超详细CP2K编译过程，GNU9.3+intel MKL+openmpi【含视频】

biogon

ShuangfeiZhu 发表于 2020-9-22 16:02
各位老师，前面都没问题，后面报错如下，请问该怎么解决

(base) [room@localhost cp2k-7.1.0]$ make -j  ...

在/cp2k/exts 路径下执行

1. git clone https://github.com/cp2k/dbcsr.git
   

复制代码

如提示fypp有问题，则再在/cp2k/exts/dbcsr下执行

1. git submodule update --init
   

复制代码

myyang

haibeih 发表于 2020-9-10 20:29
借个楼提醒一下，gcc版本最重要，特别注意用这种方法编译cp2k时，需要python也是用官网推荐的gcc版本编译 ...

您好，我想请教您一个问题： 我在make CP2K 时， popt 可以顺利通过，但psmp 就会出现错误。 而且生成的cp2k.popt 在运行使用CPU 并行 mpirun -np N  的时候会crash, 单个CPU则可以正常通过，我感觉这是openmpi 的问题（根据你的建议自己安装的最新4.0.5版），请问你遇到过这样的问题了吗？如何解决？谢谢

biogon

myyang 发表于 2021-4-27 15:23
您好，我想请教您一个问题： 我在make CP2K 时， popt 可以顺利通过，但psmp 就会出现错误。 而且生成的c ...

你的什么编译器编译的openmpi？

learnerNONE

各位老师，我目前在用toolchain的方法编译CP2K8.1, 一切顺利直到编译quip。

编译过程的信息很少：
...
==================== Installing QUIP ====================
QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705.tar.gz is found
Installing from scratch into /home/bin/cp2k_pool/cp2k-8.1/tools/toolchain/install/quip-1ff93b3400b83e804f0f2e857e70c5e4133d9705
ERROR: (./scripts/install_quip.sh, line 100) Non-zero exit code detected.

于是我去翻看了make.log文件，发现问题全在MPI的相关库文件缺失：
...
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_dblprec'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Isend'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_f2c'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Op_f2c'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_vector'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Alltoall'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Finalize'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Sendrecv'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /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/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Op_c2f'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_size'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_real'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Group_free'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_indexed'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Barrier'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_commit'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /opt/intel/compilers_and_libraries_2020.4.304/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_c2f'
/opt/rh/devtoolset-9/root/usr/libexec/gcc/x86_64-redhat-linux/9/ld: /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 `/home/bin/cp2k_pool/cp2k-8.1/tools/toolchain/build/QUIP-1ff93b3400b83e804f0f2e857e70c5e4133d9705/build/linux_x86_64_gfortran'
make: *** [Programs] Error 2

网上有人遇到类似情况（不是编译cp2k），解决方法是用intelmpi进行编译（没有说明问题原因）。但是我使用的是AMD核，且之前都没有用intelmpi编译，我怕两种编译运行后会有不兼容情况，而也并不清楚intel在AMD核上会不会比openmpi更高效。

请问这种情况有什么办法解决吗？谢谢！

abin

learnerNONE 发表于 2021-8-2 20:57
各位老师，我目前在用toolchain的方法编译CP2K8.1, 一切顺利直到编译quip。

编译过程的信息很少：

能解决你的问题吗?

http://bbs.keinsci.com/thread-24469-1-1.html

learnerNONE

abin 发表于 2021-8-2 23:35
能解决你的问题吗?

http://bbs.keinsci.com/thread-24469-1-1.html

感谢abin老师的回复！

我看了您给的教程，确实非常快捷方便，但是结尾提到这个是官方的预编译版本，我担心这会牺牲一点效率。而我目前使用的这个方法只剩一个quip无法解决，只是一步之遥了，可以的话，还是希望一套方法下来把quip编译好。之前也花了很多时间出坑，现在直接放弃，有点舍不得。

abin

learnerNONE 发表于 2021-8-3 09:50
感谢abin老师的回复！

我看了您给的教程，确实非常快捷方便，但是结尾提到这个是官方的预编译版 ...

我有提及，
如果自己本地优化编译搞不定，
那就采用预编译的版本。

效率嘛，自己测试看了。

如果采用intel套件，全程本地优化编译，
请特别留意，
保证所有的套件都才用intel来编译。

8.2.0版本，有要求，libxc cosma版本。

我试了才用intel工具链，有几个算例有错误。
不过7.1是全盘通过，可以支持AVX512指令集。

abin

learnerNONE 发表于 2021-8-2 20:57
各位老师，我目前在用toolchain的方法编译CP2K8.1, 一切顺利直到编译quip。

编译过程的信息很少：

https://github.com/cp2k/cp2k/issues/1617

Lucien1234,
这是你吗?

RHEL中, devtoolset-9, 应该是9.1.1吧?

既然自己编译, 看看CP2K官方支持说明呀.
https://www.cp2k.org/dev:compiler_support
其中 x86_64平台, GCC版本5.5, 7.3, 7.5, 8.3, 8.4, 9.3, 10.2, 均可.

大致的原因是,
你采用的编译器捣鼓的openMPI 或者MPICH, 和你所采用的MKL不兼容.

推荐方案,
更换编译器为官方推荐版本.
采用官方推荐的intel编译器对应的MKL版本.

重新打包处理OpenMPI或者MPICH.

或者, 我能搞定.
cp2k 8.1 8.2 GNU+MKL, 算例测试全通过.

祝好.

learnerNONE

abin 发表于 2021-8-3 10:53
https://github.com/cp2k/cp2k/issues/1617

Lucien1234,

非常感谢abin老师的耐心回复～

那个是我，我在github上也开了一个问题。

可能是版本的原因，但不是很确定，因为我查gcc --version的时候确实是9.3.1.后面我又按刘博i方法尝试了安装cp2k7.1，发现openmpi的版本是4.0.1，这个版本下的quip搭配2020mkl是可以正常安装的。

Intel的编译器过期了，暂时还没有新的，只能申请到了再试试...

试过多次8.1的安装无果，现已决定躺平，就用7.1的好了...

Siling_S

请问刘博，服务器默认的编译器是intelmpi，是否需要注释掉或者改成openmpi？因为按照您的方法编出来的CP2K跑多核并行的时候速度还没有单核快，所以猜是不是编译过程出了问题。。

hitvip

刘老师，您好，我的系统是 CentOS Linux release 8.4.2105
想安装 cp2k8.2，运行了：

1. > --math-mode=mkl \
   
2. > --with-openmpi=install \
   
3. > --with-scalapack=no \
   
4. > --with-ptscotch=install \
   
5. > --with-parmetis=install \
   
6. > --with-metis=install \
   
7. > --with-superlu=install \
   
8. > --with-pexsi=install \
   
9. > --with-quip=install \
   
10. > --with-plumed=install
    

复制代码

但是提示错误：不认识 metis和parmetis选项：

(./install_cp2k_toolchain.sh) Unknown flag: --with-metis=install
(./install_cp2k_toolchain.sh) Unknown flag: --with-parmetis=install

是因为我的gcc版本是8.4.1，而不是9吗？

谢谢

hitvip

也无法安装 scl 包。提示

1. sudo yum install centos-release-scl scl-utils-build
   
2. Last metadata expiration check: 1:01:59 ago on Sat 04 Sep 2021 06:39:54 AM EDT.
   
3. No match for argument: centos-release-scl
   
4. Error: Unable to find a match: centos-release-scl
   

复制代码

喵星大佬

hitvip 发表于 2021-9-4 19:33
刘老师，您好，我的系统是 CentOS Linux release 8.4.2105
想安装 cp2k8.2，运行了：

cp2k 8系列不需要写着两个，就用系统自带的gcc8.4就可以了

hitvip

喵星大佬 发表于 2021-9-5 06:38
cp2k 8系列不需要写着两个，就用系统自带的gcc8.4就可以了

非常感谢您的解答，如您所说，我去掉了那两个软件包，并且采用cent8自带的gcc 8.4.1 来编译，但是我现在就差 QUIP 编译不过去，其它都没有问题。

提示： ERROR: (./scripts/stage6/install_quip.sh, line 107) Non-zero exit code detected.
搜了下论坛，也有人遇到了这个问题（http://bbs.keinsci.com/thread-20432-1-1.html），但没有给出解决办法。麻烦大家给看看，谢谢。

这是我用的toochain：

1. ./install_cp2k_toolchain.sh \
   
2. --with-openmpi=install \
   
3. --with-cmake=install \
   
4. --with-libint=install \
   
5. --with-ptscotch=install  \
   
6. --with-pexsi=install \
   
7. --with-superlu=install \
   
8. --with-quip=install \
   
9. --with-plumed=install \
   
10. --with-sirius=install \
    
11. --with-cosma=install

复制代码

然后我查了下QUIP编译出错的log，似乎是mkl引起的问题，部分log文件内容如下：

1. Making Programs
   
2. 
   
3. ********************************************
   
4. rm -f /home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/build/linux_x86_64_gfortran/Makefile
   
5. cp /home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/src/Programs/Makefile /home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/build/linux_x86_64_gfortran/Makefile
   
6. make -C /home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/build/linux_x86_64_gfortran QUIP_ROOT=/home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd VPATH=/home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/src/Programs -I/home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd -I/home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/arch
   
7. make[1]: Entering directory '/home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/build/linux_x86_64_gfortran'
   
8. gfortran  -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC -g  -I/home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/src/libAtoms -I/home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/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  /home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/src/Programs/vacancy_map_mod.f95 -o vacancy_map_mod.o
   
9. gfortran  -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC -g  -I/home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/src/libAtoms -I/home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/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  /home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/src/Programs/quip.f95 -o quip.o
   
10. gfortran  -o quip  quip.o vacancy_map_mod.o -L. -lquiputils -lquip_core  -latoms  -O3  -L/home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/src/fox/objs.linux_x86_64_gfortran/lib -lFoX_sax -lFoX_wxml -lFoX_utils -lFoX_common -lFoX_fsys  -L/home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64 -Wl,-rpath=/home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64 -lmkl_scalapack_lp64 -Wl,--start-group -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_openmpi_lp64 -Wl,--end-group -lpthread -lm -ldl  
    
11. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Waitall'
    
12. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_comm_null'
    
13. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Abort'
    
14. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Waitany'
    
15. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_f2c'
    
16. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Wtime'
    
17. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_dup'
    
18. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_double'
    
19. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Op_free'
    
20. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_create'
    
21. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Group_incl'
    
22. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Attr_get'
    
23. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_dblcplex'
    
24. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Init'
    
25. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_create_struct'
    
26. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Bcast'
    
27. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Alltoallv'
    
28. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Cart_create'
    
29. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Scatterv'
    
30. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Initialized'
    
31. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_free'
    
32. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Iprobe'
    
33. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Testall'
    
34. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Allgatherv'
    
35. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_group'
    
36. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Cart_sub'
    
37. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_split'
    
38. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Send'
    
39. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Allreduce'
    
40. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_packed'
    
41. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_op_max'
    
42. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_op_maxloc'
    
43. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_op_min'
    
44. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Rsend'
    
45. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_byte'
    
46. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Irecv'
    
47. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_contiguous'
    
48. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Recv'
    
49. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_free'
    
50. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_comm_world'
    
51. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Address'
    
52. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_compare'
    
53. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_float'
    
54. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Reduce'
    
55. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Pack'
    
56. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_request_null'
    
57. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_cplex'
    
58. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_unsigned_short'
    
59. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_c2f'
    
60. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Gatherv'
    
61. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Wait'
    
62. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Allgather'
    
63. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_double_int'
    
64. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Op_create'
    
65. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_int'
    
66. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Pack_size'
    
67. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_long_long_int'
    
68. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Unpack'
    
69. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_integer'
    
70. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Test'
    
71. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_dblprec'
    
72. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Isend'
    
73. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_f2c'
    
74. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Op_f2c'
    
75. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_ub'
    
76. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_vector'
    
77. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Alltoall'
    
78. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Finalize'
    
79. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Sendrecv'
    
80. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_op_sum'
    
81. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Op_c2f'
    
82. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_size'
    
83. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `ompi_mpi_real'
    
84. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Group_free'
    
85. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_indexed'
    
86. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Barrier'
    
87. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_commit'
    
88. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Type_c2f'
    
89. /home/pfg/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so: undefined reference to `MPI_Comm_rank'
    
90. collect2: error: ld returned 1 exit status
    
91. make[1]: *** [Makefile:71: quip] Error 1
    
92. make[1]: Leaving directory '/home/pfg/Apps/cp2k-8.2/tools/toolchain/build/QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd/build/linux_x86_64_gfortran'
    
93. make: *** [Makefile:155: Programs] Error

复制代码

喵星大佬

hitvip 发表于 2021-9-5 10:07
非常感谢您的解答，如您所说，我去掉了那两个软件包，并且采用cent8自带的gcc 8.4.1 来编译，但是我现在 ...

不用mkl就好了。。。。