Hello. Could you please tell us versions of GCC and CUDA that you've used
to build both AMBER and PLUMED?
73, Viktor
ср, 26 авг. 2020 г., 22:04 Dmitry Karlov <dkar89.gmail.com>:
> Dear Amber community,
> May be somebody knows about the following issue:
>
> pmemd.cuda -O -i prod.in -o prod.out -p bcyd_lig.prmtop -c
> bcyd_lig_den.rst
> -r bcyd_lig_prod1.rst -x prod.nc
>
> +++ Loading the PLUMED kernel runtime +++
> +++
> PLUMED_KERNEL="/home/dkarlov/soft/plumed-2.6.0/src/lib/libplumedKernel.so"
> +++
> PLUMED: PLUMED is starting
> PLUMED: Version: 2.6.0 (git: Unknown) compiled on Mar 19 2020 at 13:57:52
> PLUMED: Please cite these papers when using PLUMED [1][2]
> PLUMED: For further information see the PLUMED web page at
> http://www.plumed.org
> PLUMED: Root: /home/dkarlov/soft/plumed-2.6.0/
> PLUMED: For installed feature, see
> /home/dkarlov/soft/plumed-2.6.0//src/config/config.txt
> PLUMED: Molecular dynamics engine: amber
> PLUMED: Precision of reals: 8
> PLUMED: Running over 1 node
> PLUMED: Number of threads: 1
> PLUMED: Cache line size: 512
> PLUMED: Number of atoms: 10428
> PLUMED: File suffix:
> PLUMED: FILE: plumed.dat
> PLUMED: Action CENTER
> PLUMED: with label cc
> PLUMED: serial associated to this virtual atom is 10429
> PLUMED: of atoms:
> PLUMED: 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67
> 68 69 70
> PLUMED: 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92
> 93 94 95
> PLUMED: 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112
> 113 114 115 116 117 118 119 120
> PLUMED: 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136
> 137 138 139 140 141 142 143 144 145
> PLUMED: 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161
> 162 163 164 165 166 167 168 169 170
> PLUMED: 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186
> 187 188 189 190 191 192
> PLUMED: using the geometric center
> PLUMED: broken molecules will be rebuilt assuming atoms are in the proper
> order
> PLUMED: Action CENTER
> PLUMED: with label cl
> PLUMED: serial associated to this virtual atom is 10430
> PLUMED: of atoms:
> PLUMED: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
> PLUMED: 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
> PLUMED: using the geometric center
> PLUMED: broken molecules will be rebuilt assuming atoms are in the proper
> order
> PLUMED: Action DISTANCE
> PLUMED: with label d
> PLUMED: between atoms 10429 10430
> PLUMED: using periodic boundary conditions
> PLUMED: Action CENTER
> PLUMED: with label o5m
> PLUMED: serial associated to this virtual atom is 10431
> PLUMED: of atoms:
> PLUMED: 61 82 103 124 145 166 187
> PLUMED: using the geometric center
> PLUMED: broken molecules will be rebuilt assuming atoms are in the proper
> order
> PLUMED: Action CENTER
> PLUMED: with label c3m
> PLUMED: serial associated to this virtual atom is 10432
> PLUMED: of atoms:
> PLUMED: 53 74 95 116 137 158 179
> PLUMED: using the geometric center
> PLUMED: broken molecules will be rebuilt assuming atoms are in the proper
> order
> PLUMED: Action TORSION
> PLUMED: with label a1
> PLUMED: between atoms 10431 10432 10 7
> PLUMED: using periodic boundary conditions
> PLUMED: Action ANGLE
> PLUMED: with label a2
> PLUMED: between atoms 10431 10432 10430
> PLUMED: using periodic boundary conditions
> PLUMED: Action METAD
> PLUMED: with label metadP
> PLUMED: with arguments d a1 a2
> PLUMED: added component to this action: metadP.bias
> PLUMED: Binsize not specified, 1/5 of sigma will be be used
> PLUMED: Gaussian width 0.050000 0.050000 0.025000 Gaussian height
> 0.300000
> PLUMED: Gaussian deposition pace 500
> PLUMED: Gaussian file HILLS
> PLUMED: Well-Tempered Bias Factor 15.000000
> PLUMED: Hills relaxation time (tau) 116.402469
> PLUMED: KbT 2.494339
> PLUMED: Grid min 0 -pi 0
> PLUMED: Grid max 6 pi pi
> PLUMED: Grid bin 600 629 629
> PLUMED: Grid uses spline interpolation
> PLUMED: added component to this action: metadP.work
> PLUMED: Bibliography [3][4]
> PLUMED: Action PRINT
> PLUMED: with label .8
> PLUMED: with stride 500
> PLUMED: with arguments d a1 a2
> PLUMED: on file COLVAR
> PLUMED: with format %f
> PLUMED: END FILE: plumed.dat
> PLUMED: Timestep: 0.002000
> PLUMED: KbT: 2.494323
> PLUMED: Relevant bibliography:
> PLUMED: [1] The PLUMED consortium, Nat. Methods 16, 670 (2019)
> PLUMED: [2] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput.
> Phys. Commun. 185, 604 (2014)
> PLUMED: [3] Laio and Parrinello, PNAS 99, 12562 (2002)
> PLUMED: [4] Barducci, Bussi, and Parrinello, Phys. Rev. Lett. 100, 020603
> (2008)
> PLUMED: Please read and cite where appropriate!
> PLUMED: Finished setup
> pmemd.cuda: Plumed.h:2605: plumed_gcreate: Assertion `plumed_gmain.p==NULL'
> failed.
>
> Program received signal SIGABRT: Process abort signal.
>
> Backtrace for this error:
> #0 0x7feb29abb2ed in ???
> #1 0x7feb29aba503 in ???
> #2 0x7feb28baafcf in ???
> #3 0x7feb28baaf47 in ???
> #4 0x7feb28bac8b0 in ???
> #5 0x7feb28b9c429 in ???
> #6 0x7feb28b9c4a1 in ???
> #7 0x55acc2998427 in ???
> #8 0x55acc299932b in ???
> #9 0x55acc29992ef in ???
> #10 0x55acc2726e89 in ???
> #11 0x55acc275fc52 in ???
> #12 0x55acc26ac37e in ???
> #13 0x7feb28b8db96 in ???
> #14 0x55acc26c29b9 in ???
> #15 0xffffffffffffffff in ???
> Aborted
>
>
> I should note that this error does not occur when I use sander instead of
> pmemd.cuda
>
> prod.in file contains following information:
> cyd metad
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=500000000,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=2, ntp=1, taup=2.0,
> ntpr=25000, ntwx=25000,
> ntt=3, gamma_ln=2.0,
> temp0=300.0, ig=-1,
> plumed = 1, plumedfile = 'plumed.dat',
> /
> --
> DK
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>
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Received on Wed Aug 26 2020 - 12:30:03 PDT
