From: Chunli Yan (utchunliyan_at_gmail.com)
Date: Sun Dec 06 2020 - 19:14:06 CST
I ran into problems to run namd QM/MM.
The job always died by following information:
ORCA finished by error termination in GTOInt
Calling Command: mpirun -np 320
/ccs/home/chunli/program/orca421/orca_gtoint_mpi
/gpfs/alpine/scratch/chunli/bip174/eABF/smd.qm.dft/0/qmmm_0.input.int.tmp
/gpfs/alpine/scratch/chunli/bip174/eABF/smd.qm.dft/0/qmmm_0.input
[file orca_tools/qcmsg.cpp, line 458]:
... aborting the run
It seems that I can not parallel ORCA.
If I remove "PAL8" not to parallel ORCA, the job was running without
problems.
Please let me know why I can not call mpirun. I really need your help.
The following is my job script for submission:
#!/bin/bash
#SBATCH -A bip174
#SBATCH -J test
#SBATCH -N 10
#SBATCH -t 48:00:00
#module load cuda/9.2.148
module load fftw
module unload openmpi
#module load spectrum-mpi
#module list
#export ORCA_DIR="/ccs/home/chunli/program/orca421"
#export PATH="$PATH:$ORCA_DIR"
export PATH="/ccs/home/chunli/namd-andes/openmpi-3.1.4/bin/:$PATH"
export
LD_LIBRARY_PATH="/ccs/home/chunli/namd-andes/openmpi-3.1.4/lib/:$LD_LIBRARY_PATH"
cd /gpfs/alpine/scratch/chunli/bip174/eABF/run.smd.dft
srun -n 320
/ccs/home/chunli/namd-andes/NAMD_2.14_Source/Linux-x86_64-g++/namd2
decarboxylase.1.conf > output.smd1.log
#NAMD CONFIGURATION FILE FOR SMD 1
#initial config
coordinates decarboxylase.0.pdb
extendedsystem decarboxylase.0r.xsc
bincoordinates decarboxylase.0r.coor
temperature 300
seed 12345
# Reaction
qmcSMD on
qmcSMDfile reaction_1.rct
#output params
binaryoutput no
outputname decarboxylase.1
outputenergies 1
outputtiming 1
outputpressure 1
binaryrestart yes
dcdfile decarboxylase.1.dcd
dcdfreq 1
XSTFreq 1
restartname decarboxylase.1r
restartfreq 1
#pme parameters
PME on
PMETolerance 10e-6
PMEInterpOrder 4
PMEGridspacing 1
#temperature control and equilibration
langevin on
langevintemp 300
langevindamping 200
#pressure control
usegrouppressure yes
useflexiblecell no
useConstantArea no
langevinpiston off
langevinpistontarget 1
langevinpistonperiod 200
langevinpistondecay 100
langevinpistontemp 300
surfacetensiontarget 0.0
strainrate 0. 0. 0.
#brnch_root_list_opt
splitpatch hydrogen
hgroupcutoff 2.8
#integrator params
timestep 0.5
firstTimestep 0
fullElectFrequency 1
nonbondedfreq 1
#force field params
structure decarboxylase.0.psf
paratypecharmm on
parameters ../toppar/par_all36_prot.prm
parameters ../toppar/par_all36_cgenff.prm
parameters ../toppar/par_all36_na.prm
parameters ../toppar/par_all36_carb.prm
parameters ../toppar/par_all36_lipid.prm
parameters ../toppar/toppar_water_ions_namd.str
parameters ../toppar/ligand.str
exclude scaled1-4
1-4scaling 1.0
rigidbonds all
rigidtolerance 0.00001
rigiditerations 400
cutoff 14.0
pairlistdist 15.0
stepspercycle 1
switching on
switchdist 12.0
wrapAll on
############################################
################################ QM STUFF ##
############################################
qmForces on
qmColumn beta
QMSimsPerNode 1
qmBondColumn occ
QMBondScheme CS
QMSwitching on
QMSwitchingType shift
QMPointChargeScheme none
qmBaseDir "/gpfs/alpine/scratch/chunli/bip174/eABF/smd.qm.dft"
QMVdWParams off
QMNoPntChrg off
QMPCStride 1
QMLiveSolventSel off
qmConfigLine "! B3LYP 6-31G Grid4 EnGrad TightSCF PAL8"
#qmConfigLine "%%pal nprocs 320 end"
qmConfigLine "%%output PrintLevel Mini Print\[ P_Mulliken \] 1
Print\[P_AtCharges_M\] 1 end"
QMChargeFromPSF on
qmMult "1 1"
qmSoftware orca
qmExecPath "/ccs/home/chunli/program/orca421/orca"
QMOutStride 1
QMPositionOutStride 1
############################################
######################### END OF QM STUFF ##
############################################
#script
minimize 500
reinitvels 300
run 10000
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Best,
*Chunli*
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