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GFN0 malloc error for dihydrogen
Describe the bug
When I run a test GFN0 calculation on H2, I frequently (but not always) see malloc errors (copied below). Occasionally the calculation just hangs and must be quit manually (after 10+ seconds). This does not happen with GFN1, GFN2, or GFN-FF.
I'm using xtb 6.5.1 updated today from conda-forge, and the problem just started happening — I don't remember when I last updated, however.
This occurs on my laptop (MacBook Pro, macOS 10.14.6).
To Reproduce Steps to reproduce the behaviour:
- happens with input (include input files) H2.xyz:
2
H2
H 0.25 0.0 0.0
H -0.25 0.0 0.0
- start
xtbwith (all the options here):xtb --gfn 0 H2.xyz - run
xtbwith your options and the--verboseflag - output showing the error:
[[A(chem) dhcp-10-250-194-185:presto cwagen$ xtb --verbose --gfn 0 test/static/H2.xyz
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
-----------------------------------------------------------
* xtb version 6.5.1 (conda-forge) compiled by '[email protected]' on 2022-07-12
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for ALPB and GBSA implicit solvation:
* S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput.,
2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, C. Hölzer
A. Katbashev, J. Koopman, C. Lavigne, S. Lehtola, F. März, M. Müller,
F. Musil, H. Neugebauer, J. Pisarek, C. Plett, P. Pracht, F. Pultar,
J. Seibert, P. Shushkov, S. Spicher, M. Stahn, M. Steiner, T. Strunk,
J. Stückrath, T. Rose, and J. Unsleber
* started run on 2022/07/26 at 16:34:31.116
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : xtb --verbose --gfn 0 test/static/H2.xyz
coordinate file : test/static/H2.xyz
xtbhome directory : /Users/cwagen
path for xtb : /Users/cwagen/.xtb-parameters/
xcontrol input file : test/static/H2.xyz
omp threads : 8
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
CONSTRAINTS & SCANS: DEBUG SECTION
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
ID Z sym. atoms
1 1 H 1, 2
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
-------------------------------------------------
| G F N 0 - x T B |
-------------------------------------------------
Reference 10.26434/chemrxiv.8326202.v1
* Hamiltonian:
H0-scaling (s, p, d) 2.000000 2.486800 2.270000
zeta-weighting 1.000000
* Dispersion:
s8 2.850000
a1 0.800000
a2 4.600000
s9 0.000000
* Repulsion:
kExp 1.500000
rExp 1.000000
* Coulomb:
alpha 0.000000
third order atomic
anisotropic false
* Polar bond correction:
rad-shift 0.053700
strength -0.012900
en-exp 3.484700
en-scale 0.509700
xtb(35213,0x10c7075c0) malloc: can't allocate region
*** mach_vm_map(size=18446744069414588416) failed (error code=3)
xtb(35213,0x700008c59000) malloc: can't allocate region
*** mach_vm_map(size=18446744069414588416) failed (error code=3)
xtb(35213,0x10c7075c0) malloc: *** set a breakpoint in malloc_error_break to debug
xtb(35213,0x70000bc6b000) malloc: can't allocate region
*** mach_vm_map(size=18446744069414588416) failed (error code=3)
xtb(35213,0x70000b468000) malloc: can't allocate region
*** mach_vm_map(size=18446744069414588416) failed (error code=3)
Operating system error: Cannot allocate memory
Allocation would exceed memory limit
Error termination. Backtrace:
xtb(35213,0x700009c5f000) malloc: can't allocate region
*** mach_vm_map(size=18446744069414588416) failed (error code=3)
xtb(35213,0x70000945c000) malloc: can't allocate region
*** mach_vm_map(size=18446744069414588416) failed (error code=3)
xtb(35213,0x700008c59000) malloc: *** set a breakpoint in malloc_error_break to debug
xtb(35213,0x70000a462000) malloc: can't allocate region
*** mach_vm_map(size=18446744069414588416) failed (error code=3)
xtb(35213,0x70000ac65000) malloc: can't allocate region
*** mach_vm_map(size=18446744069414588416) failed (error code=3)
xtb(35213,0x70000b468000) malloc: *** set a breakpoint in malloc_error_break to debug
xtb(35213,0x70000ac65000) malloc: *** set a breakpoint in malloc_error_break to debug
xtb(35213,0x70000bc6b000) malloc: *** set a breakpoint in malloc_error_break to debug
xtb(35213,0x700009c5f000) malloc: *** set a breakpoint in malloc_error_break to debug
Operating system error: Cannot allocate memory
Allocation would exceed memory limit
Error termination. Backtrace:
Operating system error: Cannot allocate memory
Allocation would exceed memory limit
Operating system error: Cannot allocate memory
Allocation would exceed memory limit
Error termination. Backtrace:
Operating system error: Cannot allocate memory
Allocation would exceed memory limit
xtb(35213,0x70000a462000) malloc: *** set a breakpoint in malloc_error_break to debug
Error termination. Backtrace:
Error termination. Backtrace:
Operating system error: Cannot allocate memory
Allocation would exceed memory limit
xtb(35213,0x70000945c000) malloc: *** set a breakpoint in malloc_error_break to debug
Error termination. Backtrace:
Operating system error: Cannot allocate memory
Allocation would exceed memory limit
Error termination. Backtrace:
Operating system error: Cannot allocate memory
Allocation would exceed memory limit
Error termination. Backtrace:
#0 0x1071ee4dc
#0 0x1071ee4dc
#0 0x1071ee4dc
#0 0x1071ee4dc
#0 0x1071ee4dc
#0 0x1071ee4dc
#0 0x1071ee4dc
#0 0x1071ee4dc
#1 0x1071ef395
#1 0x1071ef395
#1 0x1071ef395
#1 0x1071ef395
#1 0x1071ef395
#1 0x1071ef395
#1 0x1071ef395
#1 0x1071ef395
#2 0x1071ef609
#2 0x1071ef609
#2 0x1071ef609
#2 0x1071ef609
#3 0x106d191c2
#3 0x106d191c2
#3 0x106d191c2
#3 0x106d191c2
#2 0x1071ef609
#4 0x1078864c7
#3 0x106d191c2
#4 0x10788c65d
#4 0x1078864c7
#4 0x1078864c7
#4 0x1078864c7
#5 0x106d19798
#6 #2 0x1071ef609
#2 0x1071ef609
#3 0x106d191c2
#4 0x1078864c7
0x106d8db87
#2 0x1071ef609
#3 0x106d191c2
#4 0x1078864c7
Please provide all input and output file such that we confirm your report.
Expected behaviour I would like it to work.
Additional context None.
