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[Advent bug squashing] Fwd: Bug#1025953: marked as done (beast-mcmc: only usable with OpenCL)

Hi,
Andrius made a bug report for beast-mcmc, thanks to the upstream of beast2-mcmc I could find the origin lay in libhmsbeagle and I just fixed it. 

Cheers,

--
Pierre


-------- Message transféré --------
Sujet : Bug#1025953: marked as done (beast-mcmc: only usable with OpenCL)
Date : Fri, 16 Dec 2022 22:24:05 +0000
De : Debian Bug Tracking System <owner@bugs.debian.org>
Répondre à : 1025953@bugs.debian.org
Pour : Pierre Gruet <pgt@debian.org>

Your message dated Fri, 16 Dec 2022 22:20:56 +0000
with message-id <E1p6J4a-004G4d-Hf@fasolo.debian.org>
and subject line Bug#1025953: fixed in libhmsbeagle 3.1.2+dfsg-13
has caused the Debian Bug report #1025953,
regarding beast-mcmc: only usable with OpenCL
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.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


--
1025953: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1025953
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: beast-mcmc
Version: 1.10.4+dfsg-5
Severity: important
Control: block 1025424 by -1

Hello,

When launched on a system without OpenCL, beast-mcmc executable dies:

$ beast-mcmc -help
OpenCL error: CL_DEVICE_NOT_FOUND from file <GPUInterfaceOpenCL.cpp>, line 122.
From a quick glance this seems to be happening due to beast-mcmc using OpenCL version of libhmsbeagle1v5 (the line cited in the error message is in libhmsbeagle source). However, beast-mcmc seems to support CLI options to switch to libhmsbeagle1v5 CPU instance (see 'beagle_CPU' in src/dr/app/beast/BeastMain.java). Maybe it is possible to make CPU mode the default to avoid loading OpenCL-dependent libraries. 

Andrius

--- End Message ---
--- Begin Message --- 
Source: libhmsbeagle
Source-Version: 3.1.2+dfsg-13
Done: Pierre Gruet <pgt@debian.org>

We believe that the bug you reported is fixed in the latest version of
libhmsbeagle, 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 1025953@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Pierre Gruet <pgt@debian.org> (supplier of updated libhmsbeagle 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: Fri, 16 Dec 2022 22:41:31 +0100
Source: libhmsbeagle
Architecture: source
Version: 3.1.2+dfsg-13
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Pierre Gruet <pgt@debian.org>
Closes: 1025953
Changes:
 libhmsbeagle (3.1.2+dfsg-13) unstable; urgency=medium
 .
   * Team upload
   * Stopping supporting OpenCL (Closes: #1025953)
Checksums-Sha1:
 344f7c2c0cce31f09d697e76714d0fdc55b6a409 2337 libhmsbeagle_3.1.2+dfsg-13.dsc
 25a9f4aeb988b973b39a216cba2da027bd99a5a2 37220 libhmsbeagle_3.1.2+dfsg-13.debian.tar.xz
 df0753bf5759f898dee69caeb897ad1213369224 14604 libhmsbeagle_3.1.2+dfsg-13_amd64.buildinfo
Checksums-Sha256:
 307ab3ef407d70ecada6838325b2b7af25594a5c842dceb6a6c5421a22f8f07e 2337 libhmsbeagle_3.1.2+dfsg-13.dsc
 6105baa129f69c68d43d0684cc99e23f6d4e5074c431faa2eb0ee04b53dc0cb1 37220 libhmsbeagle_3.1.2+dfsg-13.debian.tar.xz
 1971546c01918c71b612a7b57397ecbdbdc09b9d83893383a532b2bd11146896 14604 libhmsbeagle_3.1.2+dfsg-13_amd64.buildinfo
Files:
 6af997f8b1e4c46455c2691c9285495b 2337 libs optional libhmsbeagle_3.1.2+dfsg-13.dsc
 1085b37ed81835856e34e419eadc76dc 37220 libs optional libhmsbeagle_3.1.2+dfsg-13.debian.tar.xz
 5984894bea0ee300b873d04a63f89225 14604 libs optional libhmsbeagle_3.1.2+dfsg-13_amd64.buildinfo

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