Debian Bug report logs - #1004005
openmm: reproducible-builds: BuildId differences triggered by RPATH

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Vagrant Cascadian <vagrant@reproducible-builds.org>

To: submit@bugs.debian.org

Subject: openmm: reproducible-builds: BuildId differences triggered by RPATH

Date: Wed, 19 Jan 2022 00:02:39 -0800

[Message part 1 (text/plain, inline)]

Source: openmm
Severity: normal
Tags: patch
User: reproducible-builds@lists.alioth.debian.org
Usertags: buildpath
X-Debbugs-Cc: reproducible-bugs@lists.alioth.debian.org

The RPATH contains the build path resulting in different buildid:

  https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/openmm.html

The attached patch to debian/rules passes
-DCMAKE_BUILD_RPATH_USE_ORIGIN=ON via a dh_auto_configure override,
which should use a relative path for RPATH.

Alternately, updating the packaging to debhelper compat level 14 should
fix this, although it is currently an experimental compat level.

With this patch applied, openmm *should* build reproducibly on
tests.reproducible-builds.org for the version currently in unstable,
although the version in experimental seems to embed the build path in
additional and/or non-deterministic ways.


Thanks for maintaining openmm!

live well,
  vagrant

[0001-debian-rules-Pass-DCMAKE_BUILD_RPATH_USE_ORIGIN-ON-v.patch (text/x-diff, inline)]

From 62bcd0ccc41cdfe087c2aefcceaf55863172127d Mon Sep 17 00:00:00 2001
From: Vagrant Cascadian <vagrant@reproducible-builds.org>
Date: Wed, 19 Jan 2022 05:05:47 +0000
Subject: [PATCH] debian/rules: Pass -DCMAKE_BUILD_RPATH_USE_ORIGIN=ON via
 dh_auto_configure override.

This avoids embedding the full path in RPATH, which triggers BuildId
differences.

https://tests.reproducible-builds.org/debian/issues/unstable/cmake_rpath_contains_build_path_issue.html
---
 debian/rules | 1 +
 1 file changed, 1 insertion(+)

diff --git a/debian/rules b/debian/rules
index 4c281f4..20f599f 100755
--- a/debian/rules
+++ b/debian/rules
@@ -13,6 +13,7 @@ CMAKE_FLAGS = \
         -DCMAKE_C_FLAGS_RELEASE="$(CFLAGS)" \
         -DCMAKE_CXX_FLAGS_RELEASE="$(CXXFLAGS)" \
         -DCMAKE_SHARED_LINKER_FLAGS_RELEASE="$(LDFLAGS)" \
+        -DCMAKE_BUILD_RPATH_USE_ORIGIN=ON \
         -DCMAKE_BUILD_TYPE=Release      \
         $(CMAKE_ARCH_FLAGS) \
         -DOPENMM_BUILD_AMOEBA_PLUGIN=ON \
-- 
2.34.1

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Message #10 received at 1004005@bugs.debian.org (full text, mbox, reply):

From: Andrius Merkys <merkys@debian.org>

To: Vagrant Cascadian <vagrant@reproducible-builds.org>, 1004005@bugs.debian.org

Subject: Re: [Debichem-devel] Bug#1004005: openmm: reproducible-builds: BuildId differences triggered by RPATH

Date: Wed, 19 Jan 2022 10:52:08 +0200

Hi,

On 2022-01-19 10:02, Vagrant Cascadian wrote:
> The attached patch to debian/rules passes
> -DCMAKE_BUILD_RPATH_USE_ORIGIN=ON via a dh_auto_configure override,
> which should use a relative path for RPATH.

Thanks a lot for the patch!

> Alternately, updating the packaging to debhelper compat level 14 should
> fix this, although it is currently an experimental compat level.
> 
> With this patch applied, openmm *should* build reproducibly on
> tests.reproducible-builds.org for the version currently in unstable,
> although the version in experimental seems to embed the build path in
> additional and/or non-deterministic ways.

Maybe a possible long-term solution would be to use chrpath to set the
RPATH to point to the absolute location of private libraries, like
/usr/lib/${DEB_HOST_MULTIARCH}/openmm ?

Best,
Andrius

Message #15 received at 1004005@bugs.debian.org (full text, mbox, reply):

From: Vagrant Cascadian <vagrant@reproducible-builds.org>

To: Andrius Merkys <merkys@debian.org>, 1004005@bugs.debian.org

Subject: Re: [Debichem-devel] Bug#1004005: openmm: reproducible-builds: BuildId differences triggered by RPATH

Date: Wed, 19 Jan 2022 07:43:01 -0800

[Message part 1 (text/plain, inline)]

On 2022-01-19, Andrius Merkys wrote:
> On 2022-01-19 10:02, Vagrant Cascadian wrote:
>> The attached patch to debian/rules passes
>> -DCMAKE_BUILD_RPATH_USE_ORIGIN=ON via a dh_auto_configure override,
>> which should use a relative path for RPATH.
>
> Thanks a lot for the patch!
>
>> Alternately, updating the packaging to debhelper compat level 14 should
>> fix this, although it is currently an experimental compat level.
>> 
>> With this patch applied, openmm *should* build reproducibly on
>> tests.reproducible-builds.org for the version currently in unstable,
>> although the version in experimental seems to embed the build path in
>> additional and/or non-deterministic ways.
>
> Maybe a possible long-term solution would be to use chrpath to set the
> RPATH to point to the absolute location of private libraries, like
> /usr/lib/${DEB_HOST_MULTIARCH}/openmm ?

I haven't yet identified the cause of the other issues.

I think the RPATH issues are solved by the submitted patch; at the very
least it massively reduces the differences!


live well,
  vagrant

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Message #20 received at 1004005@bugs.debian.org (full text, mbox, reply):

From: Vagrant Cascadian <vagrant@reproducible-builds.org>

To: Andrius Merkys <merkys@debian.org>, 1004005@bugs.debian.org

Subject: Re: [Debichem-devel] Bug#1004005: openmm: reproducible-builds: BuildId differences triggered by RPATH

Date: Wed, 19 Jan 2022 08:00:23 -0800

[Message part 1 (text/plain, inline)]

On 2022-01-19, Vagrant Cascadian wrote:
> On 2022-01-19, Andrius Merkys wrote:
>> On 2022-01-19 10:02, Vagrant Cascadian wrote:
>>> The attached patch to debian/rules passes
>>> -DCMAKE_BUILD_RPATH_USE_ORIGIN=ON via a dh_auto_configure override,
>>> which should use a relative path for RPATH.
>>
>> Thanks a lot for the patch!
>>
>>> Alternately, updating the packaging to debhelper compat level 14 should
>>> fix this, although it is currently an experimental compat level.
>>> 
>>> With this patch applied, openmm *should* build reproducibly on
>>> tests.reproducible-builds.org for the version currently in unstable,
>>> although the version in experimental seems to embed the build path in
>>> additional and/or non-deterministic ways.
>>
>> Maybe a possible long-term solution would be to use chrpath to set the
>> RPATH to point to the absolute location of private libraries, like
>> /usr/lib/${DEB_HOST_MULTIARCH}/openmm ?
>
> I haven't yet identified the cause of the other issues.
>
> I think the RPATH issues are solved by the submitted patch; at the very
> least it massively reduces the differences!

It looks like the addition of python3-simtk-dbgsym in the version in
experimental is what is causing the additional changes.

diffoscope output attached.


live well,
  vagrant

[experiment-1.diffoscope.out.gz (application/gzip, attachment)]

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Message #23 received at 1004005-submitter@bugs.debian.org (full text, mbox, reply):

From: Andrius Merkys <noreply@salsa.debian.org>

To: 1004005-submitter@bugs.debian.org

Subject: Bug#1004005 marked as pending in openmm

Date: Fri, 21 Jan 2022 18:27:21 +0000

Control: tag -1 pending

Hello,

Bug #1004005 in openmm reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:

https://salsa.debian.org/debichem-team/openmm/-/commit/46d22ae3d1e1446db462f95e4236b3f1e1de4ad3

------------------------------------------------------------------------
Setting CMAKE_BUILD_RPATH_USE_ORIGIN=ON to fix reproducibility (Closes: #1004005). Thanks Vagrant Cascadian.
------------------------------------------------------------------------

(this message was generated automatically)
-- 
Greetings

https://bugs.debian.org/1004005

Message #30 received at 1004005@bugs.debian.org (full text, mbox, reply):

From: Andrius Merkys <merkys@debian.org>

To: Vagrant Cascadian <vagrant@reproducible-builds.org>, 1004005@bugs.debian.org

Subject: Re: [Debichem-devel] Bug#1004005: Bug#1004005: openmm: reproducible-builds: BuildId differences triggered by RPATH

Date: Fri, 21 Jan 2022 20:33:08 +0200

Hi,

On 2022-01-19 18:00, Vagrant Cascadian wrote:
> On 2022-01-19, Vagrant Cascadian wrote:
>> On 2022-01-19, Andrius Merkys wrote:
>>> Maybe a possible long-term solution would be to use chrpath to set the
>>> RPATH to point to the absolute location of private libraries, like
>>> /usr/lib/${DEB_HOST_MULTIARCH}/openmm ?
>>
>> I haven't yet identified the cause of the other issues.
>>
>> I think the RPATH issues are solved by the submitted patch; at the very
>> least it massively reduces the differences!
> 
> It looks like the addition of python3-simtk-dbgsym in the version in
> experimental is what is causing the additional changes.

Thanks for the information, now it is clear to me. I have applied your 
patch - thanks a lot for providing it.

I will upload to unstable soon, after I finish resolving a couple of 
unrelated issues.

Best,
Andrius

Message #35 received at 1004005-close@bugs.debian.org (full text, mbox, reply):

From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>

To: 1004005-close@bugs.debian.org

Subject: Bug#1004005: fixed in openmm 7.7.0+dfsg-2

Date: Mon, 24 Jan 2022 07:08:03 +0000

Source: openmm
Source-Version: 7.7.0+dfsg-2
Done: Andrius Merkys <merkys@debian.org>

We believe that the bug you reported is fixed in the latest version of
openmm, 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 1004005@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andrius Merkys <merkys@debian.org> (supplier of updated openmm 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 ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Mon, 24 Jan 2022 01:45:05 -0500
Source: openmm
Architecture: source
Version: 7.7.0+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Changed-By: Andrius Merkys <merkys@debian.org>
Closes: 1004005
Changes:
 openmm (7.7.0+dfsg-2) unstable; urgency=medium
 .
   * Upload to unstable.
   * Setting CMAKE_BUILD_RPATH_USE_ORIGIN=ON to fix reproducible build
     (Closes: #1004005).
   * Cleaning up debian/rules.
   * Moving libOpenMMAmoeba.so, libOpenMMDrude.so and libOpenMMRPMD.so to
     libdevel package.
   * Updating debian/todo.
Checksums-Sha1:
 034905fcb0288565132ae4f658772ba565c4e2bb 2371 openmm_7.7.0+dfsg-2.dsc
 173346df7603fbf5c7b877fd9a74e1bddea57eea 14904 openmm_7.7.0+dfsg-2.debian.tar.xz
 3fb3feedffa3b77da4f1b86b9eb6c5d13e88bf45 8817 openmm_7.7.0+dfsg-2_source.buildinfo
Checksums-Sha256:
 f9b1c612beb7a20314560b84c707bf9a4bcfa6667233f066fe7a57f82fadf1c1 2371 openmm_7.7.0+dfsg-2.dsc
 5a2fffcf2fdf9d0aec9017c95b05a4f196aeeae4cdc07dbaeebb3a6fe7252a57 14904 openmm_7.7.0+dfsg-2.debian.tar.xz
 41133b2bb64c444f1641d7273f0a814120e1618d668ec503a7a6d7f888803b81 8817 openmm_7.7.0+dfsg-2_source.buildinfo
Files:
 d8d5d15b5101ef73739adef427e28361 2371 libs optional openmm_7.7.0+dfsg-2.dsc
 1c2e73ac816e5f4339d81971de41973a 14904 libs optional openmm_7.7.0+dfsg-2.debian.tar.xz
 ada05194c5429237fc4994e2306f222d 8817 libs optional openmm_7.7.0+dfsg-2_source.buildinfo

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