hdf5 install error at install-binSCRIPTS step


#1

Hello,

I’m attempting to install parallel enabled hdf5. This is on Ubuntu 20.04 with the openmpi 4.0.3-0ubuntu1 (installed via apt). Everything appears to configure and pass make check, but make install is failing here:

Making install in src
make[1]: Entering directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/src'
make[2]: Entering directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/src'
 /bin/mkdir -p '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/lib'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libhdf5.la '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/lib'
libtool: install: /usr/bin/install -c .libs/libhdf5.so.200.1.0 /home/glemieux/local/hdf5/hdf5-1.12.1-parallel/lib/libhdf5.so.200.1.0
libtool: install: (cd /home/glemieux/local/hdf5/hdf5-1.12.1-parallel/lib && { ln -s -f libhdf5.so.200.1.0 libhdf5.so.200 || { rm -f libhdf5.so.200 && ln -s libhdf5.so.200.1.0 libhdf5.so.200; }; })
libtool: install: (cd /home/glemieux/local/hdf5/hdf5-1.12.1-parallel/lib && { ln -s -f libhdf5.so.200.1.0 libhdf5.so || { rm -f libhdf5.so && ln -s libhdf5.so.200.1.0 libhdf5.so; }; })
libtool: install: /usr/bin/install -c .libs/libhdf5.lai /home/glemieux/local/hdf5/hdf5-1.12.1-parallel/lib/libhdf5.la
libtool: install: /usr/bin/install -c .libs/libhdf5.a /home/glemieux/local/hdf5/hdf5-1.12.1-parallel/lib/libhdf5.a
libtool: install: chmod 644 /home/glemieux/local/hdf5/hdf5-1.12.1-parallel/lib/libhdf5.a
libtool: install: ranlib /home/glemieux/local/hdf5/hdf5-1.12.1-parallel/lib/libhdf5.a
libtool: finish: PATH="/home/glemieux/.local/bin:/home/glemieux/local/gems/bin:/home/glemieux/local/conda/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/glemieux/local/cmake-3.21.5-linux-x86_64/bin:/home/glemieux/.local/bin:/home/glemieux/local/pandoc/pandoc-2.7.3/bin:/home/glemieux/local/arm/forge//bin:/sbin" ldconfig -n /home/glemieux/local/hdf5/hdf5-1.12.1-parallel/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/glemieux/local/hdf5/hdf5-1.12.1-parallel/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /bin/mkdir -p '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/include'
 /usr/bin/install -c -m 644 ../../src/hdf5-1.12.1/src/hdf5.h ../../src/hdf5-1.12.1/src/H5api_adpt.h ../../src/hdf5-1.12.1/src/H5overflow.h H5pubconf.h ../../src/hdf5-1.12.1/src/H5public.h ../../src/hdf5-1.12.1/src/H5version.h ../../src/hdf5-1.12.1/src/H5Apublic.h ../../src/hdf5-1.12.1/src/H5ACpublic.h ../../src/hdf5-1.12.1/src/H5Cpublic.h ../../src/hdf5-1.12.1/src/H5Dpublic.h ../../src/hdf5-1.12.1/src/H5Epubgen.h ../../src/hdf5-1.12.1/src/H5Epublic.h ../../src/hdf5-1.12.1/src/H5ESpublic.h ../../src/hdf5-1.12.1/src/H5Fpublic.h ../../src/hdf5-1.12.1/src/H5FDpublic.h ../../src/hdf5-1.12.1/src/H5FDcore.h ../../src/hdf5-1.12.1/src/H5FDdirect.h ../../src/hdf5-1.12.1/src/H5FDfamily.h ../../src/hdf5-1.12.1/src/H5FDhdfs.h ../../src/hdf5-1.12.1/src/H5FDlog.h ../../src/hdf5-1.12.1/src/H5FDmirror.h ../../src/hdf5-1.12.1/src/H5FDmpi.h ../../src/hdf5-1.12.1/src/H5FDmpio.h ../../src/hdf5-1.12.1/src/H5FDmulti.h ../../src/hdf5-1.12.1/src/H5FDros3.h ../../src/hdf5-1.12.1/src/H5FDsec2.h ../../src/hdf5-1.12.1/src/H5FDsplitter.h ../../src/hdf5-1.12.1/src/H5FDstdio.h ../../src/hdf5-1.12.1/src/H5FDwindows.h ../../src/hdf5-1.12.1/src/H5Gpublic.h ../../src/hdf5-1.12.1/src/H5Ipublic.h ../../src/hdf5-1.12.1/src/H5Lpublic.h ../../src/hdf5-1.12.1/src/H5Mpublic.h ../../src/hdf5-1.12.1/src/H5MMpublic.h ../../src/hdf5-1.12.1/src/H5Opublic.h ../../src/hdf5-1.12.1/src/H5Ppublic.h ../../src/hdf5-1.12.1/src/H5PLextern.h ../../src/hdf5-1.12.1/src/H5PLpublic.h ../../src/hdf5-1.12.1/src/H5Rpublic.h ../../src/hdf5-1.12.1/src/H5Spublic.h '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/include'
 /usr/bin/install -c -m 644 ../../src/hdf5-1.12.1/src/H5Tpublic.h ../../src/hdf5-1.12.1/src/H5VLconnector.h ../../src/hdf5-1.12.1/src/H5VLconnector_passthru.h ../../src/hdf5-1.12.1/src/H5VLnative.h ../../src/hdf5-1.12.1/src/H5VLpassthru.h ../../src/hdf5-1.12.1/src/H5VLpublic.h ../../src/hdf5-1.12.1/src/H5Zpublic.h '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/include'
 /bin/mkdir -p '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/lib'
 /usr/bin/install -c -m 644 libhdf5.settings '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/lib'
make[2]: Leaving directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/src'
make[1]: Leaving directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/src'
Making install in test
make[1]: Entering directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/test'
make[2]: Entering directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/test'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/test'
make[1]: Leaving directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/test'
Making install in testpar
make[1]: Entering directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/testpar'
make[2]: Entering directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/testpar'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/testpar'
make[1]: Leaving directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/testpar'
Making install in bin
make[1]: Entering directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/bin'
make[2]: Entering directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/bin'
 /bin/mkdir -p '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/bin'
 /usr/bin/install -c h5redeploy '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/bin'
/usr/bin/install: 'h5redeploy' and '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/bin/h5redeploy' are the same file
make[2]: *** [Makefile:815: install-binSCRIPTS] Error 1
make[2]: Leaving directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/bin'
make[1]: *** [Makefile:1050: install-am] Error 2
make[1]: Leaving directory '/home/glemieux/local/hdf5/hdf5-1.12.1-parallel/bin'
make: *** [Makefile:715: install-recursive] Error 1

Has anyone seen something like this before? I can provide the config.log is desired.

Thanks.