CP2K第一性原理程序在Linux中的安装方法

wuzhiyi

sobereva 发表于 2021-2-19 07:26
最近几天我会写专门的帖子。

简单来说，载入任意Multiwfn支持的含有结构信息的文件（最好也含有晶胞信 ...

非常感谢sob老师！

乐平

gog 发表于 2021-2-19 12:47
openmpi 用root权限先编译好啊。

自己编译 openmpi 和最后没有 popt 有必然联系？

乐平

gog 发表于 2021-2-19 12:47
openmpi 用root权限先编译好啊。

重新编译了一次

1. ./install_cp2k_toolchain.sh --with-mkl=system --with-openmpi=install --with-libsmm=install --with-ptscotch=install --with-superlu=install --with-pexsi=install --with-plumed=install

复制代码

直接用 CP2K 提供的 VERSION，没有自作主张加上 popt

1. make -j 40 ARCH=local VERSION="ssmp psmp"

复制代码

得到 exe/local 目录下的结果：

1. memory_utilities_unittest.ssmp
   
2. parallel_rng_types_unittest.ssmp
   
3. graph.ssmp
   
4. memory_utilities_unittest.psmp
   
5. parallel_rng_types_unittest.psmp
   
6. graph.psmp
   
7. grid_miniapp.ssmp
   
8. grid_unittest.ssmp
   
9. grid_miniapp.psmp
   
10. grid_unittest.psmp
    
11. dumpdcd.ssmp
    
12. xyz2dcd.ssmp
    
13. xyz2dcd.psmp
    
14. dumpdcd.psmp
    
15. libcp2k_unittest.ssmp
    
16. cp2k.ssmp
    
17. cp2k.sopt -> cp2k.ssmp   # 软链接
    
18. cp2k_shell.ssmp -> cp2k.ssmp # 软链接
    
19. cp2k.psmp
    
20. libcp2k_unittest.psmp
    
21. cp2k_shell.psmp -> cp2k.psmp # 软链接
    
22. cp2k.popt -> cp2k.psmp # 软链接

复制代码

可以发现，8.1 版默认用软链接把 psmp 版作为 popt 版了。

gog

乐平 发表于 2021-2-19 20:18
自己编译 openmpi 和最后没有 popt 有必然联系？

软件迭代更新、去掉了吧。刘博士的帖子回复，intelmpi编译的，也没有popt。

Penson

sobereva 发表于 2021-2-19 07:35
https://www.cp2k.org/version_history
我觉得算不上很明显的改进

了解，谢谢社长

乐平

想请教一下 sob 老师，跨节点并行应该怎么设置？用的是 openmpi 4.0.1

比如，我的服务器单个节点 16-core
mpirun -np 16 cp2k.popt -i H2O-128.inp -o H2O-128.out
可以正常运行。

如果我希望用跨两个节点，调用 32-core 应该怎么设置呢？

我尝试了用
mpirun -np 32 cp2k.popt -i H2O-128.inp -o H2O-128.out
或者
mpirun -np 32 cp2k.psmp -i H2O-128.inp -o H2O-128.out

但是任务都没法运行。

sobereva

乐平 发表于 2021-2-19 23:13
想请教一下 sob 老师，跨节点并行应该怎么设置？用的是 openmpi 4.0.1

比如，我的服务器单个节点 16-cor ...

https://www.open-mpi.org/faq/?ca ... pirun-specify-hosts

乐平

sobereva 发表于 2021-2-20 09:22
https://www.open-mpi.org/faq/?category=running#mpirun-specify-hosts

谢谢，不过似乎没看太明白。这个链接里（9）说的是在某些指定的 hosts 运行 mpi，一下小节（10）说的是在多个 hosts 上运行 mpi
openmpi 官网的帖子里说得好复杂，对于新手太不友好……



我把我的 PBS 文件修改了一下，可以跨两个节点运行了，如下。

1. #!/bin/bash
   
2. #PBS -N cp2k_H2O-512
   
3. #PBS -l nodes=2:ppn=16
   
4. #PBS -j n
   
5. #PBS -e ${PBS_JOBNAME}.e
   
6. #PBS -o ${PBS_JOBNAME}.o
   
7. #PBS -q v3
   
8. 
   
9. module load gcc/9.3.1
   
10. module load openmpi/4.0.1
    
11. source /public1/apps/cp2k-8.1/tools/toolchain/install/setup
    
12. 
    
13. 
    
14. cd $PBS_O_WORKDIR
    
15. EXEC=/public1/apps/cp2k-8.1/exe/local/cp2k.popt
    
16. 
    
17. mpirun -np 32 $EXEC -i H2O-512.inp -o H2O-512.out

复制代码

修改的地方如下：
【1】 #PBS -l nodes=2:ppn=16
修改之前是 nodes=1 ，所以只能在一个节点上运行。

【2】mpirun -np 32
32 = 2 * 16，也就是节点数乘以每个节点上的 CPU 核心数，之前只改了这里，没有改 【1】的项目，故导致任务无法运行。

ball2006

编译QUIP模块，编译不过去
==================== Installing QUIP ====================
QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705.tar.gz is found
Installing from scratch into /share/apps/soft/cp2k81/tools/toolchain/install/quip-1ff93b3400b83e804f0f2e857e70c5e4133d9705
ERROR: (./scripts/install_quip.sh, line 100) Non-zero exit code detected.

make.log有如下报错

Making Programs

********************************************
rm -f /share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/build/linux_x86_64_gfortran/Makefile
cp /share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/src/Programs/Makefile /share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/build/linux_x86_64_gfortran/Makefile
make -C /share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/build/linux_x86_64_gfortran QUIP_ROOT=/share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705 VPATH=/share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/src/Programs -I/share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705 -I/share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/arch
make[1]: Entering directory `/share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/build/linux_x86_64_gfortran'
gfortran  -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC -g  -I/share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/src/libAtoms -I/share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/src/fox/objs.linux_x86_64_gfortran/finclude -O3  -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE -D'GIT_VERSION="NOT_A_GIT_REPOSITORY"'  -D'QUIP_ARCH="linux_x86_64_gfortran"' -D'SIZEOF_FORTRAN_T=2' -DHAVE_PRECON -DHAVE_QR  -c  /share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/src/Programs/vacancy_map_mod.f95 -o vacancy_map_mod.o
gfortran  -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC -g  -I/share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/src/libAtoms -I/share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/src/fox/objs.linux_x86_64_gfortran/finclude -O3  -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE -D'GIT_VERSION="NOT_A_GIT_REPOSITORY"'  -D'QUIP_ARCH="linux_x86_64_gfortran"' -D'SIZEOF_FORTRAN_T=2' -DHAVE_PRECON -DHAVE_QR  -c  /share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/src/Programs/quip.f95 -o quip.o
gfortran  -o quip  quip.o vacancy_map_mod.o -L. -lquiputils -lquip_core  -latoms   -O3  -L/share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/src/fox/objs.linux_x86_64_gfortran/lib -lFoX_sax -lFoX_wxml -lFoX_utils -lFoX_common -lFoX_fsys  /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_scalapack_lp64.so -Wl,--start-group /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_gf_lp64.so /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_sequential.so /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_core.so /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so -Wl,--end-group -lpthread -lm -ldl  
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Waitall'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_comm_null'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Abort'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Waitany'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_f2c'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Wtime'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_dup'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_double'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Op_free'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_create'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Group_incl'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_get_attr'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_dblcplex'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Init'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_create_struct'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Bcast'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Alltoallv'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Cart_create'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Scatterv'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Initialized'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_free'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Iprobe'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Testall'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Allgatherv'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_group'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Cart_sub'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_split'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Send'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Allreduce'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_packed'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_op_max'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_op_maxloc'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_op_min'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Rsend'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_byte'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Irecv'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_contiguous'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Recv'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_free'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_comm_world'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_compare'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_float'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Reduce'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Pack'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_request_null'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_cplex'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_unsigned_short'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_c2f'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Gatherv'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Get_address'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Wait'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Allgather'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_create_resized'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_double_int'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Op_create'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_int'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Pack_size'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_long_long_int'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Unpack'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_integer'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Test'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_dblprec'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Isend'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_f2c'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Op_f2c'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_vector'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Alltoall'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Finalize'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Sendrecv'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_op_sum'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Op_c2f'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_size'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_real'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Group_free'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_indexed'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Barrier'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_commit'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_c2f'
/opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_rank'
collect2: error: ld returned 1 exit status
make[1]: *** [quip] Error 1
make[1]: Leaving directory `/share/apps/soft/cp2k81/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/build/linux_x86_64_gfortran'
make: *** [Programs] Error 2

麻烦老师们看看是啥原因

sobereva

ball2006 发表于 2021-3-24 16:22
编译QUIP模块，编译不过去
==================== Installing QUIP ====================
QUIP-1ff93b3400 ...

跟MPI库链接有问题。检查MPI方面的安装和设置

如果只有这一个过不去并且你并不使用经验势做计算，QUIP也可以不装

ball2006

好的，sob老师。
我再查查，多谢。

yiranfengbai

老师，编译make -j 4 时出现了这个问题，该怎么解决呢
Traceback (most recent call last):
  File "/calc/msi/cp2k-8.1/tools/build_utils/check_archives.py", line 69, in <module>
    main()
  File "/calc/msi/cp2k-8.1/tools/build_utils/check_archives.py", line 49, in main
    output = check_output([ar_exe, "t", archive_fn], encoding="utf8")
  File "/usr/local/lib/python3.5/subprocess.py", line 626, in check_output
    **kwargs).stdout
  File "/usr/local/lib/python3.5/subprocess.py", line 693, in run
    with Popen(*popenargs, **kwargs) as process:
TypeError: __init__() got an unexpected keyword argument 'encoding'
make[2]: *** [makedep] 错误 1
make[2]: *** 正在等待未完成的任务....
Traceback (most recent call last):
  File "/calc/msi/cp2k-8.1/tools/build_utils/check_archives.py", line 69, in <module>
    main()
  File "/calc/msi/cp2k-8.1/tools/build_utils/check_archives.py", line 49, in main
    output = check_output([ar_exe, "t", archive_fn], encoding="utf8")
  File "/usr/local/lib/python3.5/subprocess.py", line 626, in check_output
    **kwargs).stdout
  File "/usr/local/lib/python3.5/subprocess.py", line 693, in run
    with Popen(*popenargs, **kwargs) as process:
TypeError: __init__() got an unexpected keyword argument 'encoding'
make[2]: *** [makedep] 错误 1
make[2]: *** 正在等待未完成的任务....
Resolving dependencies ...
Resolving dependencies ...
make[1]: *** [ssmp] 错误 2
make[1]: *** 正在等待未完成的任务....
make[1]: *** [psmp] 错误 2
make: *** [all] 错误 2

sobereva

yiranfengbai 发表于 2021-3-26 15:33
老师，编译make -j 4 时出现了这个问题，该怎么解决呢
Traceback (most recent call last):
  File "/cal ...

信息不足，无法判断。什么系统什么编译器具体怎么编译的都得交代非常清楚

系统不要装成中文语言

yiranfengbai

sobereva 发表于 2021-3-26 19:32
信息不足，无法判断。什么系统什么编译器具体怎么编译的都得交代非常清楚

系统不要装成中文语言

抱歉老师，系统是centos7.6, gcc9.3.1。我通把这个关键词删掉之后，这个问题暂时没出来了，不知道是否正确

abin

ball2006 发表于 2021-3-24 16:22
编译QUIP模块，编译不过去
==================== Installing QUIP ====================
QUIP-1ff93b3400 ...

我记得，
使用intel2020u2没有问题。修正一下,
intel2020u2, 运行某些计算会遇到内存爆浆的问题. 请谨慎使用.   

intel2020u4， u3都有很多坑。

另，
我有编译好的
cp2k v7.1 v8.1, 分别针对E5 v3/v4 或者新的AVX2/AVX512优化的编译版本。
可以有偿提供。
需要目标机器有root授权才能完成部署。