you are showing how extension works and gives result

@alisha-kamat please update the files asap or else we'll close the issue


RedisTimeoutException: Unable to send batch after 3 retry attempts

Expected behavior
With ~800qps from 2 RedissonClients, we do not expect to see ~2qps of error rate with the following error: RedisTimeoutException: Unable to send batch after 3 retry attempts. Ideally, we should see no errors, or few errors as this isn't high load.
Actual behavior
We observe around 2qps errors (RedisTimeoutException: Unable to send batch after 3 retry attempts) that increase in a "step" up fashion. See image:

This graph is the traffic sent to redis in the same timespan:

As a side note: we are running 2 kubernetes pods, each with one RedissonClient that cumulatively are making requests/seeing the errors from the graphs above. The interesting thing to note is that for about 9hours after we start the pods (creating a new client in each) and send them traffic, they perform fine for around ~9hours and then the errors begin. We hypothesize that there is some issue in how the connections are managed.
Steps to reproduce or test case

Create 2 RedissonClient instances
Send between 400-850qps of traffic (variable) for around a day, where traffic includes batch ADD and PUT commands.
Observe failures.

Redis version
4.0.1
Redisson version
3.10.7
Redisson configuration
Cluster mode
Read mode: Master (we do not have slave nodes)
Master connection pool size: 64
Master connection pool minimum idle size: 0
Slave connection pool size: 0
Slave connection pool minimum idle size: 0
Subscription connection pool size: 0 (we do not use pubsub capabilities of redis)
Subscription connection pool minimum idle size: 0
Connect timeout: 500ms
Timeout: 500ms
Retry attempts: 3

Have you followed these suggestions - https://github.com/redisson/redisson/wiki/16.-FAQ#q-i-saw-a-redistimeoutexception-what-does-it-mean-what-shall-i-do-can-redisson-team-fix-it ?

I've looked into them and we are trying.. would you happen to know why we are experience the "step" pattern of increasing errors? If there was a lack of nettyThreads or connections, wouldn't the errors be more uniform?

Wanted to follow up from some of our trials: we have a separate RedissonClient running in SingleServer Mode with the follow config:
Connection pool size: 64
Connection pool minimum idle size: 0
Subscription connection pool size: 0 (we do not use pubsub capabilities of redis)
Subscription connection pool minimum idle size: 0
We were seeing the same RedisTimeoutException as above for this client, but we followed the FAQ guide above and increased netty threads to 48 and saw this error appear:
org.redisson.client.RedisException: Unexpected exception while processing command which further down the stack trace is caused by: Caused by: java.nio.channels.ClosedChannelException. Have you ever seen this before / know what it may mean?

Same problem here with 3.10.7

Caused by: java.nio.channels.ClosedChannelException. Have you ever seen this before / know what it may mean?

This means that connection is closed due to network issue or something.

@PaniniGelato
Which error? Did you try to follow these steps https://github.com/redisson/redisson/wiki/16.-FAQ#q-i-saw-a-redistimeoutexception-what-does-it-mean-what-shall-i-do-can-redisson-team-fix-it ?

@mrniko
got exception during load test(about 1000qps):
org.redisson.client.RedisTimeoutException: Unable to send command! Try to increase 'nettyThreads' and/or connection pool size settings Node source: NodeSource [slot=null, addr=null, redisClient=null, redirect=null, entry=MasterSlaveEntry [masterEntry=[freeSubscribeConnectionsAmount=1, freeSubscribeConnectionsCounter=value:50:queue:0, freeConnectionsAmount=1021, freeConnectionsCounter=value:1021:queue:0, freezed=false, freezeReason=null, client=[addr=redis://ip:port], nodeType=MASTER, firstFail=0]]], connection: RedisConnection@1208598866 [redisClient=[addr=redis://ip:port], channel=[id: 0xe56d57a0, L:/ip:port - R:ip:port], command=CommandsData [commands=[]]], current command in queue: null, command: (GET), params: [my_key:659472150] after 3 retry attempts

my config
        org.redisson.config.Config cc = new org.redisson.config.Config();
        cc.useSingleServer()
                .setAddress("redis://" + host + ":" + port)
                .setPingConnectionInterval(60*1000)
                .setIdleConnectionTimeout(10*60*1000)
                .setConnectionPoolSize(poolSize)
                .setTimeout(2000)
                .setKeepAlive(true)
                .setTcpNoDelay(true)
                .setRetryAttempts(1)
                .setRetryInterval(500);
        cc.setCodec(StringCodec.INSTANCE);
        cc.setTransportMode(TransportMode.EPOLL);
        cc.setNettyThreads(32);
        cc.setThreads(256);
        cc.setDecodeInExecutor(true);

enlarge nettyThreads didn't help me

@PaniniGelato
Did you try to increase connection pool?

@mrniko
poolSize=1024
trying nettyThreads=128, come back later

the client died at 784qps with
org.redisson.client.RedisTimeoutException: Unable to send command! Try to increase 'nettyThreads' and/or connection pool size settings Node source: NodeSource [slot=null, addr=null, redisClient=null, redirect=null, entry=MasterSlaveEntry [masterEntry=[freeSubscribeConnectionsAmount=1, freeSubscribeConnectionsCounter=value:50:queue:0, freeConnectionsAmount=249, freeConnectionsCounter=value:0:queue:2836, freezed=false, freezeReason=null, client=[addr=redis://ip:port], nodeType=MASTER, firstFail=0]]], connection: RedisConnection@724231806 [redisClient=[addr=redis://ip:port], channel=[id: 0x4633f9d1, L:/ip:port - R:ip:port], command=CommandData [promise=RedissonPromise [promise=ImmediateEventExecutor$ImmediatePromise@372d746b(failure: java.util.concurrent.CancellationException)], command=(ZREVRANGEBYSCORE), params=[my_key:6938743714,<PHONE_NUMBER>198, 0.0, LIMIT, 0, 3], codec=org.redisson.client.codec.StringCodec]], current command in queue: CommandData [promise=RedissonPromise [promise=ImmediateEventExecutor$ImmediatePromise@372d746b(failure: java.util.concurrent.CancellationException)], command=(ZREVRANGEBYSCORE), params=[my_key:6938743714,<PHONE_NUMBER>198, 0.0, LIMIT, 0, 3], codec=org.redisson.client.codec.StringCodec], command: (GET), params: [str:cmt:aid:17713828073626568760:cid:6823694158] after 1 retry attempts

@PaniniGelato
failure: java.util.concurrent.CancellationException was happen due to earlier cancel of command execution.
try to set retryinterval = 1500

Also make sure you redis instance is not overloaded

org.redisson.config.Config cc = new org.redisson.config.Config();
cc.useSingleServer()
        .setAddress("redis://" + host + ":" + port)
        .setIdleConnectionTimeout(10*60*1000)
        .setConnectionPoolSize(poolSize)
        .setTimeout(3000)
        .setPingConnectionInterval(60*1000)
        .setKeepAlive(true)
        .setTcpNoDelay(true);
cc.setLockWatchdogTimeout(1000);// 锁超时1s
cc.setCodec(StringCodec.INSTANCE);
cc.setTransportMode(TransportMode.EPOLL);
cc.setNettyThreads(32);
cc.setThreads(32);
return Redisson.create(cc);

using this config is able to finish 800qps load test, no TimeoutException
Are the nettyThreads only use to hand I/O?
Setting it to be cpu nums or twice should be ok for most cases
would try again later...

Are the nettyThreads only use to handle I/O?

Not only, they also participany in command decoding.

I am curious that i got freeConnectionsAmount=249 in stack trace which is far from ConnectionPoolSize, and my redis is not overloaded. It just looks like the client is not able to send command

Which poolsize did you set?


Add api key

changed the way authorization headers are generated, and left backwards compatibility for the existing (deprecated) Agent Configuration.

#65


libffi: enable static build

Motivation for this change
Flags to have libffi produces static libraries.
This won't generate any rebuild because static libraries are not built by default in this case. I tried to copy what I observed for ncurses.
ping #43795
Things done

[X] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
Built on platform(s)

[X] NixOS
[ ] macOS
[ ] other Linux distributions

[ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
[ ] Tested execution of all binary files (usually in ./result/bin/)
[ ] Determined the impact on package closure size (by running nix path-info -S before and after)
[] Assured whether relevant documentation is up to date
[X] Fits CONTRIBUTING.md.

Does this not work out of the box? We add --enable-static and --disable-shared for everything in static.nix:
https://github.com/NixOS/nixpkgs/blob/ca005338879b946d24621f2d08661cf3a539510d/pkgs/stdenv/adapters.nix#L56

@matthewbauer You are right. Sorry. I'm cloning the PR.


I can't use the "vocab_tree" method to match the images, while it works with the matching way of "sequential"

Describe the bug
I can't use the "vocab_tree" method to match the images, while it works with the matching way of "sequential"
To Reproduce
Steps to reproduce the behavior:

Use anaconda in Windows 11 to get in to the nerfstudio folder which is located in E:
Use anaconda to activate nerfstudio environment "nerfstudio" which is in C:
run"ns-process-data images ..."
See error:
error running command: colmap vocab_tree_matcher --database_path data\colmap\database.db --SiftMatching.use_gpu 1
--VocabTreeMatching.vocab_tree_path C:\Users\Username\AppData\Local\nerfstudio\nerfstudio\vocab_tree.fbow
I have changed the matching-method to "sequential" which works, the other 2 ways of matching-methods can't work due to the same error. I have change the nerfstudio folder in E: to C: , but it still can't work

Expected behavior
it should have ran the colmap correctly
Screenshots

Additional context
I have changed the matching-method to "sequential" which works, the other 2 ways of matching-methods can't work due to the same error. I have change the nerfstudio folder in E: to C: , but it still can't work

What error do you see if you run the following in the terminal?
colmap vocab_tree_matcher --database_path data\colmap\database.db --SiftMatching.use_gpu 1 --VocabTreeMatching.vocab_tree_path C:\Users\Lemon Zhong\AppData\Local\nerfstudio\nerfstudio\vocab_tree.fbow

I am having the same issue with colmap failing while running colmap feature matcher, my error after running the command you gave is this:
==============================================================================
Vocabulary tree feature matching
F0210 23:52:31.981678 1330144 cache.h:132] Check failed: max_num_elems > 0 (0 vs. 0)
*** Check failure stack trace: ***
@     0x7ff46067b1c3  google::LogMessage::Fail()
@     0x7ff46068025b  google::LogMessage::SendToLog()
@     0x7ff46067aebf  google::LogMessage::Flush()
@     0x7ff46067b6ef  google::LogMessageFatal::~LogMessageFatal()
@     0x5622e646d055  colmap::LRUCache<>::LRUCache()
@     0x5622e645b0f0  colmap::FeatureMatcherCache::Setup()
@     0x5622e6468296  colmap::VocabTreeFeatureMatcher::Run()
@     0x5622e65c3091  colmap::Thread::RunFunc()
@     0x7ff45f250de4  (unknown)
@     0x7ff45f376609  start_thread
@     0x7ff45eefb133  clone
Aborted (core dumped)

Does it work for other data? Can you also try using one of the other matchers, --matching-method exhaustive

It seems no data can work when I use vocab tree or  "exhaustive", but it works when I use the method "sequential".
---Original---
From: "Matthew @.>
Date: Sun, Feb 12, 2023 02:41 AM
To: @.>;
Cc: "Ningze<EMAIL_ADDRESS>Subject: Re: [nerfstudio-project/nerfstudio] I can't use the "vocab_tree"method to match the images, while it works with the matching way of"sequential" (Issue #1377)
Does it work for other data? Can you also try using one of the other matchers, --matching-method exhaustive
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you are subscribed to this thread.Message ID: @.***>

Is this also true if you use the data we provide, ie the poster dataset (the data is already processed, but you can run ns-process-data on the images folder)?
vocab tree requires an additional file that is downloaded the first time it is run, it's possible there is a bug there. However if exhaustive also doesn't work, this is less likely. My best guess is that colmap is struggling to find matches in the data you are using, this can be confirmed by running on data we know works (poster dataset). If it doesn't work on the poster dataset, then it might be an issue with the colmap installation.


Sample integration (parser)

Create simple parser using WebMagic or else, that parses sample html page (#176)
Parser have to receive next data:

title of event
date of event
time of start event
address
registration link
city name
price
describing text

The project is on GitLab. You should login there and say your login to Alexander Vlasov

@AndriyBaibak 4 hours


Add examples to the ack cookbook

ack 3, currently in development, will include a cookbook of examples for folks to try.  Here's an example:
Find "goats" in every file that also contains "cows"
ack -l cows | ack -x goats

What examples do you have that can get added to the cookbook?  Post them here.

From @n1vux: document use of lookbehind and other useful Perl Extended RE idioms in a separate doc section (have some a few bits now but scattered)

The example I always use in presentations:
Find all the headers used in your C programs and dedupe them:
ack '#include <(.+)>' --cc --output='$1' | sort -u

Pull out examples from the main ::Manual, especially the "TIPS" section.

Searching for a method call:
ack -- '->method'

or
ack '[-]>method'

Search for all the files that mention Sys::Hostname but don't match hostname.  Add -I because I have --smart-case on in my .ackrc.
ack -l Sys::Hostname | ack -x -L -I hostname

via @clmagic
egrep -- "\t-\t-\t-\t-\t" entries.txt |sort -k3V # Get the entries with 4+ null fields and sort the entries by IPv4 (-V) in the 3rd column.
(technically it's 4+ adjacent null fields)

Mention dirty and/or git diff --name-only.

Open list of matching files in Vim, searching for your search term:
$ ack my_search_term
<results>
$ vim $(!! -l) +/!$

!! expands to the previous command - ack my_search_term in the example
$(...) expands to the output of the command in the parens, so the output of ack my_search_term -l in the xample
+/<term> tells Vim to start searching for <term> once it opens
!$ expands to the last argument of the previous command - my_search_term in the example

Small caveat: Vim patterns and Perl regexes have some overlap, but they are different, so this doesn't work so great when you have a more complex regex as your search term.

See all the .vim files in your ~/.vim directory, except in the bundle/ directory.
ack -f --vim ~/.vim --ignore-dir=bundle

ack -g tax --ruby Finds all the ruby files that match /tax/.
vim $(ack -l taxes) open all the files that have taxes in them.
ack -f --perltest | xargs prove Find all the Perl test files and feed them to xargs which runs them all against the prove command.

We could have entire section just about ack -f and ack -g.

Find places where two methods with the same name are being called on the same line.
ack -- '->(\w+).*->\1\b'

Find all the places where I'm making a call like sort { lc $a cmp lc $b }
ack '\bsort\b.+(\w+).+\bcmp\b.+\b(\1)\b'

Show a range of lines in a file: ack --lines=830-850 filename

Find modules that are not using Test::Warn:
ack -L 'warnings?_' $(ack -l Test::Warn)

Corrolary to ack -l cows | ack -x goats is ack -L cows | ack -x goats: Goats in files that do not contain cows.

Hi. I save all the outputs of ack, together with pwd and the options, using a wrapper script. When "ack" is run without any argument,  these logs are shown by the pager, from the latest first.
I put the following code in my .bashrc:
function ack(){
    local ackLogDir=/tmp/mylogs/Ack
    mkdir -p "$ackLogDir"
    chmod 777 "$ackLogDir" &> /dev/null
    if [[ $# == 0 ]]; then
        find "$ackLogDir" -type f | xargs ls -t |xargs less
        return
    fi
    local f="$( mktemp --tmpdir=$ackLogDir )"
    echo "# Pwd: `pwd`" > $f
    echo "# ack $@" >> $f
    command ack "$@" >> "$f" 2>&1
    less $f
}

(Instead of PAGER, less is hardcoded.)
If ack itself supplies this functionality, together with some refinement, it can be much better. (So it might be better than putting in the cookbook.)
Thanks a lot for developing ack for so long. Regards.

Find all the subroutines in Perl tests and then give a count of many of each there are:
ack '^sub (\w+)' --perltest --output='$1' -h --nogroup | sort | uniq -c  | sort -n

Summarize the filetypes in your project

Search all the files that don't have foo and show their usage of bar.  Think of a better example.
ack -L foo | ack -x -w bar

Find the most-used modules in your codebase.
ack '^use ([\w+:]+)' --output='$1' -h --nogroup | sort | uniq -c  | sort -n

We could have entire section just about ack -f and ack -g.

We could. I've tried organizing a litt e more towards how user thinks ....

All the above have been added on my checkout ,  I'll proofread this weekend.
Meantime i'll put my WIP on github.com/n1vux/ack3.git fork, branch 26_cookbook
Current outline is below
(rendered as outline via perldoc -o markdown lib/App/Ack/Docs/Cookbook.pm | ack -h '^#', perhaps that's a cookbook recipe too ? ).
Feedback on organization welcome.  I haven't sorted the middle big 'section' topically yet ...
COOKBOOK
COMPOUND QUERIES
Find "goat(s)" or "cow(s(" or both
Find "goats" in every file that also contains "cows"
find goats in files that do not contain cows
Find "goats" in every farmish file
Find "goats" and "cows" in the same line, either order, as words
Search for all the files that mention Sys::Hostname but don't match hostname.
USING ACK EFFECTIVELY
Use the .ackrc file.
Use -f for working with big codesets
Use -Q when in doubt about metacharacters
Use ack to watch log files
use ack instead of find
Searching for a method call
use -w only for words
See all the .vim files in your hidden ~/.vim directory, except in the bundle/ directory.
Finds all the ruby files that match /tax/.
Find all the Perl test files and test them
Find places where two methods with the same name are being called on the same line.
Find all the places in code there's a call like sort { lc $a cmp lc $b }.
Show a range of lines in a file
Find modules that are importing but not actually using Test::Warn
TBD these are notes to be fleshed out TBD
TBD Mention dirty and/or git diff --name-only.
TBD  Search all the files that don't have foo and show their usage of bar. Think of a better example.
EXAMPLES OF --output
Find all the headers used in your C programs and dedupe them
Find the most-used modules in your codebase.
Find all the subroutines in Perl tests and then give a count of many of each there are
VERY ELEGANT ACK
Open list of matching files in Vim, searching for your search term
Extending ack your way
find log lines with 4 nulls and sort by IP address
Summarize the filetypes in your project
Fowler's Folly
KWIC: KeyWord in Context index
TBD lookahead and lookbehind

Extract part of a line from a logfile
ack '>>ip(\S+).+rq"/help' --output='$1' -h

Extract some data from JSON
I have this very long line of info in 1 file, and i want to extract  it, so that the end result look like this output.txt ? Please help !

Input.txt  [{"city":"london","first name":"peter","last name":"hansen","age":"40"},   {"city":"new york","first name":"celine","last name":"parker","age":"36"]

Output.txt
peter (40) celine (36)
From https://stackoverflow.com/questions/45538755/bash-text-extracting
The sneaky and potentially unsafe way to do it is:
ack '"first name":"([^"]+)".+"age":"(\d+)"' input.txt --output='$1 $2'

bill-n1vux   #ack
how is that "potentially unsafe" ?
andylester
Inaccurate.  Might not always work.   Unsafe is wrong word
Arguments might not be in that order.
bill-n1vux
oh right, JSON like Perl has no guarantee of sane ordering of hash elements
I'm sure it's doable correctly  with either-or and context  ...
echo '[{"city":"london","first name":"peter","last name":"hansen","age":"40"},   {"city":"new york","last name":"parker","age":"36","first name":"celine"}]' \
| ack --output '$1$4($2$3)' '{.*?"first name":"([^"]*)".*?age":"(\d+)|{.*?"age":"(\d+)".*?first name":"([^"]*?)"'
peter(40)
celine(36)

Add Elegant nearly- and not-ugly-and- exact solutions to https://github.com/beyondgrep/ack2/pull/646 that require neither hypothetical, \n as OR nor --fgrep-f .

We need lots of -f and -g examples.  Also, interesting that ag does not have -f.  If you want ack -f with ag you have to do ag -g .

Inventory all PHP sqldo functions
ack 'sqldo_\w+' --php -o -h | sort -u

Inventory of methods called on users:
ack 'users->(\w+)' --output='$1' -h | sort | uniq -c

from ack-users

I am trying to get the words in file1 that are not in file2. saving result in file3
I need equivalent awk command to the following grep
grep -F -x -v -f file1 file2 > file3
grep takes time and is being killed because file2 is about 40000 long ,and file1 is about 25000

In comm` that's the -23 option.
Column 1 is words only in file 1.
-23 is minus 2,3, omit columns 2 (file 2 words) and 3 (both files words).
The other key to comm is files must be sorted by natural sort order.
So the shell command or alias needed is
comm -23 <(sort $file1) <(sort $file2)
with modern bash <() command substitution as file-pipes.
(I may have added this one already but cataloged here to check)

Cheat to simulate "within 5 lines"
ack -i -C5 eliphalet | ack -i -C5 ricker | ack -i -C5 'eliphalet|ricker'
(Will get some false hits if either string appears in filenames alas)

Look for a method you're not sure of the name of.
I was looking for a method that I knew was called "something_follows", so I looked for method invocations like that: ack -- '->.+_follows\b'

So I can have regex like 'abc\K(def)(?=ghi)'. That will highlight ONLY 'def' in the text but only if that string is preceeded by 'abc' and 'ghi' follows.

https://news.ycombinator.com/item?id=15433310

PR#106 has above comments added to Cookbook.pm .
Items with TBD TODO  still in in file are reactioned :+1:  above in #26 (this comment stream)

What if you have a prohibition in your code against variables that use camelCase?  Find any strings that use it:
ack  -I '\b[a-z]+[A-Z]+[a-z]+'

Pick a random source file:
ack -f | shuf | head -n 1

I had a big log file of errors that looked like this:
    # (6819:1) Warning: <td> attribute "bgcolor" had invalid value "D4ED91" and has been replaced
    # (6825:1) Warning: <td> attribute "bgcolor" had invalid value "C6E2FF" and has been replaced
    # (6828:1) Warning: <td> attribute "bgcolor" had invalid value "D4ED91" and has been replaced
    # (6834:1) Warning: <td> attribute "bgcolor" had invalid value "C6E2FF" and has been replaced

To summarize the invalid values:
ack 'invalid value "(\w+)"' --output='$1' smoke.log | sort | uniq -c

What states have both a Shelbyville and a Springfield?
wget https://www2.census.gov/geo/docs/reference/codes/files/national_places.txt
comm <(ack springfield national_places.txt | cut -d| -f1 | sort | uniq)  <(ack shelbyville national_places.txt | cut -d| -f1 | sort | uniq)
(doc for data: https://www.census.gov/geo/reference/codes/place.html )
(Springfield is not most common. It's Seventh.)
perl -lan -F\| -Mstrict -Mwarnings -E 'our %Count; my ($st, $stfips, $plfips, $name,$type, $funcstat,$county)=@F;  next unless $funcstat eq q(A); $name =~ s/ \s [a-z]+$ //x; $Count{$name}++;' -E 'BEGIN { our %Count; }' -E ' END {our %Count; say qq($Count{$}\t$) for sort keys %Count;} ' national_places.txt  | sort -nr | head

stdbuf(1G) https://www.gnu.org/software/coreutils/manual/html_node/stdbuf-invocation.html as described at https://blog.plover.com/Unix/stdio-buffering.html (MJD) could be useful in an ack (or grep) pipeline.

UTF-16/UCS-2 ugly workaround could be a whole Cookbook section ... it's too big and too rare to be a FAQ, it's not asked that frequently.
See also #152 #153 https://groups.google.com/forum/#!topic/ack-users/qidCgv3S5Uo

I have tentatively assigned remaining comments above  to the existing sections, and have a plan for exposition.
TBD marks existing placeholders, also listed
USING ACK EFFECTIVELY

Edit the files i just looked at with ack (already there, but i have more for it)
TBD Do we need more C<-f> and C<-g> examples? probably enough for release

EXAMPLES OF C<< --output >>

Summarize invalid values

VERY ELEGANT ACK

TBD (workarounds for  C<--fgrep-f> needs editing)
TBD look-ahead and look-behind (do we need more than we have? probably enough for release!)
find camelCase
Pick a random source file

WHEN TO DO SOMETHING ELSE

classic Unix shell tools - What states have both a Shelbyville and a Springfield?

INFREQUENTLY Asked Questions (new section)

Unicode Workarounds (from bugs and mailinglist discussions)

ack ‘(.+),(.+)’ --output=‘mv “$1” “$2”’ filemappings.csv | sh -x

from Yagamy Light on  Ack-Users -  replacement for find -exec sed
ack -l --print0 pattern | xargs -r0 perl -i -pe 's/pattern/replacement/g'

and note that xargs -r avoids running command with stdin when no filenames provided, almost always a good idea to use that.

To see a pattern in context of subroutine / method it's in
xxx='^(package|sub|event|before|after|around|BUILD|DEMOLISH|DESTROY)\b'
pat='get_ready|do_it' ; ack --perl "$pat" -l | ack -x "$xxx|$pat"

To easily reuse a command with history when ^W or double-click and overtype would wipe out too much context , not just the keyword you want to retype, use (?x-: ) eXtended syntax option in PerlRE to make spaces not count, so can separate the Keyword from adjacent RE features.
ack --perl '(?x-:   \b Keyword \s* => )'