计算化学公社

标题: 请教gromacs做分子动力学跑预平衡过程时用GPU加速出现报错的问题 [打印本页]

作者
Author: 枝枝z 时间: 2023-9-25 18:40
标题: 请教gromacs做分子动力学跑预平衡过程时用GPU加速出现报错的问题
请教老师，用gpu加速计算时，跑预平衡过程，
报错
Fatal error:
Unexpected cudaStreamQuery failure. CUDA error #700 (cudaErrorIllegalAddress):
an illegal memory access was encountered.
是什么原因？网上查了一下报错相关问题，说是显存问题，我不太理解。
请教老师，应该怎么避免这种报错，是命令行、参数设置有问题？还是计算电脑配置问题？可以通过什么方法解决？

后续还用了命令行gmx mdrun -v -deffnm E:\gmxfile\mixc5f2g2x13\c5f2g2x13eq -nt 16 -pin on -bonded cpu -nb cpu -pme cpu -update cpu，
就没有出现
Fatal error:
Unexpected cudaStreamQuery failure. CUDA error #700 (cudaErrorIllegalAddress):
an illegal memory access was encountered.
的报错信息了。
用cpu算没有出现如上报错，所以想着应该是gpu加速这块的问题，请教老师，想用gpu加速做计算应该修改哪些参数或者命令呢？

模拟体系的原子数是30000，主要是由水分子和186原子的聚合物链构成的模拟体系。
软件是gromacs 2022.5版，在Windows环境下计算。

下面是遇到该问题具体的命令行，程序运行信息以及报错信息：
C:\Users\Administrator>gmx mdrun -v -deffnm E:\gmxfile\mixc5f2g2x13\c5f2g2x13eq -nt 16 -pin on -bonded gpu -nb gpu -pme gpu -update gpu
                  :-) GROMACS - gmx mdrun, 2022.5 (-:

Executable: D:\gromacs\bin\gmx.exe
Data prefix:  D:\gromacs
Working dir:  C:\Users\Administrator
Command line:
  gmx mdrun -v -deffnm E:\gmxfile\mixc5f2g2x13\c5f2g2x13eq -nt 16 -pin on -bonded gpu -nb gpu -pme gpu -update gpu

Highest SIMD level supported by all nodes in run: AVX2_256
SIMD instructions selected at compile time:    AVX2_128
Compiled SIMD likely not supported by hardware; program might crash.
Reading file E:\gmxfile\mixc5f2g2x13\c5f2g2x13eq.tpr, VERSION 2022.5 (single precision)
Changing nstlist from 10 to 100, rlist from 1 to 1

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 and most bonded interactions on the GPU
PP task will update and constrain coordinates on the GPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread
Using 16 OpenMP threads

starting mdrun 'water+c5f2g2x11_opt'
100000 steps, 200.0 ps.
step 0
-------------------------------------------------------
Program:    gmx mdrun, version 2022.5
Source file: src\gromacs/gpu_utils/cudautils.cuh (line 190)

Fatal error:
Unexpected cudaStreamQuery failure. CUDA error #700 (cudaErrorIllegalAddress):
an illegal memory access was encountered.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

C:\Users\Administrator>gmx mdrun -v -deffnm E:\gmxfile\mixc5f2g2x13\c5f2g2x13eq -nt 16 -pin on -bonded gpu -nb gpu -pme gpu
                  :-) GROMACS - gmx mdrun, 2022.5 (-:

Executable: D:\gromacs\bin\gmx.exe
Data prefix:  D:\gromacs
Working dir:  C:\Users\Administrator
Command line:
  gmx mdrun -v -deffnm E:\gmxfile\mixc5f2g2x13\c5f2g2x13eq -nt 16 -pin on -bonded gpu -nb gpu -pme gpu（和第一次命令行相比，命令行减去-update gpu，跑了69步后报错）

Back Off! I just backed up E:\gmxfile\mixc5f2g2x13\c5f2g2x13eq.log to E:\gmxfile\mixc5f2g2x13/#c5f2g2x13eq.log.1#
Highest SIMD level supported by all nodes in run: AVX2_256
SIMD instructions selected at compile time:    AVX2_128
Compiled SIMD likely not supported by hardware; program might crash.
Reading file E:\gmxfile\mixc5f2g2x13\c5f2g2x13eq.tpr, VERSION 2022.5 (single precision)
Changing nstlist from 10 to 100, rlist from 1 to 1

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 and most bonded 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
Using 16 OpenMP threads

Back Off! I just backed up E:\gmxfile\mixc5f2g2x13\c5f2g2x13eq.xtc to E:\gmxfile\mixc5f2g2x13/#c5f2g2x13eq.xtc.1#

Back Off! I just backed up E:\gmxfile\mixc5f2g2x13\c5f2g2x13eq.edr to E:\gmxfile\mixc5f2g2x13/#c5f2g2x13eq.edr.1#
starting mdrun 'water+c5f2g2x11_opt'
100000 steps, 200.0 ps.
step 0
Step 52, time 0.104 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.053332, max 2.134596 (between atoms 397100 and 397103)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
395240 395243 45.7 0.0973 0.0973    0.0973
397100 397103 90.0 0.0973 0.3050    0.0973
Wrote pdb files with previous and current coordinates

Step 53, time 0.106 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.028690, max 1.148184 (between atoms 394496 and 394499)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.0973 0.2090    0.0973
397100 397103 90.0 0.3050 0.0991    0.0973
Wrote pdb files with previous and current coordinates

Step 54, time 0.108 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.161245, max 6.076720 (between atoms 395426 and 395429)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.2090 0.0977    0.0973
395426 395429 90.0 0.0973 0.6886    0.0973
395612 395615 65.4 0.0973 0.0973    0.0973
396542 396545 90.0 0.0973 0.1512    0.0973
396728 396731 48.6 0.0973 0.0973    0.0973
396914 396917 38.8 0.0973 0.0973    0.0973
397100 397103 90.0 0.0991 0.3018    0.0973
Wrote pdb files with previous and current coordinates

Step 55, time 0.11 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.162835, max 5.615213 (between atoms 395798 and 395801)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.0977 0.2061    0.0973
394682 394685 33.2 0.0973 0.0973    0.0973
394868 394871 48.1 0.0973 0.0973    0.0973
395054 395057 90.0 0.0973 0.2009    0.0973
395426 395429 74.3 0.6886 0.0973    0.0973
395612 395615 50.3 0.0973 0.0973    0.0973
395798 395801 90.0 0.0973 0.6437    0.0973
395984 395987 90.0 0.0973 0.2025    0.0973
396356 396359 90.0 0.0973 0.1534    0.0973
396542 396545 72.4 0.1512 0.0973    0.0973
397100 397103 90.0 0.3018 0.1158    0.0973
397658 397661 90.0 0.0973 0.3552    0.0973
Wrote pdb files with previous and current coordinates

Step 56, time 0.112 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.177361, max 4.159923 (between atoms 395428 and 395432)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.2061 0.1104    0.0973
395054 395057 90.0 0.2009 0.0975    0.0973
395426 395429 90.0 0.0973 0.4254    0.0973
395428 395432 90.0 0.1097 0.5660    0.1097
395612 395615 45.9 0.0973 0.0973    0.0973
395798 395801 59.7 0.6437 0.0973    0.0973
395984 395987 90.0 0.2025 0.0980    0.0973
396170 396173 30.0 0.0973 0.0973    0.0973
396356 396359 72.4 0.1534 0.0973    0.0973
396542 396545 90.0 0.0973 0.1528    0.0973
397100 397103 90.0 0.1158 0.2971    0.0973
397286 397289 47.7 0.0973 0.0973    0.0973
397472 397475 90.0 0.0973 0.5003    0.0973
397658 397661 83.6 0.3552 0.0973    0.0973
Wrote pdb files with previous and current coordinates

Step 57, time 0.114 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1.781862, max 60.820023 (between atoms 395800 and 395804)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.1104 0.1986    0.0973
395054 395057 90.0 0.0975 0.1982    0.0973
395426 395429 60.3 0.4254 0.0973    0.0973
395612 395615 48.6 0.0973 0.0973    0.0973
395798 395801 90.0 0.0973 3.7080    0.0973
395800 395804 90.0 0.1097 6.7810    0.1097
395984 395987 90.0 0.0980 0.2001    0.0973
396356 396359 90.0 0.0973 0.1560    0.0973
396542 396545 90.0 0.1528 0.0989    0.0973
397100 397103 90.0 0.2971 0.1172    0.0973
397472 397475 74.5 0.5003 0.0973    0.0973
397658 397661 90.0 0.0973 0.3464    0.0973
Wrote pdb files with previous and current coordinates

Step 58, time 0.116 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.170179, max 3.970914 (between atoms 395803 and 395808)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.1986 0.1118    0.0973
395054 395057 90.0 0.1982 0.1105    0.0973
395426 395429 90.0 0.0973 0.3306    0.0973
395428 395432 60.3 0.1097 0.1097    0.1097
395430 395433 32.9 0.1097 0.1097    0.1097
395431 395436 37.5 0.1096 0.1096    0.1096
395612 395615 69.7 0.0973 0.0973    0.0973
395798 395801 56.5 3.7080 0.0973    0.0973
395800 395804 54.8 6.7810 0.1097    0.1097
395802 395805 90.0 0.1097 0.3921    0.1097
395803 395808 90.0 0.1096 0.5449    0.1096
395984 395987 90.0 0.2001 0.1114    0.0973
396356 396359 90.0 0.1560 0.0978    0.0973
396542 396545 90.0 0.0989 0.1501    0.0973
397100 397103 90.0 0.1172 0.2962    0.0973
397472 397475 90.0 0.0973 0.4572    0.0973
397658 397661 90.0 0.3464 0.1160    0.0973
Wrote pdb files with previous and current coordinates

Step 59, time 0.118 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 4.059070, max 121.903214 (between atoms 395430 and 395433)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.1118 0.1969    0.0973
395054 395057 90.0 0.1105 0.1906    0.0973
395417 395422 52.2 0.1086 0.1086    0.1086
395426 395429 90.0 0.3306 0.1383    0.0973
395428 395432 90.0 0.1097 0.3496    0.1097
395430 395433 90.0 0.1097  13.4813    0.1097
395431 395436 41.7 0.1096 0.1096    0.1096
395434 395439 90.0 0.1097 8.0741    0.1097
395612 395615 48.3 0.0973 0.0973    0.0973
395798 395801 90.0 0.0973 3.6440    0.0973
395800 395804 90.0 0.1097 7.7925    0.1097
395802 395805 90.0 0.3921 0.1584    0.1097
395803 395808 40.1 0.5449 0.1096    0.1096
395810 395814 90.0 0.1097 0.2792    0.1097
395815 395818 90.0 0.1097 0.4657    0.1097
395984 395987 90.0 0.1114 0.1925    0.0973
396356 396359 90.0 0.0978 0.1536    0.0973
396542 396545 81.0 0.1501 0.0973    0.0973
397100 397103 90.0 0.2962 0.1197    0.0973
397472 397475 90.0 0.4572 0.1045    0.0973
397658 397661 90.0 0.1160 0.3423    0.0973
Wrote pdb files with previous and current coordinates

Step 60, time 0.12 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1.304654, max 37.769939 (between atoms 395815 and 395818)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.1969 0.1187    0.0973
394682 394685 32.6 0.0973 0.0973    0.0973
395054 395057 90.0 0.1906 0.1120    0.0973
395415 395418 90.0 0.1086 0.2094    0.1086
395417 395422 90.0 0.1086 0.1158    0.1086
395426 395429 90.0 0.1383 0.3704    0.0973
395428 395432 90.0 0.3496 0.2833    0.1097
395430 395433 90.0 13.4813 0.2590    0.1097
395431 395436 55.6 0.1096 0.1096    0.1096
395434 395439 90.0 8.0741 0.2864    0.1097
395612 395615 42.3 0.0973 0.0973    0.0973
395800 395804 90.0 7.7925 1.7897    0.1097
395802 395805 90.0 0.1584 0.1514    0.1097
395803 395808 54.0 0.1096 0.1096    0.1096
395806 395811 90.0 0.1097 0.1731    0.1097
395809 395813 90.0 0.0973 0.1263    0.0973
395810 395814 90.0 0.2792 3.6318    0.1097
395815 395817 90.0 0.1076 0.1780    0.1097
395815 395818 90.0 0.4657 4.2527    0.1097
395984 395987 90.0 0.1925 0.1142    0.0973
396170 396173 36.5 0.0973 0.0973    0.0973
396356 396359 76.8 0.1536 0.0973    0.0973
396542 396545 90.0 0.0973 0.1434    0.0973
397100 397103 90.0 0.1197 0.2926    0.0973
397472 397475 90.0 0.1045 0.4553    0.0973
397658 397661 90.0 0.3423 0.1175    0.0973
Wrote pdb files with previous and current coordinates

Step 61, time 0.122 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 677486.062500, max 22656932.000000 (between atoms 395437 and 395441)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.1188 0.1816    0.0973
394682 394685 90.0 0.0973 0.4642    0.0973
395054 395057 90.0 0.1120 0.1799    0.0973
395405 395410 38.1 0.1019 0.1019    0.1019
395411 395413 80.3 0.1097 134699.2344    0.1097
395411 395414  160.0 0.1097 134729.7188    0.1097
395415 395418  156.3 0.2094 1606929.6250    0.1086
395417 395422 54.6 0.1158 0.1086    0.1086
395426 395429 64.1 0.3704 0.0973    0.0973
395428 395432 90.0 0.2834 0.1751    0.1097
395430 395433 90.0 0.2590  12.2323    0.1097
395431 395436 90.0 0.1096 0.1208    0.1096
395434 395439 90.0 0.2865 7.3465    0.1097
395437 395441  110.3 0.0973 2204519.2500    0.0973
395438 395442 55.2 0.1097 0.1097    0.1097
395440 395444 90.0 0.0973 0.1151    0.0973
395612 395615 39.4 0.0973 0.0973    0.0973
395798 395801 90.0 0.0973 0.9315    0.0973
395800 395804 90.0 1.7900 5.4213    0.1097
395802 395805 90.0 0.1514 0.1355    0.1097
395803 395808 63.2 0.1096 0.1096    0.1096
395806 395811 53.0 0.1732 0.1097    0.1097
395809 395813 90.0 0.1263 0.2244    0.0973
395810 395814 90.0 3.6324 0.3363    0.1097
395812 395816 90.0 0.0973 6.2801    0.0973
395815 395817 90.0 0.1780 7.1665    0.1097
395815 395818 90.0 4.2534 0.3808    0.1097
395984 395987 90.0 0.1142 0.1822    0.0973
396170 396173 80.1 0.0973 0.0973    0.0973
396356 396359 90.0 0.0973 0.1364    0.0973
396542 396545 74.4 0.1434 0.0973    0.0973
397100 397103 90.0 0.2926 0.1137    0.0973
397472 397475 90.0 0.4554 0.1004    0.0973
397476 397479 90.0 0.1097 0.1905    0.1097
397658 397661 90.0 0.1175 0.3241    0.0973
Wrote pdb files with previous and current coordinates

Step 62, time 0.124 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1355032.500000, max 45315580.000000 (between atoms 395437 and 395441)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.1816 0.1192    0.0973
394682 394685 90.0 0.4642 0.1015    0.0973
395054 395057 90.0 0.1799 0.1196    0.0973
395405 395410 90.0 0.1019 2.7033    0.1019
395417 395422 90.0 0.1086 0.2713    0.1086
395426 395429 90.0 0.0973 0.2578    0.0973
395428 395432 82.7 0.1751 665.7343    0.1097
395430 395433 90.0 12.2323 0.4494    0.1097
395431 395436 90.0 0.1208 4.5623    0.1096
395434 395439 90.0 7.3465 0.6956    0.1097
395438 395442 44.6 0.1097 0.1097    0.1097
395440 395444 36.9 0.1151 0.0973    0.0973
395612 395615 38.6 0.0973 0.0973    0.0973
395789 395794 44.9 0.1086 0.1086    0.1086
395791 395795 42.1 0.1086 0.1086    0.1086
395798 395801 90.0 0.9315 0.6910    0.0973
395800 395804 90.0 5.4213 1.0685    0.1097
395802 395805 90.0 0.1355 0.5417    0.1097
395803 395808 90.0 0.1096 0.1224    0.1096
395806 395811 90.0 0.1097 0.7224    0.1097
395809 395813 90.0 0.2244 0.1228    0.0973
395810 395814 90.0 0.3363 3.4242    0.1097
395812 395816 35.7 6.2801 0.0973    0.0973
395815 395817 43.4 7.1665 100.4004    0.1097
395815 395818 90.0 0.3808 4.2936    0.1097
395819 395820 30.3 0.0973 0.0973    0.0973
395984 395987 90.0 0.1822 0.1211    0.0973
396170 396173 61.5 0.0973 0.0973    0.0973
396356 396359 90.0 0.1364 0.0994    0.0973
396542 396545 90.0 0.0973 0.1418    0.0973
396914 396917 40.9 0.0973 0.0973    0.0973
397100 397103 90.0 0.1137 0.2907    0.0973
397472 397475 90.0 0.1004 0.4544    0.0973
397474 397478 30.5 0.1097 0.1097    0.1097
397476 397479 54.9 0.1905 0.1097    0.1097
397658 397661 90.0 0.3241 0.1187    0.0973
Wrote pdb files with previous and current coordinates

Step 63, time 0.126 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2032584.000000, max 67974464.000000 (between atoms 395437 and 395441)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.1192 0.1799    0.0973
394682 394685 90.0 0.1015 0.4638    0.0973
395054 395057 90.0 0.1196 0.1732    0.0973
395397 395404 90.0 0.1097 0.2171    0.1097
395405 395410 90.0 2.7033 2.9598    0.1019
395416 395420 90.0 0.1086 0.2540    0.1086
395417 395422 90.0 0.2713 0.5466    0.1086
395426 395429 90.0 0.2578 0.3326    0.0973
395430 395433 90.0 0.4494  12.5372    0.1097
395431 395436 90.0 4.5623 2.6918    0.1096
395434 395439 90.0 0.6956 7.6115    0.1097
395438 395442 90.0 0.1097 4.5586    0.1097
395440 395444 66.5 0.0973 0.0973    0.0973
395443 395445 43.9 0.1098 0.1111    0.1097
395443 395446 54.3 0.1097 0.1093    0.1097
395612 395615 37.9 0.0973 0.0973    0.0973
395789 395794 90.0 0.1086 0.1654    0.1086
395791 395795 90.0 0.1086 0.1168    0.1086
395798 395801 90.0 0.6910 1.3350    0.0973
395800 395804 90.0 1.0685 5.4075    0.1097
395802 395805 90.0 0.5417 0.5641    0.1097
395803 395808 90.0 0.1224 1.0982    0.1096
395806 395811 54.3 0.7224 0.1097    0.1097
395810 395814 90.0 3.4242 0.1887    0.1097
395812 395816 90.0 0.0973 4.2778    0.0973
395815 395818 90.0 4.2936 0.6873    0.1097
395819 395820 90.0 0.0973 0.1411    0.0973
395984 395987 90.0 0.1211 0.1749    0.0973
396170 396173 64.8 0.0973 0.0973    0.0973
396356 396359 90.0 0.0994 0.1395    0.0973
396542 396545 90.0 0.1418 0.0992    0.0973
396914 396917 90.0 0.0973 0.2590    0.0973
397100 397103 90.0 0.2907 0.1141    0.0973
397472 397475 90.0 0.4544 0.0989    0.0973
397474 397478 68.5 0.1097 0.1097    0.1097
397476 397479 90.0 0.1097 0.1482    0.1097
397658 397661 90.0 0.1187 0.3228    0.0973
Wrote pdb files with previous and current coordinates

Step 64, time 0.128 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2711198.750000, max 90633384.000000 (between atoms 395437 and 395441)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.1799 0.1207    0.0973
394682 394685 90.0 0.4638 0.1097    0.0973
395054 395057 90.0 0.1732 0.1199    0.0973
395397 395404 90.0 0.2171 0.7354    0.1097
395405 395410 90.0 2.9598 1.3845    0.1019
395416 395420 90.0 0.2540 0.8612    0.1086
395417 395422 90.0 0.5466 0.2764    0.1086
395426 395429 90.0 0.3326 0.2957    0.0973
395430 395433 90.0 12.5372 0.4957    0.1097
395431 395436 90.0 2.6918 5.5170    0.1096
395434 395439 90.0 7.6115 0.2391    0.1097
395438 395442 90.0 4.5586 5.4038    0.1097
395440 395444 90.0 0.0973 0.1027    0.0973
395443 395445 39.5 0.1111 0.1042    0.1097
395443 395446 90.0 0.1093 0.2015    0.1097
395612 395615 37.7 0.0973 0.0973    0.0973
395789 395794 50.9 0.1654 233282.2500    0.1086
395791 395795  153.8 0.1168 233284.1719    0.1086
395798 395801 90.0 1.3350 0.1356    0.0973
395800 395804 90.0 5.4075 0.4455    0.1097
395802 395805 90.0 0.5641 0.7219    0.1097
395803 395808 90.0 1.0982 0.2638    0.1096
395806 395811 90.0 0.1097 0.2706    0.1097
395809 395813 90.0 0.0973 0.1889    0.0973
395810 395814 90.0 0.1887 3.6492    0.1097
395812 395816 90.0 4.2778 0.5991    0.0973
395815 395818 90.0 0.6873 4.6719    0.1097
395984 395987 90.0 0.1749 0.1215    0.0973
396170 396173 61.2 0.0973 0.0973    0.0973
396356 396359 90.0 0.1395 0.1014    0.0973
396542 396545 90.0 0.0992 0.1332    0.0973
396914 396917 80.3 0.2590 0.0973    0.0973
397100 397103 90.0 0.1141 0.2921    0.0973
397472 397475 90.0 0.0989 0.4559    0.0973
397474 397478 54.5 0.1097 0.1097    0.1097
397476 397479 90.0 0.1482 2.0110    0.1097
397484 397488 58.0 0.1097 0.1097    0.1097
397658 397661 90.0 0.3228 0.1193    0.0973
Wrote pdb files with previous and current coordinates

Step 65, time 0.13 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 3391093.000000, max 113292432.000000 (between atoms 395437 and 395441)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.1207 0.1803    0.0973
394682 394685 90.0 0.1097 0.4506    0.0973
395054 395057 90.0 0.1199 0.1717    0.0973
395392 395398 36.8 0.1097 0.1097    0.1097
395397 395404 90.0 0.7354 1.0374    0.1097
395403 395408 72.6 0.1097 0.1086    0.1097
395405 395410 90.0 1.3845 1.0264    0.1019
395416 395420 90.0 0.8612 1.4426    0.1086
395417 395422 90.0 0.2764 0.4386    0.1086
395419 395423 90.0 0.1086 0.1736    0.1086
395426 395429 90.0 0.2957 0.3435    0.0973
395430 395433 90.0 0.4957  12.6871    0.1097
395431 395436 90.0 5.5170 2.7973    0.1096
395434 395439 90.0 0.2391 7.5034    0.1097
395438 395442 90.0 5.4038 7.4984    0.1097
395440 395444 90.0 0.1027 0.2014    0.0973
395443 395445 90.0 0.1042 0.6877    0.1097
395443 395446 90.0 0.2015 0.5308    0.1097
395612 395615 34.3 0.0973 0.0973    0.0973
395787 395790 90.0 0.1086 0.4430    0.1086
395788 395792 90.0 0.1086 0.2077    0.1086
395798 395801 90.0 0.1356 0.9179    0.0973
395800 395804 90.0 0.4455 6.7910    0.1097
395802 395805 90.0 0.7219 0.1687    0.1097
395806 395811 90.0 0.2706 0.2307    0.1097
395809 395813 90.0 0.1889 0.0991    0.0973
395810 395814 90.0 3.6492 0.2176    0.1097
395812 395816 90.0 0.5991 3.3825    0.0973
395815 395818 90.0 4.6719 0.3315    0.1097
395819 395820 90.0 0.0973 0.1178    0.0973
395984 395987 90.0 0.1215 0.1737    0.0973
396170 396173 70.6 0.0973 0.0973    0.0973
396356 396359 90.0 0.1014 0.1301    0.0973
396542 396545 90.0 0.1332 0.1010    0.0973
396728 396731 31.9 0.0973 0.0973    0.0973
396914 396917 90.0 0.0973 0.2566    0.0973
397100 397103 90.0 0.2921 0.1147    0.0973
397472 397475 90.0 0.4559 0.1003    0.0973
397474 397478 38.4 0.1097 0.1097    0.1097
397476 397479 90.0 2.0110 0.1668    0.1097
397484 397488 90.0 0.1097 0.1369    0.1097
397489 397491 90.0 0.1097 0.1375    0.1097
397658 397661 90.0 0.1193 0.3214    0.0973
Wrote pdb files with previous and current coordinates

Step 66, time 0.132 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 4071623.000000, max 135951424.000000 (between atoms 395437 and 395441)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.1803 0.1216    0.0973
394682 394685 90.0 0.4506 0.1098    0.0973
395054 395057 90.0 0.1717 0.1214    0.0973
395392 395398 90.0 0.1097 0.1689    0.1097
395397 395404 90.0 1.0374 0.9407    0.1097
395403 395408 37.5 0.1086 0.1098    0.1097
395403 395409 75.9 0.1070 0.1098    0.1097
395405 395410 90.0 1.0264 1.3076    0.1019
395416 395420 90.0 1.4426 1.1225    0.1086
395417 395422 90.0 0.4386 0.7122    0.1086
395419 395423 90.0 0.1736 0.1682    0.1086
395426 395429 90.0 0.3435 0.3331    0.0973
395430 395433 90.0 12.6871 0.4801    0.1097
395431 395436 90.0 2.7973  11.2198    0.1096
395434 395439 90.0 7.5034 0.8124    0.1097
395438 395442 90.0 7.4984  12.7531    0.1097
395440 395444 31.7 0.2014 0.0973    0.0973
395443 395445 90.0 0.6877 1.0883    0.1097
395443 395446 90.0 0.5308 0.6918    0.1097
395787 395790 90.0 0.4430 1.1006    0.1086
395788 395792 90.0 0.2077 0.1944    0.1086
395798 395801 90.0 0.9179 0.7322    0.0973
395800 395804 90.0 6.7910 1.3123    0.1097
395802 395805 90.0 0.1687 0.3059    0.1097
395803 395808 90.0 0.1096 0.5121    0.1096
395806 395811 90.0 0.2307 0.1988    0.1097
395809 395813 90.0 0.0991 0.1953    0.0973
395810 395814 90.0 0.2176 3.7251    0.1097
395812 395816 76.1 3.3825 0.0973    0.0973
395815 395818 90.0 0.3315 4.8134    0.1097
395819 395820 48.0 0.1178 0.0973    0.0973
395984 395987 90.0 0.1737 0.1230    0.0973
396170 396173 58.7 0.0973 0.0973    0.0973
396356 396359 90.0 0.1301 0.1044    0.0973
396542 396545 90.0 0.1010 0.1370    0.0973
396728 396731 31.4 0.0973 0.0973    0.0973
396914 396917 76.1 0.2566 0.0973    0.0973
397100 397103 90.0 0.1147 0.2911    0.0973
397472 397475  114.4 0.1003 1077.6273    0.0973
397474 397478 90.0 0.1097 7.8839    0.1097
397476 397479  149.4 0.1668 1466.8112    0.1097
397484 397488 90.0 0.1369 0.3313    0.1097
397489 397491 90.0 0.1375 0.2424    0.1097
397489 397492 39.9 0.1108 0.1134    0.1097
397658 397661 90.0 0.3214 0.1182    0.0973
Wrote pdb files with previous and current coordinates

Step 67, time 0.134 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 4752513.500000, max 158610272.000000 (between atoms 395437 and 395441)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.1216 0.1802    0.0973
394682 394685 90.0 0.1098 0.4634    0.0973
395054 395057 90.0 0.1214 0.1717    0.0973
395392 395398  104.9 0.1689 321.1578    0.1097
395397 395404 90.0 0.9407 0.9439    0.1097
395403 395408 90.0 0.1098  28.3751    0.1097
395403 395409 90.0 0.1098  37.8713    0.1097
395405 395410 90.0 1.3076 0.8652    0.1019
395416 395420 90.0 1.1225 0.1344    0.1086
395417 395422 90.0 0.7122 1.0133    0.1086
395419 395423 90.0 0.1682 0.9731    0.1086
395426 395429 90.0 0.3331 0.3300    0.0973
395430 395433 90.0 0.4801  12.0582    0.1097
395431 395436 90.0 11.2198 0.6028    0.1096
395434 395439 90.0 0.8124 6.6159    0.1097
395438 395442 90.0 12.7531 8.8866    0.1097
395440 395444 90.0 0.0973 0.1973    0.0973
395443 395445 90.0 1.0883 0.5847    0.1097
395443 395446 90.0 0.6918 0.4764    0.1097
395447 395448 90.0 0.0973 0.1776    0.0973
395787 395790 90.0 1.1006 0.1948    0.1086
395788 395792 53.1 0.1944 0.1086    0.1086
395798 395801 90.0 0.7322 1.3407    0.0973
395800 395804 90.0 1.3123 6.0993    0.1097
395802 395805 90.0 0.3059 0.2187    0.1097
395803 395808 90.0 0.5121 0.2566    0.1096
395806 395811 90.0 0.1988 1.0288    0.1097
395809 395813 90.0 0.1953 0.2807    0.0973
395810 395814 90.0 3.7251 0.6307    0.1097
395812 395816 90.0 0.0973 4.0219    0.0973
395815 395818 90.0 4.8134 0.5825    0.1097
395819 395820 47.7 0.0973 0.0973    0.0973
395984 395987 90.0 0.1230 0.1732    0.0973
396170 396173 74.9 0.0973 0.0973    0.0973
396356 396359 90.0 0.1044 0.1333    0.0973
396542 396545 90.0 0.1370 0.1030    0.0973
396728 396731 31.4 0.0973 0.0973    0.0973
396914 396917 90.0 0.0973 0.2576    0.0973
397100 397103 90.0 0.2911 0.1119    0.0973
397474 397478 90.0 7.8839 3.3896    0.1097
397480 397485 90.0 0.1097 4.6674    0.1097
397484 397488 90.0 0.3313 0.1510    0.1097
397489 397491 90.0 0.2424 0.1390    0.1097
397658 397661 90.0 0.1182 0.3239    0.0973
Wrote pdb files with previous and current coordinates

Step 68, time 0.136 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 5433631.500000, max 181269184.000000 (between atoms 395437 and 395441)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.1802 0.1181    0.0973
394682 394685 90.0 0.4634 0.1044    0.0973
395054 395057 90.0 0.1717 0.1228    0.0973
395390 395393 90.0 0.1097 0.1231    0.1097
395397 395404 90.0 0.9439 2.2636    0.1097
395399 395406 90.0 0.0973 0.1062    0.0973
395403 395408 90.0 28.3751  21.9182    0.1097
395403 395409 90.0 37.8713  61.0387    0.1097
395405 395410 90.0 0.8652 3.2872    0.1019
395416 395420 90.0 0.1344 0.6850    0.1086
395417 395422 90.0 1.0133 1.5656    0.1086
395419 395423 90.0 0.9731 0.4402    0.1086
395426 395429 90.0 0.3300 0.5701    0.0973
395430 395433 90.0 12.0582 0.8128    0.1097
395431 395436 90.0 0.6028  12.4716    0.1096
395434 395439 90.0 6.6159 1.4417    0.1097
395438 395442 90.0 8.8866  12.9738    0.1097
395440 395444 90.0 0.1973 0.4584    0.0973
395443 395445 90.0 0.5847 0.5822    0.1097
395443 395446 63.0 0.4764 0.1163    0.1097
395447 395448 61.1 0.1776 0.0973    0.0973
395783 395785 90.0 0.1097  24.8700    0.1097
395783 395786 90.0 0.1097  24.7530    0.1097
395787 395790 90.0 0.1948 0.7404    0.1086
395788 395792 90.0 0.1086 0.5173    0.1086
395800 395804 90.0 6.0993  34.1175    0.1097
395802 395805 90.0 0.2187 0.6628    0.1097
395803 395808 90.0 0.2566 1.2600    0.1096
395806 395811 90.0 1.0288 0.4421    0.1097
395810 395814 90.0 0.6307 3.2340    0.1097
395812 395816 90.0 4.0219 0.6627    0.0973
395815 395818 90.0 0.5825 5.0395    0.1097
395819 395820 90.0 0.0973 0.1037    0.0973
395984 395987 90.0 0.1732 0.1247    0.0973
396170 396173 90.0 0.0973 0.0975    0.0973
396356 396359 90.0 0.1333 0.1074    0.0973
396542 396545 90.0 0.1030 0.1299    0.0973
396728 396731 33.1 0.0973 0.0973    0.0973
396914 396917 90.0 0.2576 0.0983    0.0973
397100 397103 90.0 0.1119 0.2917    0.0973
397474 397478 90.0 3.3896 9.5702    0.1097
397477 397482 90.0 0.1096 0.3699    0.1096
397480 397485 90.0 4.6674 4.4045    0.1097
397484 397488 90.0 0.1510 0.4748    0.1097
397486 397490 90.0 0.0973 0.3294    0.0973
397489 397491 90.0 0.1390 0.2344    0.1097
397658 397661 90.0 0.3239 0.1199    0.0973
Wrote pdb files with previous and current coordinates

Step 69, time 0.138 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 6114902.500000, max 203928160.000000 (between atoms 395437 and 395441)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
394496 394499 90.0 0.1181 0.1834    0.0973
394682 394685 90.0 0.1044 0.4941    0.0973
394868 394871 30.1 0.0973 0.0973    0.0973
395054 395057 90.0 0.1228 0.1714    0.0973
395390 395393 90.0 0.1231 0.2525    0.1097
395391 395394 90.0 0.1097 0.1465    0.1097
395397 395404 90.0 2.2636 3.1837    0.1097
395399 395406 90.0 0.1062 0.1037    0.0973
395403 395408  109.7 21.9182  72.7234    0.1097
395403 395409 90.0 61.0387  27.3710    0.1097
395405 395410 90.0 3.2872 4.1410    0.1019
395416 395420 90.0 0.6850 1.5148    0.1086
395417 395422 90.0 1.5656 0.8261    0.1086
395419 395423 90.0 0.4402 1.2190    0.1086
395426 395429 90.0 0.5701 0.4265    0.0973
395430 395433 90.0 0.8128  12.3267    0.1097
395431 395436 90.0 12.4716 4.6069    0.1096
395434 395439 90.0 1.4417 6.8678    0.1097
395438 395442 90.0 12.9738 6.9215    0.1097
395440 395444 90.0 0.4584 0.1227    0.0973
395443 395445 90.0 0.5822 0.3493    0.1097
395443 395446 90.0 0.1163 0.3174    0.1097
395447 395448 90.0 0.0973 0.2456    0.0973
395612 395615 33.6 0.0973 0.0973    0.0973
395777 395782 90.0 0.1019 2.2755    0.1019
395783 395785 90.0 24.8700 5.5719    0.1097
395783 395786 90.0 24.7530 3.3408    0.1097
395787 395790 90.0 0.7404 0.3183    0.1086
395788 395792 90.0 0.5173 0.8065    0.1086
395798 395801 90.0 0.0973 0.4585    0.0973
395800 395804 90.0 34.1175  39.3079    0.1097
395802 395805 90.0 0.6628 3.1282    0.1097
395803 395808 90.0 1.2600 2.4867    0.1096
395806 395811 90.0 0.4421 0.2040    0.1097
395809 395813 90.0 0.0973 0.1923    0.0973
395810 395814 90.0 3.2340 0.3440    0.1097
395812 395816 90.0 0.6627 3.5244    0.0973
395815 395818 90.0 5.0395 0.3123    0.1097
395819 395820 41.0 0.1037 0.0973    0.0973
395984 395987 90.0 0.1247 0.1727    0.0973
396170 396173 90.0 0.0975 0.1126    0.0973
396356 396359 90.0 0.1074 0.1246    0.0973
396542 396545 90.0 0.1299 0.1059    0.0973
396728 396731 32.9 0.0973 0.0973    0.0973
396914 396917 90.0 0.0983 0.2643    0.0973
397100 397103 90.0 0.2917 0.1150    0.0973
397105 397110 38.2 0.1096 0.1096    0.1096
397474 397478 90.0 9.5702 4.2279    0.1097
397477 397482 90.0 0.3699 0.3139    0.1096
397480 397485 90.0 4.4045 4.0941    0.1097
397484 397488 90.0 0.4748 0.2487    0.1097
397486 397490 90.0 0.3294 0.2362    0.0973
397489 397491 90.0 0.2344 0.1486    0.1097
397489 397492 38.5 0.1089 0.1144    0.1097
397658 397661 90.0 0.1199 0.3236    0.0973
397660 397664 46.4 0.1097 0.1097    0.1097
Wrote pdb files with previous and current coordinates

-------------------------------------------------------
Program:    gmx mdrun, version 2022.5
Source file: src\gromacs/gpu_utils/cudautils.cuh (line 190)

Fatal error:
Unexpected cudaStreamQuery failure. CUDA error #700 (cudaErrorIllegalAddress):
an illegal memory access was encountered.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

C:\Users\Administrator>gmx mdrun -v -deffnm E:\gmxfile\mixc5f2g2x13\c5f2g2x13eq -nt 16 -pin on -pme gpu -update gpu -bonded gpu
                  :-) GROMACS - gmx mdrun, 2022.5 (-:

Executable: D:\gromacs\bin\gmx.exe
Data prefix:  D:\gromacs
Working dir:  C:\Users\Administrator
Command line:
  gmx mdrun -v -deffnm E:\gmxfile\mixc5f2g2x13\c5f2g2x13eq -nt 16 -pin on -pme gpu -update gpu -bonded gpu（和第一次命令行相比只减去-nb gpu，报错）

Highest SIMD level supported by all nodes in run: AVX2_256
SIMD instructions selected at compile time:    AVX2_128
Compiled SIMD likely not supported by hardware; program might crash.
Reading file E:\gmxfile\mixc5f2g2x13\c5f2g2x13eq.tpr, VERSION 2022.5 (single precision)
Changing nstlist from 10 to 100, rlist from 1 to 1

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 and most bonded interactions on the GPU
PP task will update and constrain coordinates on the GPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread
Using 16 OpenMP threads

starting mdrun 'water+c5f2g2x11_opt'
100000 steps, 200.0 ps.
step 0
-------------------------------------------------------
Program:    gmx mdrun, version 2022.5
Source file: src\gromacs/gpu_utils/cudautils.cuh (line 190)

Fatal error:
Unexpected cudaStreamQuery failure. CUDA error #700 (cudaErrorIllegalAddress):
an illegal memory access was encountered.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

作者
Author: 枝枝z 时间: 2023-9-25 18:45
(, 下载次数 Times of downloads: 6)
(, 下载次数 Times of downloads: 3)
(, 下载次数 Times of downloads: 2)
(, 下载次数 Times of downloads: 3)
(, 下载次数 Times of downloads: 2)

作者
Author: lmch 时间: 2023-9-26 01:58
绝对是拓扑的事

作者
Author: sobereva 时间: 2023-9-26 03:15
既然CPU跑没问题，先用CPU跑诸如500ps，等体系相对稳定一些了，再用GPU续跑看是否能成功。如果确认就是GPU跑有问题，也可以尝试Linux版看看

作者
Author: 枝枝z 时间: 2023-9-27 00:28

lmch 发表于 2023-9-26 01:58
绝对是拓扑的事

想请教一下老师为什么这么说，从哪能看出来

作者
Author: 枝枝z 时间: 2023-9-27 00:39

sobereva 发表于 2023-9-26 03:15
既然CPU跑没问题，先用CPU跑诸如500ps，等体系相对稳定一些了，再用GPU续跑看是否能成功。如果确认就是GPU ...

用CPU跑也有一些报错，但是能跑一段时间之后才报错，应该是我体系本身也有一定问题；
这个win版本应该GPU跑没问题，因为之前我用gromacs分子动力学课讲义上测试计算速度的成品tpr样本跑过，同样的命令行能进行正常计算；
那我先调整一下我的体系，再用CPU和GPU分别跑，用老师的方法试试看~后续有问题的话再问老师。
谢谢老师！

作者
Author: zdworld 时间: 2023-9-28 13:31
我也遇到了相同的情况，我检查后发现不是gpu的问题，单纯就是我退火温度拉太高结构出问题爆了一堆lincs warning，降低温度就没事了。建议先检查结构，cpu没保存可能单纯是慢（

作者
Author: 枝枝z 时间: 2023-9-30 19:45

zdworld 发表于 2023-9-28 13:31
我也遇到了相同的情况，我检查后发现不是gpu的问题，单纯就是我退火温度拉太高结构出问题爆了一堆lincs war ...

好的！十分感谢！我也试试做这方面调整~

欢迎光临计算化学公社 (http://bbs.keinsci.com/)