Open shenwei356 opened 8 months ago
cesarpomar
commented
8 months ago The Permission denied error is because your user doesn't have permission to access /var/run/docker.sock. Please check if you can run docker ps.
Another option is to run ignis-submit command with sudo.
Please let me know if you find any other errors
shenwei356
commented
8 months ago $ sudo docker ps
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
$ sudo ./ignis/bin/ignis-submit ignishpc/full bigseqkit
Mar 12, 2024 09:59:28 <ERROR> org.ignis.submitter.Submit.call(Submit.java:271): Key 'ignis.scheduler.type' value error, not found
org.ignis.properties.IPropertyException: Key 'ignis.scheduler.type' value error, not found
at org.ignis.properties.IProperties.getProperty(IProperties.java:69) ~[ignis-properties-1.0.jar:?]
at org.ignis.submitter.Submit.call(Submit.java:113) [ignis-submitter-1.0.jar:?]
at org.ignis.submitter.Submit.call(Submit.java:46) [ignis-submitter-1.0.jar:?]
at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.1.jar:task ':jar' property 'archiveVersion']
at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.1.jar:task ':jar' property 'archiveVersion']
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) [picocli-4.6.1.jar:task ':jar' property 'archiveVersion']
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) [picocli-4.6.1.jar:task ':jar' property 'archiveVersion']
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) [picocli-4.6.1.jar:task ':jar' property 'archiveVersion']
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.1.jar:task ':jar' property 'archiveVersion']
at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.1.jar:task ':jar' property 'archiveVersion']
at org.ignis.submitter.Submit.main(Submit.java:284) [ignis-submitter-1.0.jar:?]You should use sudo -E to preserve the environment variables defined with the export command. The error indicates that ignis.scheduler.type created with export IGNIS_SCHEDULER_TYPE=docker does not exist.
shenwei356
commented
8 months ago Oh thanks, it finally worked. However a new error comes out. It reported a file not exist error. But the input file does exist.
$ ll /home/shenwei/go/src/github.com/shenwei356/seqkit/tests/hairpin.fa
-rw-r--r-- 1 shenwei shenwei 4.6M 9月25日 08:16 /home/shenwei/go/src/github.com/shenwei356/seqkit/tests/hairpin.fa
$ sudo -E sh ./ignis/bin/ignis-submit ignishpc/full 'bigseqkit seq /home/shenwei/go/src/github.com/shenwei356/seqkit/tests/hairpin.fa | bigseqkit stats'
...
panic: stat /home/shenwei/go/src/github.com/shenwei356/seqkit/tests/hairpin.fa: no such file or directory
...Using Docker containers, only the IGNIS_DFS_ID is mounted and set as the working directory. Therefore, you can reference files within that directory using relative paths.
You can use IgnisHPC properties to manually mount other directories using -p just after the script.
...ignis-submit -p ignis.driver.bind.{containerpath}={hostpath} -p ignis.executor.bind.{containerpath}={hostpath}...
We're working on a simpler implementation, but it's not ready yet.
Hi, I'm trying to install and run BigSeqKit locally.
Here are the commands. There's an error of
Permission denied, but it remains after changing ownership of theignisdirectory.