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Bug #449

Merge in debian patches

Added by Christoph Junghans over 9 years ago. Updated over 9 years ago.

Status:
Closed
Priority:
Normal
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Before the release it would be nice to merge in
patchs 3,4,5,20 and parts of patch 11 of the debian package.

Associated revisions

Revision b2414b5f (diff)
Added by Christoph Junghans over 9 years ago

added missing manpages (fixes bug #449)

History

#1 Updated by David van der Spoel over 9 years ago

Where do those patches come from? Some of them, e.g. http://patch-tracker.debian.org/patch/series/view/gromacs/4.0.7-3/30_git_release-4.0-patches.dpatch seem to change the functionality in a non-trivial manner, such that it is difficult to understand why the patches are correct. E.g.

diff --git a/src/gmxlib/mshift.c b/src/gmxlib/mshift.c
index 58115a2..d77aa79 100644
--- a/src/gmxlib/mshift.c
++ b/src/gmxlib/mshift.c
@ -190,8 +190,15 @ static void calc_1se(t_graph g,int ftype,t_ilist *il,
if (iaa >= at_start && iaa < at_end) {
g->start=min(g->start,iaa);
g->end =max(g->end, iaa);
- /*if (interaction_function[tp].flags & IF_CHEMBOND)
/
- nbond[iaa]
+;
+ /* When making the graph we (might) link all atoms in an interaction
+ * sequentially. Therefore the end atoms add 1 to the count,
+ * the middle atoms 2.
+ */
+ if (k 1 || k nratoms) {
+ nbond[iaa] = 1;
} else {
+ nbond[iaa] = 2;
}
}
}
}

changes the mshift code in a way that I do not understand.

#2 Updated by Christoph Junghans over 9 years ago

leave out patch #30, it is anyway only a strip from release-4.0 branch of the git repository.

The other patches are fine.

#3 Updated by Christoph Junghans over 9 years ago

20_altivec_kernel.dpatch is not needed anymore due to commit a27da1b5becf1679c0b977f49c6f18fa29622602 in release-4.0 branch

#4 Updated by Christoph Junghans over 9 years ago

03_autoconf_bashisms.dpatch & 04_autoconf_mpisuffix.dpatch got merged in commit 8d972c81d4c62fd123a0302d1f58122fbe15eead - that were the simple ones....

adding LT_INIT to configure.ac (05_lt_init.dpatch) can not be done, due to the fact that the gromacs version of libtool is modified and this version is based on libtool version 1.5.26, which does not know LT_INIT macro.

@erik: Got all your modifications merged in the main line of libtool?

#5 Updated by Nicholas Breen over 9 years ago

(In reply to comment #1)

Where do those patches come from? Some of them, e.g.
http://patch-tracker.debian.org/patch/series/view/gromacs/4.0.7-3/30_git_release-4.0-patches.dpatch [...]

That one's just a pull of the git release-4.0-patches branch between the 4.0.7 release and the last time I updated that patch in May. (The patch header shows the exact commits involved.) By definition, all of those changes are already incorporated, so it should be ignored.

The 05_lt_init patch worked around a build failure in Ubuntu (but not Debian) as of early 2009, <https://bugs.launchpad.net/ubuntu/+source/gromacs/+bug/327354&gt;. It may not be necessary any more, and if 04_autoconf_mpisuffix is merged, it definitely becomes obsolete because the packaging scripts wouldn't need to re-run autotools.

#6 Updated by Christoph Junghans over 9 years ago

Thanks, Nicolas for the quick answer.

Yes, 04_autoconf_mpisuffix got merged, because I also had multiple mpi environments (lam and openmpi) @MPIP as well.

Are there any additional modification from debian? I saw some missing manpages, something else?

I think there will be one, maybe last, 4.0.X release.

#7 Updated by Nicholas Breen over 9 years ago

(In reply to comment #6)

Are there any additional modification from debian? I saw some missing manpages,
something else?

I think there will be one, maybe last, 4.0.X release.

Man pages are the only significant remaining issue. The packages also rename demux.pl and xplor2gmx.pl without their suffixes, making it an easier transition if they're ever rewritten in any language other than Perl. It also makes it possible to write man pages for them without the system treating them as the Polish language translations!

Of the man pages, g_kinetics(1) should probably be generated by admin/mknroff.pl instead; demux(1), xplor2gmx(1), and luck(1) can't be; and gromacs(7) needs some adjustments to man/Makefile that can be pulled from the version in git/4.5. These would only be for a final 4.0.x release, though -- 4.5-beta2 has a different set of missing or misnamed pages, which I'll submit as a separate bug once I finish a patch.

patch-tracker is good for the formal patches, but files added elsewhere (such as the aforementioned man pages) are easier to pull from the packaging SVN repo: http://svn.debian.org/wsvn/debichem/unstable/gromacs/debian/man/#_unstable_gromacs_debian_man_

#8 Updated by Christoph Junghans over 9 years ago

I added the missing manpages in commit b2414b5fd0a951c094dd244fc3af642607b9c1a4
on the 4.0 branch.

Looking forward to your patch for 4.5-beta2

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