- openSUSE Science

Leave
by Slawomir Siejka 31 Jul '22

31 Jul '22

Empty Message

1 0

Re: Unannounced change of shlib-policy-name-error rpmlint strictness on TW
by Stefan Brüns 14 Jul '22

14 Jul '22

On Donnerstag, 14. Juli 2022 14:34:27 CEST Richard Biener wrote: > On Thu, 14 Jul 2022, Stefan Brüns wrote: > > Hi, > > > > a few days ago any violation of shlib-policy-name-error has become a fatal > > error. > > > > This is especially problematic for many packages in the science > > repository, > > when packages are built as flavors for e.g. openmpi2/3/4, and the library > > packages carry a corresponding suffix. E.g.: > > > > libhdf5-103-openmpi4.x86_64: E: shlib-policy-name-error (Badness: 10000) > > SONAME: libhdf5.so.103 > > (/usr/lib64/mpi/gcc/openmpi4/lib64/libhdf5.so.103.3.1), expected package > > suffix: 103 > > > > This is a case not covered by https://en.opensuse.org/ > > openSUSE:Shared_library_packaging_policy > > > > Can this please be reverted until the policy has been extended to cover > > these cases? Preferably, rpmlint learns to understand this pattern. > > The policy wasn't originally supposed to apply to shared libraries > that do not reside in the default runpath which means > /usr/lib*/$package/... should have been excempted. Possibly the > implementation doesn't reflect that or the implementation > is too narrow? > > IIRC there's also a whitelist(?) - the GCC package excempts itself > via rpmlintrc filtering the check ... > > Richard. In the current code I can not find such a generic exemption. Of course one can add an exemption via rpmlintrc. I would prefer not do so: 1. There are probably about 50 source packages in science alone affected by this. 2. Each rpmlintrc entry bears the risk of hiding actual packaging errors. Regards, Stefan -- Stefan Brüns / Bergstraße 21 / 52062 Aachen phone: +49 241 53809034 mobile: +49 151 50412019

1 0

Unannounced change of shlib-policy-name-error rpmlint strictness on TW
by Stefan Brüns 14 Jul '22

14 Jul '22

Hi, a few days ago any violation of shlib-policy-name-error has become a fatal error. This is especially problematic for many packages in the science repository, when packages are built as flavors for e.g. openmpi2/3/4, and the library packages carry a corresponding suffix. E.g.: libhdf5-103-openmpi4.x86_64: E: shlib-policy-name-error (Badness: 10000) SONAME: libhdf5.so.103 (/usr/lib64/mpi/gcc/openmpi4/lib64/libhdf5.so.103.3.1), expected package suffix: 103 This is a case not covered by https://en.opensuse.org/ openSUSE:Shared_library_packaging_policy Can this please be reverted until the policy has been extended to cover these cases? Preferably, rpmlint learns to understand this pattern. Regards, Stefan -- Stefan Brüns / Bergstraße 21 / 52062 Aachen home: +49 241 53809034 mobile: +49 151 50412019

1 0

Re: RFC: Proper automatic library dependencies for MPI/serial flavors
by Egbert Eich 05 Jul '22

05 Jul '22

Hi Stefan, Stefan Brüns writes: > Hi everyone, > > we have a reocurring problem with multiple providers of libraries built as > serial and openMPI(1-4)/MVAPICH/... flavors. > > Currently, both the serial and e.g. openMPI4 flavors provide the exact same > resolvables, e.g. "libsundials_sunlinsolklu.so.4.2.0()(64bit)" [1]. This is > then manually fixed up on a case-by-case basis by manually specifying the > default package. > > Fedora solves this problem by adding the MPI flavor to the resolvable, e.g. > "libfoo.so()(64bit)(openmpi-x86_64)". For details, see [2][3]. > > I would propose for (open)SUSE to follow this notation, and finally get rid > of the manual workarounds. Indeed, this problem is not new and I believe we've talked about this some years ago already. We had the same with HPC packages as well, we 'solved' it by replacing the dependency generator by one that would ignore any dependencies pointing into the HPC directories (/usr/lib/hpc) and adding dependencies manually. I had the plan to resolve it the way you've suggested adding more 'attribute tags' do the dependency to specify it with greater detail. This of course wasn't the real solution, just a workaround. I never found time to do the real solution. So indeed, if Fedora has a solution for this already (at least for the MPI problem, for HPC packages there are further challanges), we should take this into consideration. Thanks for picking this up again! Cheers, Egbert. > > Kind regards, Stefan > > > [1] https://build.opensuse.org/package/binary/science/sundials:openmpi4/ > openSUSE_Tumbleweed/x86_64/libsundials4-openmpi4-6.2.0-19.1.x86_64.rpm > > [2] https://fedoraproject.org/wiki/Changes/RpmMPIReqProv > [3] https://packages.fedoraproject.org/pkgs/rpm-mpi-hooks/rpm-mpi-hooks/ > index.html > -- Egbert Eich (Res. & Dev.) SUSE Labs - Architect HPC Tel: +49 911-740 53 0 https://www.suse.com ----------------------------------------------------------------------- SUSE Software Solutions Germany GmbH, Maxfeldstrasse 5, 90409 Nuernberg Geschaeftsfuehrer: Ivo Totev (HRB 36809, AG Nürnberg)

1 0

RFC: Proper automatic library dependencies for MPI/serial flavors
by Stefan Brüns 05 Jul '22

05 Jul '22

Hi everyone, we have a reocurring problem with multiple providers of libraries built as serial and openMPI(1-4)/MVAPICH/... flavors. Currently, both the serial and e.g. openMPI4 flavors provide the exact same resolvables, e.g. "libsundials_sunlinsolklu.so.4.2.0()(64bit)" [1]. This is then manually fixed up on a case-by-case basis by manually specifying the default package. Fedora solves this problem by adding the MPI flavor to the resolvable, e.g. "libfoo.so()(64bit)(openmpi-x86_64)". For details, see [2][3]. I would propose for (open)SUSE to follow this notation, and finally get rid of the manual workarounds. Kind regards, Stefan [1] https://build.opensuse.org/package/binary/science/sundials:openmpi4/ openSUSE_Tumbleweed/x86_64/libsundials4-openmpi4-6.2.0-19.1.x86_64.rpm [2] https://fedoraproject.org/wiki/Changes/RpmMPIReqProv [3] https://packages.fedoraproject.org/pkgs/rpm-mpi-hooks/rpm-mpi-hooks/ index.html

1 0

Re: openblas setup screwed in science project
by Egbert Eich 05 May '22

05 May '22

Atri Bhattacharya writes: > On Wed, 2022-05-04 at 14:19 +0200, Stefan Brüns wrote: > > > > Hi Egbert, > > > > Another problem with openblas is the missing .baselibs configuration > > for 32bit > > packages. Some time ago it was still there, but then went missing > > without a > > mention in the changelog. This breaks at least arpack-ng. > > > > At least for TW, i586 (actully, somthing like P4) is still supported, > > and for > > any library package still working on i586 we should also have the > > baselibs > > configuration (IMHO). > > > > > > Related to this, I am trying to restore the baselibs.conf to openblas, > see WIP at > <https://build.opensuse.org/package/show/home:badshah400:branches:science/op… > >. That's fine, especially since you are creating it dynamically ;) You may have to specify the library files by hand as lib(64)?/ contains only links. The real libraries live in lib(64)?/openblas-<flavor>. Cheers, Egbert. > > Optionally, I made an sr to obs://science/arpack-ng to disable the - > 32bit bi-arch package generation in > <https://build.opensuse.org/request/show/974867> > but feel free to decide whether to decline this and accept the changes > to openblas (in a future sr) instead. > > Best wishes, > > > -- > Atri Bhattacharya -- Egbert Eich (Res. & Dev.) SUSE Labs - Architect HPC Tel: +49 911-740 53 0 https://www.suse.com ----------------------------------------------------------------------- SUSE Software Solutions Germany GmbH, Maxfeldstrasse 5, 90409 Nuernberg Geschaeftsfuehrer: Ivo Totev (HRB 36809, AG Nürnberg)

2 1

Re: openblas setup screwed in science project
by Egbert Eich 04 May '22

04 May '22

Hi Stefan, Stefan Brüns writes: > On Freitag, 8. April 2022 16:08:01 CEST Stefan Brüns wrote: > > Hi, > > > > someone has apparently disabled *all* builds for openblas. > > > > Whats the reason for this? > > > > As openblas 0.3.20 was never built inside science, we now have 0.3.20 in > > Factory and 0.3.17 (binary packages) in science. This causes a lot of > > unresolvables, as OBS tries to use openblas 0.3.17 from science. > > > > Kind regards, > > > > Stefan > > Hi Egbert, > > as you are the de-facto maintainer of openblas, can you shed some light here? > > Another problem with openblas is the missing .baselibs configuration for 32bit > packages. Some time ago it was still there, but then went missing without a > mention in the changelog. This breaks at least arpack-ng. > > At least for TW, i586 (actully, somthing like P4) is still supported, and for > any library package still working on i586 we should also have the baselibs > configuration (IMHO). I'm not aware that I've thrown these out. On the packages I've worked on, I've converted the static baselibs.conf files to static ones as there was no good way to use static baselibs.conf file for all the different flavors - moreover, I don't want these 32bit binaries for HPC anyway. I've looked back, the version where I've claimed I added these, did not have it. Going further back I wasn't able to find any static baselibs.conf either, which makes me believe there was never any. I personally do not care for 32-bit libraries, neither professionally nor personally - at least for openblas. I had my fair share of openblas - the upgrade to 0.3.20 gave me some grief - and I do not want to invest any more time on topics that are of no interest for me. If you feel like a baselibs.conf setup is useful and want to create one *and* maintain it, please feel free. There were some breakages introduced thru my changes - which I've hopefully rectified, they had nothing to do with a missing baselibs.conf. These issues should disappear from Factory as the fix has been accepted last night. I have no idea who disabled build of openblas in science. It wasn't me - at least not intentionally. On the bright sight, switching between netlib-lapack and openblas should be possible, now. Cheers, Egbert. > > Kind regards, > > Stefan > > -- > Stefan Brüns / Bergstraße 21 / 52062 Aachen > home: +49 241 53809034 mobile: +49 151 50412019 > -- Egbert Eich (Res. & Dev.) SUSE Labs - Architect HPC Tel: +49 911-740 53 0 https://www.suse.com ----------------------------------------------------------------------- SUSE Software Solutions Germany GmbH, Maxfeldstrasse 5, 90409 Nuernberg Geschaeftsfuehrer: Ivo Totev (HRB 36809, AG Nürnberg)

1 0

openblas setup screwed in science project
by Stefan Brüns 04 May '22

04 May '22

Hi, someone has apparently disabled *all* builds for openblas. Whats the reason for this? As openblas 0.3.20 was never built inside science, we now have 0.3.20 in Factory and 0.3.17 (binary packages) in science. This causes a lot of unresolvables, as OBS tries to use openblas 0.3.17 from science. Kind regards, Stefan -- Stefan Brüns / Bergstraße 21 / 52062 Aachen home: +49 241 53809034 mobile: +49 151 50412019

2 2

Some new scientific packages for molecular biology
by Vojtěch Zeisek 26 Nov '21

26 Nov '21

Hi, I decided not to be that much lazy and when I need to compile some software (mostly for molecular biology, genetics, ...), I package it. So far it is in https://build.opensuse.org/project/show/home:vojtaeus but I think it could be useful to submit them to https://build.opensuse.org/project/show/science but I'm still bit beginner with packaging (and biologist, not programmer), so I'm not sure if I follow all best-practice guidelines and so... Anyway, can I just do such a "mass submission" of my packages into science? Is there any special procedure? Any review? I suppose I'm then maintainer of the packages, but not of whole science repository...? There are still issues with some packages I don't know how to solve now: https://build.opensuse.org/package/show/home:vojtaeus/bamtools - I'm not sure if I'm correctly handling shared library and don't really get why it works for TW, but fails for 15.2 and 15.3... Similarly I fail with BEAGLE library (not in OBS), which should add extra support for MrBayes. https://build.opensuse.org/package/show/home:vojtaeus/bandage - I wonder if it fails for 15.2 due to "ERROR: No sufficient Category definition" and "Errors in installed desktop file detected.". Is this so different comparing to 15.3 and TW? Hint in build log doesn't really help me... :-/ I was also bit confused when looking into various Qt applications by diversity of usage of BuildRequires tags, but I hope I package it correctly... :-) https://build.opensuse.org/package/show/home:vojtaeus/bwa - I don't really get why it fails for i586 TW, but it's probably unimportant. ;-) https://build.opensuse.org/package/show/home:vojtaeus/seaview - I wonder if failures for 15.2 and 15.3 are due to errors in desktop file (which works for TW). Also, it is supposed to deliver HTML help file, which I think I package correctly (well, lines 48 and 49 of spec file can be probably dropped, the don't do what I was hoping for), but it fails to find it. Interestingly, when I packaged the RPM locally with this spec file, it can find the help, but not when I do it in OBS... I have also list of things in Java, Maven, bazel, and more which I'd like to add. Especially with thinks like IGV, GATK or Picard I don't really have any idea, how to compile it... We'll see :-) So can I just submit what I have into science, or am I supposed to undergo some sophisticated procedure? :-) Yours, V. -- Vojtěch Zeisek https://trapa.cz/ Komunita openSUSE GNU/Linuxu Community of the openSUSE GNU/Linux https://www.opensuse.org/

1 0

Re: [opensuse-science] openmpi3 pulled as dep
by Egbert Eich 22 Oct '20

22 Oct '20

Hi Nicolas! Nicolas Morey-Chaisemartin writes: > > > Le 10/22/20 à 10:57 AM, Egbert Eich a écrit : > > > > Hi Nicolas, > > > > Nicolas Morey-Chaisemartin writes: > > > > > > > > > Is this available or all MPI flavors? If so, we could just do a: > > BuildRequires: %{mpi}-macros-devel > > > > No it's only for openmpi* packages at the moment. Ok, if you can fix this for mpich and mvapich we can integrate this into more packages. I'd be easier if we were able to do things the same way for all MPI flavors. > > The define of %mpi should be avaiable to the build dependency > > script as it doesn't depend on other macro packages. > > If this is the case I will make adjustments when visiting packages > > again. > > > > > It'll provide the macros: > > > %setup_openmpi # (Load the orpper mpivars.sh) > > > %openmpi_requires # ( Add the right Requires:..... for the openmpi package) > > > %openmpi_devel_requires # same but for devel packages) > > > > > > Also for using the "default" version of openmpi (currently openmpi2), you can juste BuildRequires: openmpi-macros-devel. > > > It'll pull the macros from the default version so there is no need to specify which one and it can be changed more easily when we decide to go to openmpi 3 or 4 by default. > > > > Right. Ok, this should work as well - if 'openmpi' stands for > > 'openmpi-default' instead of 'openmpi1' it'd be fine. Right. > It does. That's the reason openmpi was renamed to openmpi1 > > We will > > build for openmpi2 twice then: once for 'default' and once for > > it explicitly and we don't build for openmpi1 at all. But maybe > > people don't care any more ... > > > > You probably don't need that. The default flavor is mostly for package which don't really care which one they use (stuff like boost and other core libs) but you need all of them to use the same one. > It was introduced as there was a huge mess of some libs building against openmpi1, some against openmpi2 so the stack wasn't working. > Package like lapack where the pick of flavor might matter should build against all, not necesseraly against the default one. Yes. I would think for many of the packages in science this is true. With multibuild this will be quite easy - one does not necessarily need all the HPC stuff with full environment module support. Thanks! Cheers, Egbert.-- To unsubscribe, e-mail: opensuse-science+unsubscribe(a)opensuse.org To contact the owner, e-mail: opensuse-science+owner(a)opensuse.org

1 0

2022

2021

2020

2019

2018

2017

openSUSE Science