[gmx-users] handling particle decomposition with distance restraints
Justin A. Lemkul
jalemkul at vt.edu
Thu Jun 25 03:53:16 CEST 2009
jayant james wrote:
> Yes my distance restraints are long because I am using FRET distances as
> distance restraints while performing MD simulations. Upon usage of this
> command
>
> mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr -c pr.gro
> -pd &
>
> I get the following error!! I did try giving yes after -pd but even
> then the same error message is repeated.
>
Anything else printed to the screen or log file? LINCS warnings or anything
else? Did energy minimization complete successfully?
-Justin
> Back Off! I just backed up md.log to ./#md.log.9#
> Reading file pr.tpr, VERSION 4.0 (single precision)
> NNODES=4, MYRANK=1, HOSTNAME=localhost.localdomain
> NODEID=1 argc=13
> NODEID=3 argc=13
> [localhost:17514] *** Process received signal ***
> [localhost:17514] Signal: Segmentation fault (11)
> [localhost:17514] Signal code: Address not mapped (1)
> [localhost:17514] Failing at address: 0x1340000
> [localhost:17514] [ 0] /lib64/libpthread.so.0 [0x38dec0f0f0]
> [localhost:17514] [ 1] /lib64/libc.so.6(memcpy+0x15b) [0x38de08432b]
> [localhost:17514] [ 2]
> /usr/lib64/openmpi/1.2.4-gcc/libmpi.so.0(ompi_convertor_pack+0x152)
> [0x3886e45392]
> [localhost:17514] [ 3]
> /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_btl_sm.so(mca_btl_sm_prepare_src+0x13d)
> [0x7f39dd118a4d]
> [localhost:17514] [ 4]
> /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_pml_ob1.so(mca_pml_ob1_send_request_start_rndv+0x140)
> [0x7f39dd735230]
> [localhost:17514] [ 5]
> /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_pml_ob1.so(mca_pml_ob1_send+0x748)
> [0x7f39dd72e508]
> [localhost:17514] [ 6]
> /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_coll_tuned.so(ompi_coll_tuned_bcast_intra_split_bintree+0x91c)
> [0x7f39dc6f735c]
> [localhost:17514] [ 7]
> /usr/lib64/openmpi/1.2.4-gcc/libmpi.so.0(MPI_Bcast+0x15c) [0x3886e4c40c]
> [localhost:17514] [ 8] mdrun_mpi(bcast_state+0x26c) [0x56d59c]
> [localhost:17514] [ 9] mdrun_mpi(mdrunner+0x1067) [0x42b807]
> [localhost:17514] [10] mdrun_mpi(main+0x3b4) [0x431c34]
> [localhost:17514] [11] /lib64/libc.so.6(__libc_start_main+0xe6)
> [0x38de01e576]
> [localhost:17514] [12] mdrun_mpi [0x413339]
> [localhost:17514] *** End of error message ***
> mpirun noticed that job rank 0 with PID 17514 on node
> localhost.localdomain exited on signal 11 (Segmentation fault).
> 3 additional processes aborted (not shown)
>
>
>
> On Wed, Jun 24, 2009 at 6:04 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> jayant james wrote:
>
>
> I just replaced the old gmx 4.0 version with the 4.0.5 version
> and still the same problem
>
> NOTE: atoms involved in distance restraints should be within the
> longest cut-off distance, if this is not the case mdrun
> generates a fatal error, in that case use particle decomposition
> (mdrun option -pd)
>
>
> Well, does it work with -pd? It looks like your distance restraints
> are indeed quite long, so this looks like it is your only option.
>
> -Justin
>
>
>
> WARNING: Can not write distance restraint data to energy file
> with domain decomposition
>
>
>
> On Wed, Jun 24, 2009 at 5:10 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> jayant james wrote:
>
> Hi!
> I am performing an mpi MD (on a quad core system) run with
> distance restraints. When I execute this command below
> without
> position restraints the MD run is distributed over 4 nodes
> perfectly well. But when I incorporate the distance
> restraints I
> hit a road block
> mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr
> -c pr.gro &
> I get this error message (below). My pr.mdp and distance
> restraints files are given below the error message
> . *
> Question.* How do I handle this sitation? Do I increase
> the long
> range cut off in the pr.mdp file? If you see my distance
> restraints file, my upper range of distances are close to
> 9nm!!
>
>
> Upgrade to the latest version (4.0.5), since there have been
> numerous improvements to domain decomposition throughout the
> development of version 4.0.
>
> -Justin
>
> Please guide.
> Thanks
> JJ
>
> ----------------------------------------------------------------------------------------------------------------------------------------------------------
> Back Off! I just backed up md.log to ./#md.log.6#
> Reading file pr.tpr, VERSION 4.0 (single precision)
>
> NOTE: atoms involved in distance restraints should be
> within the
> longest cut-off distance, if this is not the case mdrun
> generates a fatal error, in that case use particle
> decomposition
> (mdrun option -pd)
>
>
>
> WARNING: Can not write distance restraint data to energy file
> with domain decomposition
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.2 Source
> code file: domdec.c, line: 5842
> Fatal error:
> There is no domain decomposition for 4 nodes that is
> compatible
> with the given box and a minimum cell size of 9.85926 nm
> Change the number of nodes or mdrun option -rdd or -dds
>
> Look in
> the log file for details on the domain decomposition
>
>
> -----------------------------------------------------------------------------------------------------------------------------------------------
>
> *pr.mdp*
>
> ; User spoel (236)
> ; Wed Nov 3 17:12:44 1993
> ; Input file
> ;
> title = Yo
> cpp = /usr/bin/cpp
> define = -DDISRES
> constraints = none
> ;constraint_algorithm = lincs
> ;lincs_order = 4
> integrator = md
> dt = 0.001 ; ps !
> nsteps = 4000000 ; total 2.0ns.
> nstcomm = 1
> nstxout = 50000
> nstvout = 50000
> nstfout = 50000
> nstlog = 50000
> nstenergy = 500
> nstlist = 10
> ns_type = grid
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> vdwtype = cut-off
> rvdw = 1.4
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> disre = simple
> disre_weighting = equal
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = V-rescale
> tc-grps = Protein Non-Protein
> tau_t = 0.1 0.1
> ref_t = 300 300
> ; Energy monitoring
> energygrps = Protein Non-Protein
> ;tnc Non-Protein tnt NMR tni
> ; Pressure coupling is not on
> Pcoupl = parrinello-rahman
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> ;simulated annealing
> ;Type of annealing form each temperature group
> (no/single/periodic)
> ;annealing = no, no, no, single, no
> ;
> ;Number of annealing points to use for specifying
> annealing in
> each group
> ;annealing_npoints = 0, 0, 0, 9, 0
> ;
> ; List of times at the annealing points for each group
> ;annealing_time = 0 25 50 75 100 125 150 175 200
> ; Temp.at each annealing point, for each group.
> ;annealing_temp = 300 350 400 450 500 450 400 350 300
>
> *
> distance restraints file*
>
> distance_restraints ]
> ; ai aj type index type' low
> up1 up2 fac
> ;TnT240-TnI131, 145, 151, 160, 167 (ca+-7)
> 2019 3889 1 1 1 3.91
> 3.91 5.31 0.574679
> 2019 4056 1 2 1 4.86
> 4.86 6.26 0.409911
> 2019 4133 1 3 1 5.69
> 5.69 7.09 0.457947
> 2019 4207 1 4 1 6.63
> 6.63 8.03 0.323852
> 2019 4273 1 5 1 7.14
> 7.14 8.54 0.294559
> ;TnT276- Tni 131,145,151,160,167,5,17,27,40
> 2434 3889 1 6 1 1.34
> 1.34 2.74 4.884769
> 2434 4056 1 7 1 2.13
> 2.13 3.53 0.523368
> 2434 4133 1 8 1 3.66
> 3.66 5.06 0.409911
> 2434 4207 1 9 1 4.48
> 4.48 5.88 0.547825
> 2434 4273 1 10 1 5.43
> 5.43 6.83 0.285938
> 2434 2628 1 11 1 5.89
> 5.89 7.29 0.241333
> 2434 2719 1 12 1 4.76
> 4.76 6.16 0.366358
> 2434 2824 1 13 1 3.81
> 3.81 5.21 0.644145
> 2434 2972 1 14 1 3.10
> 3.10 4.50 0.431009
> ;TnT288- Tni 131,145,151,160,167,5,17,27,40
> 2557 3889 1 15 1 1.89
> 1.89 3.29 1.429688
> 2557 4056 1 16 1 3.25
> 3.25 4.65 0.32931
> 2557 4133 1 17 1 4.44
> 4.44 5.84 0.346847
> 2557 4207 1 18 1 4.80
> 4.80 6.20 0.275198
> 2557 4273 1 19 1 5.84
> 5.84 7.24 0.200744
> 2557 2628 1 20 1 4.79
> 4.79 6.19 1.046736
> 2557 2719 1 21 1 5.06
> 5.06 6.46 0.267659
> ; 2557 2824 1 22 1
> 2557 2972 1 23 1 3.99
> 3.99 5.39 0.412797
>
>
>
>
>
>
> ------------------------------------------------------------------------
>
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> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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> --
> Jayasundar Jayant James
>
> www.chick.com/reading/tracts/0096/0096_01.asp
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
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> Please don't post (un)subscribe requests to the list. Use the www
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> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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>
>
>
> --
> Jayasundar Jayant James
>
> www.chick.com/reading/tracts/0096/0096_01.asp
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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