Your message dated Tue, 21 Aug 2012 19:02:38 +0000
with message-id <[email protected]>
and subject line Bug#684879: fixed in condor 7.8.2~dfsg.1-2
has caused the Debian Bug report #684879,
regarding condor_qsub should probably not enable the file transfer mechanism
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
684879: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=684879
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Source: condor
Source-Version: 7.8.2~dfsg.1-2
We believe that the bug you reported is fixed in the latest version of
condor, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael Hanke <[email protected]> (supplier of updated condor package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Sun, 12 Aug 2012 19:20:35 +0200
Source: condor
Binary: condor condor-dev condor-doc condor-dbg libclassad-dev libclassad3
Architecture: source amd64 all
Version: 7.8.2~dfsg.1-2
Distribution: experimental
Urgency: low
Maintainer: Condor Developers <[email protected]>
Changed-By: Michael Hanke <[email protected]>
Description:
condor - distributed workload management system
condor-dbg - distributed workload management system - debugging symbols
condor-dev - distributed workload management system - development files
condor-doc - distributed workload management system - documentation
libclassad-dev - Condor classads expression language - development library
libclassad3 - Condor classads expression language - runtime library
Closes: 678425 684463 684667 684879
Changes:
condor (7.8.2~dfsg.1-2) experimental; urgency=low
.
* Make postinst script more robust against missing config variables (Closes:
#684667). Patch is courtesy of Tim Cartwright.
* Disable Condor's file transfer mechanism for jobs submitted via
condor_qsub, because a shared filesystem is assumed for these jobs
(Closes: #684879).
* This time really remove dangling symlink /usr/sbin/condor -> ../bin/condor.
This file no longer exists (Closes: #678425).
* Support deployment scenario where the administrative 'condor' user is not
a local system user, but is shared (e.g. through LDAP) by all machines in a
Condor pool (see installation manual section 3.2). The condor package will
accept to run under an existing non-system user account named 'condor',
but only when that account is locked, i.e. not login is possible
(Closes: #684463).
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