Lsb_init: initenv_:fopen(/etc/lsf.conf) failed, No such file or directory

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1

Hello,
I’m running LSF and my ondemand server is v3.0.3. I’ve configured the cluster yml file. When I try to submit to my submit host, it tells me it can’t find /etc/lsf.conf. I never told it to look for lsf.conf in /etc or /etc at all. Here is a sample of /etc/ood/config/clusters.d/my_cluster.yml

Error:
Oct 25 17:05:08 2023 23055 3 3.4.0 lsb_init: initenv_:fopen(/etc/lsf.conf) failed, No such file or directory.
lsb_init: Failed in an LSF library call: Unable to open file lsf.conf. Job not submitted.

v2:
metadata:
title: “LPC Cluster”
login:
host: “loginhost.something.edu”
job:
adapter: “lsf”
host: “lsf_resource_manager.pmacs.upenn.edu”
submit_host: “submithost.something.edu”
bindir: “/lsf/10.1/linux3.10-glibc2.17-x86_64/bin”
libdir: “/lsf/10.1/linux3.10-glibc2.17-x86_64/lib”
envdir: “/lsf/conf/lsbatch/PMACS-SCC/configdir”
serverdir: “/lsf/10.1/linux3.10-glibc2.17-x86_64/etc”
cluster: “lpc”
strict_host_checking: false
# bin_overrides:
# bsub: “/usr/local/bin/bsub”
# bjobs: “”
# bstop: “”
# bresume: “”
# bkill: “”

2

Hi, yes it seems it should be respecting serverdir.

That said - I can’t tell if the formatting is correct or not. You can use 3 backticks and yaml to provide correct formatting or just upload the file as a text file.

You want to print it out like this:

```yaml
valid_yaml: true
```

3

Also - hi and welcome!

1 Like
4

If you provide a correctly formatted file - I can try to test it out to see if it’s valid and/or if there’s a bug on our side.

5

Hi,
Thanks I fixed it.
–David

6

Hi,
So the solution was a config issue with envdir. I had to change it to /misc/lsf/conf where lsf.conf lived. Then when I submitted a job it kept telling me it could not connect to cluster. So I found out that I had to remove the “cluster: “mycluster”” statement because it thought that was the server I was sending it to. Then I added the queue name in my batch job to get it to work.

v2:
metadata:
title: “LPC Cluster”
login:
host: “loginhost.something.edu”
job:
adapter: “lsf”
host: “lsfscheduler.something.edu”
submit_host: “submithost.something.edu”
bindir: “/misc/lsf/10.1/linux3.10-glibc2.17-x86_64/bin”
libdir: “/misc/lsf/10.1/linux3.10-glibc2.17-x86_64/lib”
envdir: “/misc/lsf/conf”
serverdir: “/misc/lsf/10.1/linux3.10-glibc2.17-x86_64/etc”
#cluster: “lpc”
strict_host_checking: false
# bin_overrides:
# bsub: “/usr/local/bin/bsub”
# bjobs: “”
# bstop: “”
# bresume: “”
# bkill: “”

–David

7

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