Re: [Condor-users] jobs in R

[Ian Chesal <ichesal@xxxxxxxxxxxxxxxxxx>]

That PATH call you're making in your .bat file is completely wiping out the rest of the path. So any Windows DLLs that are required by the R runtime aren't going to be found.

Try:

set PATH=%PATH%:"c:\Program Files\R\R-2.6.1\bin"

instead.

If that doesn't work it's likely you're missing dependencies that R requires to run on the remote machine. Try USE_VISIBLE_DESKTOP=True on the execute node (you'll need to restart Condor for this setting to take effect) and watch the machine as the job runs to see if you can spot a popup error that says which DLLs are missing.

- Ian

On Tue, Aug 17, 2010 at 11:44 AM, Shruti Mudra <shruti.mudra@xxxxxxxxx> wrote:

Hi Everyone,

I'm using condor to run R jobs when I submit job to the condor it is running for 2 seconds and going back to the idle state.

Here is my submit file

universe = vanilla

Executable =  Rscript.bat

should_transfer_files = YES

when_to_transfer_output = ON_EXIT

arguments = Simulate_Normal_Data.R

input = Simulate_Normal_Data.R

transfer_input_files = bay_alpha.R

Output = test_r_out.out

Log = test_r_log.log

error = error_r.error

queue

where Rscript.bat is

set PATH=C:\Program Files\R\R-2.6.1\bin

R CMD BATCH --vanilla %1

my startlog is

08/17 11:35:38 slot1: match_info called

08/17 11:35:38 slot1: Received match <y.y.y.y:49160>#1281995849#1#...

08/17 11:35:38 slot1: State change: match notification protocol successful

08/17 11:35:38 slot1: Changing state: Unclaimed -> Matched

08/17 11:35:38 slot1: Request accepted.

08/17 11:35:38 slot1: Remote owner is owner@lab

08/17 11:35:38 slot1: State change: claiming protocol successful

08/17 11:35:38 slot1: Changing state: Matched -> Claimed

08/17 11:35:39 slot1: Got activate_claim request from shadow (<y.y.y.y:49209>)

08/17 11:35:39 slot1: Remote job ID is 52.0

08/17 11:35:39 slot1: Got universe "VANILLA" (5) from request classad

08/17 11:35:39 slot1: State change: claim-activation protocol successful

08/17 11:35:39 slot1: Changing activity: Idle -> Busy

08/17 11:35:43 slot1: Called deactivate_claim_forcibly()

08/17 11:35:43 slot1: State change: received RELEASE_CLAIM command

08/17 11:35:43 slot1: Changing state and activity: Claimed/Busy -> Preempting/Vacating

08/17 11:35:43 Starter pid 3840 exited with status 0

08/17 11:35:43 slot1: State change: starter exited

08/17 11:35:43 slot1: State change: No preempting claim, returning to owner

08/17 11:35:43 slot1: Changing state and activity: Preempting/Vacating -> Owner/Idle

08/17 11:35:43 slot1: State change: IS_OWNER is false

08/17 11:35:43 slot1: Changing state: Owner -> Unclaimed

here is my starterlog file

08/17 11:35:39 Locale: English_United States.1252

08/17 11:35:39 ******************************************************

08/17 11:35:39 ** condor_starter (CONDOR_STARTER) STARTING UP

08/17 11:35:39 ** C:\condor\bin\condor_starter.exe

08/17 11:35:39 ** SubsystemInfo: name=STARTER type=STARTER(8) class=DAEMON(1)

08/17 11:35:39 ** Configuration: subsystem:STARTER local:<NONE> class:DAEMON

08/17 11:35:39 ** $CondorVersion: 7.4.2 Mar 30 2010 BuildID: 227044 $

08/17 11:35:39 ** $CondorPlatform: INTEL-WINNT50 $

08/17 11:35:39 ** PID = 3840

08/17 11:35:39 ** Log last touched 8/16 12:51:13

08/17 11:35:39 ******************************************************

08/17 11:35:39 Using config source: C:\condor\condor_config

08/17 11:35:39 Using local config sources: 

08/17 11:35:39    C:\condor\condor_config.local

08/17 11:35:39 DaemonCore: Command Socket at <y.y.y.y:49213>

08/17 11:35:39 GLEXEC_JOB not supported on this platform; ignoring

08/17 11:35:39 Setting resource limits not implemented!

08/17 11:35:39 Communicating with shadow <y.y.y.y:49206>

08/17 11:35:39 Submitting machine is "machine_name"

08/17 11:35:39 setting the orig job name in starter

08/17 11:35:39 setting the orig job iwd in starter

08/17 11:35:40 File transfer completed successfully.

08/17 11:35:41 Job 52.0 set to execute immediately

08/17 11:35:41 Starting a VANILLA universe job with ID: 52.0

08/17 11:35:41 Tracking process family by login "condor-reuse-slot1"

08/17 11:35:41 IWD: C:\condor\execute\dir_3840

08/17 11:35:41 Input file: C:\condor\execute\dir_3840\Simulate_Normal_Data.R

08/17 11:35:41 Output file: C:\condor\execute\dir_3840\test_r_out.out

08/17 11:35:41 Error file: C:\condor\execute\dir_3840\error_r.error

08/17 11:35:41 Renice expr "10" evaluated to 10

08/17 11:35:41 About to exec C:\condor\execute\dir_3840\condor_exec.bat Simulate_Normal_Data.R

08/17 11:35:41 Executable is a batch file, running: "C:\Windows\system32\cmd.exe" /Q /C "C:\condor\execute\dir_3840\condor_exec.bat" Simulate_Normal_Data.R

08/17 11:35:41 Create_Process succeeded, pid=1916

08/17 11:35:43 Process exited, pid=1916, status=1

08/17 11:35:43 Got SIGQUIT.  Performing fast shutdown.

08/17 11:35:43 ShutdownFast all jobs.

08/17 11:35:43 **** condor_starter (condor_STARTER) pid 3840 EXITING WITH STATUS 0

can anyone help me with this 

Thanks,

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