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Package Details: hdf5-openmpi-java 1.10.5-1

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Git Clone URL:	https://aur.archlinux.org/hdf5-openmpi-java.git (read-only)
Package Base:	hdf5-openmpi-java
Description:	General purpose library and file format for storing scientific data (openmpi version) (full version including its Java Native Interfaces)
Upstream URL:	https://portal.hdfgroup.org/display/support
Licenses:	custom
Conflicts:	hdf5, hdf5-java, hdf5-openmpi
Provides:	hdf5, hdf5-cpp-fortran, hdf5-fortran-openmpi, hdf5-java, hdf5-openmpi
Replaces:	hdf5-fortran-openmpi
Submitter:	eleftg
Maintainer:	eleftg
Last Packager:	eleftg
Votes:	3
Popularity:	0.260569
First Submitted:	2017-10-19 22:30
Last Updated:	2019-05-06 08:18

Dependencies (7)

bash (bash-devel-git, bash-devel-static-git)
libaec
openmpi (openmpi-git, openmpi-cuda)
cmake (cmake-git) (make)
gcc-fortran (gcc-fortran-multilib-x32, gcc-fortran-git, gcc-fortran-multilib-git) (make)
java-environment (jdk5, zulu-jdk, jdk9-openj9-bin, jdk7, tuxjdk, jdk7-openjdk-infinality, java-8-openjdk-shenandoah, jdk8-openjdk-infinality, java-gcj-compat, jdk10-openjdk-openj9-bin, jdk9, zulu-10-bin, jdk-devel, jdk10, jdk6, jdk-dcevm, jdk8-arm, jdk8-arm64, intellij-jdk, jdk8-openj9-bin, jdk-arm, zulu-11-bin, zulu-12-bin, jdk11-openj9-bin, jetbrains-jre, amazon-corretto-8, amazon-corretto-11, jdk8-openjdk-shenandoah, jdk7-j9-bin, jdk7r1-j9-bin, jdk12-openj9-bin, jdk8-openjdk-jetbrains, jdk8-j9-bin, graal-bin, jdk8, jdk11, java-openjdk-ea-bin, jdk, zulu-embedded-jdk11, jdk-adoptopenjdk, jdk11-adoptopenjdk, jdk-openjdk, jdk10-openjdk, jdk11-openjdk, jdk7-openjdk, jdk8-openjdk) (make)
time (time-git) (make)

Required by (173)

alpscore (requires hdf5)
alpscore-git (requires hdf5)
alpscore-openmpi (requires hdf5)
alpscore-openmpi-git (requires hdf5)
animeloop-cli (requires hdf5)
armadillo (requires hdf5) (optional)
avogadrolibs-git (requires hdf5)
caffe (requires hdf5)
caffe-cmake-git (requires hdf5)
caffe-cuda (requires hdf5)
caffe-cuda-git (requires hdf5)
caffe-dr-git (requires hdf5-cpp-fortran)
caffe-git (requires hdf5)
caffe-mnc-dr-git (requires hdf5-cpp-fortran)
caffe-opencl-git (requires hdf5)
caffe-ssd (requires hdf5)
caffe-ssd-cpu (requires hdf5)
casacore (requires hdf5) (optional)
casacore-git (requires hdf5) (optional)
cbflib (requires hdf5)
cdo (requires hdf5)
cdo (requires hdf5) (make)
code_saturne (requires hdf5-openmpi)
csound-git (requires hdf5)
csound-git (requires hdf5) (make)
csxcad-git (requires hdf5)
deal-ii (requires hdf5-openmpi) (optional)
deepdetect-git (requires hdf5)
dolfin (requires hdf5)
eman2 (requires hdf5)
espressomd-git (requires hdf5) (optional)
espressomd-git (requires hdf5-openmpi) (optional)
ess-epics (requires hdf5)
ethoscope-device (requires hdf5)
expressionmatrix2-git (requires hdf5)
flann (requires hdf5)
freefem (requires hdf5)
freefem-git (requires hdf5)
gdal-curl (requires hdf5)
gdal-filegdb (requires hdf5)
gdal-hdf4 (requires hdf5)
gdal1 (requires hdf5)
glnemo2 (requires hdf5-cpp-fortran)
gnudatalanguage (requires hdf5)
h5utils (requires hdf5)
h5utils-git (requires hdf5)
hdf-eos-common (requires hdf5)
hdf-eos2 (requires hdf5)
hdf-eos5 (requires hdf5)
hdf5-lz4-filter-git (requires hdf5)
hdfview (requires hdf5-java)
hdfview-git (requires hdf5-java)
highfive (requires hdf5)
howdy (requires hdf5)
hydrus (requires hdf5)
insight-toolkit (requires hdf5-cpp-fortran)
itk-git (requires hdf5-cpp-fortran)
jhdf5 (requires hdf5)
jitterdebugger-git (requires hdf5)
kallisto (requires hdf5)
kealib (requires hdf5-cpp-fortran)
kealib (requires hdf5-cpp-fortran) (make)
kst-git (requires hdf5)
lalcore (requires hdf5)
lalsuite-git (requires hdf5)
lib32-opencv (requires hdf5) (make)
libmatio-git (requires hdf5)
libmesh (requires hdf5)
libnexus (requires hdf5-cpp-fortran)
makerbot-desktop (requires hdf5)
mantid (requires hdf5)
mathgl (requires hdf5)
med (requires hdf5)
med-openmpi (requires hdf5-openmpi)
med3 (requires hdf5)
meep (requires hdf5)
meep-git (requires hdf5)
minc-toolkit-v2 (requires hdf5)
moose (requires hdf5)
moose (requires hdf5) (make)
mothur (requires hdf5) (make)
mpb (requires hdf5)
mpb-git (requires hdf5)
mxnet (requires hdf5)
mxnet-cuda (requires hdf5)
mxnet-mkl (requires hdf5)
ncbi-vdb (requires hdf5)
ncl (requires hdf5)
nixio (requires hdf5)
nixio-git (requires hdf5)
octave-hg (requires hdf5)
octave40 (requires hdf5)
opencv-cuda (requires hdf5) (make)
opencv-cuda (requires hdf5) (optional)
opencv-cuda-git (requires hdf5-cpp-fortran)
opencv-git (requires hdf5) (make)
opencv-git (requires hdf5) (optional)
opencv-java (requires hdf5) (make)
opencv-with-python2-support (requires hdf5) (make)
opencv-with-python2-support (requires hdf5) (optional)
opencv-with-python2-support-samples (requires hdf5) (make)
opencv-with-python2-support-samples (requires hdf5) (optional)
opencv3-opt (requires hdf5) (make)
opencv3-opt (requires hdf5) (optional)
opencv3-opt-samples (requires hdf5) (optional)
opencv3-opt-samples (requires hdf5) (make)
openems (requires hdf5)
openems-git (requires hdf5)
openems-project-git (requires hdf5)
openmodelica-dev-omc (requires hdf5-openmpi)
openmodelica-dev-omedit (requires hdf5-openmpi)
openmodelica-dev-omnotebook (requires hdf5-openmpi)
openmodelica-dev-omoptim (requires hdf5-openmpi)
openmodelica-dev-omplot (requires hdf5-openmpi)
openmodelica-dev-omshell (requires hdf5-openmpi)
openmodelica-dev-qwt (requires hdf5-openmpi)
openmodelica-git (requires hdf5-openmpi)
openmodelica-omc (requires hdf5-openmpi)
openmodelica-omedit (requires hdf5-openmpi)
openmodelica-omnotebook (requires hdf5-openmpi)
openmodelica-omplot (requires hdf5-openmpi)
openmodelica-omshell (requires hdf5-openmpi)
openmodelica-qwt (requires hdf5-openmpi)
oqapy (requires hdf5)
orfeo-toolbox (requires hdf5)
ossim (requires hdf5-cpp-fortran)
paraview-opt (requires hdf5)
perl-pdl-io-hdf5 (requires hdf5)
petsc (requires hdf5) (optional)
petsc-git (requires hdf5)
python-h5py-git (requires hdf5-openmpi)
python-h5py-git (requires hdf5-openmpi) (make)
python-pyspeckit (requires hdf5) (optional)
python-rsgislib (requires hdf5-cpp-fortran) (make)
python-rsgislib (requires hdf5-cpp-fortran)
python-stfio-git (requires hdf5)
python2-h5py-git (requires hdf5-openmpi)
python2-h5py-git (requires hdf5-openmpi) (make)
python2-pynio (requires hdf5)
python2-pyspeckit (requires hdf5) (optional)
python2-rsgislib (requires hdf5-cpp-fortran)
python2-rsgislib (requires hdf5-cpp-fortran) (make)
qgis-crayfish-plugin (requires hdf5)
qgis2-crayfish-plugin (requires hdf5)
ros-melodic-opencv3 (requires hdf5) (make)
sagecal (requires hdf5) (optional)
sagecal-git (requires hdf5) (optional)
sagecal-gpu (requires hdf5) (optional)
scilab (requires hdf5)
scilab-git (requires hdf5)
sdaps-git (requires hdf5) (check)
sdaps-git (requires hdf5) (optional)
shogun (requires hdf5)
silo (requires hdf5)
slurm-llnl (requires hdf5) (optional)
slurm-llnl-dev (requires hdf5) (optional)
slurm-llnl-git (requires hdf5) (optional)
sra-tools (requires hdf5)
su2 (requires hdf5-openmpi) (make)
swarm (requires hdf5)
torch7-hdf5-git (requires hdf5-cpp-fortran) (make)
trilinos (requires hdf5-openmpi)
trinnity-caffe-cuda-git (requires hdf5)
trinnity-caffe-cudnn-git (requires hdf5)
trinnity-caffe-git (requires hdf5)
underworld2-git (requires hdf5-openmpi)
usgs-phast (requires hdf5)
vapoursynth-plugin-waifu2x-caffe-git (requires hdf5)
vigra-git (requires hdf5)
visit (requires hdf5)
vtk-git (requires hdf5)
xdmf-git (requires hdf5)
xmds (requires hdf5)

Sources (2)

Latest Comments

MartinDiehl commented on 2019-04-12 21:52

The patch for MPI 4 compatibility is not needed anymore. Please find an updated PKGBUILD for hdf5 1.10.5 on https://webshare.mpie.de/index.php?7e84df3a19

eleftg commented on 2019-02-19 22:57

@MartinDiehl: Thanks a lot for bringing this to my attention!

MartinDiehl commented on 2019-02-15 20:21

there is a new patch for MPI 4 compatibility

https://dbkt.hdfgroup.org/original/1X/2e17280ce6a1ede727c75e865c2e2af351f09696.diff

The modifications I used for this package are here https://webshare.mpie.de/index.php?685bdc8a61

greyltc commented on 2019-02-03 18:00

Please add hdf5-java to provides and conflicts.

eleftg commented on 2018-10-09 16:52

Now fixed. Thanks petronny

petronny commented on 2018-10-09 07:09

The Open MPI wrapper compiler was unable to find the specified compiler
/usr/bin/gfortran in your PATH.

Please add gcc-fortran to makedepends.

MartinDiehl commented on 2018-09-23 07:00

FYI, I have reported this already upstream: If HDF5 is build with cmake, the high level library for Fortran is called libhdf5_hl_fortran while it is called libhdf5hl_fortran when using configure. Also, the fortran module files are places in /usr/include/shared and /usr/include/static in the former case but in /usr/include in the latter.

Therefore, hdf5-openmpi-java does not fully replaces hdf5-openmpi at the moment. Would it be possible to use a similar, cmake based PKGBUILD as in hdf5-openmpi in hdf5-openmpi-java?

eleftg commented on 2018-06-18 22:19

Fixed. Thanks again

petronny commented on 2018-06-16 17:55

I get

../../java/src/hdf/overview.html:9: error: self-closing element not allowed
<p />There are a large number of functions in the HDF5
^
../../java/src/hdf/overview.html:14: error: unknown attribute: COLS
<center><table BORDER=1 COLS=1 WIDTH="71%" BGCOLOR="#dbeaf5" >
                        ^
../../java/src/hdf/overview.html:14: warning: attribute obsolete, use CSS instead: BGCOLOR
<center><table BORDER=1 COLS=1 WIDTH="71%" BGCOLOR="#dbeaf5" >
                                           ^
../../java/src/hdf/overview.html:20: error: no summary or caption for table
</table></center>
^                                                                                                                                                                                                                                                                              Generating javadoc/help-doc.html...
[done in 3789 ms]

like hdf4-java. You may need to set JAVADOC='javadoc -Xdoclint:none' too.

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