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 <jalem...@vt.edu <mailto:jalem...@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
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@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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        <mailto:gmx-users-requ...@gromacs.org>>.

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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

    ========================================
    _______________________________________________
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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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