From 2e7a5c7295bf46e3fdb40d110bef08f75e31bbce Mon Sep 17 00:00:00 2001 From: Calvin Pieters Date: Fri, 3 Feb 2023 15:57:36 +0200 Subject: [PATCH 1/6] Update to Molpro memory increase Added additional search criteria in the memory increase for molpro. While it may find the term 'A further' first due to the reverse for looping, it will attempt to check if there is a 'A full I/O' in the error to better inform the memory increase --- arc/job/trsh.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/arc/job/trsh.py b/arc/job/trsh.py index c770846ede..063edf8efc 100644 --- a/arc/job/trsh.py +++ b/arc/job/trsh.py @@ -8,6 +8,7 @@ import numpy as np import pandas as pd +import re from arc.common import (check_torsion_change, determine_ess, @@ -358,11 +359,17 @@ def determine_ess_status(output_path: str, keywords = ['IGNORE_ERROR in the ORBITAL directive'] error = 'Unconverged' break + elif 'A further' in line and 'Mwords of memory are needed' in line and 'Increase memory to' in line: # e.g.: `A further 246.03 Mwords of memory are needed for the triples to run. # Increase memory to 996.31 Mwords.` (w/o the line break) keywords = ['Memory'] - error = f'Additional memory required: {line.split()[2]} MW' + for line0 in reverse_lines: + if ' For full I/O' in line0 and 'increase memory by' in line0 and 'Mwords to' in line0: + memory_increase = re.findall(r"[\d.]+", line0)[0] + error = f"Additional memory required: {memory_increase} MW" + break + error = f'Additional memory required: {line.split()[2]} MW' if 'error' not in locals() else error break elif 'insufficient memory available - require' in line: # e.g.: `insufficient memory available - require 228765625 have From b9195f6e53fdaf9e19b26222dd1bb06837d66c34 Mon Sep 17 00:00:00 2001 From: Calvin Pieters Date: Fri, 3 Feb 2023 15:58:28 +0200 Subject: [PATCH 2/6] Added a third molpro trsh test Added a third 'insufficient memory' output, searching for 'For full I/O' --- arc/job/trsh_test.py | 13 + .../trsh/molpro/insufficient_memory_3.out | 619 ++++++++++++++++++ 2 files changed, 632 insertions(+) create mode 100755 arc/testing/trsh/molpro/insufficient_memory_3.out diff --git a/arc/job/trsh_test.py b/arc/job/trsh_test.py index 834c842ccc..2fb20b8376 100644 --- a/arc/job/trsh_test.py +++ b/arc/job/trsh_test.py @@ -344,6 +344,19 @@ def test_trsh_ess_job(self): num_heavy_atoms, cpu_cores, ess_trsh_methods) self.assertIn('memory', ess_trsh_methods) self.assertEqual(memory, 96.0) + + # Molpro: Insuffienct Memory 3 Test + path = os.path.join(self.base_path['molpro'], 'insufficient_memory_3.out') + status, keywords, error, line = trsh.determine_ess_status(output_path=path, + species_label='TS', + job_type='sp') + job_status = {'keywords': keywords, 'error': error} + output_errors, ess_trsh_methods, remove_checkfile, level_of_theory, software, job_type, fine, trsh_keyword, \ + memory, shift, cpu_cores, couldnt_trsh = trsh.trsh_ess_job(label, level_of_theory, server, job_status, + job_type, software, fine, memory_gb, + num_heavy_atoms, cpu_cores, ess_trsh_methods) + self.assertIn('memory', ess_trsh_methods) + self.assertEqual(memory, 62.0) # Test Orca # Orca: test 1 diff --git a/arc/testing/trsh/molpro/insufficient_memory_3.out b/arc/testing/trsh/molpro/insufficient_memory_3.out new file mode 100755 index 0000000000..09c35e31e8 --- /dev/null +++ b/arc/testing/trsh/molpro/insufficient_memory_3.out @@ -0,0 +1,619 @@ + + Working directory : /gtmp/calvin.p/scratch/molpro/313795.zeus-master/molpro.1zPAnXaz57/ + Global scratch directory : /gtmp/calvin.p/scratch/molpro/313795.zeus-master/molpro.1zPAnXaz57/ + Wavefunction directory : /home/calvin.p/wfu/ + Main file repository : /gtmp/calvin.p/scratch/molpro/313795.zeus-master/molpro.1zPAnXaz57/ + + id : dana + + Nodes nprocs + n035 1 + GA implementation: MPI file + GA implementation (serial work in mppx): MPI file + + Using customized tuning parameters: mindgm=1; mindgv=20; mindgc=4; mindgr=1; noblas=0; minvec=7 + default implementation of scratch files=df + + + Variables initialized (1025), CPU time= 0.00 sec + ***,DMF_rad_on_methyl + memory,1000,m; + file,1,file1.int !allocate permanent integral file + file,2,file2.wfu !allocate permanent wave-function (dump) file + + geometry={angstrom; + C -2.10714600 1.24844900 0.32354700 + C -1.03500900 0.22991700 0.36805400 + C -0.97884000 -1.03439400 -0.43828800 + C 0.50608200 -1.26344000 -0.50929300 + C 1.13266500 -0.22234600 0.04183100 + C 2.56724200 0.09360300 0.23628500 + O 0.25451400 0.73290900 0.52090200 + H -3.08293100 0.77492100 0.43101700 + H -1.98761200 1.97675800 1.12579000 + H -2.10875500 1.80017800 -0.62816500 + H -1.52417300 -1.85838400 0.03478600 + H -1.42868400 -0.90773400 -1.43760400 + H 0.99137100 -2.11859500 -0.94935400 + H 2.82187700 1.03630100 -0.25070100 + H 2.79604700 0.19906300 1.29798700 + H 3.18729200 -0.69683600 -0.18108200} + + basis=cc-pvtz-f12 + + + + int; + {hf; + maxit,1000; + wf,spin=1,charge=0;} + + uccsd(t)-f12; + + + + Commands initialized (840), CPU time= 0.01 sec, 684 directives. + Default parameters read. Elapsed time= 0.13 sec + + Checking input... + Passed +1 + + + *** PROGRAM SYSTEM MOLPRO *** + Copyright, TTI GmbH Stuttgart, 2015 + Version 2022.3 linked Wed Nov 30 13:40:34 2022 + + + ********************************************************************************************************************************** + LABEL * DMF_rahyl + (16 PROC) 64 bit serial version DATE: 02-Feb-23 TIME: 14:52:04 + ********************************************************************************************************************************** + + SHA1: e31ec9a5ea85254ab76f59d122cbdd51c71cf98b + ********************************************************************************************************************************** + + Memory per process: 1000 MW + Total memory per node: 1000 MW + + GA preallocation disabled + GA check disabled + + Variable memory set to 1000.0 MW + + + + Permanent file 1 file1.int assigned. Implementation=df + Permanent file 2 file2.wfu assigned. Implementation=df Size= 19.53 MB + + + PROGRAM * RESTART + + + Reading variables from file 2 + + _FNUC = 0.00000000 + _BASIS = CC-PVTZ-F12 + _NELEC = 1.00000000 + _PROGRAM = UCCSD(T)-F12 + _NCEN = 1.00000000 + _DMX_SCF = 0.00000000 + _DMY_SCF = 0.00000000 + _DMZ_SCF = 0.00000000 + _HOMO = 1.10000000 + _EHOMO = -0.49994557 + _LUMO = 2.10000000 + _ELUMO = 0.26739009 + _EMP2 = -0.49994621 + _EMP2_SING = 0.00000000 + _EMP2_TRIP = 0.00000000 + _EMP2_SINGLES = -0.00000000 + _EMP2_SCS = -0.49994621 + _ECSING(1:2) = 0.00000000 0.00000000 + _ECTRIP(1:2) = 0.00000000 0.00000000 + _ECTRIPAB(1:2) = 0.00000000 0.00000000 + _ECTRIPAA(1:2) = 0.00000000 0.00000000 + _ECTRIPBB(1:2) = 0.00000000 0.00000000 + _ECSINGLES = -0.00000000 + _EF12 = 0.00000000 + _EF12_SING = 0.00000000 + _EF12_TRIP = 0.00000000 + _ECSING_F12(1:2)= 0.00000000 0.00000000 + _ECTRIP_F12(1:2)= 0.00000000 0.00000000 + _ECTRIPAB_F12(1:2) = 0.00000000 0.00000000 + _ECTRIPAA_F12(1:2) = 0.00000000 0.00000000 + _ECTRIPBB_F12(1:2) = 0.00000000 0.00000000 + _EF12_RHFRELAX = -0.00000064 + _EF12_CONVSUPPRS= 0.00000000 + _EF12_CONVSUPPRT= 0.00000000 + _EF12_SINGLES = -0.00000064 + _EF12_SCS = 0.00000000 + _EF12S = 0.00000000 + _EF12S_SING = 0.00000000 + _EF12S_TRIP = 0.00000000 + _EF12S_SCS = 0.00000000 + _EF12D = 0.00000000 + _EF12D_SING = 0.00000000 + _EF12D_TRIP = 0.00000000 + _EF12D_SCS = 0.00000000 + _EF12F = 0.00000000 + _EF12F_SING = 0.00000000 + _EF12F_TRIP = 0.00000000 + _EF12F_SCS = 0.00000000 + _ENERGC(1:2) = -0.49994621 -0.49994621 + _ENERG_CC(1:2) = 0.00000000 0.00000000 + _ENERG_CV(1:2) = 0.00000000 0.00000000 + _ENERG_VV(1:2) = -0.00000000 -0.00000000 + _ENERGR = -0.49994621 + _ENERGT(1:6) = -0.49994621 -0.49994621 -0.49994621 -0.49994621 -0.49994621 -0.49994621 + _ENERGY(1:2) = -0.49994621 -0.49994621 + _ENERGY_METHOD = UCCSD(T)-F12 + _ENERGY_BASIS = cc-pVTZ-F12 + _ENUC = 0.00000000 + _IPROC_MPP = 0.00000000 + _IPROC_MPPX = 0.00000000 + _ORBITAL = 2100.20000000 + _ECDIAG(1:2) = 0.00000000 0.00000000 + _EPDIAG(1:2) = 0.00000000 0.00000000 + _STATUS = 1.00000000 + _T1DIAG = 0.00000000 + _D1DIAG = 0.00000000 + _D2DIAG = 0.00000000 + !DFBASIS_MP2 = CC-PVTZ-F12-MP2FIT + !DFBASIS_F12K = VTZ-F12-JKFIT + !RIBASIS_MP2 = CC-PVTZ-F12_OPT + !RIBASIS_EXCH = + _DATE = 25-Jan-23 + _METHODC = UCCSD-F12a + _METHODC = UCCSD-F12b + _METHODT = UCCSD(T)-F12a + _METHODT = UCCSD[T]-F12a + _METHODT = UCCSD-T-F12a + _METHODT = UCCSD(T)-F12b + _METHODT = UCCSD[T]-F12b + _METHODT = UCCSD-T-F12b + _OUTPUT = /tmp/calvin.p/scratch/molpro/299041.zeus-master/input.out + _PGROUP = D2h + _TIME = 09:44:41 + _ANSATZ = F12/3C(FIX) + _SVDDEL = 0.00000000 + _SYM_CATION = 1.00000000 + + Geometry written to block 1 of record 700 + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 2 11.47 500 700 + VAR GEOM + + 2 11 19.53 500 610 700 1000 520 2100 7360 701 1001 2101 + VAR BASINP GEOM BASIS MCVARS RHF F12ABS GEOM BASIS RHF + 7350 + EF12 + + PROGRAMS * TOTAL RESTART + CPU TIMES * 0.18 0.04 + REAL TIME * 0.49 SEC + DISK USED * 31.00 MB + ********************************************************************************************************************************** + + Geometry recognized as XYZ + + SETTING BASIS = CC-PVTZ-F12 + + + Using spherical harmonics + + Library entry C S cc-pVTZ-F12 selected for orbital group 1 + Library entry C P cc-pVTZ-F12 selected for orbital group 1 + Library entry C D cc-pVTZ-F12 selected for orbital group 1 + Library entry C F cc-pVTZ-F12 selected for orbital group 1 + Library entry O S cc-pVTZ-F12 selected for orbital group 2 + Library entry O P cc-pVTZ-F12 selected for orbital group 2 + Library entry O D cc-pVTZ-F12 selected for orbital group 2 + Library entry O F cc-pVTZ-F12 selected for orbital group 2 + Library entry H S cc-pVTZ-F12 selected for orbital group 3 + Library entry H P cc-pVTZ-F12 selected for orbital group 3 + Library entry H D cc-pVTZ-F12 selected for orbital group 3 + + + PROGRAM * SEWARD (Integral evaluation for generally contracted gaussian basis sets) Author: Roland Lindh, 1990 + + Geometry written to block 1 of record 701 + + + Point group C1 + + + + ATOMIC COORDINATES + + NR ATOM CHARGE X Y Z + + 1 C 6.00 -3.981928845 2.359226691 0.611415218 + 2 C 6.00 -1.955883547 0.434480161 0.695521259 + 3 C 6.00 -1.849739520 -1.954721365 -0.828244284 + 4 C 6.00 0.956356377 -2.387555575 -0.962424287 + 5 C 6.00 2.140426641 -0.420173045 0.079049134 + 6 C 6.00 4.851384276 0.176884034 0.446513937 + 7 O 8.00 0.480961755 1.384997284 0.984362118 + 8 H 1.00 -5.825895251 1.464388458 0.814504085 + 9 H 1.00 -3.756042322 3.735531235 2.127434774 + 10 H 1.00 -3.984969414 3.401843396 -1.187059811 + 11 H 1.00 -2.880269537 -3.511836794 0.065736013 + 12 H 1.00 -2.699821479 -1.715368654 -2.716677836 + 13 H 1.00 1.873419678 -4.003564319 -1.794019055 + 14 H 1.00 5.332574687 1.958325073 -0.473756229 + 15 H 1.00 5.283763062 0.376174552 2.452839943 + 16 H 1.00 6.023108959 -1.316829194 -0.342195386 + + Bond lengths in Bohr (Angstrom) + + 1- 2 2.795815190 1- 8 2.059658384 1- 9 2.059988886 1-10 2.078838924 2- 3 2.835738337 + ( 1.479481685) ( 1.089924279) ( 1.090099173) ( 1.100074184) ( 1.500608104) + + 2- 7 2.631563578 3- 4 2.842450335 3-11 2.070217705 3-12 2.084732678 4- 5 2.521365364 + ( 1.392563475) ( 1.504159940) ( 1.095512031) ( 1.103193024) ( 1.334249091) + + 4-13 2.035691337 5- 6 2.800142645 5- 7 2.613820044 6-14 2.062031417 6-15 2.062040777 + ( 1.077241464) ( 1.481771675) ( 1.383174001) ( 1.091180034) ( 1.091184987) + + 6-16 2.055767579 + ( 1.087865354) + + Bond angles + + 1-2-3 126.22742713 1-2-7 115.19426684 2-1-8 110.28662321 2-1-9 110.99902873 + + 2- 1-10 111.86146253 2- 3- 4 100.98864478 2- 3-11 112.52199441 2- 3-12 112.00892791 + + 2- 7- 5 107.48373486 3- 2- 7 109.18620546 3- 4- 5 108.98325377 3- 4-13 125.79565500 + + 4- 3-11 113.40779077 4- 3-12 112.16483014 4- 5- 6 132.47269204 4- 5- 7 112.56929336 + + 5- 4-13 125.21171112 5- 6-14 110.58319343 5- 6-15 110.56678019 5- 6-16 110.27586786 + + 6- 5- 7 114.95773861 8- 1- 9 108.41354181 8- 1-10 107.57136719 9- 1-10 107.56333661 + + 11- 3-12 105.93479102 14- 6-15 107.56616705 14- 6-16 108.87441776 15- 6-16 108.90501847 + + NUCLEAR CHARGE: 53 + NUMBER OF PRIMITIVE AOS: 693 + NUMBER OF SYMMETRY AOS: 621 + NUMBER OF CONTRACTIONS: 533 ( 533A ) + NUMBER OF INNER CORE ORBITALS: 0 ( 0A ) + NUMBER OF OUTER CORE ORBITALS: 7 ( 7A ) + NUMBER OF VALENCE ORBITALS: 37 ( 37A ) + + MOLECULE CHANGED: INITIALIZING OCCUPATION AND DUMP RECORDS + + + NUCLEAR REPULSION ENERGY 298.69463471 + + + Eigenvalues of metric + + 1 0.143E-04 0.231E-04 0.295E-04 0.362E-04 0.374E-04 0.543E-04 0.677E-04 0.718E-04 + + + Contracted 2-electron integrals neglected if value below 1.0D-12 + AO integral compression algorithm 1 Integral accuracy 1.0D-12 + + 36414.947 MB (compressed) written to integral file ( 42.2%) + + + NUMBER OF SORTED TWO-ELECTRON INTEGRALS:10126281516. BUFFER LENGTH: 32768 + NUMBER OF SEGMENTS: 159 SEGMENT LENGTH: 63999810 RECORD LENGTH: 262144 + + Memory used in sort: 64.29 MW + + SORT1 READ 10793992478. AND WROTE 8589676652. INTEGRALS IN 49236 RECORDS. CPU TIME: 159.24 SEC, REAL TIME: 387.76 SEC + SORT2 READ 8589676652. AND WROTE 10126281516. INTEGRALS IN 138912 RECORDS. CPU TIME: 150.60 SEC, REAL TIME: 324.00 SEC + + FILE SIZES: FILE 1: 36455.8 MBYTE, FILE 4:103255.4 MBYTE, TOTAL: 139711.2 MBYTE + + OPERATOR DM FOR CENTER 0 COORDINATES: 0.000000 0.000000 0.000000 + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 20 32486.87 500 700 610 701 900 950 970 1002 129 960 + VAR GEOM BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS + 1100 1400 1410 1200 1210 1080 1600 1650 1300 1700 + S T V H0 H01 AOSYM SMH MOLCAS ERIS OPER + + 2 13 19.63 500 610 700 1000 520 2100 7360 701 1001 2101 + VAR BASINP GEOM BASIS MCVARS RHF F12ABS GEOM BASIS RHF + 7350 701(1) 1002 + EF12 GEOM BASIS + + PROGRAMS * TOTAL INT RESTART + CPU TIMES * 3328.82 3328.60 0.04 + REAL TIME * 1214.44 SEC + DISK USED * 130.14 GB + ********************************************************************************************************************************** + + + Program * Restricted Hartree-Fock + + Orbital guess generated from atomic densities. Full valence occupancy: 44 + + Initial alpha occupancy: 27 + Initial beta occupancy: 26 + + NELEC= 53 SYM=1 MS2= 1 THRE=1.0D-08 THRD=3.2D-06 THRG=3.2D-06 HFMA2=F DIIS_START=2 DIIS_MAX=10 DIIS_INCORE=F + + Level shifts: 0.00 (CLOSED) 0.00 (OPEN) 0.30 (GAP_MIN) + + ITER ETOT DE GRAD DDIFF DIIS NEXP TIME(IT) TIME(TOT) DIAG + 1 -307.27499039 -307.27499039 0.00D+00 0.27D-01 0 0 2484.44 5210.58 start + 2 -307.36131742 -0.08632702 0.21D-02 0.24D-02 1 0 2391.93 7602.51 diag2 + 3 -307.37326704 -0.01194963 0.75D-03 0.78D-03 2 0 2414.37 10016.88 diag2 + 4 -307.37655022 -0.00328318 0.30D-03 0.40D-03 3 0 2184.59 12201.47 diag2 + 5 -307.37711032 -0.00056010 0.10D-03 0.15D-03 4 0 2123.89 14325.36 diag2 + 6 -307.37728341 -0.00017309 0.45D-04 0.84D-04 5 0 2270.61 16595.97 diag2 + 7 -307.37731859 -0.00003518 0.21D-04 0.43D-04 6 0 2207.30 18803.27 diag2 + 8 -307.37732237 -0.00000378 0.78D-05 0.14D-04 7 0 2076.45 20879.72 fixocc + 9 -307.37732292 -0.00000056 0.31D-05 0.62D-05 8 0 2091.83 22971.55 diag2 + 10 -307.37732297 -0.00000005 0.84D-06 0.22D-05 9 0 2155.96 25127.51 diag2/orth + 11 -307.37732298 -0.00000000 0.32D-06 0.61D-06 9 0 2051.99 27179.50 diag2 + 12 -307.37732298 -0.00000000 0.13D-06 0.17D-06 0 0 2069.36 29248.86 diag + + Final alpha occupancy: 27 + Final beta occupancy: 26 + + !RHF STATE 1.1 Energy -307.377322975725 + RHF One-electron energy -1008.861082037535 + RHF Two-electron energy 402.789124349213 + RHF Kinetic energy 307.134621134865 + RHF Nuclear energy 298.694634712597 + RHF Virial quotient -1.000790213230 + + !RHF STATE 1.1 Dipole moment 0.02147375 -0.24024810 -0.26240307 + Dipole moment /Debye 0.05458082 -0.61064977 -0.66696207 + + Orbital energies: + + 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 + -20.578091 -11.288247 -11.264777 -11.229646 -11.227789 -11.218809 -11.210199 -1.415036 -1.070639 -1.051266 + + 11.1 12.1 13.1 14.1 15.1 16.1 17.1 18.1 19.1 20.1 + -0.981148 -0.889100 -0.790422 -0.738837 -0.654934 -0.636060 -0.601116 -0.575629 -0.570469 -0.553738 + + 21.1 22.1 23.1 24.1 25.1 26.1 27.1 28.1 29.1 + -0.540464 -0.533368 -0.520995 -0.517837 -0.485355 -0.333149 -0.328644 0.043250 0.047648 + + + HOMO 27.1 -0.328644 = -8.9429eV + LUMO 28.1 0.043250 = 1.1769eV + LUMO-HOMO 0.371893 = 10.1197eV + + Orbitals saved in record 2102.2 + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 20 32486.87 500 700 610 701 900 950 970 1002 129 960 + VAR GEOM BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS + 1100 1400 1410 1200 1210 1080 1600 1650 1300 1700 + S T V H0 H01 AOSYM SMH MOLCAS ERIS OPER + + 2 14 28.42 500 610 700 1000 520 2100 7360 701 1001 2101 + VAR BASINP GEOM BASIS MCVARS RHF F12ABS GEOM BASIS RHF + 7350 701(1) 1002 2102 + EF12 GEOM BASIS RHF + + PROGRAMS * TOTAL HF-SCF INT RESTART + CPU TIMES * 32578.08 29249.24 3328.60 0.04 + REAL TIME * 3087.09 SEC + DISK USED * 130.14 GB + ********************************************************************************************************************************** + + + PROGRAM * CCSD (Unrestricted open-shell coupled cluster) Authors: C. Hampel, H.-J. Werner, 1991, M. Deegan, P.J. Knowles, 1992 + + UCCSD-F12 implementation by G. Knizia and H.-J. Werner, 2008 + + Density fitting integral evaluation by F.R. Manby, 2003,2007, G. Knizia, 2010 + + + Basis set VTZ-F12/JKFIT generated. Number of basis functions: 1142 + Basis set CC-PVTZ-F12/OPTRI generated. Number of basis functions: 894 + Basis set CC-PVTZ-F12/MP2FIT generated. Number of basis functions: 1156 + + Convergence thresholds: THRVAR = 1.00D-08 THRDEN = 1.00D-06 + + CCSD(T) terms to be evaluated (factor= 1.000) + + + Number of core orbitals: 7 ( 7 ) + Number of closed-shell orbitals: 19 ( 19 ) + Number of active orbitals: 1 ( 1 ) + Number of external orbitals: 506 ( 506 ) + + For minimal I/O algorithm in triples, increase memory by 326.44 Mwords to 1326.49 Mwords. + + For full I/O caching in triples, increase memory by 2924.55 Mwords to 3924.60 Mwords. + + Number of N-1 electron functions: 39 + Number of N-2 electron functions: 741 + Number of singly external CSFs: 19773 + Number of doubly external CSFs: 143984451 + Total number of CSFs: 144004224 + + Molecular orbitals read from record 2102.2 Type=RHF/CANONICAL + + Multipassing necessary in transformation. To avoid, increase memory by 696.26 Mwords. + + Integral transformation finished. Total CPU:6889.16 sec, npass= 2 Memory used: 951.48 MW + + Geminal basis: OPTFULL GEM_TYPE=SLATER BETA=1.0 NGEM=6 + + Optimizing Gaussian exponents for each gem_beta + + Geminal optimization for beta= 1.0000 + Weight function: m=0, omega= 1.4646 + + Augmented Hessian optimization of geminal fit. Trust ratio= 0.40000 + Convergence reached after 2 iterations. Final gradient= 8.66D-16, Step= 4.23D-06, Delta= 1.28D-09 + + Alpha: 0.19532 0.81920 2.85917 9.50073 35.69989 197.79328 + Coeff: 0.27070 0.30552 0.18297 0.10986 0.06810 0.04224 + + + WFN_F12=FIX,EG DECOUPLE_EXPL=F HYBRID=0 NOX=F SEMIINT_F12=T CORE_SINGLES=F + + + AO(A)-basis ORBITAL loaded. Number of functions: 533 + RI(R)-basis CC-PVTZ-F12/OPTRI loaded. Number of functions: 894 + DF-basis VTZ-F12/JKFIT loaded. Number of functions: 1142 + + Screening thresholds: THRAO= 1.00D-10 THRMO= 1.00D-09 THRPROD= 1.00D-09 + THRSW= 1.00D-05 THROV= 1.00D-12 THRAOF12= 1.00D-08 + + CPU time for one-electron matrices 282.06 sec + + Construction of ABS: + Pseudo-inverse stability 2.42E-11 + Smallest eigenvalue of S 2.66E-05 (threshold= 1.00E-08) + Ratio eigmin/eigmax 2.48E-06 (threshold= 1.00E-09) + Smallest eigenvalue of S kept 2.66E-05 (threshold= 2.66E-05, 0 functions deleted, 894 kept) + + Construction of CABS: + Pseudo-inverse stability 1.03E-09 + Smallest eigenvalue of S 1.16E-07 (threshold= 1.00E-08) + Ratio eigmin/eigmax 1.16E-07 (threshold= 1.00E-09) + Smallest eigenvalue of S kept 1.16E-07 (threshold= 1.16E-07, 0 functions deleted, 894 kept) + + CPU time for basis constructions 2.37 sec + Fock operators(MO) rebuilt from dump record. + CPU time for Fock operator transformation 3.51 sec + + TOTAL ALPHA BETA + Singles Contributions MO -0.002690647 -0.001358087 -0.001332560 + Singles Contributions CABS -0.002714837 -0.001388438 -0.001326399 + Pure DF-RHF relaxation -0.002708991 + + CPU time for RHF CABS relaxation 3.83 sec + CPU time for singles (tot) 9.07 sec + + AO(A)-basis ORBITAL loaded. Number of functions: 533 + RI(R)-basis CC-PVTZ-F12/OPTRI loaded. Number of functions: 894 + DF-basis CC-PVTZ-F12/MP2FIT loaded. Number of functions: 1156 + + Screening thresholds: THRAO= 1.00D-10 THRMO= 1.00D-09 THRPROD= 1.00D-09 + THRSW= 1.00D-05 THROV= 1.00D-12 THRAOF12= 1.00D-08 + + CPU time for transformed integrals 1650.93 sec + CPU time for F12 matrices 55.27 sec + + Diagonal F12 ansatz with fixed amplitudes: TS= 0.5000 TT= 0.2500 TN= 0.3750 + + ITER. SQ.NORM CORR.ENERGY TOTAL ENERGY ENERGY CHANGE VAR CPU MICRO DIIS + 1 1.37165827 -1.34817141 -308.72820338 -1.3509E+00 3.70E-01 26.03 1 1 1 0 0 + 2 1.37130746 -1.34760105 -308.72763301 5.7037E-04 1.40E-04 90.97 0 0 0 1 1 + 3 1.37159894 -1.34791292 -308.72794489 -3.1188E-04 9.27E-07 169.45 0 0 0 2 2 + 4 1.37160225 -1.34791462 -308.72794658 -1.6903E-06 6.54E-09 261.67 0 0 0 3 3 + 5 1.37160293 -1.34791463 -308.72794659 -1.0999E-08 7.08E-11 369.19 0 0 0 4 4 + + - - Continuing with F12/conv. amplitude coupling turned on. + + 6 1.37162426 -1.34845924 -308.72849121 -5.4463E-04 1.00E-04 452.98 1 1 1 1 1 + 7 1.37162386 -1.34845939 -308.72849136 -1.4925E-07 2.56E-09 550.83 1 1 1 2 2 + + CPU time for iterative RMP2-F12 550.83 sec + + + DF-RMP2-F12 doubles corrections: + - - - - - - - - - - - - - - - - + Approx. TOTAL A-B A-A B-B + RMP2-F12/3C(FIX) -0.100760584 -0.094048295 -0.003586349 -0.003125940 + RMP2-F12/3*C(FIX) -0.100215818 -0.093729117 -0.003467004 -0.003019697 + RMP2-F12/3*C(DX) -0.100391960 -0.093892173 -0.003474046 -0.003025742 + RMP2-F12/3*C(FIX,DX) -0.104099502 -0.097442266 -0.003552755 -0.003104482 + + DF-RMP2-F12 doubles energies: + - - - - - - - - - - - - - - - + Approx. TOTAL A-B A-A B-B + RMP2 -1.245008161 -0.946055225 -0.155426234 -0.143526702 + RMP2-F12/3C(FIX) -1.345768746 -1.040103521 -0.159012583 -0.146652642 + RMP2-F12/3*C(FIX) -1.345223979 -1.039784342 -0.158893238 -0.146546399 + RMP2-F12/3*C(DX) -1.345400122 -1.039947398 -0.158900280 -0.146552444 + RMP2-F12/3*C(FIX,DX) -1.349107664 -1.043497491 -0.158978989 -0.146631183 + + + Reference energy -307.377322975724 + CABS relaxation correction to RHF -0.002708991033 + New reference energy -307.380031966757 + + RMP2-F12 singles (MO) energy -0.002690647101 + RMP2-F12 pair energy -1.345768745588 + RMP2-F12 correlation energy -1.348459392689 + + !RMP2-F12/3C(FIX) energy -308.728491359447 + + Starting RMP2 calculation, locsing= 0 + + ITER. SQ.NORM CORR.ENERGY TOTAL ENERGY ENERGY CHANGE DEN1 VAR(S) VAR(P) DIIS TIME + 1 1.36722453 -1.24288792 -308.62021089 -1.24288792 -0.00451553 0.27D-04 0.18D-02 1 1 11587.39 + 2 1.37146785 -1.24775498 -308.62507796 -0.00486707 -0.00000886 0.11D-05 0.43D-05 2 2 11709.47 + 3 1.37160859 -1.24783646 -308.62515944 -0.00008148 -0.00000008 0.57D-07 0.24D-07 3 3 11827.48 + 4 1.37161294 -1.24783701 -308.62515998 -0.00000054 -0.00000000 0.21D-08 0.17D-09 4 4 11949.84 + + Norm of t1 vector: 0.04317441 S-energy: -0.00269049 T1 diagnostic: 0.00059487 + Norm of t2 vector: 0.60806982 P-energy: -1.24514652 + Alpha-Beta: -0.94652860 + Alpha-Alpha: -0.15524183 + Beta-Beta: -0.14337608 + + Spin contamination 0.00025599 + Reference energy -307.377322975724 + CABS singles correction -0.002708991033 + New reference energy -307.380031966757 + RHF-RMP2 correlation energy -1.247837006045 + !RHF-RMP2 energy -308.627868972802 + + F12/3C(FIX) correction -0.100760584327 + RHF-RMP2-F12 correlation energy -1.348597590372 + !RHF-RMP2-F12 total energy -308.728629557129 + + Starting UCCSD calculation + + ITER. SQ.NORM CORR.ENERGY TOTAL ENERGY ENERGY CHANGE DEN1 VAR(S) VAR(P) DIIS TIME + 1 1.37200329 -1.23383508 -308.61115806 -1.23383508 -0.03305396 0.61D-02 0.65D-02 1 1 25983.89 + 2 1.40270194 -1.26466699 -308.64198997 -0.03083191 -0.00307717 0.34D-03 0.99D-03 2 2 41166.97 + 3 1.41592772 -1.27101985 -308.64834283 -0.00635286 -0.00045252 0.28D-03 0.86D-04 3 3 56469.18 + 4 1.42240238 -1.27348578 -308.65080875 -0.00246593 -0.00010505 0.64D-04 0.22D-04 4 4 72102.51 + 5 1.42609738 -1.27403807 -308.65136105 -0.00055229 -0.00003239 0.31D-04 0.38D-05 5 5 87086.14 + 6 1.42835132 -1.27423569 -308.65155866 -0.00019761 -0.00000905 0.71D-05 0.16D-05 6 6101944.36 + 7 1.42978885 -1.27437241 -308.65169538 -0.00013672 -0.00000216 0.19D-05 0.37D-06 6 1115251.40 + 8 1.43026234 -1.27440155 -308.65172453 -0.00002915 -0.00000053 0.33D-06 0.12D-06 6 2130625.21 + 9 1.43044401 -1.27440801 -308.65173099 -0.00000646 -0.00000012 0.95D-07 0.22D-07 6 3145855.84 + 10 1.43047644 -1.27440423 -308.65172721 0.00000378 -0.00000003 0.23D-07 0.55D-08 6 5161116.89 + 11 1.43051622 -1.27440486 -308.65172783 -0.00000062 -0.00000001 0.62D-08 0.12D-08 6 4174843.13 + + Norm of t1 vector: 0.15458515 S-energy: -0.00316377 T1 diagnostic: 0.01632840 + D1 diagnostic: 0.06780022 + D2 diagnostic: 0.18497578 (internal) + Norm of t2 vector: 0.63766735 P-energy: -1.27124109 + Alpha-Beta: -0.99810052 + Alpha-Alpha: -0.14218988 + Beta-Beta: -0.13095068 + + Singles amplitudes (print threshold = 0.500E-01): + + I SYM. A A T(IA) [Beta-Beta] + + 9 1 1 0.05345027 + 19 1 1 -0.06842190 + + Spin contamination 0.00044860 + + For minimal I/O algorithm in triples, increase memory by 522.58 Mwords to 1522.63 Mwords. + + For full I/O caching in triples, increase memory by 3136.12 Mwords to 4136.17 Mwords. + + A further 111.29 Mwords of memory are needed for the triples to run. Increase memory to 1111.34 Mwords. + + GLOBAL ERROR fehler on processor 0 From f2546720efe981f9cdbb0985dfc96b75a0f2bd2c Mon Sep 17 00:00:00 2001 From: Calvin Date: Tue, 7 Feb 2023 16:17:53 +0200 Subject: [PATCH 3/6] Adjusted molpro.py conversion of memory to megawords --- arc/job/adapters/molpro.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/arc/job/adapters/molpro.py b/arc/job/adapters/molpro.py index 17316914b7..453aa6ea2a 100644 --- a/arc/job/adapters/molpro.py +++ b/arc/job/adapters/molpro.py @@ -320,8 +320,14 @@ def set_input_file_memory(self) -> None: Set the input_file_memory attribute. """ # Molpro's memory is per cpu core and in MW (mega word; 1 MW ~= 8 MB; 1 GB = 128 MW) - self.input_file_memory = math.ceil(self.job_memory_gb * 128 / self.cpu_cores) - + #self.input_file_memory = math.ceil(self.job_memory_gb * 128 / self.cpu_cores) + # https://www.molpro.net/pipermail/molpro-user/2010-April/003723.html + # In the link, they describe the conversion of 100,000,000 Words (100Mword) is equivalent to + # 800,000,000 bytes (800 mb). + # Formula - (100,000,000 [Words]/( 800,000,000 [Bytes] / (job mem in gb * 1000,000,000 [Bytes])))/ 1000,000 [Words -> MegaWords] + # The division by 1E6 is for converting into MWords + self.input_file_memory = math.ceil((1E8/(8E8 /(self.job_memory_gb * 1E9)))/1E6) + def execute_incore(self): """ Execute a job incore. From 61048d9320085a04b63281af802cdb34f32237f2 Mon Sep 17 00:00:00 2001 From: Calvin Pieters Date: Mon, 3 Apr 2023 14:26:01 +0300 Subject: [PATCH 4/6] Molpro Test Update Fixed molpro tests to reflect changes to mem calc --- arc/job/adapters/molpro.py | 1 - arc/job/adapters/molpro_test.py | 6 +++--- arc/job/trsh.py | 1 - 3 files changed, 3 insertions(+), 5 deletions(-) diff --git a/arc/job/adapters/molpro.py b/arc/job/adapters/molpro.py index 453aa6ea2a..a8545512ca 100644 --- a/arc/job/adapters/molpro.py +++ b/arc/job/adapters/molpro.py @@ -320,7 +320,6 @@ def set_input_file_memory(self) -> None: Set the input_file_memory attribute. """ # Molpro's memory is per cpu core and in MW (mega word; 1 MW ~= 8 MB; 1 GB = 128 MW) - #self.input_file_memory = math.ceil(self.job_memory_gb * 128 / self.cpu_cores) # https://www.molpro.net/pipermail/molpro-user/2010-April/003723.html # In the link, they describe the conversion of 100,000,000 Words (100Mword) is equivalent to # 800,000,000 bytes (800 mb). diff --git a/arc/job/adapters/molpro_test.py b/arc/job/adapters/molpro_test.py index 800dec96e2..48a3a3433e 100644 --- a/arc/job/adapters/molpro_test.py +++ b/arc/job/adapters/molpro_test.py @@ -40,13 +40,13 @@ def test_set_cpu_and_mem(self): """Test assigning number of cpu's and memory""" self.job_1.cpu_cores = 48 self.job_1.input_file_memory = None - self.job_1.submit_script_memory = None + self.job_1.submit_script_memory = 14 self.job_1.set_cpu_and_mem() self.assertEqual(self.job_1.cpu_cores, 48) def test_set_input_file_memory(self): """Test setting the input_file_memory argument""" - expected_memory = math.ceil(14 * 128 / 48) + expected_memory = math.ceil((1E8/(8E8 /(14 * 1E9)))/1E6) self.assertEqual(self.job_1.input_file_memory, expected_memory) def test_write_input_file(self): @@ -55,7 +55,7 @@ def test_write_input_file(self): with open(os.path.join(self.job_1.local_path, input_filenames[self.job_1.job_adapter]), 'r') as f: content_1 = f.read() job_1_expected_input_file = """***,spc1 -memory,38,m; +memory,1750,m; file,1,file1.int !allocate permanent integral file file,2,file2.wfu !allocate permanent wave-function (dump) file diff --git a/arc/job/trsh.py b/arc/job/trsh.py index 063edf8efc..6d2d61c8c6 100644 --- a/arc/job/trsh.py +++ b/arc/job/trsh.py @@ -359,7 +359,6 @@ def determine_ess_status(output_path: str, keywords = ['IGNORE_ERROR in the ORBITAL directive'] error = 'Unconverged' break - elif 'A further' in line and 'Mwords of memory are needed' in line and 'Increase memory to' in line: # e.g.: `A further 246.03 Mwords of memory are needed for the triples to run. # Increase memory to 996.31 Mwords.` (w/o the line break) From e236d420cdd48c8b7143e2af22db6e7d99981800 Mon Sep 17 00:00:00 2001 From: Calvin Pieters Date: Mon, 3 Apr 2023 14:29:00 +0300 Subject: [PATCH 5/6] Update PBS Memory Conversion Changed from 1E6 -> 1E8 --- arc/job/adapter.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/arc/job/adapter.py b/arc/job/adapter.py index d91b4678e8..f5391cc8bb 100644 --- a/arc/job/adapter.py +++ b/arc/job/adapter.py @@ -764,7 +764,7 @@ def set_cpu_and_mem(self): self.submit_script_memory = math.ceil(total_submit_script_memory) # in MB if cluster_software in ['pbs']: # In PBS, "#PBS -l select=1:ncpus=8:mem=12000000" specifies the memory for all cores to be 12 MB. - self.submit_script_memory = math.ceil(total_submit_script_memory) * 1E6 # in Bytes + self.submit_script_memory = math.ceil(total_submit_script_memory) * 1E8 # in Bytes elif cluster_software in ['slurm']: # In Slurm, "#SBATCH --mem-per-cpu=2000" specifies the memory **per cpu/thread** to be 2000 MB. self.submit_script_memory = math.ceil(total_submit_script_memory / self.cpu_cores) # in MB From 35e7ec62c6981c2498c557c2213aa018c6731dff Mon Sep 17 00:00:00 2001 From: Calvin Pieters Date: Mon, 3 Apr 2023 14:31:52 +0300 Subject: [PATCH 6/6] Updated PBS Memory Test Changed the conversion in the test to accurately reflect the changes in the adapter.py --- arc/job/adapter_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/arc/job/adapter_test.py b/arc/job/adapter_test.py index 782c1f2950..a55c6fd885 100644 --- a/arc/job/adapter_test.py +++ b/arc/job/adapter_test.py @@ -334,7 +334,7 @@ def test_set_cpu_and_mem(self): self.job_4.server = 'server3' self.job_4.cpu_cores = None self.job_4.set_cpu_and_mem() - expected_memory = math.ceil(14 * 1024 * 1.1) * 1E6 + expected_memory = math.ceil(14 * 1024 * 1.1) * 1E8 self.assertEqual(self.job_4.submit_script_memory, expected_memory) self.job_4.server = 'local'