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标题: 安装Gromacs+cp2k，编译出错 [打印本页]
作者Author: yjb 时间: 2022-5-8 14:49
标题: 安装Gromacs+cp2k，编译出错
本人使用的是Ubuntuxit
Linux test 5.4.0-94-generic #106-Ubuntu SMP Thu Jan 6 23:58:14 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
使用sob的教程先安装了9.1版本的cp2k，测试能够正常运行。
编译cp2k时，首先执行make -j ARCH=local VERSION="ssmp psmp" ，再执行 make -j ARCH=local VERSION="ssmp psmp" libcp2k
测试cp2k安装成功。
之后解压Gromacs-22安装包
mkdir build
cd build
cmake .. -DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_INSTALL_NBLIB_API=OFF -DGMX_DOUBLE=ON -DGMX_CP2K=ON -DCP2K_DIR=/home/test/soft/cp2k-9.1/lib/local/psmp -DGMX_FFT_LIBRARY=fftw3 -DFFTWF_LIBRARY=/home/test/soft/cp2k-9.1/tools/toolchain/install/fftw-3.3.10/lib -DFFTWF_INCLUDE_DIR=/home/test/soft/cp2k-9.1/tools/toolchain/install/fftw-3.3.10/include -DGMX_BLAS_USER=/home/test/soft/cp2k-9.1/tools/toolchain/install/openblas-0.3.19/lib/libopenblas.a -DGMX_LAPACK_USER=/home/test/soft/cp2k-9.1/tools/toolchain/install/scalapack-2.1.0/lib/libscalapack.a -DGMX_MPI=ON -DCP2K_LINKER_FLAGS="-Wl,--enable-new-dtags -pthread -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/elpa-2021.11.001/cpu/lib' -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/fftw-3.3.10/lib' -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/lib' -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/libxc-5.1.7/lib' -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/libxsmm-1.17/lib' -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/scalapack-2.1.0/lib' -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/elpa-2021.11.001/cpu/lib' -lelpa_openmp -lscalapack -lxsmmf -lxsmm -ldl -lpthread -lxcf03 -lxc -lint2 -lfftw3_mpi -lfftw3 -lfftw3_omp -lmpi -lopenblas -lstdc++ " -DCMAKE_INSTALL_PREFIX=/home/test/soft/gromacs-2022
上一步也没有报错
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_WARNING_EVERYTHING
-- Performing Test HAS_WARNING_EVERYTHING - Failed
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
make -j 224
[100%] Linking CXX static library ../../lib/libgromacs_mpi_d.a
[100%] Built target libgromacs
[100%] Linking CXX executable ../../bin/gmx_mpi_d
/usr/bin/ld: /home/test/soft/cp2k-9.1/lib/local/psmp/libcp2k.a(space_groups.o): in function `__space_groups_MOD_spgr_create':
/home/test/soft/cp2k-9.1/src/motion/space_groups.F:229: undefined reference to `spg_get_international'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/motion/space_groups.F:238: undefined reference to `spg_get_multiplicity'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/motion/space_groups.F:245: undefined reference to `spg_get_symmetry'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/motion/space_groups.F:248: undefined reference to `spg_get_schoenflies'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/motion/space_groups.F:256: undefined reference to `spg_get_pointgroup'
/usr/bin/ld: /home/test/soft/cp2k-9.1/lib/local/psmp/libcp2k.a(cryssym.o): in function `__cryssym_MOD_kpoint_gen':
/home/test/soft/cp2k-9.1/src/cryssym.F:281: undefined reference to `spg_get_ir_reciprocal_mesh'
/usr/bin/ld: /home/test/soft/cp2k-9.1/lib/local/psmp/libcp2k.a(cryssym.o): in function `__cryssym_MOD_crys_sym_gen':
/home/test/soft/cp2k-9.1/src/cryssym.F:161: undefined reference to `spg_get_major_version'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/cryssym.F:162: undefined reference to `spg_get_minor_version'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/cryssym.F:163: undefined reference to `spg_get_micro_version'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/cryssym.F:170: undefined reference to `spg_get_international'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/cryssym.F:175: undefined reference to `spg_get_multiplicity'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/cryssym.F:179: undefined reference to `spg_get_symmetry'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/cryssym.F:182: undefined reference to `spg_get_schoenflies'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/cryssym.F:187: undefined reference to `spg_get_pointgroup'
/usr/bin/ld: /home/test/soft/cp2k-9.1/lib/local/psmp/libcp2k.a(voronoi_interface.o): in function `__voronoi_interface_MOD_entry_voronoi_or_bqb':
/home/test/soft/cp2k-9.1/src/voronoi_interface.F:420: undefined reference to `libvori_setPrefix_Voronoi'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:421: undefined reference to `libvori_setRefinementFactor'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:422: undefined reference to `libvori_setVoronoiSkipFirst'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:423: undefined reference to `libvori_setVoriOverwrite'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:424: undefined reference to `libvori_setEMPOutput'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:474: undefined reference to `libvori_setGrid'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:499: undefined reference to `libvori_pushAtoms'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:551: undefined reference to `libvori_push_rho_zrow'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:589: undefined reference to `libvori_setRadii_User'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:426: undefined reference to `libvori_setPrefix_BQB'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:430: undefined reference to `libvori_setBQBFilename'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:431: undefined reference to `libvori_setBQBParmString'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:575: undefined reference to `libvori_setRadii_Unity'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:604: undefined reference to `libvori_step'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:619: undefined reference to `libvori_get_radius'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:621: undefined reference to `libvori_get_charge'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:623: undefined reference to `libvori_get_volume'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:626: undefined reference to `libvori_get_dipole'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:631: undefined reference to `libvori_get_quadrupole'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:636: undefined reference to `libvori_get_wrapped_pos'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:641: undefined reference to `libvori_get_charge_center'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:692: undefined reference to `libvori_processBQBFrame'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:444: undefined reference to `libvori_setBQBOptimization'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:445: undefined reference to `libvori_setBQBHistory'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:446: undefined reference to `libvori_setBQBSkipFirst'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:447: undefined reference to `libvori_setBQBCheck'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:448: undefined reference to `libvori_setBQBOverwrite'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:449: undefined reference to `libvori_setBQBStoreStep'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:596: undefined reference to `libvori_sanitycheck'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:578: undefined reference to `libvori_setRadii_Covalent'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/voronoi_interface.F:581: undefined reference to `libvori_setRadii_User'
/usr/bin/ld: /home/test/soft/cp2k-9.1/lib/local/psmp/libcp2k.a(voronoi_interface.o): in function `__voronoi_interface_MOD_finalize_libvori':
/home/test/soft/cp2k-9.1/src/voronoi_interface.F:749: undefined reference to `libvori_finalize'
/usr/bin/ld: /home/test/soft/cp2k-9.1/lib/local/psmp/libcp2k.a(metadynamics.o): in function `__metadynamics_MOD_metadyn_integrator':
/home/test/soft/cp2k-9.1/src/metadynamics.F:299: undefined reference to `plumed_gcmd'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/metadynamics.F:300: undefined reference to `plumed_gcmd'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/metadynamics.F:301: undefined reference to `plumed_gcmd'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/metadynamics.F:302: undefined reference to `plumed_gcmd'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/metadynamics.F:303: undefined reference to `plumed_gcmd'
/usr/bin/ld: /home/test/soft/cp2k-9.1/lib/local/psmp/libcp2k.a(metadynamics.o):/home/test/soft/cp2k-9.1/src/metadynamics.F:304: more undefined references to `plumed_gcmd' follow
/usr/bin/ld: /home/test/soft/cp2k-9.1/lib/local/psmp/libcp2k.a(metadynamics.o): in function `__metadynamics_MOD_metadyn_finalise_plumed':
/home/test/soft/cp2k-9.1/src/metadynamics.F:208: undefined reference to `plumed_gfinalize'
/usr/bin/ld: /home/test/soft/cp2k-9.1/lib/local/psmp/libcp2k.a(metadynamics.o): in function `__metadynamics_MOD_metadyn_initialise_plumed':
/home/test/soft/cp2k-9.1/src/metadynamics.F:166: undefined reference to `plumed_installed'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/metadynamics.F:171: undefined reference to `plumed_gcreate'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/metadynamics.F:172: undefined reference to `plumed_gcmd'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/metadynamics.F:173: undefined reference to `plumed_gcmd'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/metadynamics.F:174: undefined reference to `plumed_gcmd'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/metadynamics.F:175: undefined reference to `plumed_gcmd'
/usr/bin/ld: /home/test/soft/cp2k-9.1/src/metadynamics.F:176: undefined reference to `plumed_gcmd'
/usr/bin/ld: /home/test/soft/cp2k-9.1/lib/local/psmp/libcp2k.a(metadynamics.o):/home/test/soft/cp2k-9.1/src/metadynamics.F:177: more undefined references to `plumed_gcmd' follow
collect2: error: ld returned 1 exit status
make[2]: *** [src/programs/CMakeFiles/gmx.dir/build.make:107: bin/gmx_mpi_d] Error 1
make[1]: *** [CMakeFiles/Makefile2:6082: src/programs/CMakeFiles/gmx.dir/all] Error 2
make: *** [Makefile:166: all] Error 2
出现如上错误，我认为是/usr/bin/ld 下面的一个动态库出现了问题，请各位老师给与帮助，谢谢。
作者Author: abin 时间: 2022-5-8 17:37
这里有其他版本的gmx,
https://pan.baidu.com/s/1r7PduYXqjn3kpS-ie0H8NQ?pwd=aknc
如有需要, 自行下载.
详细信息, 查询签名连接了解.
作者Author: beyond 时间: 2022-5-26 08:32
删除-DCP2K_LINKER_FLAGS 再试试，Gromacs论坛上有人这样建议，我试过，安装成功了
作者Author: yjb 时间: 2022-5-26 10:24
-DCP2K_LINKER_FLAGS="-Wl,--enable-new-dtags -pthread -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/elpa-2021.11.001/cpu/lib' -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/fftw-3.3.10/lib' -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/lib' -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/libxc-5.1.7/lib' -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/libxsmm-1.17/lib' -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/scalapack-2.1.0/lib' -L'/home/test/soft/cp2k-9.1/tools/toolchain/install/elpa-2021.11.001/cpu/lib' -lelpa_openmp -lscalapack -lxsmmf -lxsmm -ldl -lpthread -lxcf03 -lxc -lint2 -lfftw3_mpi -lfftw3 -lfftw3_omp -lmpi -lopenblas -lstdc++ "
把这个全部删除吗？
作者Author: beyond 时间: 2022-5-26 17:26
yjb 发表于 2022-5-26 10:24
-DCP2K_LINKER_FLAGS="-Wl,--enable-new-dtags -pthread -L'/home/test/soft/cp2k-9.1/tools/toolchain/i ...
是的
作者Author: yjb 时间: 2022-5-26 18:21
好的谢谢，我试试
作者Author: yjb 时间: 2022-6-27 17:45
您好，我试了之后发现还是会出现这个错误。
作者Author: xj1318850094 时间: 2023-7-7 09:50
我也出现这个问题，请问怎样解决这个呢
作者Author: yjb 时间: 2023-7-7 13:15
没有解决这个问题
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