Error in rsync_remote yields no output

[shahrozeabbas]

I have been unable to produce an output using qsub_lapply. I only tried to run the example of incrementing 1:3 by 1. There's an error for rsync and the log files have this message:

ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'R'
export: Command not found.
export: Command not found.
MANPATH: Undefined variable.
Rscript: Command not found.

[rcannood]

Could you give me some information on the system you are trying to submit a job on? What are the usual commands you enter when submitting a job?

[shahrozeabbas]

It is a university cluster running CentOS 5.11 and I am using R 3.5.1 which has to be sourced prior to calling R. I use the command qsub myscript.sh to submit a job and qrsh for an interactive login. The cluster uses GridEngine for jobs.

These are my commands locally:
config <- create_qsub_config(remote = remote, local_tmp_path=local_tmp, remote_tmp_path=remote_tmp, execute_before=r_source)

qsub_lapply(1:3, function(x) x + 1, qsub_config=config)

This is my error:
Error in rsync_remote(remote_src = qs$remote, path_src = qs$remote_logdir, : rsync failed:

Along with those error messages in log.1.e, log.2.e, log.3.e files mentioned in the original post.

[zouter]

Just to make sure something can be executed on the remote system, could you do:
qsub::run_remote("echo hello", remote = remote) ?

If that completes successfully, could you try to rsync something to the remote system:

file <- tempfile()
write("hello", file)
qsub::rsync_remote(FALSE, file, remote, "~/test")

Because of the first error you gave, it's highly unlikely that these commands will succeed, but then we can troubleshoot further!

[shahrozeabbas]

It looks like the first command succeeded, but the second failed with the same error mentioned above.

[zouter]

Could you then run

file <- tempfile()
write("hello", file)
qsub::rsync_remote(FALSE, file, "prism", "~/test", verbose = TRUE)

and then run the first line you get (without the #) in the command line? Then we'll know the exact error

[shahrozeabbas]

This did not complete successfully. Returned the error:

Error in parse_remote(remote_dest) : object 'username' not found

I also tried running rsync_remote line by line and it seems fetch_hostname_from_config returns NULL. I tried to debug but not familiar with keep in lInes 19, 24, 29.

[zouter]

Sorry, I meant

file <- tempfile()
write("hello", file)
qsub::rsync_remote(FALSE, file, remote, "~/test", verbose = TRUE)

(prism is our remote 😉 )

[shahrozeabbas]

So the first line that was returned from that command was the rsync command and when I ran that in command line, it seems to have executed correctly. There is now a test file with 'hello' written in my remote directory.

[rcannood]

You said that this is the code you are trying to run:

config <- create_qsub_config(remote = remote, local_tmp_path=local_tmp, remote_tmp_path=remote_tmp, execute_before=r_source)
qsub_lapply(1:3, function(x) x + 1, qsub_config=config)

What is the content of r_source?

Also, could you run the following code?

library(qsub)
config <- create_qsub_config(
  remote = remote,
  local_tmp_path = local_tmp,
  remote_tmp_path = remote_tmp, 
  execute_before = r_source,
  remove_tmp_folder = FALSE
)
qsub_lapply(1:3, function(x) x + 1, qsub_config = config)

By setting remove_tmp_folder to FALSE, the folder that qsub creates at remote_tmp on the remote will not be removed, even if an error was produced. Inside, you should find a script.sh and script.R. script.sh should look something like this:

#!/bin/bash
#$ -t 1-3
#$ -N myjob
#$ -l h_vmem=10G
cd /path/to/your/folder
module unload R
Rscript --default-packages=methods,stats,utils,graphics,grDevices script.R $SGE_TASK_ID

One of the errors (Unable to locate a modulefile for 'R') will be caused by the module unload R. The other errors are likely related to whatever is in r_source. What does your script.sh look like?

[rcannood]

Closing this due to inactivity. Let me know if you have any more updates on this.