- openSUSE Science

[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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[opensuse-science] hpc phdf5
by Alin Marin Elena 10 Feb '18

10 Feb '18

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. ========= 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

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[opensuse-science] scalapack
by Alin M Elena 09 Feb '18

09 Feb '18

Dear All, I have noticed two things related to scalapack 1. has no PKG_CONFIG_PATH even if contains the right pkgconfig files 2. does not pull the right blacs package Regards, Alin -- Without Questions there are no Answers! _______________________________________________ Dr. Alin Marin ELENA http://alin.elena.space/ _______________________________________________

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[opensuse-science] pythonX-mpi4py
by Alin M Elena 03 Feb '18

03 Feb '18

Hi, I wonder if this shall be built against different flavours of mpi as per new recipe? I have also notice zypper wp mpi is a little bit out of date and incomplete. rpm -qR python3-mpi4py-2.0.0-32.8.x86_64 libc.so.6()(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.4)(64bit) libdl.so.2()(64bit) libdl.so.2(GLIBC_2.2.5)(64bit) libmpi.so.12()(64bit) libpthread.so.0()(64bit) libpython3.6m.so.1.0()(64bit) openmpi python(abi) = 3.6 rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(PayloadIsXz) <= 5.2-1 -- Without Questions there are no Answers! _______________________________________________ Dr. Alin Marin ELENA http://alin.elena.space/ _______________________________________________

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