|
|
各位老师，之前在服务器上跑gromacs，选的时间是200 ns。后来觉得可能用得着500 ns，就提交了一个新的任务
gmx convert-tpr -s md.tpr -extend 300000 -o md.tpr
gmx mdrun -v -deffnm md -cpi md.cpt
但是遗憾的是前面的才跑到197 ns，那个extend的任务就进去了，直接导致trr文件跑乱了。转换成xtc的时候就报错了：
-------------------------------------------------------
Program: gmx trjconv, version 2020.6
Source file: src/gromacs/fileio/trrio.cpp (line 113)
Fatal error:
Failed to find GROMACS magic number in trr frame header, so this is not a trr
file!
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
我想用tpbconv从197.5 ns续跑，但是gromacs提示没有这个命令了。请问这个时候怎么挽救一下呢？（主要是198 ns以后的读不出来了）
log文件相关部分如下：
Step Time
98986000 197972.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
7.02166e+04 3.09531e+05 2.42639e+05 6.36891e+03 -3.83449e+03
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
5.59984e+04 5.05290e+04 2.36441e+05 -5.63285e+06 2.10167e+04
Potential Kinetic En. Total Energy Conserved En. Temperature
-4.64395e+06 1.17365e+06 -3.47030e+06 3.04729e+07 3.00313e+02
Pressure (bar) Constr. rmsd
-4.70852e+01 4.41455e-06
Step Time
98987000 197974.00000
Writing checkpoint, step 98987000 at Fri Aug 18 05:20:34 2023
Reading checkpoint file md.cpt
file generated by: /home/lijun/WORK/yinhang/gmx2020.6.cuda/bin/gmx
file generated at: Fri Aug 18 05:20:34 2023
GROMACS double prec.: 0
simulation part #: 1
step: 98987000
time: 197974.000000
-----------------------------------------------------------
Restarting from checkpoint, appending to previous log file.
:-) GROMACS - gmx mdrun, 2020.6 (-:
Executable: /home/lijun/WORK/yinhang/gmx2020.6.cuda/bin/gmx
Data prefix: /home/lijun/WORK/yinhang/gmx2020.6.cuda
Working dir: /WORK/lijun_work/yinhang/7rqw-delta4
Process ID: 25319
Command line:
gmx mdrun -v -deffnm md -cpi md.cpt -ntomp 20 -pme gpu -nb gpu
GROMACS version: 2020.6
Verified release checksum is 2f568d8884e039acbc6b68722432516e0628be00c847969b7c905c8b53ef826f
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: CUDA
SIMD instructions: AVX_512
FFT library: fftw-3.3.10-sse2-avx-avx2-avx2_128
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: hwloc-1.11.8
Tracing support: disabled
C compiler: /apps/compilers/gcc/v9.2.0/bin/gcc GNU 9.2.0
C compiler flags: -mavx512f -mfma -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
C++ compiler: /apps/compilers/gcc/v9.2.0/bin/g++ GNU 9.2.0
C++ compiler flags: -mavx512f -mfma -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
CUDA compiler: /usr/local/cuda-11.6/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2022 NVIDIA Corporation;Built on Tue_Mar__8_18:18:20_PST_2022;Cuda compilation tools, release 11.6, V11.6.124;Build cuda_11.6.r11.6/compiler.31057947_0
CUDA compiler flags:-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-Wno-deprecated-gpu-targets;-gencode;arch=compute_35,code=compute_35;-gencode;arch=compute_50,code=compute_50;-gencode;arch=compute_52,code=compute_52;-gencode;arch=compute_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-gencode;arch=compute_70,code=compute_70;-gencode;arch=compute_75,code=compute_75;-gencode;arch=compute_80,code=compute_80;-use_fast_math;;-mavx512f -mfma -fexcess-precision=fast -funroll-all-loops -fopenmp -O3 -DNDEBUG
CUDA driver: 12.0
CUDA runtime: 11.60
Changing nstlist from 20 to 100, rlist from 1.211 to 1.326
1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
PP:0,PME:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread
Non-default thread affinity set, disabling internal thread affinity
Using 20 OpenMP threads
System total charge: 0.000
Will do PME sum in reciprocal space for electrostatic interactions.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06
Initialized non-bonded Ewald tables, spacing: 1.02e-03 size: 1176
Generated table with 1163 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1163 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1163 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Using GPU 8x8 nonbonded short-range kernels
Using a dual 8x8 pair-list setup updated with dynamic, rolling pruning:
outer list: updated every 100 steps, buffer 0.126 nm, rlist 1.326 nm
inner list: updated every 16 steps, buffer 0.005 nm, rlist 1.205 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
outer list: updated every 100 steps, buffer 0.283 nm, rlist 1.483 nm
inner list: updated every 16 steps, buffer 0.069 nm, rlist 1.269 nm
Initializing LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
The number of constraints is 75198
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
There are: 442627 Atoms
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: SOLU_MEMB
1: SOLV
Started mdrun on rank 0 Fri Aug 18 05:32:38 2023
Step Time
98987000 197974.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
7.12062e+04 3.10216e+05 2.41943e+05 6.50838e+03 -3.60176e+03
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
5.58516e+04 5.11185e+04 2.38904e+05 -5.64105e+06 2.08064e+04
Potential Kinetic En. Total Energy Conserved En. Temperature
-4.64810e+06 1.17384e+06 -3.47425e+06 3.04738e+07 3.00364e+02
Pressure (bar) Constr. rmsd
-6.36098e+01 4.45868e-06
step 98987800: timed with pme grid 144 144 144, coulomb cutoff 1.200: 2102.3 M-cycles
step 98988000: timed with pme grid 128 128 128, coulomb cutoff 1.282: 2231.1 M-cycles
|
|
发表于 Post on 2023-8-18 07:21:09
收藏 Add to favorites