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标题: cp2k2024.3的intel编译器版安装错误 [打印本页]

作者
Author: lrh4 时间: 2024-10-30 13:46
标题: cp2k2024.3的intel编译器版安装错误
前言：想在学校集群上安装cp2k和vasp（无root权限、centOS7.9，gcc-4.8.5)，但是按照sob、goldNAN、冰释之川等大佬的帖子去安装cp2k2024.3版本，安装过程出现各种错误（gcc编译），各种查资料也没办法解决。

于是开始尝试intel编译器去安装，去oneapi下载最新版的base和HPC组件，配置好环境后开始 cd ~/cp2k-2024.3/tools/toolchain/目录下

运行./install_cp2k_toolchain.sh --mpi-mode=intelmpi --math-mode=mkl --with-intelmpi=system --with-plumed=install --with-openblas=no --with-sirius=no --with-gcc=no --with-mkl=system --with-ninja --with-dftd4命令，然后到libint这里出现如下错误：

MPI is detected and it appears to be Intel MPI
Compiling with 40 processes for target native.
Step gcc took 0.00 seconds.
==================== Finding Intel compiler from system paths ====================
path to icx is /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/icx
path to icpx is /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/icpx
path to ifx is /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/ifx
CC  is /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/icx
CXX is /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/icpx
FC  is /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/ifx
Step intel took 0.00 seconds.
==================== Getting proc arch info using OpenBLAS tools ====================
OpenBLAS detected LIBCORE = haswell
OpenBLAS detected ARCH = x86_64
==================== Installing CMake ====================
cmake-3.30.0 is already installed, skipping it.
Step cmake took 0.00 seconds.
==================== Installing Ninja  ====================
ninja-v1.12.1 is already installed, skipping it.
Step ninja took 0.00 seconds.
==================== Finding Intel MPI from system paths ====================
path to mpiexec is /lustre/home/Liang4CP2K/intel/oneapi/mpi/2021.14/bin/mpiexec
path to mpiicc is /lustre/home/Liang4CP2K/intel/oneapi/mpi/2021.14/bin/mpiicc
path to mpiicpc is /lustre/home/Liang4CP2K/intel/oneapi/mpi/2021.14/bin/mpiicpc
path to mpiifort is /lustre/home/Liang4CP2K/intel/oneapi/mpi/2021.14/bin/mpiifort
Found lib directory /lustre/home/Liang4CP2K/intel/oneapi/mpi/2021.14/lib
libmpi is found in ld search path
libmpicxx is found in ld search path
I_MPI_CXX is icpx
I_MPI_CC  is icx
I_MPI_FC  is ifort
MPICXX is /lustre/home/Liang4CP2K/intel/oneapi/mpi/2021.14/bin/mpiicpc
MPICC    is /lustre/home/Liang4CP2K/intel/oneapi/mpi/2021.14/bin/mpiicc
MPIFC    is /lustre/home/Liang4CP2K/intel/oneapi/mpi/2021.14/bin/mpiifort
Step intelmpi took 0.00 seconds.
==================== Finding MKL from system paths ====================
MKLROOT is found to be /lustre/home/Liang4CP2K/intel/oneapi/mkl/2025.0
libm is found in ld search path
libdl is found in ld search path
Step mkl took 1.00 seconds.
Step fftw took 0.00 seconds.
==================== Installing LIBINT ====================
libint-v2.6.0-cp2k-lmax-5.tgz is found
Installing from scratch into /lustre/home/Liang4CP2K/cp2k-2024.3/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
Using standard ordering of solid harmonic Gaussians
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... /bin/install -c
checking for ranlib... ranlib
checking whether the C++ compiler works... no
configure: error: in `/lustre/home/Liang4CP2K/cp2k-2024.3/tools/toolchain/build/libint-v2.6.0-cp2k-lmax-5':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
sed: can't read fortran/Makefile: No such file or directory
ERROR: (./scripts/stage3/install_libint.sh, line 87) Non-zero exit code detected.

到libint目录下查看config.log文件得到如下信息：

   1  This file contains any messages produced by compilers while
   2  running configure, to aid debugging if configure makes a mistake.
   3
   4  It was created by Libint2 configure 2.6.0, which was
   5  generated by GNU Autoconf 2.69.  Invocation command line was
   6
   7 $ ./configure --prefix=/lustre/home/Liang4CP2K/cp2k-2024.3/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5 --with-cxx=/lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/icpx -O2 -fPIC -fp-model=precise -funroll-loops -g -qopenmp -qopenmp-simd -traceback -xHost -g1 --with-cxx-optflags=-O2 -fPIC -fp-model=precise -funroll-loops -g -qopenmp -qopenmp-simd -traceback -xHost -g1 --enable-fortran --with-pic --libdir=/lustre/home/Liang4CP2K/cp2k-2024.3/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/lib
   8
   9  ## --------- ##
10  ## Platform. ##
11  ## --------- ##
12
13  hostname = ln01
14  uname -m = x86_64
15  uname -r = 3.10.0-1127.el7.x86_64
16  uname -s = Linux
17  uname -v = #1 SMP Tue Mar 31 23:36:51 UTC 2020
18
19  /usr/bin/uname -p = x86_64
20  /bin/uname -X    = unknown
21
22  /bin/arch             = x86_64
23  /usr/bin/arch -k    = unknown
24  /usr/convex/getsysinfo = unknown
25  /usr/bin/hostinfo    = unknown
26  /bin/machine          = unknown
27  /usr/bin/oslevel    = unknown
28  /bin/universe       = unknown
29
30  PATH: /lustre/home/Liang4CP2K/cp2k-2024.3/tools/toolchain/install/ninja-v1.12.1/bin
31  PATH: /lustre/home/Liang4CP2K/cp2k-2024.3/tools/toolchain/install/cmake-3.30.0/bin
32  PATH: /lustre/home/Liang4CP2K/intel/oneapi/mpi/2021.14/bin
33  PATH: /lustre/home/Liang4CP2K/intel/oneapi/mkl/2025.0/bin
34  PATH: /lustre/home/Liang4CP2K/intel/oneapi/dpcpp-ct/2025.0/bin
35  PATH: /lustre/home/Liang4CP2K/intel/oneapi/dev-utilities/2025.0/bin
36  PATH: /lustre/home/Liang4CP2K/intel/oneapi/debugger/2025.0/opt/debugger/bin
37  PATH: /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin
38  PATH: /lustre/home/Liang4CP2K/anaconda3/bin
39  PATH: /lustre/home/Liang4CP2K/intel/oneapi/mpi/2021.14/bin
40  PATH: /lustre/home/Liang4CP2K/intel/oneapi/mkl/2025.0/bin
41  PATH: /lustre/home/Liang4CP2K/intel/oneapi/dpcpp-ct/2025.0/bin
42  PATH: /lustre/home/Liang4CP2K/intel/oneapi/dev-utilities/2025.0/bin
43  PATH: /lustre/home/Liang4CP2K/intel/oneapi/debugger/2025.0/opt/debugger/bin
44  PATH: /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin
45  PATH: /usr/java/jre1.8.0_151/bin
46  PATH: /usr/java/jre1.8.0_151/bin
47  PATH: /opt/software/tsce4/maui/sbin
48  PATH: /opt/software/tsce4/maui/bin
49  PATH: /opt/software/tsce4/torque6/bin
50  PATH: /opt/software/tsce4/torque6/sbin
51  PATH: /usr/local/bin
52  PATH: /usr/lib64/qt-3.3/bin
53  PATH: /usr/local/bin
54  PATH: /bin
55  PATH: /usr/bin
56  PATH: /usr/local/sbin
57  PATH: /usr/sbin
58  PATH: /opt/ibutils/bin
59  PATH: .
60  PATH: /lustre/home/Liang4CP2K/.local/bin
61  PATH: /lustre/home/Liang4CP2K/bin
62
63
64  ## ----------- ##
65  ## Core tests. ##
66  ## ----------- ##
67
68  configure:2658: checking build system type
69  configure:2672: result: x86_64-pc-linux-gnu
70  configure:2692: checking host system type
71  configure:2705: result: x86_64-pc-linux-gnu
72  configure:2725: checking target system type
73  configure:2738: result: x86_64-pc-linux-gnu
74  configure:2979: result: Using standard ordering of solid harmonic Gaussians
75  configure:3007: checking whether make sets $(MAKE)
76  configure:3029: result: yes
77  configure:3052: checking for a BSD-compatible install
78  configure:3120: result: /bin/install -c
79  configure:3174: checking for ranlib
80  configure:3190: found /bin/ranlib
81  configure:3201: result: ranlib
82  configure:3386: checking for C++ compiler version
83  configure:3395: /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/icpx -O2 -fPIC -fp-model=precise -funroll-loops -g -qopenmp -qopenmp-simd -traceback -xHost -g1 --version >&5
84  /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++)
85  /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++)
86  configure:3406: $? = 1
87  configure:3395: /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/icpx -O2 -fPIC -fp-model=precise -funroll-loops -g -qopenmp -qopenmp-simd -traceback -xHost -g1 -v >&5
88  /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++)
89  /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++)
90  configure:3406: $? = 1
91  configure:3395: /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/icpx -O2 -fPIC -fp-model=precise -funroll-loops -g -qopenmp -qopenmp-simd -traceback -xHost -g1 -V >&5
92  Intel(R) oneAPI DPC++/C++ Compiler for applications running on Intel(R) 64, Version 2025.0.0 Build 20241008
93  Copyright (C) 1985-2024 Intel Corporation. All rights reserved.
94
95  configure:3406: $? = 0
96  configure:3395: /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/icpx -O2 -fPIC -fp-model=precise -funroll-loops -g -qopenmp -qopenmp-simd -traceback -xHost -g1 -qversion >&5
97  /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++)
98  /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++)
99  configure:3406: $? = 1
100  configure:3426: checking whether the C++ compiler works
101  configure:3448: /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/icpx -O2 -fPIC -fp-model=precise -funroll-loops -g -qopenmp -qopenmp-simd -traceback -xHost -g1 -O2 -fPIC -fp-model=precise -funroll-loops -g -qopenmp -qopenmp-simd -traceback -xHost conftest.cpp  >&5
102  /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++)
103  /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++)
104  configure:3452: $? = 1
105  configure:3490: result: no
106  configure: failed program was:
107  | /* confdefs.h */
108  | #define PACKAGE_NAME "Libint2"
109  | #define PACKAGE_TARNAME "libint2"
110  | #define PACKAGE_VERSION "2.6.0"
111  | #define PACKAGE_STRING "Libint2 2.6.0"
112  | #define PACKAGE_BUGREPORT "libint@valeyev.net"
113  | #define PACKAGE_URL ""
114  | #define LIBINT2_BUILDID ""
115  | #define LIBINT2_VERSION "2.6.0"
116  | #define LIBINT_SHGSHELL_ORDERING 1
117  | /* end confdefs.h.  */
118  |
119  | int
120  | main ()
121  | {
122  |
123  | ;
124  | return 0;
125  | }
126  configure:3495: error: in `/lustre/home/Liang4CP2K/cp2k-2024.3/tools/toolchain/build/libint-v2.6.0-cp2k-lmax-5':
127  configure:3497: error: C++ compiler cannot create executables
128  See `config.log' for more details
129

请各位大佬帮忙分析是什么原因？？无root权限的我该如何解决？？十分感谢！！！

作者
Author: Uus/pMeC6H4-/キ 时间: 2024-10-30 14:15
本帖最后由 Uus/pMeC6H4-/キ于 2024-10-30 14:23 编辑

Intel编译器具体是什么版本？在学校集群上用module list和module avail查查看，有没有现成的Intel OneAPI模块可供调用？按理说这样的编译环境应该是集群管理员统一配置的，自己没root权限的话下载安装可能会有问题。用icc --version ; icpc --version ; ifort --version可以查看编译器版本。

看Finding Intel compiler from system paths那一段输出，找到的Intel编译指令是比较新的icx、icpx、ifx，但是CP2K官方的编译器支持列表认为应该用Intel的经典编译器。我之前也因为Intel编译器的问题折腾了几天，后来解决的方法是在运行install_cp2k_toolchain.sh时，用--with=intel=system并同时指定--with-intel-classic=yes，或许可以参考一下。

（这个列表也明确提到，GCC 4.8.5在x86_64系统上不能支持CP2K编译）

作者
Author: abin 时间: 2024-10-30 15:16
问题在于:
/lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by

需要高版本的GLIBC

你可以问问AI, Linux发行版,如何升级GLIBC版本?

CentOS7.9 提供的套件太古老, 无法编译cp2k.2024.3版本的.
需要其他的技能.

同时, 你采用的编译方式, 用到-xHost选项,
如果主控节点master node, 和计算节点/slave node处理器支持的指令集不同,
可能遭遇某些计算运行失败.
并不是说, 不能编译, 而是编译成功后, 会部分环节运算失败.

作者
Author: lrh4 时间: 2024-10-30 15:43

Uus/pMeC6H4-/キ发表于 2024-10-30 14:15
Intel编译器具体是什么版本？在学校集群上用module list和module avail查查看，有没有现成的Intel OneAPI模 ...

我看了您的帖子，我再试试看，十分感谢！！！

作者
Author: lrh4 时间: 2024-10-30 15:44

abin 发表于 2024-10-30 15:16
问题在于:
/lustre/home/Liang4CP2K/intel/oneapi/compiler/2025.0/bin/compiler/clang++: /lib64/libc.so ...

明白了，那还是清空所有，再老老实实装2024.1版本

。十分感谢您！！

作者
Author: zzyzz 时间: 2024-11-6 16:54

lrh4 发表于 2024-10-30 15:44
明白了，那还是清空所有，再老老实实装2024.1版本。十分感谢您！！

您好想请问一下您安装成功了吗？

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