编译MPI并行版OpenMolcas的时候，在configuring这一步总是出现“error: could not ...

wanlichuan

最近按照邹老师《编译MPI并行版OpenMolcas.md》（https://gitlab.com/jxzou/qcinsta ... %89%88OpenMolcas.md）的方法编译MPI并行版OpenMolcas，在HDF5库、GA库这两步都没遇到问题（intel编译器和GNU编译器都能成功），但是在编译MPI版OpenMolcas时，configuring这一步一直无法成功（make之前的那一步，也还没到“把Libxc放到相应目录下，让OpenMolcas自动识别并编译它”这一步），尝试了各种方法，出现的错误信息一直是一样的。

用GNU编译器所用指令和错误信息如下：

~/software/OpenMolcas-v24.02/build$CC=gcc CXX=g++ F77=gfortran FC=gfortran MPICC=mpiccMPICXX=mpicxx cmake -DLINALG=MKL -DMPI=ON -DGA=ON -DMPIEXEC_EXECUTABLE=$HOME/openmpi416/bin/mpiexec  -DCMAKE_INSTALL_PREFIX=$HOME/software/OpenMolcas2402..

-- The Fortran compiler identification isGNU 9.4.0

-- The C compiler identification is GNU9.4.0

-- Detecting Fortran compiler ABI info

-- Detecting Fortran compiler ABI info -done

-- Check for working Fortran compiler:/usr/bin/gfortran - skipped

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Check for working C compiler:/usr/bin/gcc - skipped

-- Detecting C compile features

-- Detecting C compile features - done

-- Found Python:/opt/intel/oneapi/intelpython/latest/bin/python3.9 (found version"3.9.7") found components: Interpreter

Configuring compilers:

Detecting Molcas version info:

-- OPENMOLCAS_VERSION: v24.02 ?

Detecting system info:

-- OS: Linux-x86_64

-- ADDRMODE: 64

-- PLATFORM: LINUX64

Configuring with MPI parallellization:

-- Found MPI_C: /home/wlc/openmpi416/lib/libmpi.so(found version "3.1")

-- Found MPI_Fortran: /home/wlc/openmpi416/lib/libmpi_usempif08.so(found version "3.1")

-- Found MPI: TRUE (found version"3.1")  

-- MPI_C_INCLUDE_PATH: /home/wlc/openmpi416/include

-- MPI_Fortran_INCLUDE_PATH: /home/wlc/openmpi416/include;/home/wlc/openmpi416/lib

-- MPI_C_LIBRARIES: /home/wlc/openmpi416/lib/libmpi.so

-- MPI_Fortran_LIBRARIES: /home/wlc/openmpi416/lib/libmpi_usempif08.so;/home/wlc/openmpi416/lib/libmpi_usempi_ignore_tkr.so;/home/wlc/openmpi416/lib/libmpi_mpifh.so;/home/wlc/openmpi416/lib/libmpi.so

-- MPIEXEC: /home/wlc/openmpi416/bin/mpiexec

-- MPI_IMPLEMENTATION: openmpi

Configuring HDF5 support:

-- Found HDF5: hdf5-shared (found version"1.14.4") found components: C

-- HDF5_INCLUDE_DIRS: /home/wlc/software/hdf5-1.14.4/include

-- HDF5_C_LIBRARIES: hdf5-shared

Configuring linear algebra libraries:

-- Using Intel Math Kernel Library (MKL)

-- MKLROOT = /opt/intel/oneapi/mkl/2022.0.2

-- MKL_INCLUDE_PATH =/opt/intel/oneapi/mkl/2022.0.2/include

-- MKL_LIBRARY_PATH =/opt/intel/oneapi/mkl/2022.0.2/lib

-- LINALG_LIBRARIES:/opt/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_scalapack_ilp64.so;/opt/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_gf_ilp64.so;/opt/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_core.so;/opt/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_sequential.so;/opt/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_blacs_openmpi_ilp64.so

Configuring Libxc:

-- Configuring built-in Libxc

CMake Error at/opt/cmake-3.28.6/share/cmake-3.28/Modules/ExternalProject.cmake:2919(message):

error: could not find git for clone of Libxc

Call Stack (most recent callfirst):

/opt/cmake-3.28.6/share/cmake-3.28/Modules/ExternalProject.cmake:4427(_ep_add_download_command)

CMakeLists.txt:1237 (ExternalProject_Add)

-- Configuring incomplete, errors occurred!

用intel编译器所用指令和错误信息如下：

~/software/OpenMolcas-v24.06/build$ CC=icc CXX=icpc F77=ifort FC=ifort MPICC=mpiccMPICXX=mpicxx cmake -DLINALG=MKL -DMPI=ON -DGA=ON-DMPIEXEC_EXECUTABLE=/$HOME/software/openmpi416/bin/mpiexec-DCMAKE_INSTALL_PREFIX=$HOME/software/openmolcas2406 ..

Configuring compilers:

Detecting Molcas version info:

-- OPENMOLCAS_VERSION: v24.06 ?

Detecting system info:

-- OS: Linux-x86_64

-- ADDRMODE: 64

-- PLATFORM: LINUX64

Configuring with MPI parallellization:

-- MPI_C_INCLUDE_PATH: /home/wlc/software/openmpi416/include

-- MPI_Fortran_INCLUDE_PATH: /home/wlc/software/openmpi416/include;/home/wlc/software/openmpi416/lib

-- MPI_C_LIBRARIES: /home/wlc/software/openmpi416/lib/libmpi.so

-- MPI_Fortran_LIBRARIES: /home/wlc/software/openmpi416/lib/libmpi_usempif08.so;/home/wlc/software/openmpi416/lib/libmpi_usempi_ignore_tkr.so;/home/wlc/software/openmpi416/lib/libmpi_mpifh.so;/home/wlc/software/openmpi416/lib/libmpi.so

-- MPIEXEC: /home/wlc/software/openmpi416/bin/mpiexec

-- MPI_IMPLEMENTATION: openmpi

Configuring HDF5 support:

-- HDF5_INCLUDE_DIRS: /home/wlc/software/hdf5-1-14-4/include

-- HDF5_C_LIBRARIES: hdf5-shared

Configuring linear algebra libraries:

-- Using Intel Math Kernel Library (MKL)

-- MKLROOT = /opt/intel/oneapi/mkl/2022.0.2

-- MKL_INCLUDE_PATH =/opt/intel/oneapi/mkl/2022.0.2/include

-- MKL_LIBRARY_PATH =/opt/intel/oneapi/mkl/2022.0.2/lib

-- LINALG_LIBRARIES:/opt/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_scalapack_ilp64.so;/opt/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_intel_ilp64.so;/opt/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_core.so;/opt/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_sequential.so;/opt/intel/oneapi/mkl/2022.0.2/lib/intel64/libmkl_blacs_openmpi_ilp64.so

Configuring Libxc:

-- Configuring built-in Libxc

CMake Error at/snap/cmake/1413/share/cmake-3.30/Modules/ExternalProject/shared_internal_commands.cmake:951(message):

error: could not find git for clone of Libxc

Call Stack (most recent callfirst):

/snap/cmake/1413/share/cmake-3.30/Modules/ExternalProject.cmake:3035(_ep_add_download_command)

CMakeLists.txt:1237 (ExternalProject_Add)

-- Configuring incomplete, errors occurred!

我尝试的方法有：

1）换各种版本的Libxc和OpenMolcas，尽量尝试原文教程相同的组合；

2）把解压并改名后的Libxc放在多个不同的目录下，差不多让程序随时都能找到Libxc；

3）除直接解压外，还用make& make install 命令安装了Libxc，并且也写了环境变量；

4）openMPI试过了4.1.6和4.1.1两个版本；

5）激活或不激活anaconda；

6）修改CMakeLists.txt文件，去掉configuring Libxc的部分：

#Libxc settings

#===============

message("Configuring Libxc:")

if(EXTERNAL_LIBXC)

……  ……

endif()

#Global Arrays settings

#=======================

Configure可以成功，但是到下一步的make操作，进行到26%需要build Libxc部分时仍然会出错：

[26%] Building Fortran objectCMakeFiles/dft_util/CMakeFiles/dft_util_obj.dir/libxc_parameters.F90.o

/home/wlc/software/OpenMolcas-v24.02/src/dft_util/libxc_parameters.F90(17):error #7002: Error in opening the compiled module file.  Check INCLUDE paths.   [XC_F03_LIB_M]

……  ……

一直无法解决这个错误。请大佬赐教，应该如何解决这个错误呢？

谢谢

wanlichuan

好的

wanlichuan

zjxitcc 发表于 2024-9-29 11:58
最好不要使用Intel MPI。在编译前检查一下openmpi环境变量，例如
which mpirun
mpirun --version

邹老师，一开始用的intel编译器是2022.1.2.146，openmpi是4.1.6，写指令的时候指定了openmpi目录（和which mpirun得到的相同）。make进行到67%时出现的错误本来以为是MPI的版本不合适。于是后来完全采用您教程中的版本：
Intel_Parallel_Studio_XE_2019
OpenMolcas-v22.10.tar.gz
libxc-5.2.2.tar.gz
hdf5-hdf5-1_14_1-2.tar.gz
ga-5.8.1.tar.gz
openmpi-4.1.1.tar.gz
这一次，make之前都没问题，但是执行make，运行到64%时还是出错。
后来换成GNU编译器，竟然成功了。
多谢邹老师。

zjxitcc

wanlichuan 发表于 2024-9-28 16:33
谢谢邹老师，的确，装上git后，configure就通过了。原来以为只要联网就行，没想到需要安装git。
但是make ...

最好不要使用Intel MPI。在编译前检查一下openmpi环境变量，例如
which mpirun
mpirun --version
编译时看看输出内容里MPI识别为哪一种。有的人机器上有不止一种MPI，环境变量也没写成使用目标MPI的形式，很容易发生错误。

wanlichuan

谢谢邹老师，的确，装上git后，configure就通过了。原来以为只要联网就行，没想到需要安装git。
但是make进行到67%又出现了一些新的问题：
[ 67%] Building Fortran object CMakeFiles/system_util/CMakeFiles/system_util_obj.dir/xabort.F90.o
/home/wlc/software/OpenMolcas-v24.02/src/system_util/xabort.F90(16): error #7013: This module file was not generated by any release of this compiler.   [MPI]
use mpi, only: MPI_COMM_WORLD
----^
/home/wlc/software/OpenMolcas-v24.02/src/system_util/xabort.F90(23): error #6683: A kind type parameter must be a compile-time constant.   [IWP]
integer(kind=iwp) :: rc
-------------^
……  ……
Google了一下，大概是mpi的版本不合适。我再重新编译吧，多谢邹老师。

wanlichuan

啥也不显示，看来真是没装git。我装上试试。

zjxitcc

你的机器上是不是没有git？运行which git显示啥？