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nextflow run hello: ERROR ~ a fault occurred in an unsafe memory access operation #4942
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This is commonly related to the lack of temporary disk storage. There at least of similar issues https://github.com/nextflow-io/nextflow/issues?q=is%3Aissue+unsafe+memory+is%3Aclosed |
I do not see an issue with disk storage, everywhere I look, there seems to be plenty of space. However, I did realise the following: It seems to work when I run the pipeline in my home directory. But if I run it from a directory on our lustre filesystem nextflow seems to crash: $ cd ~/temp/
$ nextflow run hello
N E X T F L O W ~ version 23.10.1
Launching `https://github.com/nextflow-io/hello` [scruffy_chandrasekhar] DSL2 - revision: 7588c46ffe [master]
executor > local (4)
[e0/3d25bb] process > sayHello (4) [100%] 4 of 4 ✔
Ciao world!
Bonjour world!
Hello world!
Hola world! $ cd /path/on/lustre
$ nextflow run hello
N E X T F L O W ~ version 23.10.1
Launching `https://github.com/nextflow-io/hello` [evil_baekeland] DSL2 - revision: 7588c46ffe [master]
ERROR ~ a fault occurred in an unsafe memory access operation
-- Check '.nextflow.log' file for details Not yet sure how this might help, but at least I can now reproduce it more systematically. |
Just wanted to add that running things in my home directory is not an option, because there I do not have enough space. |
The error happens specifically with the LevelDB cache:
I guess leveldb is memory-mapping the db file, maybe this operation is not supported by Lustre, or your particular implementation / configuration of Lustre. I would ask your sys admin about this |
Bug report
Expected behavior and actual behavior
Expected behavior:
nextflow run hello
should work.Actual behavior:
About a week ago, I installed nextflow using mamba (i.e. conda) on our clsuter, and it worked just fine. I had also tested the hello world example. Now, I wanted to start a new pipeline and got an ERROR, and I also get the same error when I try to run the hello world example, see below under Program output .
Steps to reproduce the problem
This temporarily solved the problem. But then the error came back. And I even observed that it once worked again, but then the error came back.
Program output
Environment
Additional context
It is probably hard to tell what is going on with the limited information I can provide at the moment. If anyone has ideas what I should try or which infos I should provide, I would be very grateful
nextflow.log
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