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[CP2K] cp2k 大体系进行多k点的结构弛豫时,自洽场第一步报错

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各位老师好,

我想使用cp2k计算声子谱,材料是周期性的。进行了2*2*2的扩胞后,含有320个原子。原先是使用vasp弛豫的原胞结构,计算的声子谱,在非gamma点有虚频,但是扩胞的话,320个原子,对于vasp来说是很困难的,所以改用了cp2k。

我首先对vasp的结构进行cp2k的重新优化,在结构优化的时候,进行了2*2*2的扩胞,然后通过multiwfn生成了输入文件,设置的k mesh是2*3*2。提交任务之后,第一个自洽场直接报错。这个报错是因为mpi的问题?还是内存不足呢?输入文件和输出文件如下。请各位老师指点。

我把k点改为gamma only之后,能够正常的进行计算,scf一个电子步约为5~6s。

relax.inp

5.83 KB, 下载次数 Times of downloads: 9

slurm-8637629.out

11.03 KB, 下载次数 Times of downloads: 3

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发表于 Post on 2024-5-10 23:04:33 | 只看该作者 Only view this author
CP2K没编译好,怎么以正规方式编译在http://sobereva.com/586里写明了。或者编译时的MPI和当前活动状态的MPI不一致
北京科音自然科学研究中心http://www.keinsci.com)致力于计算化学的发展和传播,长期开办极高质量的各种计算化学类培训:初级量子化学培训班中级量子化学培训班高级量子化学培训班量子化学波函数分析与Multiwfn程序培训班分子动力学与GROMACS培训班CP2K第一性原理计算培训班,内容介绍以及往届资料购买请点击相应链接查看。这些培训是计算化学从零快速入门以及进一步全面系统性提升研究水平的高速路!培训各种常见问题见《北京科音办的培训班FAQ》
欢迎加入北京科音微信公众号获取北京科音培训的最新消息,并避免错过网上有价值的计算化学文章!
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Google Scholar:https://scholar.google.com/citations?user=tiKE0qkAAAAJ
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 楼主 Author| 发表于 Post on 2024-5-13 10:35:13 | 只看该作者 Only view this author
sobereva 发表于 2024-5-10 23:04
CP2K没编译好,怎么以正规方式编译在http://sobereva.com/586里写明了。或者编译时的MPI和当前活动状态的MP ...

好的,感谢sob老师

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发表于 Post on 2025-7-5 08:29:44 | 只看该作者 Only view this author
sobereva 发表于 2024-5-10 23:04
CP2K没编译好,怎么以正规方式编译在http://sobereva.com/586里写明了。或者编译时的MPI和当前活动状态的MP ...

卢老师,我在Ubuntu系统上装的cp2k-2025.1,编译无问题。只要不是设置k点的任务都能跑,可是一设置k点,包括GAMMA在内,就报错,这是为什么呢。
:mpiexec -np 4 --bind-to socket --map-by socket cp2k.popt test.inp > test.out

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0xb1ec1823960 in ???
#1  0xb1ec1822ac5 in ???
#2  0xb1ec144251f in ???
        at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3  0xb1ec88ab1c8 in ompi_comm_invalid
        at ../../../ompi/communicator/communicator.h:494
#4  0xb1ec88ab1c8 in PMPI_Comm_size
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/tools/toolchain/build/openmpi-5.0.6/ompi/mpi/c/comm_size.c:51
#5  0xb1ec8c0c02b in ???
#6  0xb1ec853af52 in ???
#7  0xb1ec858f302 in ???
#8  0xb1ec8056690 in ???
#9  0xb1ec8055e20 in ???
#10  0xb1ec80607ec in ???
#11  0xb1ec82c7bac in ???
#12  0xb1ec82c6317 in ???
#13  0xb1ec82c591d in ???
#14  0x5d08ae9ada96 in cp_cfm_heevd_base
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/fm/cp_cfm_diag.F:156
#15  0x5d08ae9af2b8 in __cp_cfm_diag_MOD_cp_cfm_heevd
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/fm/cp_cfm_diag.F:73
#16  0x5d08ae9af2b8 in __cp_cfm_diag_MOD_cp_cfm_geeig
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/fm/cp_cfm_diag.F:217
#17  0x5d08ad3dfe66 in __qs_scf_diagonalization_MOD_do_general_diag_kp
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf_diagonalization.F:644
#18  0x5d08acaa6d7e in __qs_scf_loop_utils_MOD_qs_scf_new_mos_kp
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf_loop_utils.F:325
#19  0x5d08acd05568 in __qs_scf_MOD_scf_env_do_scf
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf.F:500
#20  0x5d08acd11f63 in __qs_scf_MOD_scf
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf.F:244
#21  0x5d08ac84119c in __qs_energy_MOD_qs_energies
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_energy.F:126
#22  0x5d08ac135bd6 in __force_env_methods_MOD_force_env_calc_energy_force
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/force_env_methods.F:260
#23  0x5d08abb91413 in cp2k_run
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k_runs.F:327
#24  0x5d08abb941b1 in __cp2k_runs_MOD_run_input
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k_runs.F:935
#25  0x5d08abb8e015 in cp2k
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k.F:379
#26  0x5d08abaf677e in main
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k.F:44
#0  0x9bf5e023960 in ???
#1  0x9bf5e022ac5 in ???
#2  0x9bf5dc4251f in ???
        at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3  0x9bf650ab1c8 in ompi_comm_invalid
        at ../../../ompi/communicator/communicator.h:494
#4  0x9bf650ab1c8 in PMPI_Comm_size
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/tools/toolchain/build/openmpi-5.0.6/ompi/mpi/c/comm_size.c:51
#5  0x9bf658c802b in ???
#6  0x9bf64d3af52 in ???
#7  0x9bf64d8f302 in ???
#8  0x9bf64856690 in ???
#9  0x9bf64855e20 in ???
#10  0x9bf648607ec in ???
#11  0x9bf64ac7bac in ???
#12  0x9bf64ac6317 in ???
#13  0x9bf64ac591d in ???
#14  0x62c8bb748a96 in cp_cfm_heevd_base
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/fm/cp_cfm_diag.F:156
#15  0x62c8bb74a2b8 in __cp_cfm_diag_MOD_cp_cfm_heevd
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/fm/cp_cfm_diag.F:73
#16  0x62c8bb74a2b8 in __cp_cfm_diag_MOD_cp_cfm_geeig
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/fm/cp_cfm_diag.F:217
#0  0x13819be23960 in ???
#1  0x13819be22ac5 in ???
#2  0x13819ba4251f in ???
        at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3  0x1381a2eab1c8 in ompi_comm_invalid
        at ../../../ompi/communicator/communicator.h:494
#4  0x1381a2eab1c8 in PMPI_Comm_size
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/tools/toolchain/build/openmpi-5.0.6/ompi/mpi/c/comm_size.c:51
#5  0x1381a36a702b in ???
#6  0x1381a2b3af52 in ???
#17  0x62c8ba17ae66 in __qs_scf_diagonalization_MOD_do_general_diag_kp
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf_diagonalization.F:644
#7  0x1381a2b8f302 in ???
#8  0x1381a2656690 in ???
#9  0x1381a2655e20 in ???
#10  0x1381a26607ec in ???
#11  0x1381a28c7bac in ???
#12  0x1381a28c6317 in ???
#13  0x1381a28c591d in ???
#14  0x6144a479ca96 in cp_cfm_heevd_base
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/fm/cp_cfm_diag.F:156
#15  0x6144a479e2b8 in __cp_cfm_diag_MOD_cp_cfm_heevd
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/fm/cp_cfm_diag.F:73
#16  0x6144a479e2b8 in __cp_cfm_diag_MOD_cp_cfm_geeig
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/fm/cp_cfm_diag.F:217
#18  0x62c8b9841d7e in __qs_scf_loop_utils_MOD_qs_scf_new_mos_kp
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf_loop_utils.F:325
#17  0x6144a31cee66 in __qs_scf_diagonalization_MOD_do_general_diag_kp
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf_diagonalization.F:644
#19  0x62c8b9aa0568 in __qs_scf_MOD_scf_env_do_scf
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf.F:500
#20  0x62c8b9aacf63 in __qs_scf_MOD_scf
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf.F:244
#18  0x6144a2895d7e in __qs_scf_loop_utils_MOD_qs_scf_new_mos_kp
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf_loop_utils.F:325
#21  0x62c8b95dc19c in __qs_energy_MOD_qs_energies
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_energy.F:126
#22  0x62c8b8ed0bd6 in __force_env_methods_MOD_force_env_calc_energy_force
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/force_env_methods.F:260
#19  0x6144a2af4568 in __qs_scf_MOD_scf_env_do_scf
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf.F:500
#20  0x6144a2b00f63 in __qs_scf_MOD_scf
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf.F:244
#21  0x6144a263019c in __qs_energy_MOD_qs_energies
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_energy.F:126
#23  0x62c8b892c413 in cp2k_run
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k_runs.F:327
#24  0x62c8b892f1b1 in __cp2k_runs_MOD_run_input
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k_runs.F:935
#25  0x62c8b8929015 in cp2k
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k.F:379
#26  0x62c8b889177e in main
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k.F:44
#22  0x6144a1f24bd6 in __force_env_methods_MOD_force_env_calc_energy_force
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/force_env_methods.F:260
#23  0x6144a1980413 in cp2k_run
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k_runs.F:327
#24  0x6144a19831b1 in __cp2k_runs_MOD_run_input
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k_runs.F:935
#25  0x6144a197d015 in cp2k
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k.F:379
#26  0x6144a18e577e in main
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k.F:44
#0  0x56414423960 in ???
#1  0x56414422ac5 in ???
#2  0x5641404251f in ???
        at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3  0x5641b4ab1c8 in ompi_comm_invalid
        at ../../../ompi/communicator/communicator.h:494
#4  0x5641b4ab1c8 in PMPI_Comm_size
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/tools/toolchain/build/openmpi-5.0.6/ompi/mpi/c/comm_size.c:51
#5  0x5641b80c02b in ???
#6  0x5641b13af52 in ???
#7  0x5641b18f302 in ???
#8  0x5641ac56690 in ???
#9  0x5641ac55e20 in ???
#10  0x5641ac607ec in ???
#11  0x5641aec7bac in ???
#12  0x5641aec6317 in ???
#13  0x5641aec591d in ???
#14  0x58ed1c242a96 in cp_cfm_heevd_base
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/fm/cp_cfm_diag.F:156
#15  0x58ed1c2442b8 in __cp_cfm_diag_MOD_cp_cfm_heevd
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/fm/cp_cfm_diag.F:73
#16  0x58ed1c2442b8 in __cp_cfm_diag_MOD_cp_cfm_geeig
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/fm/cp_cfm_diag.F:217
#17  0x58ed1ac74e66 in __qs_scf_diagonalization_MOD_do_general_diag_kp
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf_diagonalization.F:644
#18  0x58ed1a33bd7e in __qs_scf_loop_utils_MOD_qs_scf_new_mos_kp
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf_loop_utils.F:325
#19  0x58ed1a59a568 in __qs_scf_MOD_scf_env_do_scf
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf.F:500
#20  0x58ed1a5a6f63 in __qs_scf_MOD_scf
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_scf.F:244
#21  0x58ed1a0d619c in __qs_energy_MOD_qs_energies
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/qs_energy.F:126
#22  0x58ed199cabd6 in __force_env_methods_MOD_force_env_calc_energy_force
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/force_env_methods.F:260
#23  0x58ed19426413 in cp2k_run
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k_runs.F:327
#24  0x58ed194291b1 in __cp2k_runs_MOD_run_input
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k_runs.F:935
#25  0x58ed19423015 in cp2k
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k.F:379
#26  0x58ed1938b77e in main
        at /home/futuremem/wwj/software/cp2k/cp2k-2025.1/src/start/cp2k.F:44
--------------------------------------------------------------------------
prterun noticed that process rank 1 with PID 2076003 on node 550W-1 exited on
signal 11 (Segmentation fault).
目前专攻:
基于DFT、MD模拟的自由能计算
基于过渡态理论的自由能垒和反应速率常数计算
基于MD模拟的交联聚合物计算

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发表于 Post on 2025-7-5 08:37:10 | 只看该作者 Only view this author
JCenter 发表于 2025-7-5 08:29
卢老师,我在Ubuntu系统上装的cp2k-2025.1,编译无问题。只要不是设置k点的任务都能跑,可是一设置k点, ...

把cp2k.popt前面一串都去掉,如果还不行,尝试用官方预编译的ssmp版跑。如果能跑,说明就是自己编译的问题。
北京科音自然科学研究中心http://www.keinsci.com)致力于计算化学的发展和传播,长期开办极高质量的各种计算化学类培训:初级量子化学培训班中级量子化学培训班高级量子化学培训班量子化学波函数分析与Multiwfn程序培训班分子动力学与GROMACS培训班CP2K第一性原理计算培训班,内容介绍以及往届资料购买请点击相应链接查看。这些培训是计算化学从零快速入门以及进一步全面系统性提升研究水平的高速路!培训各种常见问题见《北京科音办的培训班FAQ》
欢迎加入北京科音微信公众号获取北京科音培训的最新消息,并避免错过网上有价值的计算化学文章!
欢迎加入人气极高、专业性特别强的理论与计算化学综合交流群思想家公社QQ群(群号见此链接),合计达一万多人。北京科音培训班的学员在群中可申请VIP头衔,提问将得到群主Sobereva的最优先解答。
思想家公社的门口Blog:http://sobereva.com(发布大量原创计算化学相关博文)
Multiwfn主页:http://sobereva.com/multiwfn(十分强大、极为流行的量子化学波函数分析程序)
Google Scholar:https://scholar.google.com/citations?user=tiKE0qkAAAAJ
ResearchGate:https://www.researchgate.net/profile/Tian_Lu

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实验组内的DFT计算、第一性原理、MD模拟爱好者

6#
发表于 Post on 2025-7-5 08:44:21 | 只看该作者 Only view this author
sobereva 发表于 2025-7-5 08:37
把cp2k.popt前面一串都去掉,如果还不行,尝试用官方预编译的ssmp版跑。如果能跑,说明就是自己编译的问 ...

我刚才尝试了一下。感觉像是openmpi的问题,单核跑就没问题。openmpi是通过toolchain安装的。
目前专攻:
基于DFT、MD模拟的自由能计算
基于过渡态理论的自由能垒和反应速率常数计算
基于MD模拟的交联聚合物计算

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