Add cvmfs debugging tip xref #3558

galaxyproject · Jul 21, 2022 · 606f4bf · 606f4bf
1 parent b319283
commit 606f4bf
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diff --git a/topics/admin/tutorials/cvmfs/tutorial.md b/topics/admin/tutorials/cvmfs/tutorial.md
@@ -609,6 +609,56 @@ Now all we need to do is tell Galaxy how to find it! This tutorial assumes that
 > Yes. Often admins with a cluster keep a smaller cache local to each compute node, and then setup a Squid proxy to hold the most commonly accessed data on a machine with more storage. E.g. each compute node could have 10-50GB of CVMFS storage while you might setup a Squid proxy with 200-300 GB of storage that will store everything your site uses.
 {: .question}
 
+> ### {% icon tip %} Debugging failed mounting
+>
+> Are you having issues mounting your CVMFS mount? Is it giving strange errors like "Endpoint not connected"
+> Try running this command as root:
+>
+> > > ### {% icon code-in %} Input: Bash
+> > > ```console
+> > > /usr/bin/cvmfs2 -d -o rw,system_mount,fsname=cvmfs2,allow_other,grab_mountpoint singularity.galaxyproject.org /mnt
+> > > ```
+> > {: .code-in}
+> >
+> > > ### {% icon code-out %} Output: Consolue
+> > > ```console
+> > > Debug: using library /usr/lib/libcvmfs_fuse3_stub.so
+> > > CernVM-FS: running in debug mode
+> > > CernVM-FS: loading Fuse module... (cvmfs) Parsing config file /etc/cvmfs/default.conf    [07-21-2022 11:11:20 UTC]
+> > > (cvmfs) execve'd /bin/sh (PID: 280373)    [07-21-2022 11:11:20 UTC]
+> > > (cvmfs) Parsing config file /etc/cvmfs/default.d/50-cern-debian.conf    [07-21-2022 11:11:20 UTC]
+> > > (cvmfs) execve'd /bin/sh (PID: 280375)    [07-21-2022 11:11:20 UTC]
+> > > (cvmfs) Parsing config file /etc/cvmfs/default.d/80-ansible-galaxyproject-cvmfs.conf    [07-21-2022 11:11:20 UTC]
+> > > (cvmfs) execve'd /bin/sh (PID: 280378)    [07-21-2022 11:11:20 UTC]
+> > > [...]
+> > > (dns) empty hostname    [07-21-2022 11:11:20 UTC]
+> > > (download) installed 1 proxies in 1 load-balance groups    [07-21-2022 11:11:20 UTC]
+> > > (cvmfs) DNS roaming is disabled for this repository.    [07-21-2022 11:11:20 UTC]
+> > > (catalog) constructing client catalog manager    [07-21-2022 11:11:20 UTC]
+> > > (catalog) Initialize catalog    [07-21-2022 11:11:20 UTC]
+> > > (cache) unable to read local checksum    [07-21-2022 11:11:20 UTC]
+> > > (download) escaped http://cvmfs1-psu0.galaxyproject.org/cvmfs/singularity.galaxyproject.org/.cvmfspublished to http://cvmfs1-psu0.galaxyproject.org/cvmfs/singularity.galaxyproject.org/.cvmfspublished    [07-21-2022 11:11:20 UTC]
+> > > (download) Verify downloaded url /.cvmfspublished, proxy DIRECT (curl error 0)    [07-21-2022 11:11:20 UTC]
+> > > (cache) miss ./e2/ab48b0984729d99951cb62c4312f501b3ddc6b (-2)    [07-21-2022 11:11:20 UTC]
+> > > (download) escaped http://cvmfs1-psu0.galaxyproject.org/cvmfs/singularity.galaxyproject.org/data/e2/ab48b0984729d99951cb62c4312f501b3ddc6bX to http://cvmfs1-psu0.galaxyproject.org/cvmfs/singularity.galaxyproject.org/data/e2/ab48b0984729d99951cb62c4312f501b3ddc6bX    [07-21-2022 11:11:20 UTC]
+> > > (download) Verify downloaded url /data/e2/ab48b0984729d99951cb62c4312f501b3ddc6bX, proxy DIRECT (curl error 0)    [07-21-2022 11:11:20 UTC]
+> > > (download) escaped http://cvmfs1-psu0.galaxyproject.org/cvmfs/singularity.galaxyproject.org/.cvmfswhitelist to http://cvmfs1-psu0.galaxyproject.org/cvmfs/singularity.galaxyproject.org/.cvmfswhitelist    [07-21-2022 11:11:20 UTC]
+> > > [...]
+> > > (download) escaped http://cvmfs1-psu0.galaxyproject.org/cvmfs/singularity.galaxyproject.org/data/c7/f1555f421b1868b979291dc23f34a83132eadbC to http://cvmfs1-psu0.galaxyproject.org/cvmfs/singularity.galaxyproject.org/data/c7/f1555f421b1868b979291dc23f34a83132eadbC    [07-21-2022 11:11:20 UTC]
+> > > (download) Verify downloaded url /data/c7/f1555f421b1868b979291dc23f34a83132eadbC, proxy DIRECT (curl error 0)    [07-21-2022 11:11:25 UTC]
+> > > (cache) finished downloading of /data/c7/f1555f421b1868b979291dc23f34a83132eadbC    [07-21-2022 11:11:25 UTC]
+> > > (cache) commit ./c7/f1555f421b1868b979291dc23f34a83132eadb ./txn/fetchJWcwtt    [07-21-2022 11:11:25 UTC]
+> > > (quota) pin into lru c7f1555f421b1868b979291dc23f34a83132eadb, path file catalog at singularity.galaxyproject.org:/ (c7f1555f421b1868b979291dc23f34a83132eadb)    [07-21-2022 11:11:25 UTC]
+> > > (cache) commit failed: cannot pin c7f1555f421b1868b979291dc23f34a83132eadb    [07-21-2022 11:11:25 UTC]
+> > > (catalog) failed to load catalog '' (2 - not enough space to load catalog)    [07-21-2022 11:11:25 UTC]
+> > > (catalog) failed to initialize root catalog    [07-21-2022 11:11:25 UTC]
+> > > Failed to initialize root file catalog (16 - file catalog failure)
+> > > (cache) unpinning / unloading all catalogs    [07-21-2022 11:11:25 UTC]
+> > > ```
+> > {: .code-out}
+> {: .code-2col}
+{: .tip}
+
 # Other Aspects
 
 > Right, we'll go back to our tutorial. um Yeah. Just finally, just before we