hello,everyone! I ran into a problem when I complied rosetta with option "extras=hdf5". I have installed hdf5 in /usr/local/hdf5, and I have add it to environmental variables.
command line: ./scons.py -j16 bin mode=release extras=hdf5
results:
scons: Reading SConscript files ...
Running versioning script ... Release package detected, using rosetta/main/.release.json to acquire version information...
Done. (0.0 seconds)
Number of option files updated: 0
Total 4609 options.
Finished updating ResidueProperty code
-- no changes needed
Finished updating VariantType code
-- no changes needed
scons: done reading SConscript files.
scons: Building targets ...
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/AbinitioRelax.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/AbinitioRelax.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/AnchorFinder.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/interface_design/anchored_design/AnchorFinder.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/AnchoredDesign.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/interface_design/anchored_design/AnchoredDesign.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/AnchoredPDBCreator.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/interface_design/anchored_design/AnchoredPDBCreator.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/BuildPeptide.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/flexpep_docking/BuildPeptide.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/CstfileToTheozymePDB.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/enzdes/CstfileToTheozymePDB.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/DARC.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/darc/DARC.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/DNA_methylation.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/post-translational_modification/DNA_methylation.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/FiberDiffractionFreeSet.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/fiber_diffraction/FiberDiffractionFreeSet.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/FlexPepDocking.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/flexpep_docking/FlexPepDocking.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/FloppyTail.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/scenarios/FloppyTail.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/GlycanDock.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/carbohydrates/GlycanDock.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/InterfaceAnalyzer.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/analysis/InterfaceAnalyzer.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/MakeRotLib.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/ncaa_utilities/MakeRotLib.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/MakeSegmentFile.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/pose_sewing/MakeSegmentFile.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
g++ -o build/src/release/linux/5.13/64/x86/gcc/9/hdf5/N-terminal_acetylation.hdf5.linuxgccrelease -Wl,--disable-new-dtags -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=/home/zhengjishen/Desktop/rosetta.binary.linux.release-296/main/source/build/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/release/linux/5.13/64/x86/gcc/9/hdf5/apps/public/post-translational_modification/N-terminal_acetylation.o -Lexternal/lib -Lbuild/src/release/linux/5.13/64/x86/gcc/9/hdf5 -Lsrc -Lbuild/external/release/linux/5.13/64/x86/gcc/9/hdf5 -Lexternal -L/usr/local/gromacs/lib -Lbin -L/home/zhengjishen/Desktop/rdkit-Release_2016_03_1/lib -L/usr/local/lib -L/usr/local/hdf5/lib -L/usr/local/hdf5 -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lhdf5 -lhdf5_cpp -lhdf5_hl -lhdf5_hl_cpp
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/AnchoredDesign.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/AbinitioRelax.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/FloppyTail.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/AnchorFinder.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/MakeRotLib.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/FiberDiffractionFreeSet.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/BuildPeptide.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/DNA_methylation.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/MakeSegmentFile.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/FlexPepDocking.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/AnchoredPDBCreator.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/CstfileToTheozymePDB.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/N-terminal_acetylation.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/InterfaceAnalyzer.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/GlycanDock.hdf5.linuxgccrelease] Error 1
/usr/bin/ld: build/src/release/linux/5.13/64/x86/gcc/9/hdf5/libprotocols.3.so: undefined reference to `H5::ArrayType::ArrayType(H5::DataType const&, int, unsigned long long const*)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/5.13/64/x86/gcc/9/hdf5/DARC.hdf5.linuxgccrelease] Error 1
scons: building terminated because of errors.