mlip Intel 版本安装

官方安装 tutorial：installation tutorial · Wiki · Alexander Shapeev / MLIP-2 Tutorials · GitLab、README.md · master · Alexander Shapeev / LAMMPS-MLIP interface · GitLab
先编译 mlip-2，再编译 mlip-2 与 LAMMPS 的接口
编译接口时，有多种选项：intel_cpu_intelmpi、g++_mpich、mpi、g++_serial 和 serial ，编译 intel_cpu_intelmpi 版本时，需在超算导入 oneAPI 套件
- 编译前最好先读 configure、Makefile、install.sh 等配置、编译、安装脚本源代码，了解其默认配置是什么，自定义配置需要修改哪些东西
- arm 无 intel oneapi 套件，pi 和 siyuan 有，建议在后两者平台编译
- 建议在编译 mlip-2 开始前，就 module load intel oneapi 套件，因为 ./configure 命令会自动检测所在平台是否有 mpi，若检测无只会编译串行 serial 版本，后续的接口编译也只能选择串行版本

bash

module load intel-oneapi-compilers/2021.4.0
module load intel-oneapi-mpi/2021.4.0
module load intel-oneapi-mkl/2021.4.0
module load intel-oneapi-tbb/2021.4.0

编译接口时，可以在 preinstall.sh 脚本中添加所需安装的 package，添加以下 packages
- make yes-STUBS 不需要添加，因为在 install.sh 脚本中已有 make mpi-stubs 选项（本人不知道这两者的区别，也不知道对最终的运行是否会产生影响，仅从取消该选项后能编译成功得到的判断与猜测）
- 不同版本的 lammps 可以放在同一目录下分别编译，但最后一步会将 lammps 中编译好的 lmp 可执行文件复制到 interface-lammps-mlip-2 目录中，其中一个会被覆盖，建议放在不同目录下分别编译

bash

make yes-basic
make yes-manybody
make yes-KSPACE
# make yes-STUBS

安装情况：
[x] master、pi 和 siyuan 能编译 2022 版本及最新的稳定版本（20230802）的 lammps
[ ] manager 编译 mlip-2 出错，后续无法进行（应该是 2015 版本的 intel 有些老，可以编译 mpi 版本（暂未尝试））
[ ] arm 编译 mlip-2 出错，后续无法进行（无 intel 程序）

测试 LAMMPS 2022 版本

下载

bash

wget https://github.com/lammps/lammps/archive/refs/tags/stable_23Jun2022_update4.tar.gz

tar -xzvf stable_23Jun2022_update4.tar.gz

mv lammps-stable_23Jun2022_update4 lammps-stable_23Jun2022

编译

bash

./install.sh ../lammps-stable_23Jun2022 intel_cpu_intelmpi

./install.sh ../lammps-stable_23Jun2022 g++_mpich

遇到的问题

编译成功

g++_mpich 版本

bash

mpicxx -cxx=g++ -g -O -std=c++11 main.o -L../../lib/mlip -L. -llammps_g++_mpich -l_mlip_interface -std=c++11 -lgfortran -ldl -o ../lmp_g++_mpich
size ../lmp_g++_mpich
   text data bss dec hex filename
6073025 12712 11280 6097017 5d0879 ../lmp_g++_mpich
make[1]: Leaving directory `/lustre/home/acct-mseklt/mseklt/yangsl/software/pi-softwares/lammps-stable_23Jun2022/src/Obj_g++_mpich'

intel_cpu_intelmpi 版本

bash

mpiicpc -std=c++11 -diag-disable=10441 -diag-disable=2196 -qopenmp -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -L/dssg/opt/icelake/linux-centos8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-r7h6alnulyzgb6iqvxhovmwrajvwbqxf/mkl/2021.4.0/lib/intel64/ main.o -L../../lib/mlip       -L. -llammps_intel_cpu_intelmpi -l_mlip_interface     -std=c++11 -lgfortran  -ldl -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core   -o ../lmp_intel_cpu_intelmpi
size ../lmp_intel_cpu_intelmpi
   text    data     bss     dec     hex filename
13436817         242936   14280 13694033         d0f451 ../lmp_intel_cpu_intelmpi
make[1]: Leaving directory '/dssg/home/acct-mseklt/mseklt/yangsl/src/MLIP/lammps-stable_23Jun2022/src/Obj_intel_cpu_intelmpi'

manager 编译 mlip-2 出现错误

bash

mpiicpc -O3  -I/opt/intel/composer_xe_2015.0.090/mkl/include -MMD  -DMLIP_MPI -DMLIP_INTEL_MKL  -std=c++11 -DMLIP_DEV -c /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp -o /home/yangsl/src/MLIP/mlip-2/obj/mpi/common/bfgs.cpp.o
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/multidimensional_arrays.h(13),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.h(16),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):
/usr/include/c++/5/bits/stl_iterator_base_types.h(154): error: class "std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>" has no member "iterator_category"
        typedef typename _Iterator::iterator_category iterator_category;
                                    ^
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/multidimensional_arrays.h(13),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.h(16),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):
          detected during:
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/multidimensional_arrays.h(13),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.h(16),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):
            instantiation of class "std::__iterator_traits<_Iterator, void> [with _Iterator=std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>]" at line 163
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/multidimensional_arrays.h(13),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.h(16),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):
            instantiation of class "std::iterator_traits<_Iterator> [with _Iterator=std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>]" at line 88 of "/home/yangsl/src/MLIP/mlip-2/src/common/utils.h"
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/multidimensional_arrays.h(13),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.h(16),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):

In file included from /home/yangsl/src/MLIP/mlip-2/src/common/multidimensional_arrays.h(13),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.h(16),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):
/usr/include/c++/5/type_traits(1492): error: class "std::__is_convertible_helper<<error-type>, std::input_iterator_tag, false>" has no member class "type"
      : public __is_convertible_helper<_From, _To>::type
                                                    ^
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/multidimensional_arrays.h(13),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.h(16),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):
          detected during instantiation of class "std::is_convertible<_From, _To> [with _From=<error-type>, _To=std::input_iterator_tag]" at line 88 of "/home/yangsl/src/MLIP/mlip-2/src/common/utils.h"
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/multidimensional_arrays.h(13),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.h(16),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):

In file included from /home/yangsl/src/MLIP/mlip-2/src/common/multidimensional_arrays.h(13),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.h(16),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):
/usr/include/c++/5/type_traits(1492): error: not a class or struct name
      : public __is_convertible_helper<_From, _To>::type
               ^
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/multidimensional_arrays.h(13),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.h(16),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):
          detected during instantiation of class "std::is_convertible<_From, _To> [with _From=<error-type>, _To=std::input_iterator_tag]" at line 88 of "/home/yangsl/src/MLIP/mlip-2/src/common/utils.h"
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/multidimensional_arrays.h(13),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.h(16),
                 from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):

In file included from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):
/usr/include/c++/5/bits/stl_iterator_base_types.h(154): error: class "std::vector<double, std::allocator<double>>" has no member "iterator_category"
        typedef typename _Iterator::iterator_category iterator_category;
                                    ^
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):
          detected during:
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):
            instantiation of class "std::__iterator_traits<_Iterator, void> [with _Iterator=std::vector<double, std::allocator<double>>]" at line 163
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):
            instantiation of class "std::iterator_traits<_Iterator> [with _Iterator=std::vector<double, std::allocator<double>>]" at line 78 of "/home/yangsl/src/MLIP/mlip-2/src/common/multidimensional_arrays.h"
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):
            instantiation of class "templateArray2D<F> [with F=double]" at line 272 of "/home/yangsl/src/MLIP/mlip-2/src/common/bfgs.h"
In file included from /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp(11):

compilation aborted for /home/yangsl/src/MLIP/mlip-2/src/common/bfgs.cpp (code 2)
/home/yangsl/src/MLIP/mlip-2/make/Makefile:77: recipe for target '/home/yangsl/src/MLIP/mlip-2/obj/mpi/common/bfgs.cpp.o' failed
make: *** [/home/yangsl/src/MLIP/mlip-2/obj/mpi/common/bfgs.cpp.o] Error 2

`\r` 错误

master 编译最新版 LAMMPS 出现如下错误。

原因：在 windows 上下载最新版 LAMMPS 源码，再上传到 manager 上，windows 与 linux 之间存在一定的区别，导致如下错误出现。

解决方法：直接下载到 linux 端，速度慢没办法。或者先下载 tar.gz 压缩包到 windows，再上传到 linux 端，勿源码。

bash

/home/yangsl/src/MLIP-2023/interface-lammps-mlip-2
Uninstalling package user-mlip
Depend.sh: line 3: $'\r': command not found
): No such file or directorysetlocale: LC_ALL: cannot change locale (C
': not a valid identifier: `LC_ALL
Depend.sh: line 7: $'\r': command not found
Depend.sh: line 11: $'\r': command not found
Depend.sh: line 18: $'\r': command not found
Depend.sh: line 22: $'\r': command not found
Depend.sh: line 23: syntax error near unexpected token `$'{\r''
'epend.sh: line 23: `depend () {
make: *** [Makefile:616: no-user-mlip] Error 2
Installing package user-mlip
Depend.sh: line 3: $'\r': command not found
): No such file or directorysetlocale: LC_ALL: cannot change locale (C
': not a valid identifier: `LC_ALL

ARM 平台相关报错

在 ARM 平台编译接口，load openmpi/4.1.1-gcc-9.3.0 程序，提示找不到相关共享链接库

解决方法：建议不在 arm 平台编译，arm 平台可 module load 程序少且有些旧。

bash

mpicxx -O3 -I./cblas -MMD -DMLIP_MPI -std=c++11 -DMLIP_DEV -c /lustre/home/acct-mseklt/mseklt/yangsl/software/mlip-2/src/common/bfgs.cpp -o /lustre/home/acct-mseklt/mseklt/yangsl/software/mlip-2/obj/mpi/common/bfgs.cpp.o
mpicxx: error while loading shared libraries: libpmi2.so.0: cannot open shared object file: No such file or directory
make: *** [/lustre/home/acct-mseklt/mseklt/yangsl/software/mlip-2/obj/mpi/common/bfgs.cpp.o] Error 127

编译 intel_cpu_intelmpi 版本报错

导入 mpich/3.3.2-intel-19.0.5 模块编译 intel_cpu_intelmpi，提示未找到 mpiicpc 命令

解决方法：应 load intel-oneapi 程序套件

bash

cc -O -o fastdep.exe ../DEPEND/fastdep.c
make[1]: Leaving directory `/lustre/home/acct-mseklt/mseklt/yangsl/softwares/pi-softwares/mylammps/src/Obj_intel_cpu_intelmpi'
make[1]: Entering directory `/lustre/home/acct-mseklt/mseklt/yangsl/software/pi-softwares/mylammps/src/Obj_intel_cpu_intelmpi'
mpiicpc -std=c++11 -diag-disable=10441 -diag-disable=2196 -qopenmp -qno-offload -ansi-alias -restrict -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -I/include -DLAMMPS_GZIP -I../../lib/mlip -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -DFFT_MKL -DFFT_SINGLE -lgfortran -c ../main.cpp
/lustre/opt/cascadelake/linux-centos7-cascadelake/gcc-11.2.0/intel-oneapi-mpi-2021.6.0-xyxek2osiqlzbkvzgysroekj2zdfhcg2/mpi/2021.6.0/bin/mpiicpc: line 558: icpc: command not found
make[1]: *** [main.o] Error 127
make[1]: Leaving directory `/lustre/home/acct-mseklt/mseklt/yangsl/software/pi-softwares/mylammps/src/Obj_intel_cpu_intelmpi'
make: *** [intel_cpu_intelmpi] Error 2
cp: cannot stat '../mylammps/src/lmp_intel_cpu_intelmpi': No such file or directory

`../version.h` 报错

脚本 preinstall.sh 中添加 make yes-STUBS 选项，编译 g++_mpich 和 intel_cpu_intelmpi 版本时，提示找不到 ../version.h 头文件

解决方法：注释 make yes-STUBS 所在行

bash

../mpi.cpp:18:24: fatal error: ../version.h: No such file or directory
 #include "../version.h"
                        ^
compilation terminated.
make[1]: *** [mpi.o] Error 1
make[1]: Leaving directory `/lustre/home/acct-mseklt/mseklt/yangsl/software/pi-softwares/mylammps/src/Obj_g++_mpich'
make: *** [g++_mpich] Error 2
cp: cannot stat '/lustre/home/acct-mseklt/mseklt/yangsl/software/pi-softwares/mylammps/src/lmp_g++_mpich': No such file or directory

`tbbmalloc` 报错

编译 lmp_intel_cpu_intelmpi 版本，导入 intel-oneapi-compiler、mpi、mkl 模块，提示未找到 tbbmalloc 链接库

解决方法：还需导入 intel-oneapi-tbb/2021.4.0 模块

bash

mpiicpc -std=c++11 -diag-disable=10441 -diag-disable=2196 -qopenmp -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -L/dssg/opt/icelake/linux-centos8-icelake/gcc-8.5.0/intel-oneapi-mkl-2021.4.0-r7h6alnulyzgb6iqvxhovmwrajvwbqxf/mkl/2021.4.0/lib/intel64/ main.o -L../../lib/mlip       -L. -llammps_intel_cpu_intelmpi -l_mlip_interface     -std=c++11 -lgfortran  -ldl -ltbbmalloc -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core   -o ../lmp_intel_cpu_intelmpi
ld: cannot find -ltbbmalloc
make[1]: *** [Makefile:98: ../lmp_intel_cpu_intelmpi] Error 1
make[1]: Leaving directory '/dssg/home/acct-mseklt/mseklt/yangsl/src/MLIP/lammps-stable_23Jun2022/src/Obj_intel_cpu_intelmpi'
make: *** [Makefile:393: intel_cpu_intelmpi] Error 2
cp: cannot stat '../lammps-stable_23Jun2022/src/lmp_intel_cpu_intelmpi': No such file or directory

mlip Intel 版本安装 ​

测试 LAMMPS 2022 版本 ​

遇到的问题 ​

编译成功 ​

manager 编译 mlip-2 出现错误 ​

\r 错误 ​

ARM 平台相关报错 ​

编译 intel_cpu_intelmpi 版本报错 ​

../version.h 报错 ​

tbbmalloc 报错 ​

mlip Intel 版本安装

测试 LAMMPS 2022 版本

遇到的问题

编译成功

manager 编译 mlip-2 出现错误

`\r` 错误

ARM 平台相关报错

编译 intel_cpu_intelmpi 版本报错

`../version.h` 报错

`tbbmalloc` 报错