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Re: [HTCondor-users] $basename and transfer_output
- Date: Thu, 01 Sep 2016 20:00:49 +0000
- From: John M Knoeller <johnkn@xxxxxxxxxxx>
- Subject: Re: [HTCondor-users] $basename and transfer_output
Sure sounds like it. I'm curious what condor_q -long shows for the relevant attributes of this job.
-----Original Message-----
From: HTCondor-users [mailto:htcondor-users-bounces@xxxxxxxxxxx] On Behalf Of Dimitri Maziuk
Sent: Thursday, September 1, 2016 2:04 PM
To: HTCondor-Users Mail List <htcondor-users@xxxxxxxxxxx>
Subject: [HTCondor-users] $basename and transfer_output
Hi all,
I've a program that reads XYZ.sdf and outputs XYZ.sdf_output.sdf. With this in submit file:
output = $BASENAME(molfile).stdout
error = $BASENAME(molfile).stderr
log = $BASENAME(molfile).log
should_transfer_files = Yes
transfer_input_files = ...,/var/tmp/submit/$(molfile) when_to_transfer_output = ON_EXIT
transfer_output_files = ...,$BASENAME(molfile).sdf_output.sdf
queue molfile matching [0] *.sdf
I get the output, error, and log files fine, but instead of XYZ.sdf_output.sdf I get a 0-byte XYZ.sdf.sdf_output.sdf and the job goes on hold with
> 007 (012.000.000) 09/01 13:50:32 Shadow exception!
> Error from slot1@xxxxxxxxxxxxxxxxxxxxxxxx: STARTER at 144.92.4.205 failed to send file(s) to <144.92.4.205:40052>: error reading from /var/lib/condor/execute/dir_119247/Structure3D_CID_112084.sdf.sdf_output.sdf: (errno 2) No such file or directory; SHADOW failed to receive file(s) from <144.92.4.205:52846>
> 2111 - Run Bytes Sent By Job
> 1180666 - Run Bytes Received By Job
I.e. instead of transferring $BASENAME(molfile).sdf_output.sdf it's trying to transfer $(molfile).sdf_output.sdf -- and failing as that doesn't exist.
Is there a problem with $BASENAME() or am I missing something?
TIA
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu