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#20 Build problem
Hello,
I am trying to compile a program that needs to compile pwiz-4922 as part of it. It failed with the error:
/usr/bin/ld: cannot find -lhdf5
collect2: error: ld returned 1 exit status
make[2]: *** [specplot] Error 1
If I search for hdf5 in the compilation log, I found the following lines:
gcc.link /home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5make_libsettings
/home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/src/H5make_libsettings.o: In function print_header':
Jamfile</home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/libraries/hdf5-1.8.7>.copy_libsettings /home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/libhdf5.settings
Jamfile</home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/libraries/hdf5-1.8.7>.make_libsettings /home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5lib_settings.c
/bin/sh: line 2: 103163 Segmentation fault (core dumped) "/home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5make_libsettings" > "/home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5lib_settings.c"
cd /home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi
"/home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5make_libsettings" > "/home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5lib_settings.c"
...failed Jamfile</home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/libraries/hdf5-1.8.7>.make_libsettings /home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5lib_settings.c...
...removing /home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5lib_settings.c
...skipped <p/home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi>H5lib_settings.o for lack of <p/home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi-object(c-scanner)@8701>H5lib_settings.c...
gcc.compile.c /home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5Odtype.o
gcc.compile.c /home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/src/H5detect.o
gcc.link /home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5detect
/home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/src/H5detect.o: In functionprint_header':
Jamfile.make_init /home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5Tinit.c
/bin/sh: line 1: 103203 Segmentation fault (core dumped) "/home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5detect" > "/home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5Tinit.c"
"/home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5detect" > "/home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5Tinit.c"
...failed Jamfile.make_init /home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5Tinit.c...
...removing /home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5Tinit.c
...skipped
H5Tinit.o for lack of p/home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi-object(c-scanner)@8701H5Tinit.c...
gcc.compile.c /home/oo7433/NPD/sps-source-latest/sps/src/pwiz-4922/build-linux-x86_64/libraries/hdf5-1.8.7/gcc-4.8.5/release/link-static/runtime-link-static/threading-multi/H5Tconv.o
...skipped
libhdf5.a(clean) for lack of
H5Tinit.o...
...skipped
libhdf5.a for lack of
H5Tinit.o...
...skipped
SpectrumList_SorterTest for lack of
libhdf5.a...
Does any one have an advice on how to fix this?
Thanks,
Jie