Package: condor Version: 7.8.1~dfsg.1-2 Severity: normal Tags: patch A user reports that one of FSL's compenents (package 'fsl-4.1') fails in conjuction with Condor via condor_qsub:
http://lists.alioth.debian.org/pipermail/neurodebian-users/2012-July/000471.html The reason seems to be that the submit file created by condor_qsub unconditionally enables Condor's file transfer mechanism. This does in turn invalidate relative paths for SGE task files or commands, as Condor will ignore the 'initialdir' setting and instead transfer files into a dedicated execute directory. The fix for this bug seems to be to disable file transfer entirely. This should not have further limitation than those already imposed by condor_qsub (e.g. it is impossible to specify file/data dependencies exhaustively anyway). A tentative patch would be: diff --git a/debian/condor_qsub b/debian/condor_qsub index 4673456..078bd0c 100755 --- a/debian/condor_qsub +++ b/debian/condor_qsub @@ -338,8 +338,7 @@ submit_file=$(mktemp --tmpdir condor_qsub.XXXXXXXXXXXXX) cat << EOT > $submit_file # condor_qsub call: $@ universe = vanilla -should_transfer_files = YES -when_to_transfer_output = ON_EXIT +should_transfer_files = NO #log = $log_file EOT -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected]
