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機能 #17

完了

HDF5 1.8.13をCentOS 6でRPM化

高橋 徹 さんがほぼ11年前に追加. ほぼ11年前に更新.

ステータス:
終了
優先度:
通常
担当者:
高橋 徹
カテゴリ:
-
対象バージョン:
-
開始日:
2014/08/09
期日:
進捗率:

100%

予定工数:

説明

http://www.hdfgroup.org/HDF5/
のHDF5ライブラリをCentOS 6用にRPM化する。

epelリポジトリにおいてhdf5-1.8.5が提供されているが、NetCDF 4.3.2が要求するバージョン1.8.8に満たず、netcdfのテストでエラーとなる項目があるため、最新版をRPM化する。

関連するチケット 1 (0件未完了 — 1件完了)

関連している 機能 #16: NetCDF 4.3.2をCentOS 6でRPM化終了高橋 徹2014/08/08

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 #1

高橋 徹 さんがほぼ11年前に更新

  • 関連している 機能 #16: NetCDF 4.3.2をCentOS 6でRPM化 を追加
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 #2

高橋 徹 さんがほぼ11年前に更新

  • ステータス を 新規 から 解決 に変更
  • 進捗率 を 0 から 80 に変更

HDF5のサイトを辿っていくと、なんとCentOS 6用のRPMが用意されていました。
http://www.hdfgroup.org/HDF5/release/rpms.html

~$ sudo rpm -Uvh hdf5-1.8.13-1.with.szip.encoder.el6.x86_64.rpm

準備中...                ########################################### [100%]
   1:hdf5                   ########################################### [100%]
Running /sbin/ldconfig
Update the following tools because they are now installed at a new directory
h5cc:
   current setting="/usr" 
   new     setting="/usr" 
h5fc:
   current setting="/usr" 
   new     setting="/usr" 
h5c++:
   current setting="/usr" 
   new     setting="/usr" 
Update h5cc ...
Update h5fc ...
Update h5c++ ...
Update h5cc ...
H5BLD_LDFLAGS=" " 
Update h5fc ...
H5BLD_LDFLAGS=" " 
Update h5c++ ...
H5BLD_LDFLAGS=" " 
~$

インストールされたファイル一覧

~$ rpm -ql hdf5
/usr/bin/gif2h5
/usr/bin/h52gif
/usr/bin/h5c++
/usr/bin/h5cc
/usr/bin/h5copy
/usr/bin/h5debug
/usr/bin/h5diff
/usr/bin/h5dump
/usr/bin/h5fc
/usr/bin/h5import
/usr/bin/h5jam
/usr/bin/h5ls
/usr/bin/h5mkgrp
/usr/bin/h5perf_serial
/usr/bin/h5redeploy
/usr/bin/h5repack
/usr/bin/h5repart
/usr/bin/h5stat
/usr/bin/h5unjam
/usr/include/H5ACpublic.h
/usr/include/H5AbstractDs.h
/usr/include/H5Apublic.h
/usr/include/H5ArrayType.h
/usr/include/H5AtomType.h
/usr/include/H5Attribute.h
/usr/include/H5Classes.h
/usr/include/H5CommonFG.h
/usr/include/H5CompType.h
/usr/include/H5Cpp.h
/usr/include/H5CppDoc.h
/usr/include/H5Cpublic.h
/usr/include/H5DOpublic.h
/usr/include/H5DSpublic.h
/usr/include/H5DataSet.h
/usr/include/H5DataSpace.h
/usr/include/H5DataType.h
/usr/include/H5DcreatProp.h
/usr/include/H5Dpublic.h
/usr/include/H5DxferProp.h
/usr/include/H5EnumType.h
/usr/include/H5Epubgen.h
/usr/include/H5Epublic.h
/usr/include/H5Exception.h
/usr/include/H5FDcore.h
/usr/include/H5FDdirect.h
/usr/include/H5FDfamily.h
/usr/include/H5FDlog.h
/usr/include/H5FDmpi.h
/usr/include/H5FDmpio.h
/usr/include/H5FDmulti.h
/usr/include/H5FDpublic.h
/usr/include/H5FDsec2.h
/usr/include/H5FDstdio.h
/usr/include/H5FaccProp.h
/usr/include/H5FcreatProp.h
/usr/include/H5File.h
/usr/include/H5FloatType.h
/usr/include/H5Fpublic.h
/usr/include/H5Gpublic.h
/usr/include/H5Group.h
/usr/include/H5IMpublic.h
/usr/include/H5IdComponent.h
/usr/include/H5Include.h
/usr/include/H5IntType.h
/usr/include/H5Ipublic.h
/usr/include/H5LTpublic.h
/usr/include/H5Library.h
/usr/include/H5Location.h
/usr/include/H5Lpublic.h
/usr/include/H5MMpublic.h
/usr/include/H5Object.h
/usr/include/H5Opublic.h
/usr/include/H5PLextern.h
/usr/include/H5PTpublic.h
/usr/include/H5PacketTable.h
/usr/include/H5Ppublic.h
/usr/include/H5PredType.h
/usr/include/H5PropList.h
/usr/include/H5Rpublic.h
/usr/include/H5Spublic.h
/usr/include/H5StrType.h
/usr/include/H5TBpublic.h
/usr/include/H5Tpublic.h
/usr/include/H5VarLenType.h
/usr/include/H5Zpublic.h
/usr/include/H5api_adpt.h
/usr/include/H5f90i.h
/usr/include/H5f90i_gen.h
/usr/include/H5overflow.h
/usr/include/H5pubconf.h
/usr/include/H5public.h
/usr/include/H5version.h
/usr/include/h5_dble_interface.mod
/usr/include/h5a.mod
/usr/include/h5a_provisional.mod
/usr/include/h5d.mod
/usr/include/h5d_provisional.mod
/usr/include/h5ds.mod
/usr/include/h5e.mod
/usr/include/h5e_provisional.mod
/usr/include/h5f.mod
/usr/include/h5f_provisional.mod
/usr/include/h5fortran_types.mod
/usr/include/h5g.mod
/usr/include/h5global.mod
/usr/include/h5i.mod
/usr/include/h5im.mod
/usr/include/h5l.mod
/usr/include/h5l_provisional.mod
/usr/include/h5lib.mod
/usr/include/h5lib_provisional.mod
/usr/include/h5lt.mod
/usr/include/h5o.mod
/usr/include/h5o_provisional.mod
/usr/include/h5p.mod
/usr/include/h5p_provisional.mod
/usr/include/h5r.mod
/usr/include/h5r_provisional.mod
/usr/include/h5s.mod
/usr/include/h5t.mod
/usr/include/h5t_provisional.mod
/usr/include/h5tb.mod
/usr/include/h5test_kind_sizeof_mod.mod
/usr/include/h5z.mod
/usr/include/hdf5.h
/usr/include/hdf5.mod
/usr/include/hdf5_hl.h
/usr/include/ricehdf.h
/usr/include/szip_adpt.h
/usr/include/szlib.h
/usr/lib64/libhdf5.a
/usr/lib64/libhdf5.la
/usr/lib64/libhdf5.settings
/usr/lib64/libhdf5.so
/usr/lib64/libhdf5.so.8
/usr/lib64/libhdf5.so.8.0.2
/usr/lib64/libhdf5_cpp.a
/usr/lib64/libhdf5_cpp.la
/usr/lib64/libhdf5_cpp.so
/usr/lib64/libhdf5_cpp.so.8
/usr/lib64/libhdf5_cpp.so.8.0.2
/usr/lib64/libhdf5_fortran.a
/usr/lib64/libhdf5_fortran.la
/usr/lib64/libhdf5_fortran.so
/usr/lib64/libhdf5_fortran.so.8
/usr/lib64/libhdf5_fortran.so.8.0.2
/usr/lib64/libhdf5_hl.a
/usr/lib64/libhdf5_hl.la
/usr/lib64/libhdf5_hl.so
/usr/lib64/libhdf5_hl.so.8
/usr/lib64/libhdf5_hl.so.8.0.2
/usr/lib64/libhdf5_hl_cpp.a
/usr/lib64/libhdf5_hl_cpp.la
/usr/lib64/libhdf5_hl_cpp.so
/usr/lib64/libhdf5_hl_cpp.so.8
/usr/lib64/libhdf5_hl_cpp.so.8.0.2
/usr/lib64/libhdf5hl_fortran.a
/usr/lib64/libhdf5hl_fortran.la
/usr/lib64/libhdf5hl_fortran.so
/usr/lib64/libhdf5hl_fortran.so.8
/usr/lib64/libhdf5hl_fortran.so.8.0.2
/usr/lib64/libsz.a
/usr/lib64/libsz.la
/usr/lib64/libsz.so
/usr/lib64/libsz.so.2
/usr/lib64/libsz.so.2.0.0
/usr/share/doc/hdf5-1.8.13
/usr/share/doc/hdf5-1.8.13/COPYING
/usr/share/doc/hdf5-1.8.13/RELEASE.txt
/usr/share/hdf5_examples
/usr/share/hdf5_examples/README
/usr/share/hdf5_examples/c++/chunks.cpp
/usr/share/hdf5_examples/c++/compound.cpp
/usr/share/hdf5_examples/c++/create.cpp
/usr/share/hdf5_examples/c++/extend_ds.cpp
/usr/share/hdf5_examples/c++/h5group.cpp
/usr/share/hdf5_examples/c++/h5tutr_cmprss.cpp
/usr/share/hdf5_examples/c++/h5tutr_crtatt.cpp
/usr/share/hdf5_examples/c++/h5tutr_crtdat.cpp
/usr/share/hdf5_examples/c++/h5tutr_crtgrp.cpp
/usr/share/hdf5_examples/c++/h5tutr_crtgrpar.cpp
/usr/share/hdf5_examples/c++/h5tutr_crtgrpd.cpp
/usr/share/hdf5_examples/c++/h5tutr_extend.cpp
/usr/share/hdf5_examples/c++/h5tutr_rdwt.cpp
/usr/share/hdf5_examples/c++/h5tutr_subset.cpp
/usr/share/hdf5_examples/c++/readdata.cpp
/usr/share/hdf5_examples/c++/run-c++-ex.sh
/usr/share/hdf5_examples/c++/writedata.cpp
/usr/share/hdf5_examples/c/h5_attribute.c
/usr/share/hdf5_examples/c/h5_chunk_read.c
/usr/share/hdf5_examples/c/h5_cmprss.c
/usr/share/hdf5_examples/c/h5_compound.c
/usr/share/hdf5_examples/c/h5_crtatt.c
/usr/share/hdf5_examples/c/h5_crtdat.c
/usr/share/hdf5_examples/c/h5_crtgrp.c
/usr/share/hdf5_examples/c/h5_crtgrpar.c
/usr/share/hdf5_examples/c/h5_crtgrpd.c
/usr/share/hdf5_examples/c/h5_drivers.c
/usr/share/hdf5_examples/c/h5_elink_unix2win.c
/usr/share/hdf5_examples/c/h5_extend.c
/usr/share/hdf5_examples/c/h5_extend_write.c
/usr/share/hdf5_examples/c/h5_extlink.c
/usr/share/hdf5_examples/c/h5_group.c
/usr/share/hdf5_examples/c/h5_mount.c
/usr/share/hdf5_examples/c/h5_rdwt.c
/usr/share/hdf5_examples/c/h5_read.c
/usr/share/hdf5_examples/c/h5_ref2reg.c
/usr/share/hdf5_examples/c/h5_reference.c
/usr/share/hdf5_examples/c/h5_select.c
/usr/share/hdf5_examples/c/h5_shared_mesg.c
/usr/share/hdf5_examples/c/h5_subset.c
/usr/share/hdf5_examples/c/h5_write.c
/usr/share/hdf5_examples/c/ph5example.c
/usr/share/hdf5_examples/c/run-c-ex.sh
/usr/share/hdf5_examples/fortran/compound.f90
/usr/share/hdf5_examples/fortran/h5_cmprss.f90
/usr/share/hdf5_examples/fortran/h5_crtatt.f90
/usr/share/hdf5_examples/fortran/h5_crtdat.f90
/usr/share/hdf5_examples/fortran/h5_crtgrp.f90
/usr/share/hdf5_examples/fortran/h5_crtgrpar.f90
/usr/share/hdf5_examples/fortran/h5_crtgrpd.f90
/usr/share/hdf5_examples/fortran/h5_extend.f90
/usr/share/hdf5_examples/fortran/h5_rdwt.f90
/usr/share/hdf5_examples/fortran/h5_subset.f90
/usr/share/hdf5_examples/fortran/hyperslab.f90
/usr/share/hdf5_examples/fortran/mountexample.f90
/usr/share/hdf5_examples/fortran/ph5example.f90
/usr/share/hdf5_examples/fortran/refobjexample.f90
/usr/share/hdf5_examples/fortran/refregexample.f90
/usr/share/hdf5_examples/fortran/run-fortran-ex.sh
/usr/share/hdf5_examples/fortran/selectele.f90
/usr/share/hdf5_examples/hl/c++/ptExampleFL.cpp
/usr/share/hdf5_examples/hl/c++/run-hlc++-ex.sh
/usr/share/hdf5_examples/hl/c/ex_ds1.c
/usr/share/hdf5_examples/hl/c/ex_image1.c
/usr/share/hdf5_examples/hl/c/ex_image2.c
/usr/share/hdf5_examples/hl/c/ex_lite1.c
/usr/share/hdf5_examples/hl/c/ex_lite2.c
/usr/share/hdf5_examples/hl/c/ex_lite3.c
/usr/share/hdf5_examples/hl/c/ex_table_01.c
/usr/share/hdf5_examples/hl/c/ex_table_02.c
/usr/share/hdf5_examples/hl/c/ex_table_03.c
/usr/share/hdf5_examples/hl/c/ex_table_04.c
/usr/share/hdf5_examples/hl/c/ex_table_05.c
/usr/share/hdf5_examples/hl/c/ex_table_06.c
/usr/share/hdf5_examples/hl/c/ex_table_07.c
/usr/share/hdf5_examples/hl/c/ex_table_08.c
/usr/share/hdf5_examples/hl/c/ex_table_09.c
/usr/share/hdf5_examples/hl/c/ex_table_10.c
/usr/share/hdf5_examples/hl/c/ex_table_11.c
/usr/share/hdf5_examples/hl/c/ex_table_12.c
/usr/share/hdf5_examples/hl/c/image24pixel.txt
/usr/share/hdf5_examples/hl/c/image8.txt
/usr/share/hdf5_examples/hl/c/pal_rgb.h
/usr/share/hdf5_examples/hl/c/ptExampleFL.c
/usr/share/hdf5_examples/hl/c/run-hlc-ex.sh
/usr/share/hdf5_examples/hl/fortran/ex_ds1.f90
/usr/share/hdf5_examples/hl/fortran/exlite.f90
/usr/share/hdf5_examples/hl/fortran/run-hlfortran-ex.sh
/usr/share/hdf5_examples/hl/run-hl-ex.sh
/usr/share/hdf5_examples/run-al

ということで、RPMを公式サイトから入手することができ、課題解決できてしまいました。

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 #3

高橋 徹 さんがほぼ11年前に更新

epelのhdf5-1.8.5.patch1-7との違い

次の違いがあるため、epelのhdf5-1.8.5に依存するパッケージがあると単純な差し替えは難しそうです。

epelのhdf5-1.8.5.patch1-7 hdf5-1.8.13-1
libhdf5.so.6 libhdf5.so.8
libhdf5_cpp.so.6 libhdf5_cpp.8
libhdf5_fortran.so.6 libhdf5_fortran.so.8
libhdf5_hl.so.6 libhdf5_hl.so.8
libhdf5_hl_cpp.so.6 libhdf5_hl_cpp.so.8
libhdf5_hl_fortran.so.6 libhdf5_hl_fortran.so.8

epelのlibhdf5に依存するパッケージは、sonameでlibhdf5.so.6までを参照します。
例）

$ ldd /usr/bin/gdal_grid | grep hdf5
        libhdf5.so.6 => /usr/lib64/libhdf5.so.6 (0x00007f68a8c0f000)
        libhdf5_hl.so.6 => /usr/lib64/libhdf5_hl.so.6 (0x00007f68a3346000)

そこで、hdf5-1.8.13のインストール先をデフォルトの/usrではなく、/opt/localに変更します。

$ sudo rpm -ivh --prefix=/opt/local hdf5-1.8.13-1.with.szip.encoder.el6.x86_64.rpm

途中警告が発生しました

Update h5cc ...
./h5redeploy: line 211: ed: コマンドが見つかりません

edコマンドを使うようですが、検証マシンにはedがインストールされてませんでした。

$ sudo yum install ed

これで、epelリポジトリのhdf5-1.8.5.patch1-7と、hdf5-1.8.13-1.with.szip.encoderとが共存できます。

$ rpm -qa|grep hdf5
hdf5-1.8.5.patch1-7.el6.x86_64
hdf5-static-1.8.5.patch1-7.el6.x86_64
hdf5-devel-1.8.5.patch1-7.el6.x86_64
hdf5-1.8.13-1.with.szip.encoder.el6.x86_64

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 #4

高橋 徹 さんがほぼ11年前に更新

  • ステータス を 解決 から 終了 に変更
  • 進捗率 を 80 から 100 に変更
操作
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