VMD-L Mailing List

From: hgkrug1_at_gmail.com
Date: Fri Sep 09 2022 - 03:46:55 CDT

Dear All,

I was able to run the job on a single CPU and I still get the same
error (log file attached - see: Info: Running on 1 processors, 1 nodes,
1 physical nodes.).

Any further help will be much appreciated!
Thanks!
Gert Kruger

-------- Forwarded Message --------
From: hgkrug1_at_gmail.com
To: vmd-l_at_ks.uiuc.edu
Subject: QwikMD QM Tut - FATAL ERROR: Error running command for QM
forces calculation
Date: Fri, 09 Sep 2022 09:31:37 +0200

Dear All,

I found a similar error - see
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2017-2018/1005.html
 
The (partial) solution there was to run the job in serial (not in
parallel).

Question then is, how do I change the input for a QwikMD QM
minimization so that it will only run in serial?

At least it will narrow dowm this issue?

Thanks!
Gert Kruger

-------- Forwarded Message --------
From: hgkrug1_at_gmail.com
To: vmd-l_at_ks.uiuc.edu
Cc: hgkrug1_at_gmail.com
Subject: QwikMD QM Tut - FATAL ERROR: Error running command for QM
forces calculation
Date: Tue, 06 Sep 2022 17:30:58 +0200

Dear All,            

I am doing the Qwik QM/MM tutorial at
https://www.ks.uiuc.edu/Research/qmmm/Tutorial/Tutorial.pdf 

Everything worked well until the first QM minimization step (page
15/16).

I get an Error: FATAL ERROR: Error running command for QM forces
calculation (error log file - qm.log in th main directory).

I see this problem was reported before: 
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/0237.html
 - there was an error with the QM PDB file.  I don't see the same issue
with my QM PDB file?

https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/0199.html
 - no
solution?

https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/0583.html
 - no
solution?

A  tar file with setup and run files the that were created so far can
be found at this link -
https://urldefense.com/v3/__https://stuukznac-my.sharepoint.com/:f:/g/personal/kruger_ukzn_ac_za/EgII-IBVb9BKju9lBt5zD7cBHxsxl5jf2DEtssZJRwqyCw?e=yDpXal__;!!DZ3fjg!8Ll8teDwaIxkUe9sXBLsIksiNYE7yy-FsqZADYxGA19SSD12WY1_7M52AXcA-YNtnEM-z9ZzIQ4p73pa$

I have a Dell Inc. Vostro 3670 with a Intel® Core™ i7-8700 CPU @
3.20GHz × 12 processor and a NVIDIA GeForce GT 1030/PCIe/SSE2 / NVIDIA
Corporation GP108 GPU card.

Ubuntu 22.04 LTS installed.  For NAMD I have used the binary version
NAMD_Git-2022-07-21_Linux-x86_64-multicore.tar.gz

When I perform a commandline QM minimization (using the
"Minimization.conf" file) from the provided tutorial files, I get the
same error.

I changed the NAMD version on my PC to NAMD_3.0alpha13_Linux-x86_64-
multicore-CUDA-SingleNode and ran the QM-minimization job from the
command line again. This gives a different error:  FATAL ERROR: QM
forces are not compatible with CUDA at this time

The log file is attached (for the last run).

Any kind help will be much appreciated!
Bets wishes
Gert Kruger


$ namd2 QMMM-Min.conf
Charm++> No provisioning arguments specified. Running with a single PE.
         Use +auto-provision to fully subscribe resources or +p1 to silence this message.
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads (PEs)
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.10.2-0-g7bf00fa-namd-charm-6.10.2-build-2020-Aug-05-556
Warning> Randomization of virtual memory (ASLR) is turned on in the kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try running with '+isomalloc_sync'.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 hosts (1 sockets x 6 cores x 2 PUs = 12-way SMP)
Charm++> cpu topology info is gathered in 0.000 seconds.
Info: NAMD 2.14 for Linux-x86_64-multicore
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Chem. Phys. 153:044130 (2020) doi:10.1063/5.0014475
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 61002 for multicore-linux-x86_64-iccstatic
Info: Built Mon Aug 24 10:08:36 CDT 2020 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD 2.14 Linux-x86_64-multicore 1 werkubuntu gert
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00228935 s
CkLoopLib is used in SMP with simple dynamic scheduling (converse-level notification)
Info: 31.0312 MB of memory in use based on /proc/self/stat
Info: Configuration file is QMMM-Min.conf
Info: Working in the current directory /home/gert/onedrive/ubuntu_werk/namd_vmd/junk/CBM_QM/run
TCL: Suspending until startup complete.
Warning: The following variables were set in the
Warning: configuration file but will be ignored:
Warning: ionConcentration (GBIS)
Warning: alphaCutoff (GBIS)
Info: EXTENDED SYSTEM FILE QMMM-Min.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 0.5
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 1
Info: PERIODIC CELL BASIS 1 58.8481 0 0
Info: PERIODIC CELL BASIS 2 0 55.5702 0
Info: PERIODIC CELL BASIS 3 0 0 69.6404
Info: PERIODIC CELL CENTER 1.10762 0.431464 1.59686
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 200 steps
Info: FIRST LDB TIMESTEP 5
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH 40
Info: INITIAL TEMPERATURE 0
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME QMMM-Min.dcd
Info: DCD FREQUENCY 1
Info: DCD FIRST STEP 1
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME QMMM-Min.xst
Info: XST FREQUENCY 1
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME QMMM-Min
Info: RESTART FILENAME QMMM-Min.restart
Info: RESTART FREQUENCY 1
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 14
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 0.495
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16.995
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1
Info: PRESSURE OUTPUT STEPS 1
Info: HARMONIC CONSTRAINTS ACTIVE
Info: HARMONIC CONS EXP 2
Info: HARMONIC CONS SCALING 2
Info: QM FORCES ACTIVE
Info: QM PDB PARAMETER FILE: CBM_QM_QwikMD_qm-input.pdb
Info: QM SOFTWARE: MOPAC
Info: QM ATOM CHARGES FROM QM SOFTWARE: MULLIKEN
Info: QM EXECUTABLE PATH: /Scr/rcbernardi-new/Software/mopac/MOPAC2016.exe
Info: QM COLUMN: beta
Info: QM BOND COLUMN: occ
Info: QM WILL DETECT BONDS BETWEEN QM AND MM ATOMS.
Info: QM-MM BOND SCHEME: Charge Shift.
Info: QM BASE DIRECTORY: /home/gert/onedrive/ubuntu_werk/namd_vmd/junk/CBM_QM/run/qmmm_exec/QMMM-Min
Info: QM CONFIG LINE: PM7 XYZ T=2M 1SCF MOZYME CUTOFF=9.0 AUX LET GRAD QMMM GEO-OK
Info: QM CONFIG LINE: Test System
Info: QM POINT CHARGES WILL BE SELECTED EVERY 1 STEPS.
Info: QM Point Charge Switching: ON.
Info: QM Point Charge SCHEME: round.
Info: QM executions per node: 1
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 0
Info: LANGEVIN USING BBK INTEGRATOR
Info: LANGEVIN DAMPING COEFFICIENT IS 50 INVERSE PS
Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 200 FS
Info: DECAY TIME IS 100 FS
Info: PISTON TEMPERATURE IS 273 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 2.79525e-05 2.79525e-05 2.79525e-05
Info: CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 60 56 72
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from FFTW_NAMD_2.14_Linux-x86_64-multicore.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.14_Linux-x86_64-multicore.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RANDOM NUMBER SEED 1662711292
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB CBM_QM_QwikMD.pdb
Info: STRUCTURE FILE CBM_QM_QwikMD.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS Retinal_schiff_based_qwikmd.str
Info: PARAMETERS toppar_water_ions_namd.str
Info: PARAMETERS toppar_all36_carb_glycopeptide.str
Info: PARAMETERS par_all36_lipid.prm
Info: PARAMETERS par_all36_na.prm
Info: PARAMETERS par_all36_prot.prm
Info: PARAMETERS par_all36_carb.prm
Info: PARAMETERS par_all36_cgenff.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SUMMARY OF PARAMETERS:
Info: 942 BONDS
Info: 2731 ANGLES
Info: 6593 DIHEDRAL
Info: 211 IMPROPER
Info: 6 CROSSTERM
Info: 357 VDW
Info: 6 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 0.369044
Info: Reading pdb file CBM_QM_QwikMD.pdb
Info: TIME FOR READING PDB FILE: 0.0218417
Info:
Info: Using the following PDB file for QM parameters: CBM_QM_QwikMD_qm-input.pdb
Info: Number of QM atoms (excluding Dummy atoms): 148
Info: We found 6 QM-MM bonds.
Info: Applying user defined multiplicity 1 to QM group ID 1
Info: 1) Group ID: 1 ; Group size: 148 atoms ; Total PSF charge: 0
Info: Found user defined charge 0 for QM group ID 1. Will ignore PSF charge.
Info: MM-QM pair: 643:660 -> Value (distance or ratio): 1.09 (QM Group 0 ID 1)
Info: MM-QM pair: 723:715 -> Value (distance or ratio): 1.09 (QM Group 0 ID 1)
Info: MM-QM pair: 1795:1805 -> Value (distance or ratio): 1.09 (QM Group 0 ID 1)
Info: MM-QM pair: 1857:1844 -> Value (distance or ratio): 1.09 (QM Group 0 ID 1)
Info: MM-QM pair: 1861:1868 -> Value (distance or ratio): 1.09 (QM Group 0 ID 1)
Info: MM-QM pair: 1894:1886 -> Value (distance or ratio): 1.09 (QM Group 0 ID 1)
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 23334 ATOMS
Info: 16326 BONDS
Info: 11163 ANGLES
Info: 6132 DIHEDRALS
Info: 426 IMPROPERS
Info: 150 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 609 CONSTRAINTS
Info: 70002 DEGREES OF FREEDOM
Info: 8230 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 8230 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 144108 amu
Info: TOTAL CHARGE = 1.10641e-06 e
Info: MASS DENSITY = 1.05078 g/cm^3
Info: ATOM DENSITY = 0.10246 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 22.7918 s, 50.5781 MB of memory in use
Info: Startup phase 0 took 0.000112345 s, 50.5781 MB of memory in use
Info: The QM region will remove 144 bonds, 237 angles, 333 dihedrals, 25 impropers and 6 crossterms.
Info: ADDED 33513 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.0316892 s, 51.7148 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 2.64698e-23 AT 11.9138
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.40436e-16 AT 11.9138
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 4.10282e-22 AT 11.9138
Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 3.56912e-15 AT 11.9138
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.86076e-32 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 4.62223e-32 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.12237e-15 AT 11.9138
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-25 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-26 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97409e-16 AT 11.9138
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.00289143 s, 55.9648 MB of memory in use
Info: Startup phase 3 took 3.7329e-05 s, 55.9648 MB of memory in use
Info: Startup phase 4 took 0.0101146 s, 55.9648 MB of memory in use
Info: Startup phase 5 took 4.1077e-05 s, 55.9648 MB of memory in use
Info: PATCH GRID IS 3 (PERIODIC) BY 3 (PERIODIC) BY 4 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0 0 0
Info: LARGEST PATCH (22) HAS 736 ATOMS
Info: TORUS A SIZE 1 USING 0
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
Info: Placed 100% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.00504412 s, 61.3164 MB of memory in use
Info: PME using 1 and 1 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 0
Info: PME TRANS LOCATIONS: 0
Info: PME USING 1 GRID NODES AND 1 TRANS NODES
Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done.
Info: Startup phase 7 took 0.00043569 s, 61.3164 MB of memory in use
Info: Startup phase 8 took 4.5516e-05 s, 61.3164 MB of memory in use
Info: Startup phase 9 took 3.7019e-05 s, 61.3164 MB of memory in use
Info: Startup phase 10 took 3.4701e-05 s, 61.3164 MB of memory in use
Info: Startup phase 11 took 3.556e-05 s, 61.3164 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 12 took 0.000110685 s, 61.3164 MB of memory in use
Info: CREATING 763 COMPUTE OBJECTS
Info: Startup phase 13 took 0.00835758 s, 63.1523 MB of memory in use
Info: Startup phase 14 took 6.4339e-05 s, 63.1523 MB of memory in use
Info: Startup phase 15 took 0.000343877 s, 67.668 MB of memory in use
Info: Finished startup at 22.8512 s, 67.668 MB of memory in use

TCL: Minimizing for 100 steps
Info: List of ranks running QM simulations: 0.
FATAL ERROR: Error running command for QM forces calculation.
FATAL ERROR: Error running command for QM forces calculation.
[Partition 0][Node 0] End of program