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grimme-lab / xtb

Semiempirical Extended Tight-Binding Program Package
https://xtb-docs.readthedocs.io/
GNU Lesser General Public License v3.0
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forrtl: severe (174): SIGSEGV, segmentation fault occurred #393

Closed adpressa closed 3 years ago

adpressa commented 3 years ago

Attempting to run xtb on a cluster

Happens with the following input file:

#!/bin/ksh -l
#PBS -q small
#PBS -l ncpus=16
#PBS -S /bin/ksh
#PBS -j oe
#PBS -e cwd
cd $PBS_O_WORKDIR
module load xtb/6.3.3

Commands

xtb csa1.xyz --opt loose --alpb chloroform --acc 0.0001 --iterations 1000 --charge 0
  1. start xtb with (all the options here)

Happens with the following input file:

#!/bin/ksh -l
#PBS -q small
#PBS -l ncpus=16
#PBS -S /bin/ksh
#PBS -j oe
#PBS -e cwd
cd $PBS_O_WORKDIR
module load xtb/6.3.3
# Commands 
xtb csa1.xyz --opt loose --alpb chloroform --acc 0.0001 --iterations 1000 --charge 0

  1. run xtb with your options and the --verbose flag

    
  -----------------------------------------------------------      
 |                   =====================                   |     
 |                           x T B                           |     
 |                   =====================                   |     
 |                         S. Grimme                         |     
 |          Mulliken Center for Theoretical Chemistry        |     
 |                    University of Bonn                     |     
  -----------------------------------------------------------      

* xtb version 6.3.3 (5b13467) compiled by 'ehlert@majestix' on 2020-09-17

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,
 e01493. DOI: 10.1002/wcms.1493

for GFN2-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN1-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
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 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

with help from (in alphabetical order)
C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher, M. Checinski,
S. Dohm, S. Ehlert, S. Ehrlich, F. März, H. Neugebauer, J. Pisarek,
P. Pracht, P. Shushkov, and S. Spicher.

* started run on 2020/12/08 at 22:33:49.526     

       -------------------------------------------------
      |                Calculation Setup                |
       -------------------------------------------------

      program call               : xtb csa1.xyz --opt loose --alpb chloroform --acc 0.0001 --iterations 1000 --charge 0 --verbose
      hostname                   : bmbhpcpx013.merck.com
      coordinate file            : csa1.xyz
      xtbhome directory          : /SFS/user/bm/adpressa
      path for xtb               : /SFS/user/bm/adpressa
      xcontrol input file        : csa1.xyz
      omp threads                :                    16
      number of atoms            :                   196
      number of electrons        :                   486
      charge                     :                     0
      spin                       :                   0.0
      first test random number   :      0.48779992687655
      a pointer address          :            0x3EF9C0E9
      random memory content      :      3FDF381D2F3B4350

$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ CONSTRAINTS & SCANS: DEBUG SECTION $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$ ID Z sym. atoms 1 6 C 1-4, 7, 8, 11, 12, 15, 16, 19, 20, 23, 24, 27, 28, 31, 32, 35, 36, 39, 40, 43, 44, 47-53, 55-85 2 8 O 5, 9, 13, 17, 21, 25, 29, 33, 37, 41, 45, 54 3 7 N 6, 10, 14, 18, 22, 26, 30, 34, 38, 42, 46 4 1 H 86-196 $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

       -------------------------------------------------
      |                 G F N 2 - x T B                 |
       -------------------------------------------------

    Reference                      10.1021/acs.jctc.8b01176
  * Hamiltonian:
    H0-scaling (s, p, d)           1.850000    2.230000    2.230000
    zeta-weighting                 0.500000
  * Dispersion:
    s8                             2.700000
    a1                             0.520000
    a2                             5.000000
    s9                             5.000000
  * Repulsion:
    kExp                           1.500000    1.000000
    rExp                           1.000000
  * Coulomb:
    alpha                          2.000000
    third order                    shell-resolved
    anisotropic                    true
    a3                             3.000000
    a5                             4.000000
    cn-shift                       1.200000
    cn-exp                         4.000000
    max-rad                        5.000000

  * Solvation model:               ALPB
    Solvent                        chloroform
    Parameter file                 internal GFN2-xTB/ALPB
    Dielectric constant                4.8100E+00
    Reference state                gsolv [1 M gas/solution]
    Free energy shift                  3.8910E-03 Eh       2.4417E+00 kcal/mol
    Temperature                        2.9815E+02 K
    Density                            1.4900E+00 kg/L
    Solvent mass                       1.1938E+02 g/mol
    Interaction kernel             P16
    Born radius scaling (c1)           1.3274E+00
    Born radii integrator          GBOBC
    Born offset                        0.0000E+00 a0       0.0000E+00 AA
    H-bond correction              false
    Ion screening                  false
    Surface tension                    1.0000E-05 Eh       1.5569E+01 dyn/cm
    Grid points                               230 per atom

      ...................................................
      :                      SETUP                      :
      :.................................................:
      :  # basis functions                 451          :
      :  # atomic orbitals                 451          :
      :  # shells                          281          :
      :  # electrons                       486          :
      :  max. iterations                  1000          :
      :  Hamiltonian                  GFN2-xTB          :
      :  restarted?                      false          :
      :  GBSA solvation                   true          :
      :  PC potential                    false          :
      :  electronic temp.          300.0000000     K    :
      :  accuracy                    0.0001000          :
      :  -> integral cutoff          0.6500000E+02      :
      :  -> integral neglect         0.1000000E-11      :
      :  -> SCF convergence          0.1000000E-09 Eh   :
      :  -> wf. convergence          0.1000000E-07 e    :
      :  Broyden damping             0.4000000          :
      ...................................................

forrtl: severe (174): SIGSEGV, segmentation fault occurred forrtl: severe (174): SIGSEGV, segmentation fault occurred forrtl: severe (174): SIGSEGV, segmentation fault occurred forrtl: severe (174): SIGSEGV, segmentation fault occurred


4. output showing the error
-----------------------------------------------------------      
 |                   =====================                   |     
 |                           x T B                           |     
 |                   =====================                   |     
 |                         S. Grimme                         |     
 |          Mulliken Center for Theoretical Chemistry        |     
 |                    University of Bonn                     |     
  -----------------------------------------------------------

Please provide all input and output file such that we confirm your report.

Expected behaviour A clear and concise description of what you expected to happen.

Expected a geometry optimization to run on a 'cluster'.

Additional context Add any other context about the problem here.

awvwgk commented 3 years ago

Thanks for the report, did you check and setup xtb according to https://xtb-docs.readthedocs.io/en/latest/setup.html#setting-up-xtb?

Also have a look at previous issues were this came up: https://github.com/grimme-lab/xtb/issues/83, https://github.com/grimme-lab/xtb/issues/191

ekwan commented 3 years ago

I had a look at my colleague's problem here. The job runs properly with ulimit -s unlimited and an OMP_STACK_SIZE of 4 GB. The problem seems to be due to our PBS queueing system, which does not allow ulimit commands. We're trying to get that fixed.

awvwgk commented 3 years ago

@ekwan Thanks for looking into this. Seems like there is nothing I can do about this from the xtb site. I'll close this issue as “resolved” for now.