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  1. :-) G R O M A C S (-:
  2.  
  3. Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm
  4.  
  5. :-) VERSION 4.6.2 (-:
  6.  
  7. Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
  8. Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
  9. Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
  10. Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
  11. Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
  12. Michael Shirts, Alfons Sijbers, Peter Tieleman,
  13.  
  14. Berk Hess, David van der Spoel, and Erik Lindahl.
  15.  
  16. Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  17. Copyright (c) 2001-2012,2013, The GROMACS development team at
  18. Uppsala University & The Royal Institute of Technology, Sweden.
  19. check out http://www.gromacs.org for more information.
  20.  
  21. This program is free software; you can redistribute it and/or
  22. modify it under the terms of the GNU Lesser General Public License
  23. as published by the Free Software Foundation; either version 2.1
  24. of the License, or (at your option) any later version.
  25.  
  26. :-) /scratch/lustre/visvaldas/gromacs462/bin/grompp_mpi_d (double precision) (-:
  27.  
  28. Option Filename Type Description
  29. ------------------------------------------------------------
  30. -f /scratch/lustre/home/vyra6599/emamber.mdp Input grompp input
  31. file with MD parameters
  32. -po mdout.mdp Output grompp input file with MD parameters
  33. -c 1oyn-1oyn6wat1994-15a_vconf-docking_1_fix_solvated_bonded_GMX.gro Input
  34. Structure file: gro g96 pdb tpr etc.
  35. -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
  36. -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
  37. -n index.ndx Input, Opt. Index file
  38. -p 1oyn-1oyn6wat1994-15a_vconf-docking_1_fix_solvated_bonded_GMX.top Input
  39. Topology file
  40. -pp processed.top Output, Opt. Topology file
  41. -o em.tpr Output Run input file: tpr tpb tpa
  42. -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
  43. -e ener.edr Input, Opt. Energy file
  44. -ref rotref.trr In/Out, Opt. Full precision trajectory: trr trj cpt
  45.  
  46. Option Type Value Description
  47. ------------------------------------------------------
  48. -[no]h bool no Print help info and quit
  49. -[no]version bool no Print version info and quit
  50. -nice int 0 Set the nicelevel
  51. -[no]v bool no Be loud and noisy
  52. -time real -1 Take frame at or first after this time.
  53. -[no]rmvsbds bool yes Remove constant bonded interactions with virtual
  54. sites
  55. -maxwarn int 2 Number of allowed warnings during input
  56. processing. Not for normal use and may generate
  57. unstable systems
  58. -[no]zero bool no Set parameters for bonded interactions without
  59. defaults to zero instead of generating an error
  60. -[no]renum bool yes Renumber atomtypes and minimize number of
  61. atomtypes
  62.  
  63.  
  64. Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
  65.  
  66. NOTE 1 [file /scratch/lustre/home/vyra6599/emamber.mdp]:
  67. nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
  68. nstcomm to nstcalcenergy
  69.  
  70. Generated 666 of the 666 non-bonded parameter combinations
  71. Generating 1-4 interactions: fudge = 0.5
  72. Generated 666 of the 666 1-4 parameter combinations
  73. Excluding 3 bonded neighbours molecule type '1oyn-1oyn6wat1994-15a_vconf-docking_1_fix_solvated_bonded'
  74. Excluding 1 bonded neighbours molecule type 'NA+'
  75. Excluding 2 bonded neighbours molecule type 'WAT'
  76.  
  77. NOTE 2 [file 1oyn-1oyn6wat1994-15a_vconf-docking_1_fix_solvated_bonded_GMX.top, line 50698]:
  78. System has non-zero total charge: -0.003802
  79. Total charge should normally be an integer. See
  80. http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  81. for discussion on how close it should be to an integer.
  82.  
  83.  
  84.  
  85. Number of degrees of freedom in T-Coupling group rest is 197592.00
  86. Estimate for the relative computational load of the PME mesh part: 0.30
  87.  
  88. There were 2 notes
  89.  
  90. Back Off! I just backed up em.tpr to ./#em.tpr.3#
  91.  
  92. gcq#289: "The Candlelight Was Just Right" (Beastie Boys)
  93.  
  94. Analysing residue names:
  95. There are: 334 Protein residues
  96. There are: 3 Other residues
  97. There are: 17 Ion residues
  98. There are: 20144 Water residues
  99. Analysing Protein...
  100. Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
  101. Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
  102. Largest charge group radii for Van der Waals: 0.040, 0.040 nm
  103. Largest charge group radii for Coulomb: 0.081, 0.081 nm
  104. Calculating fourier grid dimensions for X Y Z
  105. Using a fourier grid of 80x96x80, spacing 0.114 0.103 0.110
  106. This run will generate roughly 5 Mb of data
  107. :-) G R O M A C S (-:
  108.  
  109. Gnomes, ROck Monsters And Chili Sauce
  110.  
  111. :-) VERSION 4.6.2 (-:
  112.  
  113. Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
  114. Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
  115. Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
  116. Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
  117. Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
  118. Michael Shirts, Alfons Sijbers, Peter Tieleman,
  119.  
  120. Berk Hess, David van der Spoel, and Erik Lindahl.
  121.  
  122. Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  123. Copyright (c) 2001-2012,2013, The GROMACS development team at
  124. Uppsala University & The Royal Institute of Technology, Sweden.
  125. check out http://www.gromacs.org for more information.
  126.  
  127. This program is free software; you can redistribute it and/or
  128. modify it under the terms of the GNU Lesser General Public License
  129. as published by the Free Software Foundation; either version 2.1
  130. of the License, or (at your option) any later version.
  131.  
  132. :-) /scratch/lustre/visvaldas/gromacs462/bin/mdrun_mpi_d (double precision) (-:
  133.  
  134. Option Filename Type Description
  135. ------------------------------------------------------------
  136. -s em.tpr Input Run input file: tpr tpb tpa
  137. -o em.trr Output Full precision trajectory: trr trj cpt
  138. -x em.xtc Output, Opt. Compressed trajectory (portable xdr format)
  139. -cpi em.cpt Input, Opt. Checkpoint file
  140. -cpo em.cpt Output, Opt. Checkpoint file
  141. -c em.gro Output Structure file: gro g96 pdb etc.
  142. -e em.edr Output Energy file
  143. -g em.log Output Log file
  144. -dhdl em.xvg Output, Opt. xvgr/xmgr file
  145. -field em.xvg Output, Opt. xvgr/xmgr file
  146. -table em.xvg Input, Opt. xvgr/xmgr file
  147. -tabletf em.xvg Input, Opt. xvgr/xmgr file
  148. -tablep em.xvg Input, Opt. xvgr/xmgr file
  149. -tableb em.xvg Input, Opt. xvgr/xmgr file
  150. -rerun em.trr Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
  151. -tpi em.xvg Output, Opt. xvgr/xmgr file
  152. -tpid em.xvg Output, Opt. xvgr/xmgr file
  153. -ei em.edi Input, Opt. ED sampling input
  154. -eo em.xvg Output, Opt. xvgr/xmgr file
  155. -j em.gct Input, Opt. General coupling stuff
  156. -jo em.gct Output, Opt. General coupling stuff
  157. -ffout em.xvg Output, Opt. xvgr/xmgr file
  158. -devout em.xvg Output, Opt. xvgr/xmgr file
  159. -runav em.xvg Output, Opt. xvgr/xmgr file
  160. -px em.xvg Output, Opt. xvgr/xmgr file
  161. -pf em.xvg Output, Opt. xvgr/xmgr file
  162. -ro em.xvg Output, Opt. xvgr/xmgr file
  163. -ra em.log Output, Opt. Log file
  164. -rs em.log Output, Opt. Log file
  165. -rt em.log Output, Opt. Log file
  166. -mtx em.mtx Output, Opt. Hessian matrix
  167. -dn em.ndx Output, Opt. Index file
  168. -multidir em Input, Opt., Mult. Run directory
  169. -plumed em.dat Input, Opt. Generic data file
  170. -membed em.dat Input, Opt. Generic data file
  171. -mp em.top Input, Opt. Topology file
  172. -mn em.ndx Input, Opt. Index file
  173.  
  174. Option Type Value Description
  175. ------------------------------------------------------
  176. -[no]h bool no Print help info and quit
  177. -[no]version bool no Print version info and quit
  178. -nice int 0 Set the nicelevel
  179. -deffnm string em Set the default filename for all file options
  180. -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
  181. -[no]pd bool no Use particle decompostion
  182. -dd vector 0 0 0 Domain decomposition grid, 0 is optimize
  183. -ddorder enum interleave DD node order: interleave, pp_pme or cartesian
  184. -npme int -1 Number of separate nodes to be used for PME, -1
  185. is guess
  186. -nt int 0 Total number of threads to start (0 is guess)
  187. -ntmpi int 0 Number of thread-MPI threads to start (0 is guess)
  188. -ntomp int 0 Number of OpenMP threads per MPI process/thread
  189. to start (0 is guess)
  190. -ntomp_pme int 0 Number of OpenMP threads per MPI process/thread
  191. to start (0 is -ntomp)
  192. -pin enum auto Fix threads (or processes) to specific cores:
  193. auto, on or off
  194. -pinoffset int 0 The starting logical core number for pinning to
  195. cores; used to avoid pinning threads from
  196. different mdrun instances to the same core
  197. -pinstride int 0 Pinning distance in logical cores for threads,
  198. use 0 to minimize the number of threads per
  199. physical core
  200. -gpu_id string List of GPU id's to use
  201. -[no]ddcheck bool yes Check for all bonded interactions with DD
  202. -rdd real 0 The maximum distance for bonded interactions with
  203. DD (nm), 0 is determine from initial coordinates
  204. -rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
  205. -dlb enum auto Dynamic load balancing (with DD): auto, no or yes
  206. -dds real 0.8 Minimum allowed dlb scaling of the DD cell size
  207. -gcom int -1 Global communication frequency
  208. -nb enum auto Calculate non-bonded interactions on: auto, cpu,
  209. gpu or gpu_cpu
  210. -[no]tunepme bool yes Optimize PME load between PP/PME nodes or GPU/CPU
  211. -[no]testverlet bool no Test the Verlet non-bonded scheme
  212. -[no]v bool no Be loud and noisy
  213. -[no]compact bool yes Write a compact log file
  214. -[no]seppot bool no Write separate V and dVdl terms for each
  215. interaction type and node to the log file(s)
  216. -pforce real -1 Print all forces larger than this (kJ/mol nm)
  217. -[no]reprod bool no Try to avoid optimizations that affect binary
  218. reproducibility
  219. -cpt real 15 Checkpoint interval (minutes)
  220. -[no]cpnum bool no Keep and number checkpoint files
  221. -[no]append bool yes Append to previous output files when continuing
  222. from checkpoint instead of adding the simulation
  223. part number to all file names
  224. -nsteps step -2 Run this number of steps, overrides .mdp file
  225. option
  226. -maxh real -1 Terminate after 0.99 times this time (hours)
  227. -multi int 0 Do multiple simulations in parallel
  228. -replex int 0 Attempt replica exchange periodically with this
  229. period (steps)
  230. -nex int 0 Number of random exchanges to carry out each
  231. exchange interval (N^3 is one suggestion). -nex
  232. zero or not specified gives neighbor replica
  233. exchange.
  234. -reseed int -1 Seed for replica exchange, -1 is generate a seed
  235. -[no]ionize bool no Do a simulation including the effect of an X-Ray
  236. bombardment on your system
  237.  
  238.  
  239. Back Off! I just backed up em.log to ./#em.log.3#
  240. Reading file em.tpr, VERSION 4.6.2 (double precision)
  241. Using 12 MPI processes
  242.  
  243. Can not set thread affinities on the current platform. On NUMA systems this
  244. can cause performance degradation. If you think your platform should support
  245. setting affinities, contact the GROMACS developers.
  246.  
  247.  
  248. Can not set thread affinities on the current platform. On NUMA systems this
  249. can cause performance degradation. If you think your platform should support
  250. setting affinities, contact the GROMACS developers.
  251. Can not set thread affinities on the current platform. On NUMA systems this
  252. can cause performance degradation. If you think your platform should support
  253. setting affinities, contact the GROMACS developers.
  254.  
  255. Can not set thread affinities on the current platform. On NUMA systems this
  256. can cause performance degradation. If you think your platform should support
  257. setting affinities, contact the GROMACS developers.
  258.  
  259.  
  260. Can not set thread affinities on the current platform. On NUMA systems this
  261. can cause performance degradation. If you think your platform should support
  262. setting affinities, contact the GROMACS developers.
  263. Can not set thread affinities on the current platform. On NUMA systems this
  264. can cause performance degradation. If you think your platform should support
  265. setting affinities, contact the GROMACS developers.
  266.  
  267. Can not set thread affinities on the current platform. On NUMA systems this
  268. can cause performance degradation. If you think your platform should support
  269. setting affinities, contact the GROMACS developers.
  270. Can not set thread affinities on the current platform. On NUMA systems this
  271. can cause performance degradation. If you think your platform should support
  272. setting affinities, contact the GROMACS developers.
  273.  
  274.  
  275.  
  276. Can not set thread affinities on the current platform. On NUMA systems this
  277. can cause performance degradation. If you think your platform should support
  278. setting affinities, contact the GROMACS developers.
  279.  
  280. Can not set thread affinities on the current platform. On NUMA systems this
  281. can cause performance degradation. If you think your platform should support
  282. setting affinities, contact the GROMACS developers.
  283. Can not set thread affinities on the current platform. On NUMA systems this
  284. can cause performance degradation. If you think your platform should support
  285. setting affinities, contact the GROMACS developers.
  286.  
  287. Can not set thread affinities on the current platform. On NUMA systems this
  288. can cause performance degradation. If you think your platform should support
  289. setting affinities, contact the GROMACS developers.
  290.  
  291. Back Off! I just backed up em.trr to ./#em.trr.3#
  292.  
  293. Back Off! I just backed up em.edr to ./#em.edr.3#
  294.  
  295. Polak-Ribiere Conjugate Gradients:
  296. Tolerance (Fmax) = 1.00000e+03
  297. Number of steps = 1000
  298. F-max = 8.94698e+03 on atom 3664
  299. F-Norm = 9.28656e+02
  300.  
  301.  
  302. Step -1:
  303. The charge group starting at atom 5420 moved more than the distance allowed by the domain decomposition (0.820340) in direction Y
  304. distance out of cell 1.136278
  305. Old coordinates: 6.426 5.195 6.096
  306. New coordinates: 7.618 6.879 5.759
  307. Old cell boundaries in direction Y: 4.922 5.742
  308. New cell boundaries in direction Y: 4.922 5.742
  309.  
  310. -------------------------------------------------------
  311. Program mdrun_mpi_d, VERSION 4.6.2
  312. Source code file: /scratch/lustre/visvaldas/gromacs-4.6.2/src/mdlib/domdec.c, line: 4348
  313.  
  314. Fatal error:
  315. A charge group moved too far between two domain decomposition steps
  316. This usually means that your system is not well equilibrated
  317. For more information and tips for troubleshooting, please check the GROMACS
  318. website at http://www.gromacs.org/Documentation/Errors
  319. -------------------------------------------------------
  320.  
  321. "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)
  322.  
  323. Error on node 6, will try to stop all the nodes
  324. Halting parallel program mdrun_mpi_d on CPU 6 out of 12
  325.  
  326. gcq#248: "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)
  327.  
  328. --------------------------------------------------------------------------
  329. MPI_ABORT was invoked on rank 6 in communicator MPI_COMM_WORLD
  330. with errorcode -1.
  331.  
  332. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
  333. You may or may not see output from other processes, depending on
  334. exactly when Open MPI kills them.
  335. --------------------------------------------------------------------------
  336. --------------------------------------------------------------------------
  337. mpirun has exited due to process rank 6 with PID 31464 on
  338. node lxibm038 exiting without calling "finalize". This may
  339. have caused other processes in the application to be
  340. terminated by signals sent by mpirun (as reported here).
  341. --------------------------------------------------------------------------
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