- openSUSE Science

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)

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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

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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/

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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

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

22 Oct '20

Hi Nicolas, Nicolas Morey-Chaisemartin writes: > > > Le 10/21/20 à 9:58 AM, Nicolas Morey-Chaisemartin a écrit : > > > > > > Le 10/21/20 à 9:35 AM, Egbert Eich a écrit : > >> > >> Hi Alin, > >> > >> please specify what system you are using (Leap<version>, Tumbleweed ...). > >> It seems you are mixing HPC (openmpi4-gnu-hpc-devel) and non-HPC packages. > >> Moreover, there is no scalapack-openmpi4 (not even among the non-HPC > >> packages). > >> > >> There is a bit of a problem with MPI depenendencies with non-HPC packages. > >> It seems like both openmpi3 and 4 provide libmpi.so.40()(64bit). > >> @Nicolas - is this correct? > > > > Yes they do. > > But in theory, packages depending on a specific MPI version like this should > > require the right openmpi, not just the libmpi.so Yes, this is what we do for the HPC versions. We even strip these 'generic' library dependencies from the list using our own dependency generator. > > WHich lapack does not seem to be doing/ > > BuildRequires: %{mpi_flavor}%{?mpi_ext}-devel > > > > It's only a BuildRequires but a > > Requires: %{mpi_flavor}%{?mpi_ext}-libs is also needed. > > Scratch some of that (it works but there is a newer/better way) > openmpi* packages were cleaned up some time back. > What should be done for all openmpi (at least non hpc) dependant packages is: > BuildRequires: openmpi<N>-macros-devel Ok. Is this available or all MPI flavors? If so, we could just do a: BuildRequires: %{mpi}-macros-devel 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. 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 ... Thanks! Cheers, Egbert. > > Nicolas > > > > > > > Nicolas > > > >> > >> For the HPC variants this has been fixed. > >> If both openmpi3 and openmpi4 provide the libmpi.so.4 ABI, then you > >> will have to install openmpi4-libs explicitly, I'm afraid - or use > >> the HPC variant of scalapack. > >> > >> Cheers, > >> Egbert. > >> > >> Alin Marin Elena writes: > >> > Hi. > >> > > >> > I try to install openmpi4 but somehow openmpi3 is pulled see below. > >> > > >> > drFaustroll@circassia:~> sudo zypper in scalapack-openmpi4 > >> > openmpi4-gnu-hpc-devel > >> > Problem retrieving files from 'oneAPI'. > >> > Permission to access > >> > 'https://yum.repos.intel.com/oneapi/media.1/media' denied. > >> > Please see the above error message for a hint. > >> > Warning: Skipping repository 'oneAPI' because of the above error. > >> > Some of the repositories have not been refreshed because of an error. > >> > Loading repository data... > >> > Reading installed packages... > >> > 'scalapack-openmpi4' not found in package names. Trying capabilities. > >> > Resolving package dependencies... > >> > > >> > The following 31 NEW packages are going to be installed: > >> > gcc-c++ gnu-compilers-hpc gnu-compilers-hpc-devel infiniband-diags > >> > libfabric1 libibmad5 libibnetdisc5 libibumad3 libinfinipath4 > >> > libopenmpi_4_0_5-gnu-hpc > >> > libpsm2-2 libpsm_infinipath1 libscalapack2-openmpi4 libucm0 libucp0 > >> > libucs0 libuct0 lua53 lua53-luafilesystem lua53-luaposix lua53-luaterm > >> > lua-lmod > >> > mpi-selector openmpi3 openmpi3-libs openmpi_4_0_5-gnu-hpc > >> > openmpi_4_0_5-gnu-hpc-devel openmpi4-config openmpi4-gnu-hpc-devel > >> > rdma-core-devel rsocket > >> > > >> > The following recommended package was automatically selected: > >> > openmpi4-config > >> > > >> > 31 new packages to install. > >> > > >> > Without Questions there are no Answers! > >> > ______________________________________________________________________ > >> > Dr. Alin Marin ELENA > >> > http://alin.elena.space/ > >> > ______________________________________________________________________ > >> > -- > >> > To unsubscribe, e-mail: opensuse-science+unsubscribe(a)opensuse.org > >> > To contact the owner, e-mail: opensuse-science+owner(a)opensuse.org > >> -- Egbert Eich (Res. & Dev.) SUSE Labs - Project Manager HPC Tel: +49 911-740 53 0 https://www.suse.com ----------------------------------------------------------------------- SUSE Software Solutions Germany GmbH, Maxfeldstrasse 5, 90409 Nuernberg Geschaeftsfuehrer: Felix Imendoerffer (HRB 36809, AG Nürnberg) -- To unsubscribe, e-mail: opensuse-science+unsubscribe(a)opensuse.org To contact the owner, e-mail: opensuse-science+owner(a)opensuse.org

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Re: [opensuse-science] openmpi3 pulled as dep
by Egbert Eich 21 Oct '20

21 Oct '20

Hi Alin, please specify what system you are using (Leap<version>, Tumbleweed ...). It seems you are mixing HPC (openmpi4-gnu-hpc-devel) and non-HPC packages. Moreover, there is no scalapack-openmpi4 (not even among the non-HPC packages). There is a bit of a problem with MPI depenendencies with non-HPC packages. It seems like both openmpi3 and 4 provide libmpi.so.40()(64bit). @Nicolas - is this correct? For the HPC variants this has been fixed. If both openmpi3 and openmpi4 provide the libmpi.so.4 ABI, then you will have to install openmpi4-libs explicitly, I'm afraid - or use the HPC variant of scalapack. Cheers, Egbert. Alin Marin Elena writes: > Hi. > > I try to install openmpi4 but somehow openmpi3 is pulled see below. > > drFaustroll@circassia:~> sudo zypper in scalapack-openmpi4 > openmpi4-gnu-hpc-devel > Problem retrieving files from 'oneAPI'. > Permission to access > 'https://yum.repos.intel.com/oneapi/media.1/media' denied. > Please see the above error message for a hint. > Warning: Skipping repository 'oneAPI' because of the above error. > Some of the repositories have not been refreshed because of an error. > Loading repository data... > Reading installed packages... > 'scalapack-openmpi4' not found in package names. Trying capabilities. > Resolving package dependencies... > > The following 31 NEW packages are going to be installed: > gcc-c++ gnu-compilers-hpc gnu-compilers-hpc-devel infiniband-diags > libfabric1 libibmad5 libibnetdisc5 libibumad3 libinfinipath4 > libopenmpi_4_0_5-gnu-hpc > libpsm2-2 libpsm_infinipath1 libscalapack2-openmpi4 libucm0 libucp0 > libucs0 libuct0 lua53 lua53-luafilesystem lua53-luaposix lua53-luaterm > lua-lmod > mpi-selector openmpi3 openmpi3-libs openmpi_4_0_5-gnu-hpc > openmpi_4_0_5-gnu-hpc-devel openmpi4-config openmpi4-gnu-hpc-devel > rdma-core-devel rsocket > > The following recommended package was automatically selected: > openmpi4-config > > 31 new packages to install. > > Without Questions there are no Answers! > ______________________________________________________________________ > Dr. Alin Marin ELENA > http://alin.elena.space/ > ______________________________________________________________________ > -- > To unsubscribe, e-mail: opensuse-science+unsubscribe(a)opensuse.org > To contact the owner, e-mail: opensuse-science+owner(a)opensuse.org -- Egbert Eich (Res. & Dev.) SUSE Labs - Project Manager HPC Tel: +49 911-740 53 0 https://www.suse.com ----------------------------------------------------------------------- SUSE Software Solutions Germany GmbH, Maxfeldstrasse 5, 90409 Nuernberg Geschaeftsfuehrer: Felix Imendoerffer (HRB 36809, AG Nürnberg) -- To unsubscribe, e-mail: opensuse-science+unsubscribe(a)opensuse.org To contact the owner, e-mail: opensuse-science+owner(a)opensuse.org

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[opensuse-science] openmpi3 pulled as dep
by Alin Marin Elena 21 Oct '20

21 Oct '20

Hi. I try to install openmpi4 but somehow openmpi3 is pulled see below. drFaustroll@circassia:~> sudo zypper in scalapack-openmpi4 openmpi4-gnu-hpc-devel Problem retrieving files from 'oneAPI'. Permission to access 'https://yum.repos.intel.com/oneapi/media.1/media' denied. Please see the above error message for a hint. Warning: Skipping repository 'oneAPI' because of the above error. Some of the repositories have not been refreshed because of an error. Loading repository data... Reading installed packages... 'scalapack-openmpi4' not found in package names. Trying capabilities. Resolving package dependencies... The following 31 NEW packages are going to be installed: gcc-c++ gnu-compilers-hpc gnu-compilers-hpc-devel infiniband-diags libfabric1 libibmad5 libibnetdisc5 libibumad3 libinfinipath4 libopenmpi_4_0_5-gnu-hpc libpsm2-2 libpsm_infinipath1 libscalapack2-openmpi4 libucm0 libucp0 libucs0 libuct0 lua53 lua53-luafilesystem lua53-luaposix lua53-luaterm lua-lmod mpi-selector openmpi3 openmpi3-libs openmpi_4_0_5-gnu-hpc openmpi_4_0_5-gnu-hpc-devel openmpi4-config openmpi4-gnu-hpc-devel rdma-core-devel rsocket The following recommended package was automatically selected: openmpi4-config 31 new packages to install. Without Questions there are no Answers! ______________________________________________________________________ Dr. Alin Marin ELENA http://alin.elena.space/ ______________________________________________________________________ -- To unsubscribe, e-mail: opensuse-science+unsubscribe(a)opensuse.org To contact the owner, e-mail: opensuse-science+owner(a)opensuse.org

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[opensuse-science] Re: Change Leap/SLE Build Targets from *:GA to *:Update
by Egbert Eich 14 Sep '20

14 Sep '20

Adrian Schröter writes: > On Montag, 14. September 2020, 11:34:26 CEST Egbert Eich wrote: > > > > Hi! > > > > I would like to change the Leap and SLE build targets of project 'science' > > from *:GA to *:Update for Leap 15.0/SLE-15 and later versions/service packs. > > > > This allows packages to be based on new or fixed packages which have > > been updated after the release. > > > > Are there any objections to this? > > question is why this is needed at build time, since the packages in :Update > are supposed to be fully backward compatible at runtime at least. Apart from issues that we have discovered and fixed since. It doesn't happen often and should not happen but I remember cases - especially around building. > Are you sure you do not hide some other issue by that? Also, new packages are not available in :GA. Cheers, Egbert. > > -- > > Adrian Schroeter <adrian(a)suse.de> > Build Infrastructure Project Manager > > SUSE Software Solutions Germany GmbH, Maxfeldstr. 5, 90409 Nuernberg, Germany > (HRB 247165, AG München), Geschäftsführer: Felix Imendörffer > > > -- Egbert Eich (Res. & Dev.) SUSE Labs - Project Manager HPC Tel: +49 911-740 53 0 https://www.suse.com ----------------------------------------------------------------------- SUSE Software Solutions Germany GmbH, Maxfeldstrasse 5, 90409 Nuernberg Geschaeftsfuehrer: Felix Imendoerffer (HRB 36809, AG Nürnberg) -- To unsubscribe, e-mail: opensuse-science+unsubscribe(a)opensuse.org To contact the owner, e-mail: opensuse-science+owner(a)opensuse.org

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[opensuse-science] Change Leap/SLE Build Targets from *:GA to *:Update
by Egbert Eich 14 Sep '20

14 Sep '20

Hi! I would like to change the Leap and SLE build targets of project 'science' from *:GA to *:Update for Leap 15.0/SLE-15 and later versions/service packs. This allows packages to be based on new or fixed packages which have been updated after the release. Are there any objections to this? Cheers, Egbert. -- Egbert Eich (Res. & Dev.) SUSE Labs - Project Manager HPC Tel: +49 911-740 53 0 https://www.suse.com ----------------------------------------------------------------------- SUSE Software Solutions Germany GmbH, Maxfeldstrasse 5, 90409 Nuernberg Geschaeftsfuehrer: Felix Imendoerffer (HRB 36809, AG Nürnberg) -- To unsubscribe, e-mail: opensuse-science+unsubscribe(a)opensuse.org To contact the owner, e-mail: opensuse-science+owner(a)opensuse.org

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Re: [opensuse-science] openmpi 4
by Egbert Eich 20 Jul '20

20 Jul '20

Hi Alin, sorry, I was extremely busy - even over the weekend. So it took me a while. Alin Marin Elena writes: > Hi, > > I fail miserable for fftw3 > https://build.opensuse.org/package/show/home:ealin:branches:multimedia:libs… > for a reason seems to still use openmpi3... and I do not see the error. > > can anyone have a look and pinpoint the issue please? I've found typo in the spec file which was not at all related to your changes. If you don't mind I will fix this and add your patch to my changes. Thanks for pointing out this issue! Cheers, Egbert. > > > Alin > Without Questions there are no Answers! > ______________________________________________________________________ > Dr. Alin Marin ELENA > http://alin.elena.space/ > ______________________________________________________________________ > > On Tue, 23 Jun 2020 at 19:39, Egbert Eich <eich(a)suse.com> wrote: > > > > > > Hi Alin, > > > > Alin Marin Elena writes: > > > Hi, > > > > > > I see openmpi 4 is nicely in the science and hpc packages but nothing > > > else seems to be built against it. > > > > > > Is there any reason why we do not build against openmpi4? > > > > Well, mostly time, I'd guess - thing with higher priority. > > > > As sonn as I find time, I will do it - unless someone beats > > me to it ;) > > > > Cheers, > > Egbert. > > > > > > > > Regards, > > > Alin > > > > > > Without Questions there are no Answers! > > > ______________________________________________________________________ > > > Dr. Alin Marin ELENA > > > http://alin.elena.space/ > > > ______________________________________________________________________ > > > -- > > > To unsubscribe, e-mail: opensuse-science+unsubscribe(a)opensuse.org > > > To contact the owner, e-mail: opensuse-science+owner(a)opensuse.org > > > > -- > > Egbert Eich (Res. & Dev.) SUSE Labs - Project Manager HPC > > Tel: +49 911-740 53 0 https://www.suse.com > > ----------------------------------------------------------------------- > > SUSE Software Solutions Germany GmbH, Maxfeldstrasse 5, 90409 Nuernberg > > Geschaeftsfuehrer: Felix Imendoerffer > > (HRB 36809, AG Nürnberg) > > -- > > To unsubscribe, e-mail: opensuse-science+unsubscribe(a)opensuse.org > > To contact the owner, e-mail: opensuse-science+owner(a)opensuse.org > > > -- > To unsubscribe, e-mail: opensuse-science+unsubscribe(a)opensuse.org > To contact the owner, e-mail: opensuse-science+owner(a)opensuse.org -- Egbert Eich (Res. & Dev.) SUSE Labs - Project Manager HPC Tel: +49 911-740 53 0 https://www.suse.com ----------------------------------------------------------------------- SUSE Software Solutions Germany GmbH, Maxfeldstrasse 5, 90409 Nuernberg Geschaeftsfuehrer: Felix Imendoerffer (HRB 36809, AG Nürnberg) -- To unsubscribe, e-mail: opensuse-science+unsubscribe(a)opensuse.org To contact the owner, e-mail: opensuse-science+owner(a)opensuse.org

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