CP2K Restart

Niccolò Di Eugenio

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Jul 22, 2024, 4:45:17 AM (5 days ago) Jul 22

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Dear all,

I am trying to restart a DFT calculation. I am currently doing so by running the .restart file instead of the .inp file, as:

srun /project/ML_YBCO/nic/cp2k/exe/CRAY-XC50-gcc/cp2k.psmp BaYCuOopt-1_8.restart > Ba2Y1Cu3O6_mp-1021507.out

However, I am getting the following error:

Rank 0 [Sat Jul 20 21:02:42 2024] [c0-0c0s1n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:
#0 0x7fffeb5b849f in ???
#1 0x7fffeb5b8420 in ???
#2 0x7fffeb5b9a00 in ???
#3 0x7fffecb8a267 in ???
#4 0x7fffeca975e5 in ???
#5 0x7fffecadea84 in ???
#6 0x20d10af in __message_passing_MOD_mp_abort
at /project/ML_YBCO/nic/cp2k/src/mpiwrap/message_passing.F:1270
#7 0x20d3d24 in __base_hooks_MOD_cp_abort
at /project/ML_YBCO/nic/cp2k/obj/CRAY-XC50-gcc/psmp/base_hooks.F90:76
#8 0x20d3ed0 in __base_hooks_MOD_cp__a
at /project/ML_YBCO/nic/cp2k/obj/CRAY-XC50-gcc/psmp/base_hooks.F90:163
#9 0xba743b in __atoms_input_MOD_read_atoms_input
at /project/ML_YBCO/nic/cp2k/src/atoms_input.F:122
#10 0x7b82c0 in coordinate_control
at /project/ML_YBCO/nic/cp2k/src/topology.F:588
#11 0x7b82c0 in __topology_MOD_topology_control
at /project/ML_YBCO/nic/cp2k/src/topology.F:197
#12 0xa49e9c in __cp_subsys_methods_MOD_cp_subsys_create
at /project/ML_YBCO/nic/cp2k/src/cp_subsys_methods.F:161
#13 0x90b5fa in __qs_subsys_methods_MOD_qs_subsys_create
at /project/ML_YBCO/nic/cp2k/src/qs_subsys_methods.F:98
#14 0x8d2610 in __qs_environment_MOD_qs_init
at /project/ML_YBCO/nic/cp2k/src/qs_environment.F:317
#15 0xafbda4 in __f77_interface_MOD_create_force_env
at /project/ML_YBCO/nic/cp2k/src/f77_interface.F:805
#16 0x410d22 in cp2k_run
at /project/ML_YBCO/nic/cp2k/src/start/cp2k_runs.F:314
#17 0x41464e in __cp2k_runs_MOD_run_input
at /project/ML_YBCO/nic/cp2k/src/start/cp2k_runs.F:983
#18 0x40b4c6 in cp2k
at /project/ML_YBCO/nic/cp2k/src/start/cp2k.F:379
#19 0x40988c in main
at /project/ML_YBCO/nic/cp2k/obj/CRAY-XC50-gcc/psmp/cp2k.F90:44
srun: error: nid00007: task 0: Aborted
srun: launch/slurm: _step_signal: Terminating StepId=1303919.0
slurmstepd: error: *** STEP 1303919.0 ON nid00007 CANCELLED AT 2024-07-20T21:02:43 ***
srun: error: nid00007: task 1: Terminated
srun: error: nid00008: tasks 2-3: Terminated
srun: Force Terminated StepId=1303919.0

How could I solve this? Thank you very much.

Krack Matthias

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Jul 22, 2024, 5:04:37 AM (5 days ago) Jul 22

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Hi

There seems to be a problem reading the atomic coordinates. However, without further information, it is difficult to give further guidance.

Best

Matthias

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Niccolò Di Eugenio

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Jul 22, 2024, 5:07:59 AM (5 days ago) Jul 22

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Hi,

This is the input file I am using:

&FORCE_EVAL

&PRINT
&FORCES

&END FORCES

&END PRINT
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT_UZH
POTENTIAL_FILE_NAME GTH_POTENTIALS
&POISSON
POISSON_SOLVER PERIODIC
PERIODIC XYZ
&END POISSON

&MGRID
NGRIDS 5
CUTOFF 400
REL_CUTOFF 80

&END MGRID
&QS
METHOD GPW
EPS_PGF_ORB 1E-16

&END QS
&SCF
&SMEAR ON
ELECTRONIC_TEMPERATURE 2000
METHOD FERMI_DIRAC
&END SMEAR
ADDED_MOS 2000
CHOLESKY INVERSE
SCF_GUESS RESTART
EPS_SCF 1.0E-6
MAX_SCF 200

&DIAGONALIZATION ON
ALGORITHM STANDARD
&END DIAGONALIZATION
&MIXING T
METHOD BROYDEN_MIXING
ALPHA 0.2
BETA 1.5
NBUFFER 15

&END MIXING

&END SCF
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&END XC

&END DFT
&SUBSYS

&TOPOLOGY
MULTIPLE_UNIT_CELL 4 4 4
COORD_FILE_FORMAT XYZ
COORD_FILE Ba2Y1Cu3O6_mp-1021507.xyz
&END TOPOLOGY
&CELL
MULTIPLE_UNIT_CELL 4 4 4
SYMMETRY CUBIC
ABC 3.886234 3.911377 11.840840
PERIODIC XYZ
&END CELL
&KIND Ba
BASIS_SET DZVP-MOLOPT-PBE-GTH-q10
POTENTIAL GTH-PBE-q10
&END KIND
&KIND Y
BASIS_SET DZVP-MOLOPT-PBE-GTH-q11
POTENTIAL GTH-PBE-q11
&END KIND
&KIND Cu
BASIS_SET DZVP-MOLOPT-PBE-GTH-q11
POTENTIAL GTH-PBE-q11
&END KIND
&KIND O
BASIS_SET DZVP-MOLOPT-PBE-GTH-q6
POTENTIAL GTH-PBE-q6
&END KIND
&PRINT
&CELL HIGH

&END CELL
&END PRINT

&END SUBSYS
STRESS_TENSOR ANALYTICAL

&END FORCE_EVAL
&GLOBAL
PROJECT BaYCuOopt
RUN_TYPE CELL_OPT
PRINT_LEVEL MEDIUM
PREFERRED_DIAG_LIBRARY SL

&END GLOBAL

&MOTION

&CELL_OPT

KEEP_SYMMETRY .TRUE.
OPTIMIZER BFGS
KEEP_ANGLES
EXTERNAL_PRESSURE 1 0 0 0 1 0 0 0 1

&END CELL_OPT

&END MOTION

Are there any mistakes here? It was working fine before introducing the restart.

Niccolò

Krack Matthias

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Jul 22, 2024, 5:17:04 AM (5 days ago) Jul 22

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Hi

Check your coordinate file and make sure that it fits the MULTIPLE_UNIT_CELLS keyword. Note, that the atomic coordinates from a run using MULTIPLE_UNIT_CELLS are expanded by CP2K to the full set. I guess that you will have to remove/comment the MULTIPLE_UNIT_CELL keyword to get it work.

HTH

Matthias

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Niccolò Di Eugenio

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Jul 22, 2024, 5:28:46 AM (5 days ago) Jul 22

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Hi all and thanks Mr. Krack for your kind response,

I am sorry: that was the input file used to run the cp2k calculation before the HPC wall time. When restarting, I am calling the .restart file that looks like this:

# Version information for this restart file
# current date 2024-07-17 19:40:31.049
# current working dir /project/ML_YBCO/nic/cp2k/YBCO/Ba2Y1Cu3O6_mp-1021507
# Program compiled at Tue Jul 9 18:29:51 JST 2024
# Program compiled on csc3
# Program compiled for CRAY-XC50-gcc
# Source code revision number git:b4a17a5
&GLOBAL
PREFERRED_DIAG_LIBRARY SCALAPACK
PRINT_LEVEL MEDIUM
PROJECT_NAME "BaYCuOopt"
RUN_TYPE CELL_OPT
&END GLOBAL
&MOTION
&CELL_OPT
OPTIMIZER BFGS
STEP_START_VAL 8
EXTERNAL_PRESSURE 1.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 \
1.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 1.0000000000000000E+000
KEEP_ANGLES T
KEEP_SYMMETRY T
&END CELL_OPT
&END MOTION
&FORCE_EVAL
METHOD QS
STRESS_TENSOR ANALYTICAL

&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT_UZH
POTENTIAL_FILE_NAME GTH_POTENTIALS

&SCF
MAX_SCF 200
EPS_SCF 9.9999999999999995E-007
CHOLESKY INVERSE
SCF_GUESS ATOMIC
ADDED_MOS 2000
&DIAGONALIZATION T
ALGORITHM STANDARD
&END DIAGONALIZATION
&SMEAR T
METHOD FERMI_DIRAC
ELECTRONIC_TEMPERATURE 2.0000000000000000E+003
&END SMEAR
&MIXING T
METHOD BROYDEN_MIXING
ALPHA 2.0000000000000001E-001
BETA 1.5000000000000000E+000

NBUFFER 15
&END MIXING
&END SCF

&QS
EPS_PGF_ORB 9.9999999999999998E-017
METHOD GPW
&END QS
&MGRID
NGRIDS 5
CUTOFF 4.0000000000000000E+002

REL_CUTOFF 8.0000000000000000E+001
&END MGRID
&XC
DENSITY_CUTOFF 1.0000000000000000E-010
GRADIENT_CUTOFF 1.0000000000000000E-010
TAU_CUTOFF 1.0000000000000000E-010
&XC_FUNCTIONAL NO_SHORTCUT
&PBE T
&END PBE
&END XC_FUNCTIONAL
&END XC

&POISSON
POISSON_SOLVER PERIODIC
PERIODIC XYZ
&END POISSON

&END DFT
&SUBSYS
&CELL
A 2.8184601333333330E+001 0.0000000000000000E+000 0.0000000000000000E+000
B 0.0000000000000000E+000 2.8184601333333330E+001 0.0000000000000000E+000
C 0.0000000000000000E+000 0.0000000000000000E+000 2.8184601333333330E+001
PERIODIC XYZ
MULTIPLE_UNIT_CELL 1 1 1
SYMMETRY CUBIC
&END CELL
&COORD
Ba 2.0881355223116063E+000 2.1081336076904886E+000 1.0731644357464377E+001
Ba 2.1105353811046417E+000 2.1050866536731037E+000 1.9416636361470143E+000
Y 2.0978449531699890E+000 2.0865232904996378E+000 6.5189374554766406E+000
Cu -8.5497041237671094E-003 -5.2291919964740198E-003 8.2677063595696030E+000
Cu -6.1654838371616076E-003 -2.5558110197782817E-003 4.6274667132335576E+000
Cu 7.2188942183468640E-003 -1.5860703738888510E-002 -2.0735700509928981E-001
O -9.2063279084127236E-004 2.1144441548333401E+000 -1.0811122621217063E-001
O 2.0922308957407263E+000 1.1438570991530483E-002 7.9708449287024701E+000
O 2.0919516195129284E+000 8.4705075099355594E-003 4.8674895316140319E+000
O -1.4222229365387621E-002 2.1116784982821857E+000 7.8242627460067347E+000
O 7.0885470607998362E-003 -1.0359230964127018E-003 1.0562381339474765E+001
O 5.3226273407098415E-004 3.5207032981484435E-003 2.2767440065454108E+000

[...]

&END COORD

&KIND "Ba"
BASIS_SET "DZVP-MOLOPT-PBE-GTH-q10"
POTENTIAL "GTH-PBE-q10"

&POTENTIAL
4 6
5.4000000000000004E-001 2 2.4526780700000000E+001 -2.4686700099999999E+000
4
4.9206839000000002E-001 2 9.5150929999999995E-002 1.1693184000000001E+000
-1.5095835700000000E+000
3.9148929999999998E-001 2 8.0018261000000002E-001 -1.6168390699999999E+000
1.9130697900000000E+000
6.7217347999999999E-001 1 3.8853100000000002E-001
3.0049773000000002E-001 1 -1.9653794520000002E+001
# Potential name: GTH-PBE-Q10 for element symbol: BA
# Potential read from the potential filename: GTH_POTENTIALS
&END POTENTIAL

&END KIND
&KIND "Y"
BASIS_SET "DZVP-MOLOPT-PBE-GTH-q11"
POTENTIAL "GTH-PBE-q11"

&POTENTIAL
4 6 1
4.7499999999999998E-001 2 1.2167769040000000E+001 -2.3285510299999999E+000
3
2.4674070000000001E-001 2 2.3450271950000001E+001 -8.3253574799999992E+000
1.0747990290000001E+001
2.9656397000000001E-001 2 5.9786340100000004E+000 -5.8523496399999999E+000
6.9245934800000004E+000
4.5045569000000002E-001 2 1.1874904799999999E+000 -1.3186733100000001E+000
1.4952349899999999E+000
# Potential name: GTH-PBE-Q11 for element symbol: Y
# Potential read from the potential filename: GTH_POTENTIALS
&END POTENTIAL

&END KIND
&KIND "Cu"
BASIS_SET "DZVP-MOLOPT-PBE-GTH-q11"
POTENTIAL "GTH-PBE-q11"

&POTENTIAL
1 0 10
5.3000000000000003E-001 0
3
4.3135505000000002E-001 3 9.6938050699999998E+000 -6.4701653500000003E+000 1.9359521500000001E+000
1.1501773960000000E+001 -4.9986069600000000E+000
3.9675212700000002E+000
5.6139154999999996E-001 2 2.5454732999999998E+000 -7.8463572999999998E-001
9.2839351999999997E-001
2.6455485000000001E-001 1 -1.2828614060000000E+001
# Potential name: GTH-PBE-Q11 for element symbol: CU
# Potential read from the potential filename: GTH_POTENTIALS
&END POTENTIAL

&END KIND
&KIND "O"
BASIS_SET "DZVP-MOLOPT-PBE-GTH-q6"
POTENTIAL "GTH-PBE-q6"

&POTENTIAL

2 4
2.4455430000000000E-001 2 -1.6667214800000000E+001 2.4873113199999999E+000
2
2.2095592000000000E-001 1 1.8337458110000000E+001
2.1133246999999999E-001 0
# Potential name: GTH-PBE-Q6 for element symbol: O
# Potential read from the potential filename: GTH_POTENTIALS
&END POTENTIAL
&END KIND
&TOPOLOGY
COORD_FILE_NAME Ba2Y1Cu3O6_mp-1021507.xyz
COORD_FILE_FORMAT XYZ
NUMBER_OF_ATOMS 768
MULTIPLE_UNIT_CELL 1 1 1
&END TOPOLOGY

&PRINT
&CELL HIGH
&END CELL
&END PRINT
&END SUBSYS

&PRINT
&FORCES SILENT
&END FORCES
&END PRINT
&END FORCE_EVAL

Should I follow the same advice you gave me before?

Thanks again,

Niccolò Di Eugenio

Krack Matthias

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Jul 22, 2024, 5:37:46 AM (5 days ago) Jul 22

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The .restart file written by CP2K should run as is. Did you change that file by hand?

To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/7f439de2-9e07-498a-b554-ad2613d7af75n%40googlegroups.com.

Niccolò Di Eugenio

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Jul 22, 2024, 5:49:24 AM (5 days ago) Jul 22

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Hi,

I did not, this is how it came out. The files in my folder are:

Ba2Y1Cu3O6_mp-1021507.inp Ba2Y1Cu3O6.sh BaYCuOopt-1_3.restart BaYCuOopt-1_6.restart BaYCuOopt-1.restart BaYCuOopt-pos-1.xyz template.inp
Ba2Y1Cu3O6_mp-1021507.out BaYCuOopt-1_1.restart BaYCuOopt-1_4.restart BaYCuOopt-1_7.restart BaYCuOopt-1.restart.bak-1 BaYCuOopt-RESTART.wfn
Ba2Y1Cu3O6_mp-1021507.xyz BaYCuOopt-1_2.restart BaYCuOopt-1_5.restart BaYCuOopt-1_8.restart BaYCuOopt-BFGS.Hessian BaYCuOopt-RESTART.wfn.bak-1

And I am running the BaYCuOopt-1_8.restart with the command srun /project/ML_YBCO/nic/cp2k/exe/CRAY-XC50-gcc/cp2k.psmp BaYCuOopt-1_8.restart > Ba2Y1Cu3O6_mp-1021507.out

Niccolò

Krack Matthias

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Jul 22, 2024, 6:06:01 AM (5 days ago) Jul 22

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Can you try to comment the lines COORD_FILE_NAME and COORD_FILE_FORMAT in the .restart file?

Maybe, I am mistaken and the .restart file does not work in all cases as is.

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Niccolò Di Eugenio

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Jul 22, 2024, 11:49:45 AM (5 days ago) Jul 22

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Hi all,

This was solved, thank you very much!

Niccolò

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