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...<br>JJ<br><br><div class="gmail_quote">
On Wed, Jun 24, 2009 at 6:53 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
jayant james wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Yes my distance restraints are long because I am using FRET distances as distance restraints while performing MD simulations. Upon usage of this command<br>
<br>
mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr -c pr.gro -pd &<br>
<br>
I get the following error!! I did try giving yes after -pd but even then the same error message is repeated.<br>
<br>
</blockquote>
<br></div>
Anything else printed to the screen or log file? LINCS warnings or anything else? Did energy minimization complete successfully?<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
Back Off! I just backed up md.log to ./#md.log.9#<br>
Reading file pr.tpr, VERSION 4.0 (single precision)<br>
NNODES=4, MYRANK=1, HOSTNAME=localhost.localdomain<br>
NODEID=1 argc=13<br>
NODEID=3 argc=13<br>
[localhost:17514] *** Process received signal ***<br>
[localhost:17514] Signal: Segmentation fault (11)<br>
[localhost:17514] Signal code: Address not mapped (1)<br>
[localhost:17514] Failing at address: 0x1340000<br>
[localhost:17514] [ 0] /lib64/libpthread.so.0 [0x38dec0f0f0]<br>
[localhost:17514] [ 1] /lib64/libc.so.6(memcpy+0x15b) [0x38de08432b]<br>
[localhost:17514] [ 2] /usr/lib64/openmpi/1.2.4-gcc/libmpi.so.0(ompi_convertor_pack+0x152) [0x3886e45392]<br>
[localhost:17514] [ 3] /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_btl_sm.so(mca_btl_sm_prepare_src+0x13d) [0x7f39dd118a4d]<br>
[localhost:17514] [ 4] /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_pml_ob1.so(mca_pml_ob1_send_request_start_rndv+0x140) [0x7f39dd735230]<br>
[localhost:17514] [ 5] /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_pml_ob1.so(mca_pml_ob1_send+0x748) [0x7f39dd72e508]<br>
[localhost:17514] [ 6] /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_coll_tuned.so(ompi_coll_tuned_bcast_intra_split_bintree+0x91c) [0x7f39dc6f735c]<br>
[localhost:17514] [ 7] /usr/lib64/openmpi/1.2.4-gcc/libmpi.so.0(MPI_Bcast+0x15c) [0x3886e4c40c]<br>
[localhost:17514] [ 8] mdrun_mpi(bcast_state+0x26c) [0x56d59c]<br>
[localhost:17514] [ 9] mdrun_mpi(mdrunner+0x1067) [0x42b807]<br>
[localhost:17514] [10] mdrun_mpi(main+0x3b4) [0x431c34]<br>
[localhost:17514] [11] /lib64/libc.so.6(__libc_start_main+0xe6) [0x38de01e576]<br>
[localhost:17514] [12] mdrun_mpi [0x413339]<br>
[localhost:17514] *** End of error message ***<br>
mpirun noticed that job rank 0 with PID 17514 on node localhost.localdomain exited on signal 11 (Segmentation fault).<br>
3 additional processes aborted (not shown)<br>
<br>
<br>
<br></div></div><div class="im">
On Wed, Jun 24, 2009 at 6:04 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
jayant james wrote:<br>
<br>
<br>
I just replaced the old gmx 4.0 version with the 4.0.5 version<br>
and still the same problem<br>
<br>
NOTE: atoms involved in distance restraints should be within the<br>
longest cut-off distance, if this is not the case mdrun<br>
generates a fatal error, in that case use particle decomposition<br>
(mdrun option -pd) <br>
<br>
Well, does it work with -pd? It looks like your distance restraints<br>
are indeed quite long, so this looks like it is your only option.<br>
<br>
-Justin<br>
<br>
<br>
<br>
WARNING: Can not write distance restraint data to energy file<br>
with domain decomposition<br>
<br>
<br>
<br>
On Wed, Jun 24, 2009 at 5:10 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
jayant james wrote:<br>
<br>
Hi!<br>
I am performing an mpi MD (on a quad core system) run with<br>
distance restraints. When I execute this command below<br>
without<br>
position restraints the MD run is distributed over 4 nodes<br>
perfectly well. But when I incorporate the distance<br>
restraints I<br>
hit a road block<br>
mpirun -np 4 mdrun_mpi -s pr -e pr -g md -o traj.trr<br>
-c pr.gro &<br>
I get this error message (below). My pr.mdp and distance<br>
restraints files are given below the error message<br>
. *<br>
Question.* How do I handle this sitation? Do I increase<br>
the long<br>
range cut off in the pr.mdp file? If you see my distance<br>
restraints file, my upper range of distances are close to<br>
9nm!!<br>
<br>
<br>
Upgrade to the latest version (4.0.5), since there have been<br>
numerous improvements to domain decomposition throughout the<br>
development of version 4.0.<br>
<br>
-Justin<br>
<br>
Please guide.<br>
Thanks<br>
JJ<br>
----------------------------------------------------------------------------------------------------------------------------------------------------------<br>
Back Off! I just backed up md.log to ./#md.log.6#<br>
Reading file pr.tpr, VERSION 4.0 (single precision)<br>
<br>
NOTE: atoms involved in distance restraints should be<br>
within the<br>
longest cut-off distance, if this is not the case mdrun<br>
generates a fatal error, in that case use particle<br>
decomposition<br>
(mdrun option -pd) <br>
WARNING: Can not write distance restraint data to energy file<br>
with domain decomposition<br>
<br>
-------------------------------------------------------<br>
Program mdrun_mpi, VERSION 4.0.2 Source<br>
code file: domdec.c, line: 5842 Fatal error:<br>
There is no domain decomposition for 4 nodes that is<br>
compatible<br>
with the given box and a minimum cell size of 9.85926 nm<br>
Change the number of nodes or mdrun option -rdd or -dds Look in<br>
the log file for details on the domain decomposition -----------------------------------------------------------------------------------------------------------------------------------------------<br>
<br>
*pr.mdp*<br>
<br>
; User spoel (236)<br>
; Wed Nov 3 17:12:44 1993<br>
; Input file<br>
;<br>
title = Yo<br>
cpp = /usr/bin/cpp<br>
define = -DDISRES<br>
constraints = none<br>
;constraint_algorithm = lincs<br>
;lincs_order = 4<br>
integrator = md<br>
dt = 0.001 ; ps !<br>
nsteps = 4000000 ; total 2.0ns.<br>
nstcomm = 1<br>
nstxout = 50000<br>
nstvout = 50000<br>
nstfout = 50000<br>
nstlog = 50000<br>
nstenergy = 500<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 1.0<br>
coulombtype = PME<br>
rcoulomb = 1.0<br>
vdwtype = cut-off<br>
rvdw = 1.4<br>
fourierspacing = 0.12<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
disre = simple<br>
disre_weighting = equal<br>
; Berendsen temperature coupling is on in two groups<br>
Tcoupl = V-rescale<br>
tc-grps = Protein Non-Protein<br>
tau_t = 0.1 0.1<br>
ref_t = 300 300<br>
; Energy monitoring<br>
energygrps = Protein Non-Protein<br>
;tnc Non-Protein tnt NMR tni<br>
; Pressure coupling is not on<br>
Pcoupl = parrinello-rahman<br>
tau_p = 0.5<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
;simulated annealing<br>
;Type of annealing form each temperature group<br>
(no/single/periodic)<br>
;annealing = no, no, no, single, no<br>
;<br>
;Number of annealing points to use for specifying<br>
annealing in<br>
each group<br>
;annealing_npoints = 0, 0, 0, 9, 0<br>
;<br>
; List of times at the annealing points for each group<br>
;annealing_time = 0 25 50 75 100 125 150 175 200<br>
; Temp.at each annealing point, for each group.<br>
;annealing_temp = 300 350 400 450 500 450 400 350 300<br>
<br>
*<br>
distance restraints file*<br>
<br>
distance_restraints ]<br>
; ai aj type index type' low up1 up2 fac<br>
;TnT240-TnI131, 145, 151, 160, 167 (ca+-7)<br>
2019 3889 1 1 1 3.91 3.91 5.31 0.574679<br>
2019 4056 1 2 1 4.86 4.86 6.26 0.409911<br>
2019 4133 1 3 1 5.69 5.69 7.09 0.457947<br>
2019 4207 1 4 1 6.63 6.63 8.03 0.323852<br>
2019 4273 1 5 1 7.14 7.14 8.54 0.294559<br>
;TnT276- Tni 131,145,151,160,167,5,17,27,40<br>
2434 3889 1 6 1 1.34 1.34 2.74 4.884769<br>
2434 4056 1 7 1 2.13 2.13 3.53 0.523368<br>
2434 4133 1 8 1 3.66 3.66 5.06 0.409911<br>
2434 4207 1 9 1 4.48 4.48 5.88 0.547825<br>
2434 4273 1 10 1 5.43 5.43 6.83 0.285938<br>
2434 2628 1 11 1 5.89 5.89 7.29 0.241333<br>
2434 2719 1 12 1 4.76 4.76 6.16 0.366358<br>
2434 2824 1 13 1 3.81 3.81 5.21 0.644145<br>
2434 2972 1 14 1 3.10 3.10 4.50 0.431009<br>
;TnT288- Tni 131,145,151,160,167,5,17,27,40<br>
2557 3889 1 15 1 1.89 1.89 3.29 1.429688<br>
2557 4056 1 16 1 3.25 3.25 4.65 0.32931<br>
2557 4133 1 17 1 4.44 4.44 5.84 0.346847<br>
2557 4207 1 18 1 4.80 4.80 6.20 0.275198<br>
2557 4273 1 19 1 5.84 5.84 7.24 0.200744<br>
2557 2628 1 20 1 4.79 4.79 6.19 1.046736<br>
2557 2719 1 21 1 5.06 5.06 6.46 0.267659<br>
; 2557 2824 1 22 1<br>
2557 2972 1 23 1 3.99 3.99 5.39 0.412797<br>
<br>
<br>
<br>
<br>
<br>
------------------------------------------------------------------------<br>
<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<div class="im">
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231-9080<br>
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-- Jayasundar Jayant James<br>
<br>
<a href="http://www.chick.com/reading/tracts/0096/0096_01.asp" target="_blank">www.chick.com/reading/tracts/0096/0096_01.asp</a><br>
<<a href="http://www.chick.com/reading/tracts/0096/0096_01.asp" target="_blank">http://www.chick.com/reading/tracts/0096/0096_01.asp</a>><br>
<<a href="http://www.chick.com/reading/tracts/0096/0096_01.asp" target="_blank">http://www.chick.com/reading/tracts/0096/0096_01.asp</a>>)<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<br>
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<br>
</div></div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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