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标题: cp2k 大体系进行多k点的结构弛豫时，自洽场第一步报错 [打印本页]

作者
Author: Shana 时间: 2024-5-10 18:01
标题: cp2k 大体系进行多k点的结构弛豫时，自洽场第一步报错
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。
(, 下载次数 Times of downloads: 41)

作者
Author: sobereva 时间: 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MPI不一致

作者
Author: Shana 时间: 2024-5-13 10:35

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

作者
Author: JCenter 时间: 2025-7-5 08:29

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).

作者
Author: sobereva 时间: 2025-7-5 08:37

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。

作者
Author: JCenter 时间: 2025-7-5 08:44

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。

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