[gmx-users] handling particle decomposition with distance restraints
jayant james
jayant.james at gmail.com
Thu Jun 25 21:17:30 CEST 2009
The energy minimization went on without any problem on 4 processors but the
problem occurs when I perform the MD run. Also, I did not get any error
message with relevance to LINCS etc...
JJ
On Wed, Jun 24, 2009 at 6:53 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
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>> Please search the archive at http://www.gromacs.org/searchbefore
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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
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> --
>> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Jayasundar Jayant James
www.chick.com/reading/tracts/0096/0096_01.asp)
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