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
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/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> 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> 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; 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; chenweiguan...@126.com ****************************************************************************
