RE: [gmx-users] Gromacs in Parallel
Yes, many people have encountered this problem with mpich 1.2.7 Use a version of MPICH2 (like OpenMPI) v1.3 Jim -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Andrew Paluch Sent: Monday, August 10, 2009 10:53 AM To: gmx-users@gromacs.org Subject: [gmx-users] Gromacs in Parallel To whom this may concern, I am receiving the following errors when attempting to run Gromacs in parallel: Making 1D domain decomposition 4 x 1 x 1 p2_21562: p4_error: Timeout in establishing connection to remote process: 0 p2_21562: (302.964844) net_send: could not write to fd=5, errno = 32 where I am using mpich 1.2.7 for 64 bit processors. From what I can find, it seems as if this is a mpich issue and not an issue of Gromacs. Has anyone else encountered such a problem? Also, does anyone have any suggestions for a solution? Thank you, Andrew ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs in Parallel
Andrew Paluch wrote: To whom this may concern, I am receiving the following errors when attempting to run Gromacs in parallel: Making 1D domain decomposition 4 x 1 x 1 p2_21562: p4_error: Timeout in establishing connection to remote process: 0 p2_21562: (302.964844) net_send: could not write to fd=5, errno = 32 where I am using mpich 1.2.7 for 64 bit processors. From what I can find, it seems as if this is a mpich issue and not an issue of Gromacs. Has anyone else encountered such a problem? Also, does anyone have any suggestions for a solution? Indeed, this is not a problem intrinsic to GROMACS. I'm not aware of problems with particular MPI libraries, but you might try compiling GROMACS with another such library. Whoever configured this machine should probably look into the problem. Mark ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs in Parallel
I agree. Mpich 1 is very old, you should try mpich 2 or lam or openmpi. Tom --On Tuesday, August 11, 2009 09:16:54 +1000 Mark Abraham mark.abra...@anu.edu.au wrote: Andrew Paluch wrote: To whom this may concern, I am receiving the following errors when attempting to run Gromacs in parallel: Making 1D domain decomposition 4 x 1 x 1 p2_21562: p4_error: Timeout in establishing connection to remote process: 0 p2_21562: (302.964844) net_send: could not write to fd=5, errno = 32 where I am using mpich 1.2.7 for 64 bit processors. From what I can find, it seems as if this is a mpich issue and not an issue of Gromacs. Has anyone else encountered such a problem? Also, does anyone have any suggestions for a solution? Indeed, this is not a problem intrinsic to GROMACS. I'm not aware of problems with particular MPI libraries, but you might try compiling GROMACS with another such library. Whoever configured this machine should probably look into the problem. Mark ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed
Hi Recently I successfully installed the gromacs-4.0.5 mpi version. I could run in 8 cpu. but the speed is very slow. Total number of atoms in the system is 78424. while running all 8 cpu showing 95-100% CPU. How to speed up the calculation. Thanks ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed
On Thu, 2009-06-11 at 14:35 +0800, Thamu wrote: Hi Recently I successfully installed the gromacs-4.0.5 mpi version. I could run in 8 cpu. but the speed is very slow. Total number of atoms in the system is 78424. while running all 8 cpu showing 95-100% CPU. That's normal for a system that atoms/cpu ratio. What's your system and what mdp file are you using? -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed
Thamu wrote: Hi Recently I successfully installed the gromacs-4.0.5 mpi version. Possibly. I could run in 8 cpu. but the speed is very slow. Total number of atoms in the system is 78424. while running all 8 cpu showing 95-100% CPU. How to speed up the calculation. You haven't given us any diagnostic information. The problem could be that you're not running an MPI GROMACS (show us your configure line, your mdrun command line and the top 50 lines of your .log file). Mark ___ gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed
Hi Mark,
The top md.log is below. The mdrun command was mpirun -np 8
~/software/bin/mdrun_mpi -deffnm md
:-) G R O M A C S (-:
GROup of MAchos and Cynical Suckers
:-) VERSION 4.0.5 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) /home/thamu/software/bin/mdrun_mpi (-:
PLEASE READ AND CITE THE FOLLOWING REFERENCE
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
--- Thank You ---
Input Parameters:
integrator = md
nsteps = 1000
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 100
nstxout = 1000
nstvout = 0
nstfout = 0
nstenergy= 100
nstxtcout= 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 70
nky = 70
nkz = 70
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = V-rescale
epc = Parrinello-Rahman
epctype = Isotropic
tau_p= 0.5
ref_p (3x3):
ref_p[0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.4
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
nwall= 0
wall_type= 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre= No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc= 1000
dr_tau = 0
nstdisreout =
Re: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed
On 06/11/09, Thamu asth...@gmail.com wrote:
Hi Mark,
The top md.log is below. The mdrun command was mpirun -np 8
~/software/bin/mdrun_mpi -deffnm md
In my experience, correctly-configured MPI gromacs running in parallel reports
information about the number of nodes and the identity of the node writing the
.log file. This is missing, so something is wrong with your setup.
I've assumed that you've compared this 8-processor runtime with a
single-processor runtime and found them comparable...
Mark
:-) G R O M A C S (-:
GROup of MAchos and Cynical Suckers
:-) VERSION 4.0.5 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org (http://www.gromacs.org) for
more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) /home/thamu/software/bin/mdrun_mpi (-:
PLEASE READ AND CITE THE FOLLOWING REFERENCE
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
--- Thank You ---
Input Parameters:
integrator = md
nsteps = 1000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 100
nstxout = 1000
nstvout = 0
nstfout = 0
nstenergy = 100
nstxtcout = 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 70
nky = 70
nkz = 70
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = V-rescale
epc = Parrinello-Rahman
epctype = Isotropic
tau_p = 0.5
ref_p (3x3):
ref_p[ 0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[ 1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[ 2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[ 0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[ 1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[ 2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed = 815131
rlist = 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.4
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy
RE: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed
Mark is correct. You should see node information at the top of the md log
file if you are truly running in parallel.
Apparently the default host (or machines) file (which contains the list of
available nodes on your cluster) has not been /is not being populated
correctly.
Your can build your own hosts file and then rerun the job using the command
line:
mpirun -np 8 -hostfile hostfile ~/software/bin/mdrun_mpi -deffnm md
The content and structure of the hostfile will depend on what version of MPI
you are using. Hopefully, you are not using MPICH 1 but instead are using
OpenMPI, MPICH2, or Intel MPI.
Jim
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Thamu
Sent: Thursday, June 11, 2009 9:13 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed
Hi Mark,
The top md.log is below. The mdrun command was mpirun -np 8
~/software/bin/mdrun_mpi -deffnm md
:-) G R O M A C S (-:
GROup of MAchos and Cynical Suckers
:-) VERSION 4.0.5 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) /home/thamu/software/bin/mdrun_mpi (-:
PLEASE READ AND CITE THE FOLLOWING REFERENCE
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
--- Thank You ---
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
--- Thank You ---
Input Parameters:
integrator = md
nsteps = 1000
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode= Linear
nstlog = 100
nstxout = 1000
nstvout = 0
nstfout = 0
nstenergy= 100
nstxtcout= 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 70
nky = 70
nkz = 70
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = V-rescale
epc = Parrinello-Rahman
epctype = Isotropic
tau_p= 0.5
ref_p (3x3):
ref_p[0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.4
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent
Re: [gmx-users] gromacs in parallel version
Looks like you are using MPICH2 as mpi software. Try including mpirun before mdrun_mpi. mpirun -n 4 mdun_mpi -v -s topol.tpr If that doesn't work you shoud run start the MPI DAEMON ( MPD ) before mpirun: mpdboot mpirun -n 2 mdun_mpi -v -s topol.tpr after you job finishes you might want to stop the mpi daemon by running: mpdallexit Diego. -- = Diego Enry B Gomes | PhD Student @ UFRJ - Brazil /tmp/home/@ Pacific Northwest National Laboratory Richland, WA. +1 (509) 372.6363 diegoenry.go...@pnl.gov = On Mar 6, 2009, at 5:13 AM, ANINDITA GAYEN wrote: Dear all, Sorry for the former post without any subject. I want to install gromacs in parallel version. I already have the normal version of gromacs and i want an MPI version of mdrun. The commands i have used are as followed. make distclean ./configure --enable-float --enable-mpi --prefix=/home/x --program- suffix=_mpi make mdrun -j 4 make install-mdrun [ i have installed fftw with --prefix=/home/x/fftw-3.2.1 and in .bashrc include ... export CPPFLAGS=-I/home/x/fftw-3.2.1/include export LDFFLAGS=-L/home/x/fftw-3.2.1/lib] grmmacs installation run successfully. But when i run mdrun_mpi ..i got the message Can't read MPIRUN_MPD and the mdrun_mpi program does not run. Any suggestion regarding this problem will be highly acceptable. thanks in advance, Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Add more friends to your messenger and enjoy! Invite them now.___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromacs in parallel version
Dear all, Sorry for the former post without any subject. I want to install gromacs in parallel version. I already have the normal version of gromacs and i want an MPI version of mdrun. The commands i have used are as followed. make distclean ../configure --enable-float --enable-mpi --prefix=/home/x --program-suffix=_mpi make mdrun -j 4 make install-mdrun [ i have installed fftw with --prefix=/home/x/fftw-3.2.1 and in .bashrc include ... export CPPFLAGS=-I/home/x/fftw-3.2.1/include export LDFFLAGS=-L/home/x/fftw-3.2.1/lib] grmmacs installation run successfully. But when i run mdrun_mpi ..i got the message Can't read MPIRUN_MPD and the mdrun_mpi program does not run. Any suggestion regarding this problem will be highly acceptable. thanks in advance, Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Connect with friends all over the world. Get Yahoo! India Messenger at http://in.messenger.yahoo.com/?wm=n/___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs in parallel version
ANINDITA GAYEN wrote: Dear all, Sorry for the former post without any subject. I want to install gromacs in parallel version. I already have the normal version of gromacs and i want an MPI version of mdrun. The commands i have used are as followed. *make distclean* *./configure --enable-float --enable-mpi --prefix=/home/x --program-suffix=_mpi* *make mdrun -j 4* *make install-mdrun* [ i have installed fftw with --prefix=/home/x/fftw-3.2.1 and in .bashrc include ... export CPPFLAGS=-I/home/x/fftw-3.2.1/include export LDFFLAGS=-L/home/x/fftw-3.2.1/lib] grmmacs installation run successfully. But when i run mdrun_mpi ..i got the message Can't read MPIRUN_MPD and the mdrun_mpi program does not run. What command are you actually issuing to run mdrun_mpi? This sounds like more of an MPI environment problem, not a Gromacs problem. -Justin Any suggestion regarding this problem will be highly acceptable. thanks in advance, Ms. Anindita Gayen C/O Dr. Chaitali Mukhopadhyay Senior Research Fellow Department of Chemistry University of Calcutta 92, A. P. C. Road Kolkata-700 009 India Add more friends to your messenger and enjoy! Invite them now. http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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 listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs-4.0.2, parallel performance in two quadcore xeon machines
Hi Nikos, I experienced the same king of things with a core i7 on one node and a corequad on an second node (Gromacs 4.0.3). Running on 8 threads (i7) or 4 cores in a single node is 30% faster than 8 or 12 cores on 2 nodes. I noticed that my gigabit switch is not limiting bandwidth using openmpi with rsh (~30 Gbps/70 max). Running on a single node cpu is 100% used by user (mdruns) while using 2 nodes each cpu is only 50% used by user, the 50% remaining being used by system. The top command shows 4 mdrun jobs using 100% CPU. I guess system usage is for network transferts ... Using ssh, system usage is quite the same and bandwidth is doubled. Any ideas about that system activity and how to reduce it ? Thanks Berk Hess a écrit : Hi, Oops, I meant 72000, which is only a factor of 10. I guess it might be faster one two nodes then, but probably not 2 times. If you use PME you can also experiment with putting all the PME nodes on one machine and the non-PME nodes on the other, probably with mdrun -ddorder pp_pme Gromacs supports near to maxint atoms. The question is much more what kind of system size you are scientifically interested in. Ethernet will never scale very well for small numbers of atoms per core. Infiniband will scale very well. Berk Date: Wed, 18 Feb 2009 12:56:16 -0800 From: lastexile...@yahoo.de Subject: RE: [gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines To: gmx-users@gromacs.org Hello, thank you for your answer. I just wondering though. How am I supposed to have a system with more than 9 atoms, while the gro file has a fixed format giving up to 5 digits in the number of atoms? What else should I change in order to succeed better performance from my hardware if I can succeed having a much bigger system? You say so that ethernet has reached its limits.. I was concidering using a supercomputing center in Europe and as far as I know they are using nodes which are using the Cell 9 core processors technology in each node. How someone there can accomplish a better performance using gromacs 4 using more nodes? Which might be the limit there in such machines. Thank you once again, Nikos --- Berk Hess /g...@hotmail.com/ schrieb am *Mi, 18.2.2009: * *Von: Berk Hess g...@hotmail.com Betreff: RE: [gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines An: lastexile...@yahoo.de Datum: Mittwoch, 18. Februar 2009, 19:16 * * Hi, You can not scale a system of just 7200 atoms to 16 cores which are connected by ethernet. 400 atoms per core is already the scaling limit of Gromacs on current hardware with the fastest available network. On ethernet a system 100 times as large might scale well to two nodes. Berk * *Date: Wed, 18 Feb 2009 09:40:28 -0800 From: lastexile...@yahoo.de To: gmx-users@gromacs.org Subject: [gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines * Hello, we have built a cluster with nodes that are comprised by the following: dual core Intel(R) Xeon(R) CPU E3110 @ 3.00GHz. The memory of each node has 16Gb of memory. The switch that we use is a dell power connect model. Each node has a Gigabyte ethernet card.. I tested the performance for a system of 7200 atoms in 4cores of one node, in 8 cores of one node and in 16 cores of two nodes. In one node the performance is getting better. The problem I get is that moving from one node to two, the performance decreases dramatically (almost two days for a run that finishes in less than 3 hours!). I have compiled gromacs with --enable-mpi option. I also have read previous archives from Mr Kurtzner, yet from what I saw is that they are focused on errors in gromacs 4 or on problems that previous versions of gromacs had. I get no errors, just low performance. Is there any option that I must enable in order to succeed better performance in more than one nodes? Or do you think according to your experience that the switch we use might be the problem? Or maybe should we have to activate anything from the nodes? Thank you in advance, Nikos * * *Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ * Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01
[gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines
Hello, we have built a cluster with nodes that are comprised by the following: dual core Intel(R) Xeon(R) CPU E3110 @ 3.00GHz. The memory of each node has 16Gb of memory. The switch that we use is a dell power connect model. Each node has a Gigabyte ethernet card. I tested the performance for a system of 7200 atoms in 4cores of one node, in 8 cores of one node and in 16 cores of two nodes. In one node the performance is getting better. The problem I get is that moving from one node to two, the performance decreases dramatically (almost two days for a run that finishes in less than 3 hours!). I have compiled gromacs with --enable-mpi option. I also have read previous archives from Mr Kurtzner, yet from what I saw is that they are focused on errors in gromacs 4 or on problems that previous versions of gromacs had. I get no errors, just low performance. Is there any option that I must enable in order to succeed better performance in more than one nodes? Or do you think according to your experience that the switch we use might be the problem? Or maybe should we have to activate anything from the nodes? Thank you in advance, Nikos ___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines
Hello,thank you for your answer. I just wondering though. How am I supposed to
have a system with more than 9 atoms, while the gro file has a fixed format
giving up to 5 digits in the number of atoms?
What else should I change in order to succeed better performance from my
hardware if I can succeed having a much bigger system? You say so that ethernet
has reached its limits. I was concidering using a supercomputing center in
Europe and as far as I know they are using nodes which are using the Cell 9
core processors technology in each node. How someone there can accomplish a
better performance using gromacs 4 using more nodes? Which might be the limit
there in such machines. Thank you once again,Nikos
--- Berk Hess g...@hotmail.com schrieb am Mi, 18.2.2009:
Von: Berk Hess g...@hotmail.com
Betreff: RE: [gmx-users] gromacs-4.0.2, parallel performance in two quad core
xeon machines
An: lastexile...@yahoo.de
Datum: Mittwoch, 18. Februar 2009, 19:16
#yiv278737063 .hmmessage P
{
margin:0px;padding:0px;}
#yiv278737063 {
font-size:10pt;font-family:Verdana;}
Hi,
You can not scale a system of just 7200 atoms
to 16 cores which are connected by ethernet.
400 atoms per core is already the scaling limit of Gromacs
on current hardware with the fastest available network.
On ethernet a system 100 times as large might scale well to two nodes.
Berk
Date: Wed, 18 Feb 2009 09:40:28 -0800
From: lastexile...@yahoo.de
To: gmx-users@gromacs.org
Subject: [gmx-users] gromacs-4.0.2, parallel performance in two quad core
xeon machines
Hello,
we have built a cluster with nodes that are comprised by the following: dual
core Intel(R) Xeon(R) CPU E3110 @ 3.00GHz. The memory of each node has 16Gb of
memory. The switch that we use is a dell power connect model. Each node has a
Gigabyte ethernet card..
I tested the performance for a system of 7200 atoms in 4cores of one node, in 8
cores of one node and in 16 cores of two nodes. In one node the performance is
getting better.
The problem I get is that moving from one node to two, the performance
decreases dramatically (almost two days for a run that finishes in less than 3
hours!).
I have compiled gromacs with --enable-mpi option. I also have read previous
archives from Mr Kurtzner, yet from what I saw is that they are focused on
errors in gromacs 4 or on problems that previous versions of gromacs had. I get
no errors, just low
performance.
Is there any option that I must enable in order to succeed better performance
in more than one nodes? Or do you think according to your experience that the
switch we use might be the problem? Or maybe should we have to activate
anything from the nodes?
Thank you in advance,
Nikos
Express yourself instantly with MSN Messenger! MSN Messenger
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RE: [gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines
Hi, Oops, I meant 72000, which is only a factor of 10. I guess it might be faster one two nodes then, but probably not 2 times. If you use PME you can also experiment with putting all the PME nodes on one machine and the non-PME nodes on the other, probably with mdrun -ddorder pp_pme Gromacs supports near to maxint atoms. The question is much more what kind of system size you are scientifically interested in. Ethernet will never scale very well for small numbers of atoms per core. Infiniband will scale very well. Berk Date: Wed, 18 Feb 2009 12:56:16 -0800 From: lastexile...@yahoo.de Subject: RE: [gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines To: gmx-users@gromacs.org Hello, thank you for your answer. I just wondering though. How am I supposed to have a system with more than 9 atoms, while the gro file has a fixed format giving up to 5 digits in the number of atoms? What else should I change in order to succeed better performance from my hardware if I can succeed having a much bigger system? You say so that ethernet has reached its limits.. I was concidering using a supercomputing center in Europe and as far as I know they are using nodes which are using the Cell 9 core processors technology in each node. How someone there can accomplish a better performance using gromacs 4 using more nodes? Which might be the limit there in such machines. Thank you once again, Nikos --- Berk Hess g...@hotmail.com schrieb am Mi, 18.2.2009: Von: Berk Hess g...@hotmail.com Betreff: RE: [gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines An: lastexile...@yahoo.de Datum: Mittwoch, 18. Februar 2009, 19:16 Hi, You can not scale a system of just 7200 atoms to 16 cores which are connected by ethernet. 400 atoms per core is already the scaling limit of Gromacs on current hardware with the fastest available network. On ethernet a system 100 times as large might scale well to two nodes. Berk Date: Wed, 18 Feb 2009 09:40:28 -0800 From: lastexile...@yahoo.de To: gmx-users@gromacs.org Subject: [gmx-users] gromacs-4.0.2, parallel performance in two quad core xeon machines Hello, we have built a cluster with nodes that are comprised by the following: dual core Intel(R) Xeon(R) CPU E3110 @ 3.00GHz. The memory of each node has 16Gb of memory. The switch that we use is a dell power connect model. Each node has a Gigabyte ethernet card.. I tested the performance for a system of 7200 atoms in 4cores of one node, in 8 cores of one node and in 16 cores of two nodes. In one node the performance is getting better. The problem I get is that moving from one node to two, the performance decreases dramatically (almost two days for a run that finishes in less than 3 hours!). I have compiled gromacs with --enable-mpi option. I also have read previous archives from Mr Kurtzner, yet from what I saw is that they are focused on errors in gromacs 4 or on problems that previous versions of gromacs had. I get no errors, just low performance. Is there any option that I must enable in order to succeed better performance in more than one nodes? Or do you think according to your experience that the switch we use might be the problem? Or maybe should we have to activate anything from the nodes? Thank you in advance, Nikos Express yourself instantly with MSN Messenger! MSN Messenger _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS in parallel on a multicore PC?
Hi everybody, Sorry for a somewhat technical question, but I'd like to know which is the best way to run GROMACS on a SMP machine (in particular, a multicore PC). The (known) points of interest are: - Does GROMACS support multithreaded execution how efficient is it? - Should I rather use some kind of MPI which (LAM/Open/MPICH) is better why? Surely, there's always the option to run two serial jobs instead with a greater efficiency, but having some means to boost the single job performance by something like 1.9x would be very useful... Thanks in advance, Vasilii ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS in parallel on a multicore PC?
Hi Vasilii, Vasilii Artyukhov wrote: Hi everybody, Sorry for a somewhat technical question, but I'd like to know which is the best way to run GROMACS on a SMP machine (in particular, a multicore PC). The (known) points of interest are: - Does GROMACS support multithreaded execution how efficient is it? As far as I know this is planned, but not supported yet. - Should I rather use some kind of MPI which (LAM/Open/MPICH) is better why? Yes. This is the way to go. On an SMP box you will probably not see large differences between the different MPI implementations, but why not try a few? My own experience is that LAM tends to be the fastest, partly due to the memory mangager it uses. Carsten Surely, there's always the option to run two serial jobs instead with a greater efficiency, but having some means to boost the single job performance by something like 1.9x would be very useful... Thanks in advance, Vasilii ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department Am Fassberg 11 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/research/dep/grubmueller/ http://www.gwdg.de/~ckutzne ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS in parallel on a multicore PC?
Thanks for the quick response :) 2007/11/21, Carsten Kutzner [EMAIL PROTECTED] : Hi Vasilii, - Does GROMACS support multithreaded execution how efficient is it? As far as I know this is planned, but not supported yet. Ok, but what about the underlying math libs? Would using threaded libs boost performance to any noticeable extent? ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS in parallel on a multicore PC?
Vasilii Artyukhov wrote: Thanks for the quick response :) 2007/11/21, Carsten Kutzner [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]: Hi Vasilii, - Does GROMACS support multithreaded execution how efficient is it? As far as I know this is planned, but not supported yet. Ok, but what about the underlying math libs? Would using threaded libs boost performance to any noticeable extent? No. We're not using any. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS in parallel on a multicore PC?
On 11/21/2007 7:33 PM, Vasilii Artyukhov wrote: Hi everybody, Sorry for a somewhat technical question, but I'd like to know which is the best way to run GROMACS on a SMP machine (in particular, a multicore PC). The (known) points of interest are: - Does GROMACS support multithreaded execution how efficient is it? No. - Should I rather use some kind of MPI which (LAM/Open/MPICH) is better why? Yes. This is the only way. Surely, there's always the option to run two serial jobs instead with a greater efficiency, but having some means to boost the single job performance by something like 1.9x would be very useful... Thanks in advance, Vasilii ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GRomacs 3.3.1 parallel run
Good morning, I started using Gromacs only few months ago doing MD on proteins in membranes. I' m using GRomacs 3.3.1 in parallel but I have some problems. I'm doing my simulations on a 70 nodes cluster using 4 nodes (16 processors). the system uses PBS torque and SCALIMPI libraries. When I run my jobs, the jobs start with no problems, even if there is the following error message : Jul 30 15:56:05: ([EMAIL PROTECTED])(2688) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(2690) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(4367) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(4370) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(4369) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(4368) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(2687) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(2689) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(698) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(32587) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(696) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(32584) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(32585) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(32586) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(695) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory Jul 30 15:56:05: ([EMAIL PROTECTED])(697) Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf failed: No such file or directory NNODES=16, MYRANK=9, HOSTNAME=avogadro-61.n16.chimica.unipd.it NNODES=16, MYRANK=11, HOSTNAME=avogadro-61.n16.chimica.unipd.it NNODES=16, MYRANK=8, HOSTNAME=avogadro-61.n16.chimica.unipd.it NNODES=16, MYRANK=10, HOSTNAME=avogadro-61.n16.chimica.unipd.it NNODES=16, MYRANK=7, HOSTNAME=avogadro-60.n16.chimica.unipd.it NNODES=16, MYRANK=5, HOSTNAME=avogadro-60.n16.chimica.unipd.it NNODES=16, MYRANK=0, HOSTNAME=avogadro-22.n16.chimica.unipd.it NNODES=16, MYRANK=4, HOSTNAME=avogadro-60.n16.chimica.unipd.it NNODES=16, MYRANK=2, HOSTNAME=avogadro-22.n16.chimica.unipd.it NNODES=16, MYRANK=15, HOSTNAME=avogadro-62.n16.chimica.unipd.it NNODES=16, MYRANK=13, HOSTNAME=avogadro-62.n16.chimica.unipd.it NNODES=16, MYRANK=6, HOSTNAME=avogadro-60.n16.chimica.unipd.it NNODES=16, MYRANK=3, HOSTNAME=avogadro-22.n16.chimica.unipd.it NNODES=16, MYRANK=1, HOSTNAME=avogadro-22.n16.chimica.unipd.it NODEID=2 argc=12 NODEID=1 argc=12 NODEID=0 argc=12 NODEID=3 argc=12 :-) G R O M A C S (-: Groningen Machine for Chemical Simulation :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun-0(mpi:[EMAIL PROTECTED]) (-: Option Filename Type Description .. When I want to delete a job, I use qdel; at this point the job desappears from queue, but apparently the job is still running on the processors. The output files are not updated and I have to enter the nodes and force killing the processes with kill -9 . This happens also if MD starts but crashes in a few seconds due for example two overlapping atoms. The job desappears from queue but is apparently running on nodes. The error message is the following: --- mpimon --- Aborting run after interrupt --- Jul 30 15:57:07:
[gmx-users] GROMACS 3.3.1 Parallel Run
Hi, I am trying to run my simulation using parallel Gmx 3.3.1 on a cluster with Linux 2.6.9-42.0.3.ELsmp, gcc 3.4.6 and ScaliMPI. My simulation causes abortion with the following error message: --- mpimon --- Aborting run after process-3 terminated abnormally Childprocess 26151 exited with exitcode 0 --- Each time it reports a different process being terminated such as process-1 or process-10 in addition to the process-3 as above. The Gmx examples such as tutor/water can be run on this system. Also, my simulation has successfully run on another system under Gmx 3.3.1 parallel run. I'd like to know what causes the abortion in my simulation on this system. Is it caused by ScaliMPI? Thanks, Sunny _ The average US Credit Score is 675. The cost to see yours: $0 by Experian. http://www.freecreditreport.com/pm/default.aspx?sc=660600bcd=EMAILFOOTERAVERAGE ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS 3.3.1 Parallel Run
Sunny wrote: Hi, I am trying to run my simulation using parallel Gmx 3.3.1 on a cluster with Linux 2.6.9-42.0.3.ELsmp, gcc 3.4.6 and ScaliMPI. My simulation causes abortion with the following error message: --- mpimon --- Aborting run after process-3 terminated abnormally Childprocess 26151 exited with exitcode 0 --- Each time it reports a different process being terminated such as process-1 or process-10 in addition to the process-3 as above. The Gmx examples such as tutor/water can be run on this system. So what's different between them and your attempted simulation? Also, my simulation has successfully run on another system under Gmx 3.3.1 parallel run. I'd like to know what causes the abortion in my simulation on this system. Is it caused by ScaliMPI? We can't tell yet. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS in parallel
Dear Sir I am trying to install GROMACS. I have tried to install program and it goes through okay. However, when I try to compile the program in parallel using the enable-mpi option, it gives me an error: Cannot compile and link MPI code with cc See below for the command and the error. Can you suggest what I can do to fix the same? _ redwood r0914/gromacs-3.3.1 ./configure --prefix=/ptmp/r0914/gromacsp --enable-mpi checking build system type... ia64-unknown-linux-gnu checking host system type... ia64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... cpio checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ANSI C... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... no checking for mpcc... no checking for hcc... no checking whether the MPI cc command works... configure: error: Cannot compile and link MPI code with cc _ Regards Akshay Akshay Patny Graduate Research Assistant Faser Hall 417, Department of Medicinal Chemistry Research Institute of Pharmaceutical Sciences University of Mississippi University, MS 38677 E-mail: [EMAIL PROTECTED] Tel: 662-915-1286 (office); Web: www.olemiss.edu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS in parallel
Akshay Patny wrote: Dear Sir I am trying to install GROMACS. I have tried to install program and it goes through okay. However, when I try to compile the program in parallel using the –enable-mpi option, it gives me an error: “Cannot compile and link MPI code with cc” See below for the command and the error. Can you suggest what I can do to fix the same? Use an MPI compiler. Find out what it is called on your system and take steps to use it - see ./configure --help for some options that can help here. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
