One of my import jobs is failing continuously with the error "Errors encountered during job execution. System error"
Job id is bqjob_r2257fe91a590a308_0000014e3e922faf_1
I can get the following information from the system
root#6bd6c7262e96:/opt/batch/jobs# bq show -j bqjob_r2257fe91a590a308_0000014e3e922faf_1
Job infra-bedrock-861:bqjob_r2257fe91a590a308_0000014e3e922faf_1
Job Type State Start Time Duration Bytes Processed
---------- --------- ----------------- ---------- -----------------
load FAILURE 29 Jun 09:07:42 0:00:02
Errors encountered during job execution. System error. The error has been logged and we will investigate.
Any idea what can cause this?
Related
I am running snakemake using this command:
snakemake --profile slurm -j 1 --cores 1 --cluster-cancel "scancel"
which writes this to standard out:
Submitted job 224 with external jobid 'Submitted batch job 54174212'.
but after I cancel the run with ctrl + c, I get the following error:
scancel: error: Invalid job id Submitted batch job 54174212
What I would guess is that the jobid is 'Submitted batch job 54174212'
and snakemake tries to run scancel 'Submitted batch job 54174212' instead of the expected scancel 54174212. If this is the case, how do I change the jobid to something that works with scancel?
Your suspicion is probably correct, snakemake probably tries to cancel the wrong job (id Submitted batch job 54174212).
Check your slurm profile for snakemake which you invoke (standard location ~/.config/snakemake/slurm/config.yaml):
Does it contain the --parsable flag for sbatch?
Missing to include that flag is a mistake I made before. Adding the flag solved it for me.
I have 14 scheduled queries that run hourly from Google Sheets but they fail half of the time. I don't understand the error status though as the queries do run successfully half of the time. The error reads:
Error status: Invalid value Error while reading table: tester-253410.test1.Table_View_2_Agent_Targets, error message: Failed to read the spreadsheet. Errors: Deadline=118.888051456s; JobID: tester-253410:5e59a150-0000-2421-b469-001a1144591c
Is there anything that I can try?
The overall problem I'm trying to solve is a way to count the number of reads present in each file at every step of a QC pipeline I'm building. I have a shell script I've used in the past which takes in a directory and outputs the number of reads per file. Since I'm looking to use a directory as input, I tried following the format laid out by Rasmus in this post:
https://bitbucket.org/snakemake/snakemake/issues/961/rule-with-folder-as-input-and-output
Here is some example input created earlier in the pipeline:
$ ls -1 cut_reads/
97_R1_cut.fastq.gz
97_R2_cut.fastq.gz
98_R1_cut.fastq.gz
98_R2_cut.fastq.gz
99_R1_cut.fastq.gz
99_R2_cut.fastq.gz
And a simplified Snakefile to first aggregate all reads by creating symlinks in a new directory, and then use that directory as input for the read counting shell script:
import os
configfile: "config.yaml"
rule all:
input:
"read_counts/read_counts.txt"
rule agg_count:
input:
cut_reads = expand("cut_reads/{sample}_{rdir}_cut.fastq.gz", rdir=["R1", "R2"], sample=config["forward_reads"])
output:
cut_dir = directory("read_counts/cut_reads")
run:
os.makedir(output.cut_dir)
for read in input.cut_reads:
abspath = os.path.abspath(read)
shell("ln -s {abspath} {output.cut_dir}")
rule count_reads:
input:
cut_reads = "read_counts/cut_reads"
output:
"read_counts/read_counts.txt"
shell:
'''
readcounts.sh {input.cut_reads} >> {output}
'''
Everything's fine in the dry-run, but when I try to actually execute it, I get a fairly cryptic error message:
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 agg_count
1 all
1 count_reads
3
[Tue Jun 18 11:31:22 2019]
rule agg_count:
input: cut_reads/99_R1_cut.fastq.gz, cut_reads/98_R1_cut.fastq.gz, cut_reads/97_R1_cut.fastq.gz, cut_reads/99_R2_cut.fastq.gz, cut_reads/98_R2_cut.fastq.gz, cut_reads/97_R2_cut.fastq.gz
output: read_counts/cut_reads
jobid: 2
Job counts:
count jobs
1 agg_count
1
[Tue Jun 18 11:31:22 2019]
Error in rule agg_count:
jobid: 0
output: read_counts/cut_reads
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/douglas/snakemake/scrap_directory/.snakemake/log/2019-06-18T113122.202962.snakemake.log
read_counts/ was created, but there's no cut_reads/ directory inside. No other error messages are present in the complete log. Anyone know what's going wrong or how to receive a more descriptive error message?
I'm also (obviously) fairly new to snakemake, so there might be a better way to go about this whole process. Any help is much appreciated!
... And it was a typo. Typical. os.makedir(output.cut_dir) should be os.makedirs(output.cut_dir). I'm still really curious why snakemake isn't displaying the AttributeError python throws when you try to run this:
AttributeError: module 'os' has no attribute 'makedir'
Is there somewhere this is stored or can be accessed to prevent future headaches?
Are you sure the error message is due to the typo in os.makedir? In this test script os.makedir does throw AttributeError ...:
rule all:
input:
'tmp.done',
rule one:
output:
x= 'tmp.done',
xdir= directory('tmp'),
run:
os.makedir(output.xdir)
When executed:
Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 all
1 one
2
[Wed Jun 19 09:05:57 2019]
rule one:
output: tmp.done, tmp
jobid: 1
Job counts:
count jobs
1 one
1
[Wed Jun 19 09:05:57 2019]
Error in rule one:
jobid: 0
output: tmp.done, tmp
RuleException:
AttributeError in line 10 of /home/dario/Tritume/Snakefile:
module 'os' has no attribute 'makedir'
File "/home/dario/Tritume/Snakefile", line 10, in __rule_one
File "/home/dario/miniconda3/envs/tritume/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/dario/Tritume/.snakemake/log/2019-06-19T090557.113876.snakemake.log
Use f-string to resolve local variables like {abspath}:
for read in input.cut_reads:
abspath = os.path.abspath(read)
shell(f"ln -s {abspath} {output.cut_dir}")
Wrap the wildcards that snakemake resolves automatically into double braces inside of f-strings.
I am using IBM LSF and trying to get usage statistics during a certain period. I found that bhist does the job, but the short form bhist output does not show all of the fields I need.
What I want to know is:
Is bhist's output field customizable? The fields I need are:
<jobid>
<user>
<queue>
<job_name>
<project_name>
<job_description>
<submission_time>
<pending_time>
<run_time>
If 1 is not possible, the long form (bhist -l) output shows everything I need, but the format is hard to manipulate. I've pasted an example of the format below.
For example, the number of line between records is not fixed, and the word wrap in each event may break the line in the middle of a word I'm trying to scan for. How do I parse this format with sed and awk?
JobId <1531>, User <user1>, Project <default>, Command< example200>
Fri Dec 27 13:04:14: Submitted from host <hostA> to Queue <priority>, CWD <$H
OME>, Specified Hosts <hostD>;
Fri Dec 27 13:04:19: Dispatched to <hostD>;
Fri Dec 27 13:04:19: Starting (Pid 8920);
Fri Dec 27 13:04:20: Running with execution home </home/user1>, Execution CWD
</home/user1>, Execution Pid <8920>;
Fri Dec 27 13:05:49: Suspended by the user or administrator;
Fri Dec 27 13:05:56: Suspended: Waiting for re-scheduling after being resumed
by user;
Fri Dec 27 13:05:57: Running;
Fri Dec 27 13:07:52: Done successfully. The CPU time used is 28.3 seconds.
Summary of time in seconds spent in various states by Sat Dec 27 13:07:52 1997
PEND PSUSP RUN USUSP SSUSP UNKWN TOTAL
5 0 205 7 1 0 218
------------------------------------------------------------
.... repeat
I'm adding a second answer because it might help you with your problem without actually having to write your own solution (depending on the usage statistics you're after).
LSF already has a utility called bacct that computes and prints out various usage statistics about historical LSF jobs filtered by various criteria.
For example, to get summary usage statistics about jobs that were dispatched/completed/submitted between time0 and time1, you can use (respectively):
bacct -D time0,time1
bacct -C time0,time1
bacct -S time0,time1
Statistics about jobs submitted by a particular user:
bacct -u <username>
Statistics about jobs submitted to a particular queue:
bacct -q <queuename>
These options can be combined as well, so for example if you wanted statistics about jobs that were submitted and completed within a particular time window for a particular project, you can use:
bacct -S time0,time1 -C time0,time1 -P <projectname>
The output provides some summary information about all jobs that match the provided criteria like so:
$ bacct -u bobbafett -q normal
Accounting information about jobs that are:
- submitted by users bobbafett,
- accounted on all projects.
- completed normally or exited
- executed on all hosts.
- submitted to queues normal,
- accounted on all service classes.
------------------------------------------------------------------------------
SUMMARY: ( time unit: second )
Total number of done jobs: 0 Total number of exited jobs: 32
Total CPU time consumed: 46.8 Average CPU time consumed: 1.5
Maximum CPU time of a job: 9.0 Minimum CPU time of a job: 0.0
Total wait time in queues: 18680.0
Average wait time in queue: 583.8
Maximum wait time in queue: 5507.0 Minimum wait time in queue: 0.0
Average turnaround time: 11568 (seconds/job)
Maximum turnaround time: 43294 Minimum turnaround time: 40
Average hog factor of a job: 0.00 ( cpu time / turnaround time )
Maximum hog factor of a job: 0.02 Minimum hog factor of a job: 0.00
Total Run time consumed: 351504 Average Run time consumed: 10984
Maximum Run time of a job: 1844674 Minimum Run time of a job: 0
Total throughput: 0.24 (jobs/hour) during 160.32 hours
Beginning time: Nov 11 17:55 Ending time: Nov 18 10:14
This command also has a long form output that provides some bhist -l-like information about each job that might be a bit easier to parse (although still not all that easy):
$ bacct -l -u bobbafett -q normal
Accounting information about jobs that are:
- submitted by users bobbafett,
- accounted on all projects.
- completed normally or exited
- executed on all hosts.
- submitted to queues normal,
- accounted on all service classes.
------------------------------------------------------------------------------
Job <101>, User <bobbafett>, Project <default>, Status <EXIT>, Queue <normal>,
Command <sleep 100000000>
Wed Nov 11 17:37:45: Submitted from host <endor>, CWD <$HOME>;
Wed Nov 11 17:55:05: Completed <exit>; TERM_OWNER: job killed by owner.
Accounting information about this job:
CPU_T WAIT TURNAROUND STATUS HOG_FACTOR MEM SWAP
0.00 1040 1040 exit 0.0000 0M 0M
------------------------------------------------------------------------------
...
Long form output is pretty hard to parse. I know bjobs has an option for unformatted output (-UF) in older LSF versions which makes it a bit easier, and the most recent version of LSF allows you to customize which columns get printed in short form output with -o.
Unfortunately, neither of these options are available with bhist. The only real possibilities for historical information are:
Figure out some way to parse bhist -l -- impractical and maybe not even possible due to inconsistent formatting as you've discovered.
Write a C program to do what you want using the LSF API, which exposes the functions that bhist itself uses to parse the lsb.events file. This is the file that stores all the historical information about the LSF cluster, and is what bhist reads to generate its ouptut.
If C is not an option for you, then you could try writing a script to parse the lsb.events file directly -- the format is documented in the configuration reference. This is hard, but not impossible. Here is the relevant document for LSF 9.1.3.
My personal recommendation would be #2 -- the function you're looking for is lsb_geteventrec(). You'd basically read each line in lsb.events one at a time and pull out the information you need.
The status is shown as success but the file is not actually transferred to big-query.
# bq show -j abc
Job Type State Start Time Duration Bytes Processed
---------- --------- ----------------- ---------- -----------------
load SUCCESS 05 Jul 15:32:45 0:26:24
From web interface, I can see the actual error.
Line:9732968, Too few columns: expected 27 column(s) but got 9 column(s)
Line:10893908 / Field:1, Bad character (ASCII 0) encountered. Rest of file not processed.
1) How do I know which bad character needs to be removed?
2) Why does "success" shown as job status?
Update:
Job ID: summary_2012_07_09_to_2012_07_10a2
The error that I got at command prompt:
BigQuery error in load operation: Backend Error
A lot of lines were not processed at all. The details from web interface:
Line:9857286 / Field:1, Bad character (ASCII 0) encountered: field starts with: <15>
Line:9857287 / Field:1, Bad character (ASCII 0) encountered. Rest of file not processed.
All the lines where successfully processed in the second attempt:
job_id: summary_2012_07_09_to_2012_07_10a3
Update 2:
Line:174952407 / Field:1, Bad character (ASCII 0) encountered. Rest of file not processed.
Job ID: job_19890847cbc3410495c3cecaf79b31fb
Sorry for the slow response, the holiday weekend meant most of the bigquery team was not answering support questions. The 'bad character' looks like it may be a known bug with some gzipped files where we improperly detect an ascii 0 value at the end of the file.
If the job is actually failing but reporting success, that sounds like a problem but we'll need the job id of the failing job in order to be able to debug. Also if you can reproduce it that would be helpful since we may not have the logs around for the original job anymore.