Why are you searching your miniconda environment for library files? All the HDF5 stuff from the Arch package gets installed in standard library locations.
On 7/23/19 9:47 PM, Weiguang Chen wrote: > Thanks for you fast response. > I have installed hdf5 by pacman -S hdf5 > (base) [zznu@archlinux ~]$ locate hdf5 > /home/zznu/.virtualenvs/aiida/lib/python3.7/site-packages/scipy/io/matlab/tests/data/testhdf5_7.4_GLNX86.mat > /home/zznu/magenta/lib/python2.7/site-packages/scipy/io/matlab/tests/data/testhdf5_7.4_GLNX86.mat > /home/zznu/magenta/tensorflow/tensorflow/tensorflow/examples/learn/hdf5_classification.py > /home/zznu/miniconda3/conda-meta/hdf5-1.10.4-hb1b8bf9_0.json > /home/zznu/miniconda3/include/hdf5.h > /home/zznu/miniconda3/include/hdf5.mod > /home/zznu/miniconda3/include/hdf5_hl.h > /home/zznu/miniconda3/include/vtk-8.2/vtk_hdf5.h > /home/zznu/miniconda3/lib/libhdf5.a > /home/zznu/miniconda3/lib/libhdf5.settings > /home/zznu/miniconda3/lib/libhdf5.so > /home/zznu/miniconda3/lib/libhdf5.so.103 > /home/zznu/miniconda3/lib/libhdf5.so.103.0.0 > /home/zznu/miniconda3/lib/libhdf5_cpp.a > /home/zznu/miniconda3/lib/libhdf5_cpp.so > /home/zznu/miniconda3/lib/libhdf5_cpp.so.103 > /home/zznu/miniconda3/lib/libhdf5_cpp.so.103.0.0 > /home/zznu/miniconda3/lib/libhdf5_fortran.a > /home/zznu/miniconda3/lib/libhdf5_fortran.so > /home/zznu/miniconda3/lib/libhdf5_fortran.so.100 > /home/zznu/miniconda3/lib/libhdf5_fortran.so.100.1.2 > /home/zznu/miniconda3/lib/libhdf5_hl.a > /home/zznu/miniconda3/lib/libhdf5_hl.so > /home/zznu/miniconda3/lib/libhdf5_hl.so.100 > /home/zznu/miniconda3/lib/libhdf5_hl.so.100.1.1 > /home/zznu/miniconda3/lib/libhdf5_hl_cpp.a > /home/zznu/miniconda3/lib/libhdf5_hl_cpp.so > /home/zznu/miniconda3/lib/libhdf5_hl_cpp.so.100 > /home/zznu/miniconda3/lib/libhdf5_hl_cpp.so.100.1.2 > /home/zznu/miniconda3/lib/libhdf5hl_fortran.a > /home/zznu/miniconda3/lib/libhdf5hl_fortran.so > /home/zznu/miniconda3/lib/libhdf5hl_fortran.so.100 > /home/zznu/miniconda3/lib/libhdf5hl_fortran.so.100.0.3 > /home/zznu/miniconda3/lib/cmake/vtk-8.2/Modules/vtkhdf5.cmake > /home/zznu/miniconda3/lib/python3.7/site-packages/scipy/io/matlab/tests/data/testhdf5_7.4_GLNX86.mat > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0.tar.bz2 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/gif2h5 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h52gif > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5c++ > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5cc > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5clear > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5copy > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5debug > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5diff > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5dump > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5fc > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5format_convert > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5import > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5jam > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5ls > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5mkgrp > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5perf_serial > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5redeploy > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5repack > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5repart > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5stat > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5unjam > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/bin/h5watch > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5ACpublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5AbstractDs.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Apublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5ArrayType.h > > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Epublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Exception.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5FDcore.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5FDdirect.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5FDfamily.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5FDlog.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5FDmpi.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5FDmpio.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5FDmulti.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5FDpublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5FDsec2.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5FDstdio.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5FaccProp.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5FcreatProp.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5File.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5FloatType.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Fpublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Gpublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Group.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5IMpublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5IdComponent.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Include.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5IntType.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Ipublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5LDpublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5LTpublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5LaccProp.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5LcreatProp.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Library.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Location.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Lpublic.h > > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Spublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5StrType.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5TBpublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Tpublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5VarLenType.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5Zpublic.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5api_adpt.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5f90i.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5f90i_gen.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5overflow.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5pubconf.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5public.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/H5version.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5_gen.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5a.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5d.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5ds.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5e.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5f.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5fortkit.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5fortran_types.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5g.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5global.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5i.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5im.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5l.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5lib.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5lt.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5lt_const.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5o.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/h5p.mod > > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/hdf5.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/hdf5_hl.h > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/tstds.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/tstds_tests.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/tstimage.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/tstimage_tests.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/tstlite.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/tstlite_tests.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/tsttable.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/include/tsttable_tests.mod > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/LICENSE.txt > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/about.json > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/files > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/git > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/has_prefix > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/hash_input.json > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/index.json > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/paths.json > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/repodata_record.json > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/run_exports.json > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/test > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/0001-ppc64le-uses-special-algorithm-for-long-double.patch > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/0002-long-double-conversion-tests-on-ppc64le.patch > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/README.md > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/TEST_FILES_LICENSE.md > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/bld.bat > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/build.sh > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/compound_fortran2003.f90 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/conda_build_config.yaml > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/h5_cmprss.c > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/h5_cmprss.f90 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/h5tutr_cmprss.cpp > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/meta.yaml > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/meta.yaml.template > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/osx_configure.patch > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/run_test.sh > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/test_Makefile.in.patch > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/recipe/yum_requirements.txt > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/test/compound_fortran2003.f90 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/test/h5_cmprss.c > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/test/h5_cmprss.f90 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/test/h5tutr_cmprss.cpp > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/test/run_test.sh > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/info/test/test_time_dependencies.json > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5.a > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5.settings > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5.so > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5.so.103 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5.so.103.0.0 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_cpp.a > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_cpp.so > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_cpp.so.103 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_cpp.so.103.0.0 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_fortran.a > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_fortran.so > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_fortran.so.100 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_fortran.so.100.1.2 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_hl.a > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_hl.so > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_hl.so.100 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_hl.so.100.1.1 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_hl_cpp.a > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_hl_cpp.so > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_hl_cpp.so.100 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5_hl_cpp.so.100.1.2 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5hl_fortran.a > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5hl_fortran.so > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5hl_fortran.so.100 > /home/zznu/miniconda3/pkgs/hdf5-1.10.4-hb1b8bf9_0/lib/libhdf5hl_fortran.so.100.0.3 > /home/zznu/miniconda3/pkgs/scipy-1.2.1-py37h7c811a0_0/lib/python3.7/site-packages/scipy/io/matlab/tests/data/testhdf5_7.4_GLNX86.mat > /home/zznu/miniconda3/pkgs/vtk-8.2.0-py37haa4764d_200/include/vtk-8.2/vtk_hdf5.h > /home/zznu/miniconda3/pkgs/vtk-8.2.0-py37haa4764d_200/lib/cmake/vtk-8.2/Modules/vtkhdf5.cmake > /usr/include/hdf5.h > /usr/include/hdf5.mod > /usr/include/hdf5_hl.h > /usr/lib/libhdf5.a > /usr/lib/libhdf5.settings > /usr/lib/libhdf5.so > /usr/lib/libhdf5.so.103 > /usr/lib/libhdf5.so.103.1.0 > /usr/lib/libhdf5_cpp.a > /usr/lib/libhdf5_cpp.so > /usr/lib/libhdf5_cpp.so.103 > /usr/lib/libhdf5_cpp.so.103.1.0 > /usr/lib/libhdf5_fortran.a > /usr/lib/libhdf5_fortran.so > /usr/lib/libhdf5_fortran.so.102 > /usr/lib/libhdf5_fortran.so.102.0.0 > /usr/lib/libhdf5_hl.a > /usr/lib/libhdf5_hl.so > /usr/lib/libhdf5_hl.so.100 > /usr/lib/libhdf5_hl.so.100.1.2 > /usr/lib/libhdf5_hl_cpp.a > /usr/lib/libhdf5_hl_cpp.so > /usr/lib/libhdf5_hl_cpp.so.100 > /usr/lib/libhdf5_hl_cpp.so.100.1.3 > /usr/lib/libhdf5_hl_fortran.a > /usr/lib/libhdf5_hl_fortran.so > /usr/lib/libhdf5hl_fortran.a > /usr/lib/libhdf5hl_fortran.so > /usr/lib/libhdf5hl_fortran.so.100 > /usr/lib/libhdf5hl_fortran.so.100.0.4 > /usr/lib/pkgconfig/hdf5-1.10.5.pc > /usr/lib/pkgconfig/hdf5_cpp-1.10.5.pc > /usr/lib/pkgconfig/hdf5_hl-1.10.5.pc > /usr/lib/pkgconfig/hdf5_hl_cpp-1.10.5.pc > /usr/share/doc/hdf5 > /usr/share/doc/hdf5/examples > /usr/share/doc/hdf5/examples/README > /usr/share/doc/hdf5/examples/c > /usr/share/doc/hdf5/examples/c++ > /usr/share/doc/hdf5/examples/fortran > /usr/share/doc/hdf5/examples/hl > /usr/share/doc/hdf5/examples/run-all-ex.sh > /usr/share/doc/hdf5/examples/c/h5_attribute.c > /usr/share/doc/hdf5/examples/c/h5_chunk_read.c > /usr/share/doc/hdf5/examples/c/h5_cmprss.c > /usr/share/doc/hdf5/examples/c/h5_compound.c > /usr/share/doc/hdf5/examples/c/h5_crtatt.c > /usr/share/doc/hdf5/examples/c/h5_crtdat.c > /usr/share/doc/hdf5/examples/c/h5_crtgrp.c > /usr/share/doc/hdf5/examples/c/h5_crtgrpar.c > /usr/share/doc/hdf5/examples/c/h5_crtgrpd.c > /usr/share/doc/hdf5/examples/c/h5_drivers.c > /usr/share/doc/hdf5/examples/c/h5_elink_unix2win.c > /usr/share/doc/hdf5/examples/c/h5_extend.c > /usr/share/doc/hdf5/examples/c/h5_extend_write.c > /usr/share/doc/hdf5/examples/c/h5_extlink.c > /usr/share/doc/hdf5/examples/c/h5_group.c > /usr/share/doc/hdf5/examples/c/h5_mount.c > /usr/share/doc/hdf5/examples/c/h5_rdwt.c > /usr/share/doc/hdf5/examples/c/h5_read.c > /usr/share/doc/hdf5/examples/c/h5_ref2reg.c > /usr/share/doc/hdf5/examples/c/h5_reference.c > /usr/share/doc/hdf5/examples/c/h5_select.c > /usr/share/doc/hdf5/examples/c/h5_shared_mesg.c > /usr/share/doc/hdf5/examples/c/h5_subset.c > /usr/share/doc/hdf5/examples/c/h5_vds-eiger.c > /usr/share/doc/hdf5/examples/c/h5_vds-exc.c > /usr/share/doc/hdf5/examples/c/h5_vds-exclim.c > /usr/share/doc/hdf5/examples/c/h5_vds-percival-unlim-maxmin.c > /usr/share/doc/hdf5/examples/c/h5_vds-percival-unlim.c > /usr/share/doc/hdf5/examples/c/h5_vds-percival.c > /usr/share/doc/hdf5/examples/c/h5_vds-simpleIO.c > /usr/share/doc/hdf5/examples/c/h5_vds.c > /usr/share/doc/hdf5/examples/c/h5_write.c > /usr/share/doc/hdf5/examples/c/ph5example.c > /usr/share/doc/hdf5/examples/c/run-c-ex.sh > /usr/share/doc/hdf5/examples/c++/chunks.cpp > /usr/share/doc/hdf5/examples/c++/compound.cpp > /usr/share/doc/hdf5/examples/c++/create.cpp > /usr/share/doc/hdf5/examples/c++/extend_ds.cpp > /usr/share/doc/hdf5/examples/c++/h5group.cpp > /usr/share/doc/hdf5/examples/c++/h5tutr_cmprss.cpp > /usr/share/doc/hdf5/examples/c++/h5tutr_crtatt.cpp > /usr/share/doc/hdf5/examples/c++/h5tutr_crtdat.cpp > /usr/share/doc/hdf5/examples/c++/h5tutr_crtgrp.cpp > /usr/share/doc/hdf5/examples/c++/h5tutr_crtgrpar.cpp > /usr/share/doc/hdf5/examples/c++/h5tutr_crtgrpd.cpp > /usr/share/doc/hdf5/examples/c++/h5tutr_extend.cpp > /usr/share/doc/hdf5/examples/c++/h5tutr_rdwt.cpp > /usr/share/doc/hdf5/examples/c++/h5tutr_subset.cpp > /usr/share/doc/hdf5/examples/c++/readdata.cpp > /usr/share/doc/hdf5/examples/c++/run-c++-ex.sh > /usr/share/doc/hdf5/examples/c++/writedata.cpp > /usr/share/doc/hdf5/examples/fortran/compound.f90 > /usr/share/doc/hdf5/examples/fortran/compound_complex_fortran2003.f90 > /usr/share/doc/hdf5/examples/fortran/compound_fortran2003.f90 > /usr/share/doc/hdf5/examples/fortran/h5_cmprss.f90 > /usr/share/doc/hdf5/examples/fortran/h5_crtatt.f90 > /usr/share/doc/hdf5/examples/fortran/h5_crtdat.f90 > /usr/share/doc/hdf5/examples/fortran/h5_crtgrp.f90 > /usr/share/doc/hdf5/examples/fortran/h5_crtgrpar.f90 > /usr/share/doc/hdf5/examples/fortran/h5_crtgrpd.f90 > /usr/share/doc/hdf5/examples/fortran/h5_extend.f90 > /usr/share/doc/hdf5/examples/fortran/h5_rdwt.f90 > /usr/share/doc/hdf5/examples/fortran/h5_subset.f90 > /usr/share/doc/hdf5/examples/fortran/hyperslab.f90 > /usr/share/doc/hdf5/examples/fortran/mountexample.f90 > /usr/share/doc/hdf5/examples/fortran/nested_derived_type.f90 > /usr/share/doc/hdf5/examples/fortran/ph5example.f90 > /usr/share/doc/hdf5/examples/fortran/refobjexample.f90 > /usr/share/doc/hdf5/examples/fortran/refregexample.f90 > /usr/share/doc/hdf5/examples/fortran/run-fortran-ex.sh > /usr/share/doc/hdf5/examples/fortran/rwdset_fortran2003.f90 > /usr/share/doc/hdf5/examples/fortran/selectele.f90 > /usr/share/doc/hdf5/examples/hl/c > /usr/share/doc/hdf5/examples/hl/c++ > /usr/share/doc/hdf5/examples/hl/fortran > /usr/share/doc/hdf5/examples/hl/run-hl-ex.sh > /usr/share/doc/hdf5/examples/hl/c/ex_ds1.c > /usr/share/doc/hdf5/examples/hl/c/ex_image1.c > /usr/share/doc/hdf5/examples/hl/c/ex_image2.c > /usr/share/doc/hdf5/examples/hl/c/ex_lite1.c > /usr/share/doc/hdf5/examples/hl/c/ex_lite2.c > /usr/share/doc/hdf5/examples/hl/c/ex_lite3.c > /usr/share/doc/hdf5/examples/hl/c/ex_table_01.c > /usr/share/doc/hdf5/examples/hl/c/ex_table_02.c > /usr/share/doc/hdf5/examples/hl/c/ex_table_03.c > /usr/share/doc/hdf5/examples/hl/c/ex_table_04.c > /usr/share/doc/hdf5/examples/hl/c/ex_table_05.c > /usr/share/doc/hdf5/examples/hl/c/ex_table_06.c > /usr/share/doc/hdf5/examples/hl/c/ex_table_07.c > /usr/share/doc/hdf5/examples/hl/c/ex_table_08.c > /usr/share/doc/hdf5/examples/hl/c/ex_table_09.c > /usr/share/doc/hdf5/examples/hl/c/ex_table_10.c > /usr/share/doc/hdf5/examples/hl/c/ex_table_11.c > /usr/share/doc/hdf5/examples/hl/c/ex_table_12.c > /usr/share/doc/hdf5/examples/hl/c/image24pixel.txt > /usr/share/doc/hdf5/examples/hl/c/image8.txt > /usr/share/doc/hdf5/examples/hl/c/pal_rgb.h > /usr/share/doc/hdf5/examples/hl/c/ptExampleFL.c > /usr/share/doc/hdf5/examples/hl/c/run-hlc-ex.sh > /usr/share/doc/hdf5/examples/hl/c++/ptExampleFL.cpp > /usr/share/doc/hdf5/examples/hl/c++/run-hlc++-ex.sh > /usr/share/doc/hdf5/examples/hl/fortran/ex_ds1.f90 > /usr/share/doc/hdf5/examples/hl/fortran/exlite.f90 > /usr/share/doc/hdf5/examples/hl/fortran/run-hlfortran-ex.sh > /usr/share/licenses/hdf5 > /usr/share/licenses/hdf5/COPYING > > I just reinstalled hdf5, but the error still exist. > > Philip Kovacs <pkde...@yahoo.com <mailto:pkde...@yahoo.com>> 于2019年7月 > 24日周三 上午9:21写道： > > Looks like you need to install hdf5, development headers and libraries. > > > On Tuesday, July 23, 2019, 08:52:06 PM EDT, Weiguang Chen > <chenweiguan...@gmail.com <mailto:chenweiguan...@gmail.com>> wrote: > > > > Hi, > > I’m installing slurm in my Archlinux Server. > > At the beginning, I used AUR helper yaourt to install it. > > yaourt -S slurm-llnl > > But an error occur while compiling sh5util, as follow: > > libtool: link: gcc -DNUMA_VERSION1_COMPATIBILITY -march=x86-64 > -mtune=generic -O2 -pipe -pthread -ggdb3 -Wall -g -O1 > -fno-strict-aliasing -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl > > ,-z -Wl,relro -Wl,-z -Wl,lazy -o .libs/sh5util sh5util.o > -Wl,-rpath=/usr/lib/slurm -Wl,--export-dynamic > -L/home/zznu/miniconda3/lib -L../../../../../src/api/.libs > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/api/.libs/libslurmfull.so > ../.libs/libhdf5_api.a -lm -ldl -lz -lpthread -lrt -lhdf5 -pthread > -Wl,-rpath -Wl,/usr/lib/slurm > > /usr/bin/ld: sh5util.o: in function `_extract_series_table': > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1079: > undefined reference to `H5PTopen' > > /usr/bin/ld: sh5util.o: in function `_extract_totals': > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:935: > undefined reference to `H5PTget_num_packets' > > /usr/bin/ld: > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:939: > undefined reference to `H5PTget_next' > > /usr/bin/ld: sh5util.o: in function `_extract_series_table': > > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1089: > undefined reference to `H5PTget_num_packets' > > /usr/bin/ld: > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1094: > undefined reference to `H5PTget_next' > > /usr/bin/ld: > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1125: > undefined reference to `H5PTclose' > > /usr/bin/ld: > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1126: > undefined reference to `H5PTclose' > > /usr/bin/ld: > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1116: > undefined reference to `H5PTclose' > > /usr/bin/ld: sh5util.o: in function `_extract_item_step': > > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1551: > undefined reference to `H5PTopen' > > /usr/bin/ld: > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1555: > undefined reference to `H5PTget_num_packets' /usr/bin/ld: > sh5util.o: in function `_item_analysis_uint': > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1275: > undefined reference to `H5PTget_next' /usr/bin/ld: sh5util.o: in > function `_extract_item_step': > > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1590: > undefined reference to `H5PTclose' /usr/bin/ld: > sh5util.o: in function `_item_analysis_double': > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1376: > undefined reference to `H5PTget_next' > > /usr/bin/ld: sh5util.o: in function `_extract_item_step': > > > /tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util/sh5util.c:1605: > undefined reference to `H5PTclose' collect2: error: ld returned 1 > exit status > > make[6]: *** [Makefile:572: sh5util] Error 1 make[6]: Leaving > directory > > '/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5/sh5util' > make[5]: *** [Makefile:722: all-recursive] Error 1 > make[5]: > Leaving directory > > '/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile/hdf5' > make[4]: *** [Makefile:521: all-recursive] Error 1 make[4]: Leaving > directory > > '/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins/acct_gather_profile' > make[3]: *** [Makefile:552: all-recursive] Error 1 > make[3]: Leaving directory > > '/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src/plugins' > make[2]: *** [Makefile:546: all-recursive] Error 1 make[2]: Leaving > directory > '/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1/src' > make[1]: *** > [Makefile:674: all-recursive] Error 1 make[1]: Leaving directory > '/tmp/yaourt-tmp-zznu/aur-slurm-llnl/src/slurm-slurm-19-05-0-1' > > Then, I directly download the source code from slurm official > website, ./configure & make. Same error occored. > > I don’t know what the problem is, how to fix it. > > Thanks. > > > -- > > ***************************************************************************** > * Chen, Weiguang, Ph.D > * Quantum Materials Research Center & > * College of Physics and Electronic Engineering > * No.6, Yingcai Road, Physics Building Rm#3511 > * Zhengzhou Normal University, Zhengzhou, 450044 Henan, China > * > * Tel: 86-13783677861; Fax: 86-371-65502273; > * Email: chenweiguan...@gmail.com > <mailto:chenweiguan...@gmail.com>; chenweiguan...@126.com > <mailto:chenweiguan...@126.com> > > **************************************************************************** > > > > > -- > ***************************************************************************** > * Chen, Weiguang, Ph.D > * Quantum Materials Research Center & > * College of Physics and Electronic Engineering > * No.6, Yingcai Road, Physics Building Rm#3511 > * Zhengzhou Normal University, Zhengzhou, 450044 Henan, China > * > * Tel: 86-13783677861; Fax: 86-371-65502273; > * Email: chenweiguan...@gmail.com <mailto:chenweiguan...@gmail.com>; > chenweiguan...@126.com <mailto:chenweiguan...@126.com> > **************************************************************************** > > > This message is from an external sender. Learn more about why this > matters. <https://ut.service-now.com/sp?id=kb_article&number=KB0011401> > >
