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@gromacs.org <mailto:gmx-users@gromacs.org>>
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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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<mailto:gmx-users-requ...@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>
<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@gromacs.org
<mailto:gmx-users@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
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@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>)
