* Package: sci-libs/h5part-1.6.6  * Repository: gentoo  * Maintainer: junghans@gentoo.org sci@gentoo.org  * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU  * FEATURES: preserve-libs sandbox splitdebug test userpriv usersandbox  * Package: sci-libs/h5part-1.6.6  * Repository: gentoo  * Maintainer: junghans@gentoo.org sci@gentoo.org  * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU  * FEATURES: preserve-libs sandbox splitdebug test userpriv usersandbox >>> Unpacking source... >>> Unpacking H5Part-1.6.6.tar.gz to /var/tmp/portage/sci-libs/h5part-1.6.6/work >>> Source unpacked in /var/tmp/portage/sci-libs/h5part-1.6.6/work >>> Preparing source in /var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6 ... * Applying h5part-1.6.6-mpio.patch ...  [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6 ... * econf: updating H5Part-1.6.6/config.guess with /usr/share/gnuconfig/config.guess * econf: updating H5Part-1.6.6/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --docdir=/usr/share/doc/h5part-1.6.6 --htmldir=/usr/share/doc/h5part-1.6.6/html --libdir=/usr/lib64 --enable-parallel --enable-shared --disable-static CC=mpicc CXX=mpicxx checking for a BSD-compatible install... /usr/lib/portage/python3.10/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking whether make sets $(MAKE)... (cached) yes checking for x86_64-pc-linux-gnu-mpicc... mpicc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether mpicc accepts -g... yes checking for mpicc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of mpicc... none checking whether we are using the GNU C++ compiler... yes checking whether mpicxx accepts -g... yes checking dependency style of mpicxx... none checking for a BSD-compatible install... /usr/lib/portage/python3.10/ebuild-helpers/xattr/install -c checking for gawk... (cached) gawk checking if debug is enabled... no checking if fortran interface enabled... no checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by mpicc... /usr/x86_64-pc-linux-gnu/bin/ld checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump checking how to recognize dependent libraries... pass_all checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking command to parse /usr/bin/nm -B output from mpicc object... ok checking how to run the C preprocessor... mpicc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if mpicc supports -fno-rtti -fno-exceptions... no checking for mpicc option to produce PIC... -fPIC -DPIC checking if mpicc PIC flag -fPIC -DPIC works... yes checking if mpicc static flag -static works... no checking if mpicc supports -c -o file.o... yes checking if mpicc supports -c -o file.o... (cached) yes checking whether the mpicc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... mpicxx -E checking for ld used by mpicxx... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the mpicxx linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking for mpicxx option to produce PIC... -fPIC -DPIC checking if mpicxx PIC flag -fPIC -DPIC works... yes checking if mpicxx static flag -static works... no checking if mpicxx supports -c -o file.o... yes checking if mpicxx supports -c -o file.o... (cached) yes checking whether the mpicxx linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if parallel interface enabled... yes checking if we can compile MPI code without setting flags... yes checking whether tools are enabled... no checking for HDF5 root ... checking looking in /usr ... ... found checking if we need to link to libsz ... no checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for int64_t... yes checking for size_t... yes checking for ssize_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for memset... yes checking for pow... yes checking for strchr... yes checking for strdup... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating doc/Makefile config.status: creating test/Makefile config.status: creating tools/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands Summary: Host OS: linux-gnu Host CPU: x86_64 Host vendor: pc Build libraries: libH5Part Build test programs: test Build tools: CC = mpicc CXX = mpicxx FC = CFLAGS = -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK CXXFLAGS = -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK FFLAGS = -O2 -pipe -ggdb -g -DPARALLEL_IO INCLUDES = -I/usr/include LDFLAGS = -Wl,-O1 -Wl,--as-needed -L/usr/lib LIBS = -lhdf5 -lz -lm HDF5ROOT = /usr >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6 ... make -j16 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6' Making all in doc make[2]: Entering directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/doc' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/doc' Making all in src make[2]: Entering directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/src' /bin/sh ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c -o H5Part.lo H5Part.c /bin/sh ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c -o H5PartAttrib.lo H5PartAttrib.c /bin/sh ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c -o H5Block.lo H5Block.c /bin/sh ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c -o H5BlockReadWrite.lo H5BlockReadWrite.c /bin/sh ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c -o H5MultiBlock.lo H5MultiBlock.c /bin/sh ../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c -o H5MultiBlockReadWrite.lo H5MultiBlockReadWrite.c libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c H5Part.c -fPIC -DPIC -o .libs/H5Part.o libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c H5Block.c -fPIC -DPIC -o .libs/H5Block.o libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c H5BlockReadWrite.c -fPIC -DPIC -o .libs/H5BlockReadWrite.o libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c H5MultiBlock.c -fPIC -DPIC -o .libs/H5MultiBlock.o libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c H5PartAttrib.c -fPIC -DPIC -o .libs/H5PartAttrib.o libtool: compile: mpicc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c H5MultiBlockReadWrite.c -fPIC -DPIC -o .libs/H5MultiBlockReadWrite.o /bin/sh ../libtool --tag=CC --mode=link mpicc -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -version-info 0:0:0 -Wl,-O1 -Wl,--as-needed -L/usr/lib -o libH5Part.la -rpath /usr/lib64 H5Part.lo H5PartAttrib.lo H5Block.lo H5BlockReadWrite.lo H5MultiBlock.lo H5MultiBlockReadWrite.lo -lhdf5 -lz -lm libtool: link: mpicc -shared .libs/H5Part.o .libs/H5PartAttrib.o .libs/H5Block.o .libs/H5BlockReadWrite.o .libs/H5MultiBlock.o .libs/H5MultiBlockReadWrite.o -L/usr/lib -lhdf5 -lz -lm -Wl,-O1 -Wl,--as-needed -Wl,-soname -Wl,libH5Part.so.0 -o .libs/libH5Part.so.0.0.0 /usr/lib/gcc/x86_64-pc-linux-gnu/11.2.1/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm /usr/lib/gcc/x86_64-pc-linux-gnu/11.2.1/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm /usr/lib/gcc/x86_64-pc-linux-gnu/11.2.1/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/lib/gcc/x86_64-pc-linux-gnu/11.2.1/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc libtool: link: (cd ".libs" && rm -f "libH5Part.so.0" && ln -s "libH5Part.so.0.0.0" "libH5Part.so.0") libtool: link: (cd ".libs" && rm -f "libH5Part.so" && ln -s "libH5Part.so.0.0.0" "libH5Part.so") libtool: link: ( cd ".libs" && rm -f "libH5Part.la" && ln -s "../libH5Part.la" "libH5Part.la" ) make[2]: Leaving directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/src' Making all in test make[2]: Entering directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/test' mpicc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c test.c mpicc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c testframe.c mpicc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c write.c mpicc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -c read.c /bin/sh ../libtool --tag=CC --mode=link mpicc -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wl,-O1 -Wl,--as-needed -L/usr/lib -o test test.o testframe.o write.o read.o ../src/libH5Part.la -lhdf5 -lz -lm libtool: link: mpicc -O2 -pipe -ggdb -g -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK -Wl,-O1 -Wl,--as-needed -o .libs/test test.o testframe.o write.o read.o -L/usr/lib ../src/.libs/libH5Part.so -lhdf5 -lz -lm /usr/lib/gcc/x86_64-pc-linux-gnu/11.2.1/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm /usr/lib/gcc/x86_64-pc-linux-gnu/11.2.1/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm /usr/lib/gcc/x86_64-pc-linux-gnu/11.2.1/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/lib/gcc/x86_64-pc-linux-gnu/11.2.1/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc make[2]: Leaving directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/test' Making all in tools make[2]: Entering directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/tools' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/tools' make[2]: Entering directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6' make[2]: Leaving directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6' make[1]: Leaving directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6' >>> Source compiled. >>> Test phase: sci-libs/h5part-1.6.6 make -j16 check Making check in doc make[1]: Entering directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/doc' make[1]: Nothing to be done for 'check'. make[1]: Leaving directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/doc' Making check in src make[1]: Entering directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/src' make[1]: Nothing to be done for 'check'. make[1]: Leaving directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/src' Making check in test make[1]: Entering directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/test' make check-TESTS make[2]: Entering directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/test' For help use: /var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/test/.libs/test -help Linked with hdf5 version 1.10 release 5 Linked with H5Part version 1.6.6 [0] Testing -- Write 32-bit data (write1) [0] =============================================== [0] Opening file once, write-truncate [0] Setting throttle [0] Writing 32-bit data [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing file attributes [0] =============================================== [0] There were 0 errors detected. [0] Testing -- Read 32-bit data (read1) [0] =============================================== [0] Opening file once, read-only [0] Reading file attributes [0] Reading 32-bit data [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] =============================================== [0] There were 0 errors detected. [0] Testing -- Write 32-bit strided data (write2) [0] =============================================== [0] Opening file twice, write-append + read-only [0] Writing 32-bit strided data [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing step attributes [0] Writing file attributes [0] =============================================== [0] There were 0 errors detected. [0] Testing -- Read 32-bit strided data (read2) [0] =============================================== [0] Opening file twice, read-only [0] Reading 32-bit strided data [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading step attributes [0] Reading file attributes [0] =============================================== [0] There were 0 errors detected. [0] Testing -- Write 64-bit strided data (write3) [0] =============================================== [0] Opening file once, write-truncate, lustre filesyste, MPI-POSIX VFD, 1KB alignment [amd64-qusr-test:00055] *** An error occurred in MPI_Info_dup [amd64-qusr-test:00055] *** reported by process [578617345,0] [amd64-qusr-test:00055] *** on communicator MPI_COMM_WORLD [amd64-qusr-test:00055] *** MPI_ERR_INFO: invalid info object [amd64-qusr-test:00055] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, [amd64-qusr-test:00055] *** and potentially your MPI job) FAIL: test ==================================== 1 of 1 tests failed Please report to h5part@lists.psi.ch ==================================== make[2]: *** [Makefile:362: check-TESTS] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/test' make[1]: *** [Makefile:461: check-am] Error 2 make[1]: Leaving directory '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6/test' make: *** [Makefile:284: check-recursive] Error 1 * ERROR: sci-libs/h5part-1.6.6::gentoo failed (test phase): * Make check failed. See above for details. * * Call stack: * ebuild.sh, line 127: Called src_test * environment, line 405: Called default * phase-functions.sh, line 858: Called default_src_test * phase-functions.sh, line 887: Called __eapi0_src_test * phase-helpers.sh, line 809: Called die * The specific snippet of code: * $emake_cmd ${internal_opts} check || \ * die "Make check failed. See above for details." * * If you need support, post the output of `emerge --info '=sci-libs/h5part-1.6.6::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/h5part-1.6.6::gentoo'`. * The complete build log is located at '/var/log/portage/build/sci-libs/h5part-1.6.6:20220113-081756.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/h5part-1.6.6/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/h5part-1.6.6/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6' * S: '/var/tmp/portage/sci-libs/h5part-1.6.6/work/H5Part-1.6.6'