<div>Hi all and thanks Mr. Krack for your kind response,</div><div>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:<br /></div><div><br /></div><div># Version information for this restart file<br /> # current date 2024-07-17 19:40:31.049<br /> # current working dir /project/ML_YBCO/nic/cp2k/YBCO/Ba2Y1Cu3O6_mp-1021507<br /> # Program compiled at Tue Jul 9 18:29:51 JST 2024<br /> # Program compiled on csc3<br /> # Program compiled for CRAY-XC50-gcc<br /> # Source code revision number git:b4a17a5<br /> &GLOBAL<br /> PREFERRED_DIAG_LIBRARY SCALAPACK<br /> PRINT_LEVEL MEDIUM<br /> PROJECT_NAME "BaYCuOopt"<br /> RUN_TYPE CELL_OPT<br /> &END GLOBAL<br /> &MOTION<br /> &CELL_OPT<br /> OPTIMIZER BFGS<br /> STEP_START_VAL 8<br /> EXTERNAL_PRESSURE 1.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 \<br /> 1.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 1.0000000000000000E+000<br /> KEEP_ANGLES T<br /> KEEP_SYMMETRY T<br /> &END CELL_OPT<br /> &END MOTION<br /> &FORCE_EVAL<br /> METHOD QS<br /> STRESS_TENSOR ANALYTICAL<br /> &DFT<br /> BASIS_SET_FILE_NAME BASIS_MOLOPT_UZH<br /> POTENTIAL_FILE_NAME GTH_POTENTIALS<br /> &SCF<br /> MAX_SCF 200<br /> EPS_SCF 9.9999999999999995E-007<br /> CHOLESKY INVERSE<br /> SCF_GUESS ATOMIC<br /> ADDED_MOS 2000<br /> &DIAGONALIZATION T<br /> ALGORITHM STANDARD<br /> &END DIAGONALIZATION<br /> &SMEAR T<br /> METHOD FERMI_DIRAC<br /> ELECTRONIC_TEMPERATURE 2.0000000000000000E+003<br /> &END SMEAR<br /> &MIXING T<br /> METHOD BROYDEN_MIXING<br /> ALPHA 2.0000000000000001E-001<br /> BETA 1.5000000000000000E+000<br /> NBUFFER 15<br /> &END MIXING<br /> &END SCF<br /> &QS<br /> EPS_PGF_ORB 9.9999999999999998E-017<br /> METHOD GPW<br /> &END QS<br /> &MGRID<br /> NGRIDS 5<br /> CUTOFF 4.0000000000000000E+002</div><div>REL_CUTOFF 8.0000000000000000E+001<br /> &END MGRID<br /> &XC<br /> DENSITY_CUTOFF 1.0000000000000000E-010<br /> GRADIENT_CUTOFF 1.0000000000000000E-010<br /> TAU_CUTOFF 1.0000000000000000E-010<br /> &XC_FUNCTIONAL NO_SHORTCUT<br /> &PBE T<br /> &END PBE<br /> &END XC_FUNCTIONAL<br /> &END XC<br /> &POISSON<br /> POISSON_SOLVER PERIODIC<br /> PERIODIC XYZ<br /> &END POISSON<br /> &END DFT<br /> &SUBSYS<br /> &CELL<br /> A 2.8184601333333330E+001 0.0000000000000000E+000 0.0000000000000000E+000<br /> B 0.0000000000000000E+000 2.8184601333333330E+001 0.0000000000000000E+000<br /> C 0.0000000000000000E+000 0.0000000000000000E+000 2.8184601333333330E+001<br /> PERIODIC XYZ<br /> MULTIPLE_UNIT_CELL 1 1 1<br /> SYMMETRY CUBIC<br /> &END CELL<br /> &COORD<br /> Ba 2.0881355223116063E+000 2.1081336076904886E+000 1.0731644357464377E+001<br /> Ba 2.1105353811046417E+000 2.1050866536731037E+000 1.9416636361470143E+000<br /> Y 2.0978449531699890E+000 2.0865232904996378E+000 6.5189374554766406E+000<br /> Cu -8.5497041237671094E-003 -5.2291919964740198E-003 8.2677063595696030E+000<br /> Cu -6.1654838371616076E-003 -2.5558110197782817E-003 4.6274667132335576E+000<br /> Cu 7.2188942183468640E-003 -1.5860703738888510E-002 -2.0735700509928981E-001<br /> O -9.2063279084127236E-004 2.1144441548333401E+000 -1.0811122621217063E-001<br /> O 2.0922308957407263E+000 1.1438570991530483E-002 7.9708449287024701E+000<br /> O 2.0919516195129284E+000 8.4705075099355594E-003 4.8674895316140319E+000<br /> O -1.4222229365387621E-002 2.1116784982821857E+000 7.8242627460067347E+000<br /> O 7.0885470607998362E-003 -1.0359230964127018E-003 1.0562381339474765E+001<br /> O 5.3226273407098415E-004 3.5207032981484435E-003 2.2767440065454108E+000<br /></div><div><br /></div><div> [...]</div><div><br /></div><div>&END COORD<br /> &KIND "Ba"<br /> BASIS_SET "DZVP-MOLOPT-PBE-GTH-q10"<br /> POTENTIAL "GTH-PBE-q10"<br /> &POTENTIAL<br /> 4 6<br /> 5.4000000000000004E-001 2 2.4526780700000000E+001 -2.4686700099999999E+000<br /> 4<br /> 4.9206839000000002E-001 2 9.5150929999999995E-002 1.1693184000000001E+000<br /> -1.5095835700000000E+000<br /> 3.9148929999999998E-001 2 8.0018261000000002E-001 -1.6168390699999999E+000<br /> 1.9130697900000000E+000<br /> 6.7217347999999999E-001 1 3.8853100000000002E-001<br /> 3.0049773000000002E-001 1 -1.9653794520000002E+001<br /> # Potential name: GTH-PBE-Q10 for element symbol: BA<br /> # Potential read from the potential filename: GTH_POTENTIALS<br /> &END POTENTIAL<br /> &END KIND<br /> &KIND "Y"<br /> BASIS_SET "DZVP-MOLOPT-PBE-GTH-q11"<br /> POTENTIAL "GTH-PBE-q11"<br /> &POTENTIAL<br /> 4 6 1<br /> 4.7499999999999998E-001 2 1.2167769040000000E+001 -2.3285510299999999E+000<br /> 3<br /> 2.4674070000000001E-001 2 2.3450271950000001E+001 -8.3253574799999992E+000<br /> 1.0747990290000001E+001<br /> 2.9656397000000001E-001 2 5.9786340100000004E+000 -5.8523496399999999E+000<br /> 6.9245934800000004E+000<br /> 4.5045569000000002E-001 2 1.1874904799999999E+000 -1.3186733100000001E+000<br /> 1.4952349899999999E+000<br /> # Potential name: GTH-PBE-Q11 for element symbol: Y<br /> # Potential read from the potential filename: GTH_POTENTIALS<br /> &END POTENTIAL<br /> &END KIND<br /> &KIND "Cu"<br /> BASIS_SET "DZVP-MOLOPT-PBE-GTH-q11"<br /> POTENTIAL "GTH-PBE-q11"<br /> &POTENTIAL<br /> 1 0 10<br /> 5.3000000000000003E-001 0<br /> 3<br /> 4.3135505000000002E-001 3 9.6938050699999998E+000 -6.4701653500000003E+000 1.9359521500000001E+000<br /> 1.1501773960000000E+001 -4.9986069600000000E+000<br /> 3.9675212700000002E+000<br /> 5.6139154999999996E-001 2 2.5454732999999998E+000 -7.8463572999999998E-001<br /> 9.2839351999999997E-001<br /> 2.6455485000000001E-001 1 -1.2828614060000000E+001<br /> # Potential name: GTH-PBE-Q11 for element symbol: CU<br /> # Potential read from the potential filename: GTH_POTENTIALS<br /> &END POTENTIAL<br /> &END KIND<br /> &KIND "O"<br /> BASIS_SET "DZVP-MOLOPT-PBE-GTH-q6"<br /> POTENTIAL "GTH-PBE-q6"<br /> &POTENTIAL</div><div>2 4<br /> 2.4455430000000000E-001 2 -1.6667214800000000E+001 2.4873113199999999E+000<br /> 2<br /> 2.2095592000000000E-001 1 1.8337458110000000E+001<br /> 2.1133246999999999E-001 0<br /> # Potential name: GTH-PBE-Q6 for element symbol: O<br /> # Potential read from the potential filename: GTH_POTENTIALS<br /> &END POTENTIAL<br /> &END KIND<br /> &TOPOLOGY<br /> COORD_FILE_NAME Ba2Y1Cu3O6_mp-1021507.xyz<br /> COORD_FILE_FORMAT XYZ<br /> NUMBER_OF_ATOMS 768<br /> MULTIPLE_UNIT_CELL 1 1 1<br /> &END TOPOLOGY<br /> &PRINT<br /> &CELL HIGH<br /> &END CELL<br /> &END PRINT<br /> &END SUBSYS<br /> &PRINT<br /> &FORCES SILENT<br /> &END FORCES<br /> &END PRINT<br /> &END FORCE_EVAL</div><div><br /></div><div>Should I follow the same advice you gave me before?</div><div>Thanks again,</div><div><br /></div><div>Niccolò Di Eugenio<br /></div><div> <br /><br /><br /></div><br /><div><div dir="auto">Il giorno lunedì 22 luglio 2024 alle 11:17:04 UTC+2 Krack Matthias ha scritto:<br /></div><blockquote style="margin: 0px 0px 0px 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div lang="en-CH" style="overflow-wrap: break-word;">
<div>
<p><span lang="EN-US" style="font-size: 11pt;">Hi
<u></u><u></u></span></p>
<p><span lang="EN-US" style="font-size: 11pt;"><u></u> <u></u></span></p>
<p><span lang="EN-US" style="font-size: 11pt;">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.<u></u><u></u></span></p>
<p><span lang="EN-US" style="font-size: 11pt;"><u></u> <u></u></span></p>
<p><span lang="EN-US" style="font-size: 11pt;">HTH<u></u><u></u></span></p>
<p><span lang="EN-US" style="font-size: 11pt;"><u></u> <u></u></span></p>
<p><span lang="EN-US" style="font-size: 11pt;">Matthias<u></u><u></u></span></p>
<p><span lang="EN-US" style="font-size: 11pt;"><u></u> <u></u></span></p>
<div>
<div></div></div></div></div><div lang="en-CH" style="overflow-wrap: break-word;"><div><div><div>
<div style="border-width: 1pt medium medium; border-style: solid none none; border-color: rgb(181, 196, 223) currentcolor currentcolor; border-image: none; padding: 3pt 0cm 0cm;">
<p style="margin-right: 0cm; margin-bottom: 12pt; margin-left: 36pt;">
<b><span style="color: black;">From: </span></b><span style="color: black;"><a href="" rel="nofollow">cp...@googlegroups.com</a> <<a href="" rel="nofollow">cp...@googlegroups.com</a>> on behalf of Niccolò Di Eugenio <<a href="" rel="nofollow">niccolod...@gmail.com</a>><br />
<b>Date: </b>Monday, 22 July 2024 at 11:08<br />
<b>To: </b>cp2k <<a href="" rel="nofollow">cp...@googlegroups.com</a>><br />
<b>Subject: </b>Re: [CP2K:20474] CP2K Restart<u></u><u></u></span></p>
</div>
<div>
<p style="margin-left: 36pt;">Hi,<u></u><u></u></p>
</div>
<div>
<p style="margin-left: 36pt;">This is the input file I am using:<u></u><u></u></p>
</div>
<div>
<p style="margin-left: 36pt;"><u></u> <u></u></p>
</div>
<div>
<p style="margin-left: 36pt;">&FORCE_EVAL<br />
<br />
&PRINT<br />
&FORCES<br />
<br />
&END FORCES<br />
<br />
&END PRINT<br />
METHOD Quickstep<br />
&DFT<br />
BASIS_SET_FILE_NAME BASIS_MOLOPT_UZH<br />
POTENTIAL_FILE_NAME GTH_POTENTIALS<br />
&POISSON<br />
POISSON_SOLVER PERIODIC<br />
PERIODIC XYZ<br />
&END POISSON<br />
<br />
&MGRID<br />
NGRIDS 5<br />
CUTOFF 400<br />
REL_CUTOFF 80<br />
<br />
&END MGRID<br />
&QS<br />
METHOD GPW<br />
EPS_PGF_ORB 1E-16<br />
<br />
&END QS<br />
&SCF<br />
&SMEAR ON<br />
ELECTRONIC_TEMPERATURE 2000<br />
METHOD FERMI_DIRAC<br />
&END SMEAR<br />
ADDED_MOS 2000<br />
CHOLESKY INVERSE<br />
SCF_GUESS RESTART<br />
EPS_SCF 1.0E-6<br />
MAX_SCF 200<br />
<br />
&DIAGONALIZATION ON<br />
ALGORITHM STANDARD<br />
&END DIAGONALIZATION<br />
&MIXING T<br />
METHOD BROYDEN_MIXING<br />
ALPHA 0.2<br />
BETA 1.5<br />
NBUFFER 15<br />
<br />
&END MIXING<br />
<br />
&END SCF<br />
&XC<br />
&XC_FUNCTIONAL PBE<br />
&END XC_FUNCTIONAL<br />
&END XC<br />
<br />
&END DFT<br />
&SUBSYS<br />
<br />
&TOPOLOGY<br />
MULTIPLE_UNIT_CELL 4 4 4<br />
COORD_FILE_FORMAT XYZ<br />
COORD_FILE Ba2Y1Cu3O6_mp-1021507.xyz<br />
&END TOPOLOGY<br />
&CELL<br />
MULTIPLE_UNIT_CELL 4 4 4<br />
SYMMETRY CUBIC<br />
ABC 3.886234 3.911377 11.840840<br />
PERIODIC XYZ<br />
&END CELL<br />
&KIND Ba<br />
BASIS_SET DZVP-MOLOPT-PBE-GTH-q10<br />
POTENTIAL GTH-PBE-q10<br />
&END KIND<br />
&KIND Y<br />
BASIS_SET DZVP-MOLOPT-PBE-GTH-q11<br />
POTENTIAL GTH-PBE-q11<br />
&END KIND<br />
&KIND Cu<br />
BASIS_SET DZVP-MOLOPT-PBE-GTH-q11<br />
POTENTIAL GTH-PBE-q11<br />
&END KIND<br />
&KIND O<br />
BASIS_SET DZVP-MOLOPT-PBE-GTH-q6<br />
POTENTIAL GTH-PBE-q6<br />
&END KIND<br />
&PRINT<br />
&CELL HIGH<br />
<br />
&END CELL<br />
&END PRINT<br />
<br />
&END SUBSYS<br />
STRESS_TENSOR ANALYTICAL<br />
<br />
&END FORCE_EVAL<br />
&GLOBAL<br />
PROJECT BaYCuOopt<br />
RUN_TYPE CELL_OPT<br />
PRINT_LEVEL MEDIUM<br />
PREFERRED_DIAG_LIBRARY SL<br />
<br />
&END GLOBAL<br />
<br />
&MOTION<br />
<br />
&CELL_OPT<br />
<br />
KEEP_SYMMETRY .TRUE.<br />
OPTIMIZER BFGS<br />
KEEP_ANGLES<br />
EXTERNAL_PRESSURE 1 0 0 0 1 0 0 0 1<br />
<br />
&END CELL_OPT<br />
<br />
&END MOTION<br />
<br />
Are there any mistakes here? It was working fine before introducing the restart.<u></u><u></u></p>
</div>
<div>
<p style="margin-left: 36pt;"><u></u> <u></u></p>
</div>
<div>
<p style="margin-left: 36pt;">Niccolò
<u></u><u></u></p>
</div>
<div>
<div>
<p style="margin-left: 36pt;">Il giorno lunedì 22 luglio 2024 alle 11:04:37 UTC+2 Krack Matthias ha scritto:<u></u><u></u></p>
</div>
<blockquote style="border-width: medium medium medium 1pt; border-style: none none none solid; border-color: currentcolor currentcolor currentcolor rgb(204, 204, 204); border-image: none; padding: 0cm 0cm 0cm 6pt; margin-left: 4.8pt; margin-right: 0cm;">
<div>
<div>
<p style="margin-left: 36pt;">
<span lang="DE-CH" style="font-size: 11pt;">Hi</span><u></u><u></u></p>
<p style="margin-left: 36pt;">
<span lang="DE-CH" style="font-size: 11pt;"> </span><u></u><u></u></p>
<p style="margin-left: 36pt;">
<span lang="EN-US" style="font-size: 11pt;">There seems to be a problem reading the atomic coordinates. However, without further information, it is difficult to give further guidance.</span><u></u><u></u></p>
<p style="margin-left: 36pt;">
<span lang="EN-US" style="font-size: 11pt;"> </span><u></u><u></u></p>
<p style="margin-left: 36pt;">
<span lang="EN-US" style="font-size: 11pt;">Best</span><u></u><u></u></p>
<p style="margin-left: 36pt;">
<span lang="EN-US" style="font-size: 11pt;"> </span><u></u><u></u></p>
<p style="margin-left: 36pt;">
<span lang="EN-US" style="font-size: 11pt;">Matthias</span><u></u><u></u></p>
<p style="margin-left: 36pt;">
<span lang="EN-US" style="font-size: 11pt;"> </span><u></u><u></u></p>
</div>
</div>
<div>
<div>
<div>
<div>
<div style="border-width: 1pt medium medium; border-style: solid none none; border-color: rgb(181, 196, 223) currentcolor currentcolor; border-image: none; padding: 3pt 0cm 0cm;">
<p style="margin-bottom: 12pt; margin-left: 72pt;">
<b><span style="color: black;">From: </span></b><span style="color: black;"><span><a href="" rel="nofollow">cp...@googlegroups.com</a></span> <<span><a href="" rel="nofollow">cp...@googlegroups.com</a></span>> on behalf of Niccolò Di Eugenio <<span><a href="" rel="nofollow">niccolod...@gmail.com</a></span>><br />
<b>Date: </b>Monday, 22 July 2024 at 10:45<br />
<b>To: </b>cp2k <<span><a href="" rel="nofollow">cp...@googlegroups.com</a></span>><br />
<b>Subject: </b>[CP2K:20471] CP2K Restart</span><u></u><u></u></p>
</div>
<div>
<p style="margin-left: 72pt;">
Dear all, <u></u><u></u></p>
</div>
<div>
<p style="margin-left: 72pt;">
I am trying to restart a DFT calculation. I am currently doing so by running the .restart file instead of the .inp file, as:<u></u><u></u></p>
</div>
<div>
<p style="margin-left: 72pt;">
<u></u><u></u></p>
</div>
<div>
<p style="margin-left: 72pt;">
srun /project/ML_YBCO/nic/cp2k/exe/CRAY-XC50-gcc/cp2k.psmp BaYCuOopt-1_8.restart > Ba2Y1Cu3O6_mp-1021507.out<u></u><u></u></p>
</div>
<div>
<p style="margin-left: 72pt;">
<u></u><u></u></p>
</div>
<div>
<p style="margin-left: 72pt;">
However, I am getting the following error:<u></u><u></u></p>
</div>
<div>
<p style="margin-left: 72pt;">
<u></u><u></u></p>
</div>
<div>
<p style="margin-left: 72pt;">
Rank 0 [Sat Jul 20 21:02:42 2024] [c0-0c0s1n3] application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0<br />
<br />
Program received signal SIGABRT: Process abort signal.<br />
<br />
Backtrace for this error:<br />
#0 0x7fffeb5b849f in ???<br />
#1 0x7fffeb5b8420 in ???<br />
#2 0x7fffeb5b9a00 in ???<br />
#3 0x7fffecb8a267 in ???<br />
#4 0x7fffeca975e5 in ???<br />
#5 0x7fffecadea84 in ???<br />
#6 0x20d10af in __message_passing_MOD_mp_abort<br />
at /project/ML_YBCO/nic/cp2k/src/mpiwrap/message_passing.F:1270<br />
#7 0x20d3d24 in __base_hooks_MOD_cp_abort<br />
at /project/ML_YBCO/nic/cp2k/obj/CRAY-XC50-gcc/psmp/base_hooks.F90:76<br />
#8 0x20d3ed0 in __base_hooks_MOD_cp__a<br />
at /project/ML_YBCO/nic/cp2k/obj/CRAY-XC50-gcc/psmp/base_hooks.F90:163<br />
#9 0xba743b in __atoms_input_MOD_read_atoms_input<br />
at /project/ML_YBCO/nic/cp2k/src/atoms_input.F:122<br />
#10 0x7b82c0 in coordinate_control<br />
at /project/ML_YBCO/nic/cp2k/src/topology.F:588<br />
#11 0x7b82c0 in __topology_MOD_topology_control<br />
at /project/ML_YBCO/nic/cp2k/src/topology.F:197<br />
#12 0xa49e9c in __cp_subsys_methods_MOD_cp_subsys_create<br />
at /project/ML_YBCO/nic/cp2k/src/cp_subsys_methods.F:161<br />
#13 0x90b5fa in __qs_subsys_methods_MOD_qs_subsys_create<br />
at /project/ML_YBCO/nic/cp2k/src/qs_subsys_methods.F:98<br />
#14 0x8d2610 in __qs_environment_MOD_qs_init<br />
at /project/ML_YBCO/nic/cp2k/src/qs_environment.F:317<br />
#15 0xafbda4 in __f77_interface_MOD_create_force_env<br />
at /project/ML_YBCO/nic/cp2k/src/f77_interface.F:805<br />
#16 0x410d22 in cp2k_run<br />
at /project/ML_YBCO/nic/cp2k/src/start/cp2k_runs.F:314<br />
#17 0x41464e in __cp2k_runs_MOD_run_input<br />
at /project/ML_YBCO/nic/cp2k/src/start/cp2k_runs.F:983<br />
#18 0x40b4c6 in cp2k<br />
at /project/ML_YBCO/nic/cp2k/src/start/cp2k.F:379<br />
#19 0x40988c in main<br />
at /project/ML_YBCO/nic/cp2k/obj/CRAY-XC50-gcc/psmp/cp2k.F90:44<br />
srun: error: nid00007: task 0: Aborted<br />
srun: launch/slurm: _step_signal: Terminating StepId=1303919.0<br />
slurmstepd: error: *** STEP 1303919.0 ON nid00007 CANCELLED AT 2024-07-20T21:02:43 ***<br />
srun: error: nid00007: task 1: Terminated<br />
srun: error: nid00008: tasks 2-3: Terminated<br />
srun: Force Terminated StepId=1303919.0<u></u><u></u></p>
</div>
<div>
<p style="margin-left: 72pt;">
<u></u><u></u></p>
</div>
<div>
<p style="margin-left: 72pt;">
How could I solve this? Thank you very much.<u></u><u></u></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p style="margin-left: 72pt;">
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</div>
</div>
</div>
</div>
</blockquote>
</div>
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https://groups.google.com/d/msgid/cp2k/78230b66-fb84-4739-b3cf-8fb4891ac81bn%40googlegroups.com</a>.<u></u><u></u></p>
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