Re: [opensuse-science] openmpi3 pulled as dep
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@opensuse.org To contact the owner, e-mail: opensuse-science+owner@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@opensuse.org To contact the owner, e-mail: opensuse-science+owner@opensuse.org
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 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. 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@opensuse.org To contact the owner, e-mail: opensuse-science+owner@opensuse.org
-- To unsubscribe, e-mail: opensuse-science+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse-science+owner@opensuse.org
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 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 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. 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@opensuse.org > To contact the owner, e-mail: opensuse-science+owner@opensuse.org
-- To unsubscribe, e-mail: opensuse-science+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse-science+owner@opensuse.org
Hi, sorry I am using tumbleweed. yes was my mistake in mixing things but that showed the problem. installing this libscalapack2-openmpi4 pulls the openmpi3 and not 4/ Not an issue for me since i use hpc but may be for others. Regards, Alin Without Questions there are no Answers! ______________________________________________________________________ Dr. Alin Marin ELENA http://alin.elena.space/ ______________________________________________________________________ On Wed, 21 Oct 2020 at 09:05, Nicolas Morey-Chaisemartin <nmoreychaisemartin@suse.com> wrote:
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 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
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.
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@opensuse.org To contact the owner, e-mail: opensuse-science+owner@opensuse.org
-- To unsubscribe, e-mail: opensuse-science+unsubscribe@opensuse.org To contact the owner, e-mail: opensuse-science+owner@opensuse.org
participants (3)
-
Alin Marin Elena -
Egbert Eich -
Nicolas Morey-Chaisemartin