I've been having trouble uploading to Synapse using the Synapse R client.
The synStore command works fine on my laptop, but I receive this error when I try it on our server:
Error in writeFileAndUnlock(cacheMapFile, cacheRecordJson, lockExpiration) :
File lock exceeded for /home/dpolioud/.synapseCache/792/10833792/.cacheMap
Thanks!
-Damon
Created by Damon Polioudakis damon237 You are on an NFS-mounted drive? If so, the issue is probably the same (not the Synapse client, but the server hosting the NFS drive).
It's not immediately obvious why this could be a problem while running `synTableQuery`, but under the hood that function fetches a CSV file to disk and then reads it in. So there is a disk write operation happening.
If not, I'm blaming the eclipse. This just happened to me with the WGS = synTableQuery("select * from syn9843361") command. I ran it last month without issue.
R version 3.0.1 RC (2013-05-12 r62742) and 3.3.1
Mac 10.11.6
nfs
I do get a message saying Please upgrade to the latest version of the Synapse Client, 1.15-0, by running the following commands:
source('http://depot.sagebase.org/CRAN.R')
pkgInstall("synapseClient")
I am taking care of this, and maybe it will fix the error. Well, that's good news and bad news.
Good news is that it's probably the same issue, which we fixed before by increasing the file lock timeout to 60 seconds. However, if the difference in timestamps is more than that you're gonna have a bad time (which could probably happen for a number of reasons, way out of my skill set to determine). Bad news is you'll probably have to reach out to the sysadmins of this server to check on the NTP daemon that's running on the machine serving the files over NFS. It's noted in the issue I linked to ([SYNR-476, comment-21547](https://sagebionetworks.jira.com/browse/SYNR-476?focusedCommentId=21547&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#comment-21547)) that a change to the `ntp.conf` file was the issue. I'm not exactly sure what the change was, but if your sysadmins can't decipher what the problem could be then please update this post and I'll track down what the change made was. You're right it looks like it is nfs
mount -l | grep '/home/jhoekstr*'
10.1.10.220:/export/home/jhoekstr on /home/jhoekstr type nfs (rw,nfsvers=3,sloppy,addr=10.1.10.220)
mount -l | grep '/home/dpolioud*'
10.1.10.220:/export/home/dpolioud on /home/dpolioud type nfs (rw,nfsvers=3,sloppy,addr=10.1.10.220)
Synapse client is the same (synapseClient_1.13-4) Thank you. That's a relatively new version of the R Synapse client, way beyond the version that this error was previously seen. Can you confirm if you're using the same version on your laptop as on the server?
Lastly, let's make sure you're filesystem is local using the `mount` command. We're looking for things that have `type nfs`. You can just find the mount point you are writing to and the mount point for your home directory, which is where the `synapseCache` is located (`/home/dpolioud/`).
After that, I'll check with our engineers and re-open that issue if I can't figure anything out. Synapse client: synapseClient_1.13-4
R: 3.2.3
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)
I accessed the server via ssh on which the data is stored and attempted to upload to Synapse by running R via command line on the server. I think the directory is local to the server.
Let me know if anymore information would be helpful.
Thanks! Can you provide some more info?
1. Version of Synapse client
1. Version of R
1. OS of the server that this happens on
1. If the directory you are writing to is local or network-based (e.g., NFS-mounted)
This issue has been noted in a quite old version of the Synapse client here, and it's a server issue with the system time and writing to an NFS-mounted drive. In summary the NFS clock is different than that of the machine you are logged into, and this causes an error:
https://sagebionetworks.jira.com/browse/SYNR-476
Thanks!
Drop files to upload
Error uploading files to Synapse: File lock exceeded page is loading…