[HTCondor-users] $basename and transfer_output

[Dimitri Maziuk <dmaziuk@xxxxxxxxxxxxx>]

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

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