February 2018 - openSUSE Science - openSUSE Mailing Lists

Re: [opensuse-science] gnu-hpc packages
by Egbert Eich 31 Mar '18

31 Mar '18

Hi Peter, I did overlook your message as at the time you wrote it, I was extremely busy to get a release out. I need to apologize for the delay and that I'm only answering now. Peter Hill writes: > Hello, > > I just noticed the gnu-hpc packages in Tumbleweed recently, and I was > wondering if there is an explanation of how they work somewhere? I had > a look for some information or discussion, but I've not been able to > find anything so far. Right, I should probably have blogged about this - and I may still do. > > I gather they are linked somehow to environment modules, but it's not > clear to me how exactly. For instance, "petsc-devel" installs a module > for PETSc, but "hdf5-devel" does not install one for HDF5. Are there > certain packages we're supposed to install to get this functionality? This could have been a bug that has been fixed meanwhile. Let me get a very brief overview: The theory is that 1. the runtime library package installs a module. 2. the devel package pulls in the runtime library package and any other package that may be needed for building. 3. There are packages which have the version numbers in the package name. Other packages don't - these are the 'master packages' which will pull in the latest version of a package thru a dependency. This allows to have mutliple version of the same base code. 4. Environment modules are used to select toolchain flavor/version, MPI flavor/version and packages and versions. By default, the latest version of a package is loaded, however, you can specify a version explicitly if you need an older version. The modules enforce some dependencies between libraries, ie you will have to select a toolchain for most of the libraries and you need to select the MPI version for MPI dependent libraries. Without this, these libraries will not become available. 5. For environment modules we use Lmod: https://lmod.readthedocs.io/en/latest/ There is the 'module' command available to load/unload, list, switch the modules. To get a help, call 'module help', modules are loaded with 'module load <module_name>[/<version>]', to get a list of accessible modules, do 'module avail', to get a list of all modules, call'module spider'. > Also, are they supposed to play nice with pkg-config? petsc-devel does > install PETSc.pc, but loading the module doesn't update > $PKG_CONFIG_PATH to be able to find it. This is a bug as well, lemme check if it is still there ... The module file of the package I'm looking at right now has: prepend-path PKG_CONFIG_PATH /usr/lib/hpc/gnu7.2/openmpi3/petsc/3.7.6/lib64/pkgconfig Thus it should work. If you find any more issues, please let me know - or create a ticket on bugzilla.opensuse.org. Please add hpc-maintainer-bugs(a)forge.provo.novell.com as the assignee. Plan is to provide these packages with openSUSE Leap 42.3. This should give you a more stable (and enterprise grade!) environment than openSUSE Tumbleweed. 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] hdf5
by Egbert Eich 13 Feb '18

13 Feb '18

Alin Marin Elena writes: > Hi, > > i was looking today at hdf5 to use it. All nice for the parallel > version but then i noticed there is no hpc version for the serial > version. > > Would be nice to have one with compiler as dependency (fortran > interface will have a lot of .mod which are compiler depedent). Also > the serial version seems to miss a .pc The 'serial' version is there mostly for 'legacy' purposes: Other packages which require hdf5 may use it. For those packages .mod files are not really interesting as they usually do not use the fortran API. Since the hdf5 package does not create .pc files these are generated by special macros which are only available in the HPC build. Whoever maintains the non-HPC build is welcome to add a .pc file. However, bottom line: one should use the HPC version when building user software. There is a little overhead involved using modules, however this can easily be used to the users environment. 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] hdf5
by Egbert Eich 12 Feb '18

12 Feb '18

Alin Marin Elena writes: > Hi, > > i was looking today at hdf5 to use it. All nice for the parallel > version but then ir noticed there is no hpc version for the serial > version. There should be the following 'serial' packages (packages without an mpi flavor on the name should be 'serial'): hdf5-gnu-hpc-devel hdf5_1_10_1-gnu-hpc hdf5_1_10_1-gnu-hpc-devel hdf5_1_10_1-gnu-hpc-devel-static hdf5_1_10_1-gnu-hpc-module libhdf5-gnu-hpc libhdf5_1_10_1-gnu-hpc libhdf5_cpp-gnu-hpc libhdf5_cpp_1_10_1-gnu-hpc libhdf5_fortran-gnu-hpc libhdf5_fortran_1_10_1-gnu-hpc libhdf5_hl-gnu-hpc libhdf5_hl_1_10_1-gnu-hpc libhdf5_hl_cpp-gnu-hpc libhdf5_hl_cpp_1_10_1-gnu-hpc libhdf5_hl_fortran-gnu-hpc libhdf5hl_fortran_1_10_1-gnu-hpc > Would be nice to have one with compiler as dependency (fortran > interface will have a lot of .mod which are compiler depedent). Also > the serial version seems to miss a .pc Let me check this tomorrow. 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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[opensuse-science] hdf5
by Alin Marin Elena 12 Feb '18

12 Feb '18

Hi, i was looking today at hdf5 to use it. All nice for the parallel version but then i noticed there is no hpc version for the serial version. Would be nice to have one with compiler as dependency (fortran interface will have a lot of .mod which are compiler depedent). Also the serial version seems to miss a .pc 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

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Re: [opensuse-science] scalapack
by Egbert Eich 11 Feb '18

11 Feb '18

Alin Marin Elena writes: > Brilliant shall be one since usually using scalapack requires, as you > probably know > -lblacs -lscalapack -l[blas|openblas] -llapack I'm considering to add a 'Recommends:' connecting the two lib packages (and maybe also the devel packages). Cheers, Egbert. > > > Alin > Without Questions there are no Answers! > ______________________________________________________________________ > Dr. Alin Marin ELENA > http://alin.elena.space/ > ______________________________________________________________________ > > > On 10 February 2018 at 18:02, Egbert Eich <eich(a)suse.com> wrote: > > Alin Marin Elena writes: > > > Thanks Egbert! > > > > > > I do not know if 2 is actually fixed. it does not list blacs ( > > > libblacs2_2_0_2-gnu-openmpi3-hpc > > > ) as dependency and it should... > > > > It doesn't as there is no dependency between the > > two libraries. > > Of course I can add one manually. > > > > Cheers, > > Egbert. > > > > -- > > 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 > -- 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] scotch and superlu
by Egbert Eich 10 Feb '18

10 Feb '18

Hi Alin! Alin Marin Elena writes: > Any chance to get scotch and superlu hpc versions? > I see both are actively maintained. superlu is on our list, scotch not (yet). 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] scalapack
by Egbert Eich 10 Feb '18

10 Feb '18

Alin Marin Elena writes: > Thanks Egbert! > > I do not know if 2 is actually fixed. it does not list blacs ( > libblacs2_2_0_2-gnu-openmpi3-hpc > ) as dependency and it should... It doesn't as there is no dependency between the two libraries. Of course I can add one manually. 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] hpc phdf5
by Egbert Eich 10 Feb '18

10 Feb '18

Hi Alin! Alin Marin Elena writes: > Hi, > > phdf5 on science seems to have a broken module file seems paths for > libs are listed as lib instead of lib64 on a 64 bit insall... also > PKG_CONFIG is missing even if the packages has one. I've fixed the latter just a while ago, OBS is a bit slow today so my fixes may not be pubished, yet. The former is indeed wrong - I do know what is behind it and I've just fixed it in science. Thanks for pointing this out! Cheers, Egbert. > > ========= module show phdf5 > ------------------------------------------------------------------------------------------------------------------------------------------------------------------- > /usr/share/lmod/moduledeps/gnu-7-openmpi-3/phdf5/1.10.1: > ------------------------------------------------------------------------------------------------------------------------------------------------------------------- > whatis("Name: hdf5 built with gnu toolchain ") > whatis("Version: 1.10.1 ") > whatis("Category: runtime library ") > whatis("Description: Command-line programs for the HDF5 scientific > data format ") > whatis("http://www.hdfgroup.org/HDF5/ ") > prepend_path("PATH","/usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1/bin") > prepend_path("LD_LIBRARY_PATH","/usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1/lib") > setenv("HDF5_DIR","/usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1") > setenv("HDF5_BIN","/usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1/bin") > setenv("HDF5_LIB","/usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1/lib") > prepend_path("LIBRARY_PATH","/usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1/lib") > prepend_path("CPATH","/usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1/include") > prepend_path("C_INCLUDE_PATH","/usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1/include") > prepend_path("CPLUS_INCLUDE_PATH","/usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1/include") > prepend_path("INCLUDE","/usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1/include") > setenv("HDF5_INC","/usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1/include") > family("hdf5") > help([[ > This module loads the hdf5 library built with the gnu compiler toolchain. > > Version 1.10.1 > > ]]) > > ========ls /usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1/lib > ls: cannot access '/usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1/lib': No > such file or directory > ===== ls /usr/lib/hpc/gnu7/openmpi3/hdf5/1.10.1/lib64/ > libdynlib1.so libdynlibadd.so libdynlibvers.so > libhdf5hl_fortran.so libhdf5_hl.so.100 libhdf5.so.101 > libdynlib2.so libdynlibdiff.so libhdf5_fortran.so > libhdf5hl_fortran.so.100 libhdf5_hl.so.100.0.1 > libhdf5.so.101.0.0 > libdynlib3.so libdynlibdump.so libhdf5_fortran.so.100 > libhdf5hl_fortran.so.100.0.1 libhdf5.settings pkgconfig > libdynlib4.so libdynlibls.so libhdf5_fortran.so.100.1.0 libhdf5_hl.so > > 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 > -- 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] scalapack
by Egbert Eich 10 Feb '18

10 Feb '18

Hi Alin! Alin M Elena writes: > Dear All, > > I have noticed two things related to scalapack > > 1. has no PKG_CONFIG_PATH even if contains the right pkgconfig files Indeed! It should be fixed now. > 2. does not pull the right blacs package I found other issues with headers and the setting of LIBRAY_PATH. Not sure if you were referring to one of these. In any case, these are fixed now as well. It will take a while to show up in TW, the devel project 'science' has the lastest fixes already. Thanks for pointing these issues out! 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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[opensuse-science] scotch and superlu
by Alin Marin Elena 10 Feb '18

10 Feb '18

Any chance to get scotch and superlu hpc versions? I see both are actively maintained. 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

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