Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Bpipe error #8

Open
Marina-Blmz opened this issue Mar 15, 2023 · 1 comment
Open

Bpipe error #8

Marina-Blmz opened this issue Mar 15, 2023 · 1 comment

Comments

@Marina-Blmz
Copy link

Marina-Blmz commented Mar 15, 2023 •
edited
Loading

Hej Gab,

trying to run bpipe from this container.

The command i am running: bpipe run -n 4 pipeline.bpipe *mnc

The error I am getting:

=========================================== Bpipe Error ============================================

An error occurred executing your pipeline:

                   Cannot run program "qsub": error=2, No such file or directory                    


Please see the details below for more information.

"========================================== Error Details ===========================================

java.io.IOException: Cannot run program "qsub": error=2, No such file or directory
	at bpipe.Utils.executeCommand(Utils.groovy:944)
	at bpipe.Utils.executeCommand(Utils.groovy)
	at bpipe.Utils$executeCommand$12.call(Unknown Source)
	at bpipe.executor.SgeCommandExecutor.start(SgeCommandExecutor.groovy:165)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.executor.ThrottledDelegatingCommandExecutor.doStart(ThrottledDelegatingCommandExecutor.groovy:120)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.executor.ThrottledDelegatingCommandExecutor.start(ThrottledDelegatingCommandExecutor.groovy:94)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.CommandManager.start(CommandManager.groovy:149)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineContext.async(PipelineContext.groovy:2304)
	at bpipe.PipelineContext.async(PipelineContext.groovy)
	at bpipe.PipelineContext.execImpl(PipelineContext.groovy:1841)
	at bpipe.PipelineContext.exec(PipelineContext.groovy:1826)
	at bpipe.PipelineContext.exec(PipelineContext.groovy)
	at bpipe.PipelineContext.exec(PipelineContext.groovy:1792)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineContext.invokeMethod(PipelineContext.groovy)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineDelegate.methodMissing(PipelineDelegate.groovy:163)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineDelegate.invokeMethod(PipelineDelegate.groovy)
	at minc-library.bpipe$_run_closure1$_closure24.doCall(minc-library.bpipe.bpipe:45)
	at minc-library.bpipe$_run_closure1$_closure24.doCall(minc-library.bpipe.bpipe)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineContext.produceImpl(PipelineContext.groovy:1461)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineContext.produceImpl(PipelineContext.groovy:1251)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.TransformOperation$_execute_closure1.doCall(TransformOperation.groovy:208)
	at bpipe.TransformOperation$_execute_closure1.doCall(TransformOperation.groovy)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineContext.withInputs(PipelineContext.groovy:2689)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.TransformOperation.execute(TransformOperation.groovy:207)
	at bpipe.TransformOperation.to(TransformOperation.groovy:179)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.TransformOperation.to(TransformOperation.groovy:89)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at minc-library.bpipe$_run_closure1.doCall(minc-library.bpipe.bpipe:44)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy:383)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy)
	at jdk.internal.reflect.GeneratedMethodAccessor163.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.runWrappedBody(PipelineStage.groovy:382)
	at bpipe.PipelineStage.runBody(PipelineStage.groovy:357)
	at bpipe.PipelineStage.run(PipelineStage.groovy:241)
	at bpipe.PipelineCategory$_plus_closure4.doCall(PipelineCategory.groovy:189)
	at jdk.internal.reflect.GeneratedMethodAccessor164.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy:383)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy)
	at jdk.internal.reflect.GeneratedMethodAccessor163.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.runWrappedBody(PipelineStage.groovy:382)
	at bpipe.PipelineStage.runBody(PipelineStage.groovy:357)
	at bpipe.PipelineStage.run(PipelineStage.groovy:241)
	at bpipe.PipelineCategory$_plus_closure4.doCall(PipelineCategory.groovy:189)
	at jdk.internal.reflect.GeneratedMethodAccessor164.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy:383)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy)
	at jdk.internal.reflect.GeneratedMethodAccessor163.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.runWrappedBody(PipelineStage.groovy:382)
	at bpipe.PipelineStage.runBody(PipelineStage.groovy:357)
	at bpipe.PipelineStage.run(PipelineStage.groovy:241)
	at bpipe.PipelineCategory$_plus_closure4.doCall(PipelineCategory.groovy:189)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy:383)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.runWrappedBody(PipelineStage.groovy:382)
	at bpipe.PipelineStage.runBody(PipelineStage.groovy:357)
	at bpipe.PipelineStage.run(PipelineStage.groovy:241)
	at bpipe.PipelineCategory$_plus_closure4.doCall(PipelineCategory.groovy:189)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy:383)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.runWrappedBody(PipelineStage.groovy:382)
	at bpipe.PipelineStage.runBody(PipelineStage.groovy:357)
	at bpipe.PipelineStage.run(PipelineStage.groovy:241)
	at bpipe.PipelineCategory$_plus_closure4.doCall(PipelineCategory.groovy:189)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy:383)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.runWrappedBody(PipelineStage.groovy:382)
	at bpipe.PipelineStage.runBody(PipelineStage.groovy:357)
	at bpipe.PipelineStage.run(PipelineStage.groovy:241)
	at bpipe.PipelineCategory$_plus_closure4.doCall(PipelineCategory.groovy:189)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.invokeMethod(PipelineStage.groovy)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy:383)
	at bpipe.PipelineStage$_runWrappedBody_closure2.doCall(PipelineStage.groovy)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at bpipe.PipelineStage.runWrappedBody(PipelineStage.groovy:382)
	at bpipe.PipelineStage.runBody(PipelineStage.groovy:357)
	at bpipe.PipelineStage.run(PipelineStage.groovy:241)
	at bpipe.PipelineStage$run.call(Unknown Source)
	at bpipe.Pipeline.runSegment(Pipeline.groovy:643)
	at bpipe.BranchRunner.run(BranchRunner.groovy:69)
Caused by: java.io.IOException: error=2, No such file or directory
	... 157 more"

Not sure if it's me doing smth wrong or a bug, but reporting in a case it might be the latter.

Thank you in any case!
@gdevenyi
Copy link
Member

Looks like you probably have the residual bpipe.config file from minc-bpipe-library which is turning on the job submission, which is not available in the container. You will need to remove it.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@gdevenyi @Marina-Blmz