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SebWouters / CheMPS2

CheMPS2: a spin-adapted implementation of DMRG for ab initio quantum chemistry
GNU General Public License v2.0
68 stars 34 forks source link

HDF5 and PyCheMPS2 #54

Closed SebWouters closed 7 years ago

SebWouters commented 7 years ago

@loriab

I think your build changes broke the python interface: seba@latitude-7350:~/debichem/chemps2-1.8.1$ debuild

 dpkg-buildpackage -rfakeroot -D -us -uc
dpkg-buildpackage: source package chemps2
dpkg-buildpackage: source version 1.8.1-1
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Sebastian Wouters <sebastianwouters@gmail.com>
 dpkg-source --before-build chemps2-1.8.1
dpkg-buildpackage: host architecture amd64
 fakeroot debian/rules clean
dh clean --with python2
   dh_testdir
   dh_auto_clean
   debian/rules override_dh_clean
make[1]: Entering directory '/home/seba/debichem/chemps2-1.8.1'
dh_clean
rm -rf build-sphinx PyCheMPS2/build PyCheMPS2/PyCheMPS2.cpp PyCheMPS2/*.pyc
make[1]: Leaving directory '/home/seba/debichem/chemps2-1.8.1'
 dpkg-source -b chemps2-1.8.1
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building chemps2 using existing ./chemps2_1.8.1.orig.tar.gz
dpkg-source: info: building chemps2 in chemps2_1.8.1-1.debian.tar.xz
dpkg-source: info: building chemps2 in chemps2_1.8.1-1.dsc
 debian/rules build
dh build --with python2
   dh_testdir
   dh_update_autotools_config
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/home/seba/debichem/chemps2-1.8.1'
dh_auto_configure -- -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu \
                             -DENABLE_XHOST=OFF \
                             -DBUILD_SPHINX=ON \
                             -DHDF5_INCLUDE_DIRS=/usr/include/hdf5/serial \
                             -DCMAKE_BUILD_TYPE=release
      cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DENABLE_XHOST=OFF -DBUILD_SPHINX=ON -DHDF5_INCLUDE_DIRS=/usr/include/hdf5/serial -DCMAKE_BUILD_TYPE=release
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc
-- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++
-- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- The CMake build type is release
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Performing Test HAS_IPO
-- Performing Test HAS_IPO - Failed
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE  
-- A library with BLAS API found.
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.8.16") 
-- Found Sphinx: /usr/bin/sphinx-build  
-- Configuring done
-- Generating done
-- Build files have been written to: /home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu
make[1]: Leaving directory '/home/seba/debichem/chemps2-1.8.1'
   debian/rules override_dh_auto_build
make[1]: Entering directory '/home/seba/debichem/chemps2-1.8.1'
dh_auto_build
      make -j1
make[2]: Entering directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
make[3]: Entering directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
make[4]: Entering directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
Scanning dependencies of target chemps2-base
make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
make[4]: Entering directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
[  1%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/CASPT2.cpp.o
[  2%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/CASSCF.cpp.o
[  3%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/CASSCFdebug.cpp.o
[  4%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/CASSCFnewtonraphson.cpp.o
[  5%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/CASSCFpt2.cpp.o
[  6%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/ConjugateGradient.cpp.o
[  7%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/ConvergenceScheme.cpp.o
[  8%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Correlations.cpp.o
[  9%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Cumulant.cpp.o
[ 10%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Davidson.cpp.o
[ 11%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DIIS.cpp.o
[ 13%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRG.cpp.o
[ 14%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGfock.cpp.o
[ 15%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGmpsio.cpp.o
[ 16%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGoperators.cpp.o
[ 17%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGoperators3RDM.cpp.o
[ 18%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGSCFindices.cpp.o
[ 19%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGSCFintegrals.cpp.o
[ 20%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGSCFmatrix.cpp.o
[ 21%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGSCFoptions.cpp.o
[ 22%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGSCFrotations.cpp.o
[ 23%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGSCFunitary.cpp.o
[ 25%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGSCFwtilde.cpp.o
[ 26%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/DMRGtechnics.cpp.o
[ 27%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/EdmistonRuedenberg.cpp.o
[ 28%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Excitation.cpp.o
[ 29%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/FCI.cpp.o
[ 30%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/FourIndex.cpp.o
[ 31%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Hamiltonian.cpp.o
[ 32%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Heff.cpp.o
[ 33%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/HeffDiagonal.cpp.o
[ 34%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/HeffDiagrams1.cpp.o
[ 35%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/HeffDiagrams2.cpp.o
[ 36%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/HeffDiagrams3.cpp.o
[ 38%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/HeffDiagrams4.cpp.o
[ 39%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/HeffDiagrams5.cpp.o
[ 40%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Initialize.cpp.o
[ 41%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Irreps.cpp.o
[ 42%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Molden.cpp.o
[ 43%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/PrintLicense.cpp.o
[ 44%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Problem.cpp.o
[ 45%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Sobject.cpp.o
[ 46%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/SyBookkeeper.cpp.o
[ 47%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Tensor3RDM.cpp.o
[ 48%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TensorF0.cpp.o
[ 50%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TensorF1.cpp.o
[ 51%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TensorGYZ.cpp.o
[ 52%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TensorKM.cpp.o
[ 53%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TensorL.cpp.o
[ 54%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TensorO.cpp.o
[ 55%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TensorOperator.cpp.o
[ 56%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TensorQ.cpp.o
[ 57%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TensorS0.cpp.o
[ 58%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TensorS1.cpp.o
[ 59%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TensorT.cpp.o
[ 60%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TensorX.cpp.o
[ 61%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/ThreeDM.cpp.o
[ 63%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TwoDM.cpp.o
[ 64%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/TwoIndex.cpp.o
[ 65%] Building CXX object CheMPS2/CMakeFiles/chemps2-base.dir/Wigner.cpp.o
make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
[ 65%] Built target chemps2-base
make[4]: Entering directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
Scanning dependencies of target chemps2-static
make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
make[4]: Entering directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
[ 66%] Linking CXX static library libchemps2.a
/usr/bin/ar: CMakeFiles/chemps2-base.dir/CASPT2.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/CASSCF.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/CASSCFdebug.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/CASSCFnewtonraphson.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/CASSCFpt2.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/ConjugateGradient.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/ConvergenceScheme.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/Correlations.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/Cumulant.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/Davidson.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DIIS.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DMRG.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DMRGfock.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DMRGmpsio.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DMRGoperators.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DMRGoperators3RDM.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DMRGSCFindices.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DMRGSCFintegrals.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DMRGSCFmatrix.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DMRGSCFoptions.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DMRGSCFrotations.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DMRGSCFunitary.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DMRGSCFwtilde.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/DMRGtechnics.cpp.o: plugin needed to handle lto object
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/usr/bin/ar: CMakeFiles/chemps2-base.dir/FourIndex.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/Hamiltonian.cpp.o: plugin needed to handle lto object
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/usr/bin/ar: CMakeFiles/chemps2-base.dir/TensorF1.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/TensorGYZ.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/TensorKM.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/TensorL.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/TensorO.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/TensorOperator.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/TensorQ.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/TensorS0.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/TensorS1.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/TensorT.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/TensorX.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/ThreeDM.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/TwoDM.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/TwoIndex.cpp.o: plugin needed to handle lto object
/usr/bin/ar: CMakeFiles/chemps2-base.dir/Wigner.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: CASPT2.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: CASSCF.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: CASSCFdebug.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: CASSCFnewtonraphson.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: CASSCFpt2.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: ConjugateGradient.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: ConvergenceScheme.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: Correlations.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: Cumulant.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: Davidson.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DIIS.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DMRG.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DMRGfock.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DMRGmpsio.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DMRGoperators.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DMRGoperators3RDM.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DMRGSCFindices.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DMRGSCFintegrals.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DMRGSCFmatrix.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DMRGSCFoptions.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DMRGSCFrotations.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DMRGSCFunitary.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DMRGSCFwtilde.cpp.o: plugin needed to handle lto object
/usr/bin/ranlib: DMRGtechnics.cpp.o: plugin needed to handle lto object
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/usr/bin/ranlib: Heff.cpp.o: plugin needed to handle lto object
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/usr/bin/ranlib: ThreeDM.cpp.o: plugin needed to handle lto object
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/usr/bin/ranlib: Wigner.cpp.o: plugin needed to handle lto object
make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
[ 66%] Built target chemps2-static
make[4]: Entering directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
Scanning dependencies of target chemps2-shared
make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
make[4]: Entering directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
[ 67%] Linking CXX shared library libchemps2.so
make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
[ 67%] Built target chemps2-shared
make[4]: Entering directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
Scanning dependencies of target chemps2-bin
make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
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[ 68%] Building CXX object CheMPS2/CMakeFiles/chemps2-bin.dir/executable.cpp.o
[ 69%] Linking CXX executable chemps2
make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
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Scanning dependencies of target test14
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Scanning dependencies of target test13
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Scanning dependencies of target test12
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Scanning dependencies of target test11
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[ 77%] Building CXX object tests/CMakeFiles/test11.dir/tests/test11.cpp.o
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Scanning dependencies of target test2
make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
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[ 79%] Building CXX object tests/CMakeFiles/test2.dir/tests/test2.cpp.o
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Scanning dependencies of target test4
make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
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[ 81%] Building CXX object tests/CMakeFiles/test4.dir/tests/test4.cpp.o
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make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
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Scanning dependencies of target test3
make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
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[ 83%] Building CXX object tests/CMakeFiles/test3.dir/tests/test3.cpp.o
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Scanning dependencies of target test1
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Scanning dependencies of target test9
make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
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Scanning dependencies of target test10
make[4]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
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[ 92%] Building CXX object tests/CMakeFiles/test5.dir/tests/test5.cpp.o
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Scanning dependencies of target test6
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[ 94%] Building CXX object tests/CMakeFiles/test6.dir/tests/test6.cpp.o
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Scanning dependencies of target test7
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Scanning dependencies of target test8
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[100%] Linking CXX executable test8
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[100%] Built target test8
make[3]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
make[2]: Leaving directory '/home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu'
# https://wiki.debian.org/Python/LibraryStyleGuide: info on sphinx-build
PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -b html \
                                                           -c obj-x86_64-linux-gnu/sphinx/ \
                                                           -D html_theme=default \
                                                           -D mathjax_path="/usr/share/javascript/mathjax/MathJax.js" sphinx/ build-sphinx/html
Running Sphinx v1.3.6
making output directory...
loading pickled environment... not yet created
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 13 source files that are out of date
updating environment: 13 added, 0 changed, 0 removed
reading sources... [  7%] caspt2
reading sources... [ 15%] dmrgscf
reading sources... [ 23%] dmrgscfcalcs
reading sources... [ 30%] handson
reading sources... [ 38%] index
reading sources... [ 46%] inoutput
reading sources... [ 53%] interfaces
reading sources... [ 61%] matrixelements
reading sources... [ 69%] method
reading sources... [ 76%] publications
reading sources... [ 84%] resources
reading sources... [ 92%] sourcecode
reading sources... [100%] symmetry

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  7%] caspt2
writing output... [ 15%] dmrgscf
writing output... [ 23%] dmrgscfcalcs
writing output... [ 30%] handson
writing output... [ 38%] index
writing output... [ 46%] inoutput
writing output... [ 53%] interfaces
writing output... [ 61%] matrixelements
writing output... [ 69%] method
writing output... [ 76%] publications
writing output... [ 84%] resources
writing output... [ 92%] sourcecode
writing output... [100%] symmetry

generating indices... genindex
writing additional pages... search
copying images... [ 12%] Comparison.png
copying images... [ 25%] handson_orbitals.png
copying images... [ 37%] single_node_h2o.png
copying images... [ 50%] ComparisonN2.png
copying images... [ 62%] handson_comparison.png
copying images... [ 75%] ExtrapolationN2reorder.png
copying images... [ 87%] polyene_scaling.png
copying images... [100%] multi_node_h2o.png

copying static files... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded.
# I know it's ugly, but sphinx splits strings at equality signs: http://svn.python.org/projects/doctools/trunk/sphinx/cmdline.py
cd build-sphinx/html && sed -i "s/MathJax.js/MathJax.js?config=TeX-AMS-MML_HTMLorMML/" *.html
# Solving the complaints from lintian about jquery.js & underscore.js
cd build-sphinx/html && sed -i "s/_static\/jquery.js/\/usr\/share\/javascript\/jquery\/jquery.js/" *.html
cd build-sphinx/html && sed -i "s/_static\/underscore.js/\/usr\/share\/javascript\/underscore\/underscore.js/" *.html
cd build-sphinx/html/_static && rm jquery*.js underscore*.js
cd PyCheMPS2 && CPATH=../CheMPS2/include:/usr/include/hdf5/serial python2 setup.py build_ext -L ../obj-x86_64-linux-gnu/CheMPS2
running build_ext
cythoning PyCheMPS2.pyx to PyCheMPS2.cpp
building 'PyCheMPS2' extension
creating build
creating build/temp.linux-x86_64-2.7
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c PyCheMPS2.cpp -o build/temp.linux-x86_64-2.7/PyCheMPS2.o
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from PyCheMPS2.cpp:251:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
creating build/lib.linux-x86_64-2.7
c++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-2.7/PyCheMPS2.o -L../obj-x86_64-linux-gnu/CheMPS2 -lchemps2 -o build/lib.linux-x86_64-2.7/PyCheMPS2.so
make[1]: Leaving directory '/home/seba/debichem/chemps2-1.8.1'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/home/seba/debichem/chemps2-1.8.1'
cd obj-x86_64-linux-gnu/ && ctest -R "^test3|^test5|^test8"
Test project /home/seba/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu
    Start 3: test3
1/3 Test #3: test3 ............................   Passed   17.07 sec
    Start 5: test5
2/3 Test #5: test5 ............................   Passed   16.55 sec
    Start 8: test8
3/3 Test #8: test8 ............................   Passed   17.66 sec

100% tests passed, 0 tests failed out of 3

Total Test time (real) =  51.27 sec
cd PyCheMPS2/tests && PYTHONPATH=../.././PyCheMPS2/build/lib.linux-x86_64-2.7:.. \
                              LD_LIBRARY_PATH=../../obj-x86_64-linux-gnu/CheMPS2:/usr/lib/x86_64-linux-gnu/hdf5/serial \
                              python2 test1.py
Traceback (most recent call last):
  File "test1.py", line 22, in <module>
    import PyCheMPS2
ImportError: ../../obj-x86_64-linux-gnu/CheMPS2/libchemps2.so.2: undefined symbol: H5T_NATIVE_INT_g
debian/rules:46: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1
make[1]: Leaving directory '/home/seba/debichem/chemps2-1.8.1'
debian/rules:70: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
debuild: fatal error at line 1376:
dpkg-buildpackage -rfakeroot -D -us -uc failed

And it's caused by not linking HDF5 to the library: seba@latitude-7350:~/debichem/chemps2-1.8.1/obj-x86_64-linux-gnu/CheMPS2$ ldd libchemps2.so.2

linux-vdso.so.1 =>  (0x00007ffcc2682000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fa29d4ae000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fa29d1a5000)
libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007fa29cf83000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fa29cd6c000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fa29c9a3000)
/lib64/ld-linux-x86-64.so.2 (0x000055e5a6a0a000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fa29c79f000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fa29c581000)

Can you please fix it?