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本帖最后由 lrh4 于 2025-4-2 14:54 编辑
前言:想在学校集群上安装cp2k-2025.1(无root权限、centOS7.9,gcc-4.8.5),超算上有module,输入module av得到:
------------------------------------------------------------------------------- /public/software/modules --------------------------------------------------------------------------------
apps/abinit/intelmpi/9.4.2 benchmark/hpcg/intelmpi/2017 compiler/cmake/3.20.1 mathlib/hdf5/gnu/1.12.0 mathlib/netcdf/intel/4.7.4
apps/anaconda3/2021.05 benchmark/hpl/intelmpi/2.2 compiler/gcc/7.3.1 mathlib/hdf5/intel/1.12.0 mathlib/petsc/intelmpi/3.15.0
apps/arwpost/intel/3.0 benchmark/i7z/gnu/0.28 compiler/intel/2021.3.0 mathlib/jasper/gnu/1.900.1 mpi/intelmpi/2021.3.0
apps/cp2k/intelmpi/8.1 benchmark/imb/intelmpi/2017 mathlib/fftw/intelmpi/3.3.9_double mathlib/jasper/intel/1.900.1 mpi/openmpi/gnu/4.0.3
apps/gromacs/intelmpi/2021.5 benchmark/iozone/gnu/3.430 mathlib/fftw/intelmpi/3.3.9_single mathlib/lapack/gnu/3.9.1 mpi/openmpi/intel/4.0.3
apps/ncl/gnu/6.6.2 benchmark/mpigraph/intelmpi/1.4 mathlib/gsl/gnu/2.6 mathlib/lapack/intel/3.9.1
apps/vasp/intelmpi/5.4.4 benchmark/stream/intel/5.10 mathlib/gsl/intel/2.6 mathlib/netcdf/gnu/4.7.4
但是不知道能否满足cp2k-2025.1的按照需求。按照社长的教程安装时总是在gcc这一步出错,无法安装gcc-14,故考虑使用其他方法安装。
因此这一次尝试使用spack安装cp2k。按照帖子使用包管理器spack安装cp2k的方法分享 - 第一性原理 (First Principle) - 计算化学公社 (keinsci.com)以及帖子记在超算上用spack安装cp2k 2024.1的过程的步骤。
前面几步都挺成功,能够安装gcc-14.2.0,openmpi5.0.6。但是接下来想安装带有dftd4的cp2k-2025.1时出错。
通过以下命令安装:spack install cp2k@2025.1 %gcc@14.2.0 +plumed +dftd4 ^openmpi@5.0.6
进行到 Installing multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy [49/62] 时出现错误:
(base) [llshu219@admin2 spack]$ spack install cp2k@2025.1 %gcc@14.2.0 +plumed +dftd4 ^openmpi@5.0.6
[+] /usr (external glibc-2.17-pjghjgm7je36u4vfmhdpecf3ileqewnj)
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/compiler-wrapper-1.0-lhacife6xviglorxk2bws22rtxssd5zm
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/gcc-runtime-4.8.5-ijk5nxbjzrc3dzmz5q6bwbotwf5lppd6
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/gcc-runtime-14.2.0-63x7leuv62km4hjbpxq4rkj22t4q4q3i
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/zlib-ng-2.2.3-ygo5tstc5lvdzxfkafvb7xwsfeo4idbv
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/gmake-4.4.1-ozr7xh2blngvw5b7r7gvgahuyv23n7vl
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/libxc-7.0.0-b63rhgde6pnvoot57wmachssbmejojra
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/ninja-1.12.1-fkxjme5hkfumqcqboockiqsptawulrvf
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/pigz-2.8-vktqf7edpgjdzsp47mkrwtbezfi63dim
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/pkgconf-2.3.0-4losfnewdjcieqjzons5sqqcgj7zkhdt
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/libxcrypt-4.4.38-xls5l4mphvj7njzq3p2s5wobhaop7hgv
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/xz-5.6.3-mpxab7xvoybghi3biw6cf5bda2uugmmh
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/openssl-3.4.1-zlad2u7en6j6bnftiw56ny45insafjzj
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/icu4c-74.2-a4iq2mfoh7ghluwqxzmf5vgwy5shai3u
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/bzip2-1.0.8-wg4gewicfzhof7nk74vci7zmoorx4544
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/zstd-1.5.6-zqmzoo64nqese7t77dk3z3ef3ogywtnk
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/libxsmm-1.17-w7levva45avbtlpv2ws7jcs45cz5xbpn
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/eigen-3.4.0-tydzwtnn2idtzua4kwjmgyvukhhdvtpt
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/openblas-0.3.29-m6sd4467gr4oyiyrfkl2n4iq67hb6hvj
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/numactl-2.0.18-5calyfaym4pa5wdudhpw3y3trrwmcjgj
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/gmp-6.3.0-pqszx4fmnjx6ut7ojzcjwnikyrhsthl5
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/libffi-3.4.6-vvnd6of5xa3pcvr7jwj6i6aficifw4sc
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/libmd-1.1.0-icdxg4x7jpbqwpgh3raqpw5zxubaea6l
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/libiconv-1.17-rdvq5mqsaeoz3hbdhlqua3abovupitiz
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/gsl-2.8-s6ad7zslwfv7n2nusrvcfqx4mxz7gybl
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/libpciaccess-0.17-xb4b7nk6d4qqdr2vhxfhsnikyznqaqrm
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/mctc-lib-0.3.1-bgx22narruurio3vka22hqraoprpsa6u
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/nghttp2-1.65.0-nrszzp5dc4opefouwthcn67ttrg4kuga
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/ncurses-6.5-axb2g2wrzcmz5yzzzb7oxsjgzm5skemc
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/util-linux-uuid-2.40.4-zh2bwhvubpf3pursrji2nz53bu72vhqv
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/libevent-2.1.12-ccp3jctntqjm2ppxkjyy2ed725lkrxpt
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/boost-1.87.0-kictyfbz6jx4lmssb2vew6rxufpgj7ky
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/mpfr-4.2.1-wlhonemw7ivgrn6kcizktjxejxvk7lme
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/libbsd-0.12.2-p7yejspsckimub7gjpfreoowsl2ww7i7
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/libxml2-2.13.5-6vgysaw3igozoymrlvtnemkthbc6aesc
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/tar-1.35-47265wgnuq6bqz5vzclabahfpovqzoic
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/curl-8.11.1-3umyngjgsypohjikyis5t2godfnqi7xg
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/readline-8.2-72wtvcoznfrfyn2iiouamgdje4lbp22j
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/libedit-3.1-20240808-5gvvzbsjcjnmkzte547ns4fg7pioxnww
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/libint-2.9.0-xvjhuczrrw3hau4opstrh252wsdpwhq7
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/mpc-1.3.1-c2d7qdhhur2gakhltxn765q66hotm7hi
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/expat-2.7.1-yi2fjkly635ybrd6xdlg3gdxuxuqxeng
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/hwloc-2.11.1-fnvlavgrh4su4fic5rhl4w7jvdlferuu
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/gettext-0.21.1-4x557vbab6yu754bmbeine3a5566assm
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/cmake-3.31.6-rdak4y4ert3gua5zyfov4pkvmgdsu7mj
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/sqlite-3.46.0-hk47mrzqos5w5ezdrpfd75rul4qjwvoy
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/gdbm-1.23-xyvj5qtprslvvc3cub7a2xgikvafs2eq
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/gcc-14.2.0-vlcduxsnfrb6y5jilblel2so7guydnwx
==> Installing multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy [49/62]
==> No binary for multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy found: installing from source
==> Using cached archive: /mnt/public/home/llshu219/spack/spack/var/spack/cache/_source-cache/archive/18/180541714c26804a2d66edd892c8cd4cb40a21acbaf7edb24aaf04d580368b97.tar.xz
==> No patches needed for multicharge
==> multicharge: Executing phase: 'cmake'
==> multicharge: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
'/mnt/public/home/llshu219/spack/spack/opt/spack/linux-haswell/gmake-4.4.1-ozr7xh2blngvw5b7r7gvgahuyv23n7vl/bin/make' '-j16'
19 errors found in build log:
73 [ 23%] Building Fortran object subprojects/mstore/CMakeFiles/mstore-lib.dir/src/mstore_version.f90.o
74 cd /tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-build-tgea2dc/subprojects/mstore && /usr/bin/f95 -I/tmp/llshu219/spack-st
age/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-build-tgea2dc/subprojects/mstore/include -I/mnt/public/home/llshu219/spack/spack/opt/spack/linux-ca
scadelake/mctc-lib-0.3.1-bgx22narruurio3vka22hqraoprpsa6u/include -I/mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/mctc-lib-0.3.1-bgx22narruurio3vka22hqr
aoprpsa6u/include/mctc-lib/GNU-14.2.0 -O3 -Jinclude -fPIC -c /tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-src/subprojects/
mstore/src/mstore_version.f90 -o CMakeFiles/mstore-lib.dir/src/mstore_version.f90.o
75 /tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-src/src/multicharge/data/covrad.f90:17.7:
76
77 use mctc_env, only : wp
78 1
>> 79 Fatal Error: File 'mctc_env.mod' opened at (1) is not a GNU Fortran module file
>> 80 make[2]: *** [CMakeFiles/multicharge-lib.dir/build.make:81: CMakeFiles/multicharge-lib.dir/src/multicharge/data/covrad.f90.o] Error 1
81 /tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-src/src/multicharge/ewald.f90:17.7:
82
83 use mctc_env, only : wp
84 1
>> 85 Fatal Error: File 'mctc_env.mod' opened at (1) is not a GNU Fortran module file
86 make[2]: *** Waiting for unfinished jobs....
>> 87 make[2]: *** [CMakeFiles/multicharge-lib.dir/build.make:146: CMakeFiles/multicharge-lib.dir/src/multicharge/ewald.f90.o] Error 1
88 /tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-src/src/multicharge/ncoord.f90:17.7:
89
90 use mctc_env, only : wp
91 1
>> 92 Fatal Error: File 'mctc_env.mod' opened at (1) is not a GNU Fortran module file
>> 93 make[2]: *** [CMakeFiles/multicharge-lib.dir/build.make:185: CMakeFiles/multicharge-lib.dir/src/multicharge/ncoord.f90.o] Error 1
94 /tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-src/src/multicharge/cutoff.f90:17.7:
95
96 use mctc_env, only : wp
97 1
>> 98 Fatal Error: File 'mctc_env.mod' opened at (1) is not a GNU Fortran module file
>> 99 make[2]: *** [CMakeFiles/multicharge-lib.dir/build.make:120: CMakeFiles/multicharge-lib.dir/src/multicharge/cutoff.f90.o] Error 1
100 /tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-src/src/multicharge/blas.F90:22.7:
101
102 use mctc_env, only : sp, dp, ik => i4
103 1
>> 104 Fatal Error: File 'mctc_env.mod' opened at (1) is not a GNU Fortran module file
105 /tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-src/src/multicharge/param/eeq2019.f90:22.7:
106
107 use mctc_env, only : wp
108 1
>> 109 Fatal Error: File 'mctc_env.mod' opened at (1) is not a GNU Fortran module file
110 /tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-src/src/multicharge/lapack.F90:21.7:
111
112 use mctc_env, only : sp, dp, ik => i4
113 1
>> 114 Fatal Error: File 'mctc_env.mod' opened at (1) is not a GNU Fortran module file
>> 115 make[2]: *** [CMakeFiles/multicharge-lib.dir/build.make:107: CMakeFiles/multicharge-lib.dir/src/multicharge/blas.F90.o] Error 1
>> 116 make[2]: *** [CMakeFiles/multicharge-lib.dir/build.make:94: CMakeFiles/multicharge-lib.dir/src/multicharge/param/eeq2019.f90.o] Error 1
>> 117 make[2]: *** [CMakeFiles/multicharge-lib.dir/build.make:159: CMakeFiles/multicharge-lib.dir/src/multicharge/lapack.F90.o] Error 1
118 make[2]: Leaving directory '/tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-build-tgea2dc'
>> 119 make[1]: *** [CMakeFiles/Makefile2:432: CMakeFiles/multicharge-lib.dir/all] Error 2
120 make[1]: *** Waiting for unfinished jobs....
121 /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/cmake-3.31.6-rdak4y4ert3gua5zyfov4pkvmgdsu7mj/bin/cmake -E cmake_copy_f90_mod subprojects/mstore/include/m
store_version.mod subprojects/mstore/CMakeFiles/mstore-lib.dir/mstore_version.mod.stamp GNU
122 /tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-src/subprojects/mstore/src/mstore/data/record.f90:17.7:
123
124 use mctc_io, only : structure_type
125 1
>> 126 Fatal Error: File 'mctc_io.mod' opened at (1) is not a GNU Fortran module file
>> 127 make[2]: *** [subprojects/mstore/CMakeFiles/mstore-lib.dir/build.make:94: subprojects/mstore/CMakeFiles/mstore-lib.dir/src/mstore/data/record.f90.o] Error 1
128 make[2]: *** Waiting for unfinished jobs....
129 make[2]: Leaving directory '/tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-build-tgea2dc'
>> 130 make[1]: *** [CMakeFiles/Makefile2:464: subprojects/mstore/CMakeFiles/mstore-lib.dir/all] Error 2
131 make[1]: Leaving directory '/tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-build-tgea2dc'
>> 132 make: *** [Makefile:149: all] Error 2
See build log for details:
/tmp/llshu219/spack-stage/spack-stage-multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy/spack-build-out.txt
==> Warning: Skipping build of dftd4-3.7.0-3ii4z7zeganssfirpeb75cdno6ctfavx since multicharge-0.3.1-tgea2dcpxgcmjafko5ibmjok4sanvezy failed
==> Warning: Skipping build of cp2k-2025.1-r5vezn4pja35bcd26c64cnu62xjebboi since dftd4-3.7.0-3ii4z7zeganssfirpeb75cdno6ctfavx failed
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/krb5-1.21.3-uy76oglzn37dsmqbistkjjrpynmpyp34
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/python-3.13.2-iq3m32hkr2ouc7zuqsgsyys2n37ajmcv
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/pmix-5.0.5-b6kp3d5wpqx7cfqg5x6yzl76ney6mdof
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/openssh-9.9p1-u2t766z6cgjahgd5wxk7nwpxnmu2wvne
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/python-venv-1.0-pr5j47r2k2isay2ymcvlw2ze3j3qqbyn
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/openmpi-5.0.6-37t2tbxpjbon4rn36i2v6gluze2jgoi3
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/py-fypp-3.1-rpjq4px7tru4biacl6oguaonixgzvjvk
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/netlib-scalapack-2.2.2-pwr42nwufms3s2qfjvh2c33byr5omcnb
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/fftw-3.3.10-cibmu357csqndrekigmaj4z2sjae4hx4
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/plumed-2.9.2-myxktfbphwi26slgxcgfvnguga42iyci
==> Installing dbcsr-2.8.0-xfnuchcktgnjc5doni4jkavq474ooext [60/62]
==> No binary for dbcsr-2.8.0-xfnuchcktgnjc5doni4jkavq474ooext found: installing from source
==> Using cached archive: /mnt/public/home/llshu219/spack/spack/var/spack/cache/_source-cache/archive/d5/d55e4f052f28d1ed0faeaa07557241439243287a184d1fd27f875c8b9ca6bd96.tar.gz
==> No patches needed for dbcsr
==> dbcsr: Executing phase: 'cmake'
==> dbcsr: Executing phase: 'build'
==> dbcsr: Executing phase: 'install'
==> dbcsr: Successfully installed dbcsr-2.8.0-xfnuchcktgnjc5doni4jkavq474ooext
Stage: 0.24s. Cmake: 25.92s. Build: 1m 30.59s. Install: 4.19s. Post-install: 0.47s. Total: 2m 7.86s
[+] /mnt/public/home/llshu219/spack/spack/opt/spack/linux-cascadelake/dbcsr-2.8.0-xfnuchcktgnjc5doni4jkavq474ooext
==> Error: cp2k-2025.1-r5vezn4pja35bcd26c64cnu62xjebboi: Package was not installed
==> Error: Installation request failed. Refer to reported errors for failing package(s).
请大佬帮帮分析是什么原因?如何解决这个问题? 或者能有什么办法安装cp2k-2025.1?
更新报错txt(在附件)
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error.txt
3.85 KB, 下载次数 Times of downloads: 3
spack-build-out.txt
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