Re: [gmx-users] Energy minimization problem with Double precision and mpi
Josiah Zayner wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Sunday, June 24, 2007 4:18 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:gmx-users- [EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, June 23, 2007 4:36 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: I managed to install mdrun_d from CVS and the problem is fixed you didn't say which cvs solved your problem. was it the release_3_3_patches branch? Mdrun_d says version: 3.3.99_development_20070413 It was the main branch. OK, this branch is not yet quite stable, we are still testing things there. It would be good to know whether the release_3_3_patches branch also solves your problem. Installing the release-3-3-patches branch also solves the problem. I only tested it on two nodes ie. -np 2 but I assume it would also work for more. Thanks, that is good to hear. It could be due to parallel minimization, but if it is fixed in CVS I won't investigate it further. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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] Energy minimization problem with Double precision and mpi
> -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of David van der Spoel > Sent: Sunday, June 24, 2007 4:18 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Energy minimization problem with Double precision > andmpi > > Josiah Zayner wrote: > > -Original Message- > > From: [EMAIL PROTECTED] [mailto:gmx-users- > [EMAIL PROTECTED] > > On Behalf Of David van der Spoel > > Sent: Saturday, June 23, 2007 4:36 PM > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Energy minimization problem with Double > precision > > andmpi > > > > Josiah Zayner wrote: > >> I managed to install mdrun_d from CVS and the problem is fixed > > > > > >>> you didn't say which cvs solved your problem. was it the > >>> release_3_3_patches branch? > > > > Mdrun_d says version: 3.3.99_development_20070413 > > It was the main branch. > > > OK, > > this branch is not yet quite stable, we are still testing things there. > It would be good to know whether the release_3_3_patches branch also > solves your problem. Installing the release-3-3-patches branch also solves the problem. I only tested it on two nodes ie. -np 2 but I assume it would also work for more. > > -- > David. > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596,75124 Uppsala, Sweden > phone:46 18 471 4205 fax: 46 18 511 755 > [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 ___ 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] Energy minimization problem with Double precision and mpi
Josiah Zayner wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, June 23, 2007 4:36 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: I managed to install mdrun_d from CVS and the problem is fixed you didn't say which cvs solved your problem. was it the release_3_3_patches branch? Mdrun_d says version: 3.3.99_development_20070413 It was the main branch. OK, this branch is not yet quite stable, we are still testing things there. It would be good to know whether the release_3_3_patches branch also solves your problem. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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] Energy minimization problem with Double precision and mpi
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, June 23, 2007 4:36 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: > I managed to install mdrun_d from CVS and the problem is fixed >>you didn't say which cvs solved your problem. was it the >>release_3_3_patches branch? Mdrun_d says version: 3.3.99_development_20070413 It was the main branch. > > -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of Josiah Zayner > Sent: Saturday, June 23, 2007 1:05 PM > To: gmx-users@gromacs.org > Subject: [gmx-users] Energy minimization problem with Double precision and > mpi > > Each time I try to run mdrun with double precision and more than one node, I > always receive some atom with infinite Fmax, no matter what I do, Always on > Step=0. The strangest thing is that it still attempts the minimization but > the values never change except for Dmax in a steepest descent. If I change > the coordinates of the atom that has the inf value another one has infinite > value and so on. I use lam/mpi, with the command 'mpirun -np 5 mdrun_d -v > -deffnm potd'. My double precision was configured with both --enable-mpi and > --enable-double. Here is a copy of the mdp file I use: > > title = potd > cpp = /usr/bin/cpp > constraints = none > integrator= steep > nsteps= 0 > ns_type = grid > nstcomm = 1 > nstlist = 10 > rlist = 1.4 > coulombtype = Shift > vdw_type = Shift > rcoulomb = 1.2 > rvdw = 1.2 > rcoulomb_switch = 1.0 > rvdw_switch = 1.0 > epsilon_r = 6.0 > optimize_fft = yes > > > emtol = 1000 > emstep= 0.01 > nstcgsteep= 100 > > It doesn't matter if it is in vaccum or water. I have minimized to an emtol > of 10 and mdrun_d still does not work. I am using gromacs 3.3.1. I have > tried changing or removing almost every value in the mdp file. I have tried > different pdb files. Tried using grompp and grompp_d. Tried with -sort > -shuffle and without. Is this another one of those compiler issues like > genion? Any help would be great. > > Thanks, > Josiah Zayner > > ___ > 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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 ___ 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] Energy minimization problem with Double precision and mpi
Josiah Zayner wrote: I managed to install mdrun_d from CVS and the problem is fixed you didn't say which cvs solved your problem. was it the release_3_3_patches branch? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Josiah Zayner Sent: Saturday, June 23, 2007 1:05 PM To: gmx-users@gromacs.org Subject: [gmx-users] Energy minimization problem with Double precision and mpi Each time I try to run mdrun with double precision and more than one node, I always receive some atom with infinite Fmax, no matter what I do, Always on Step=0. The strangest thing is that it still attempts the minimization but the values never change except for Dmax in a steepest descent. If I change the coordinates of the atom that has the inf value another one has infinite value and so on. I use lam/mpi, with the command 'mpirun -np 5 mdrun_d -v -deffnm potd'. My double precision was configured with both --enable-mpi and --enable-double. Here is a copy of the mdp file I use: title = potd cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 0 ns_type = grid nstcomm = 1 nstlist = 10 rlist = 1.4 coulombtype = Shift vdw_type= Shift rcoulomb= 1.2 rvdw= 1.2 rcoulomb_switch = 1.0 rvdw_switch = 1.0 epsilon_r = 6.0 optimize_fft= yes emtol = 1000 emstep = 0.01 nstcgsteep = 100 It doesn't matter if it is in vaccum or water. I have minimized to an emtol of 10 and mdrun_d still does not work. I am using gromacs 3.3.1. I have tried changing or removing almost every value in the mdp file. I have tried different pdb files. Tried using grompp and grompp_d. Tried with -sort -shuffle and without. Is this another one of those compiler issues like genion? Any help would be great. Thanks, Josiah Zayner ___ 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 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [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] Energy minimization problem with Double precision and mpi
I managed to install mdrun_d from CVS and the problem is fixed -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Josiah Zayner Sent: Saturday, June 23, 2007 1:05 PM To: gmx-users@gromacs.org Subject: [gmx-users] Energy minimization problem with Double precision and mpi Each time I try to run mdrun with double precision and more than one node, I always receive some atom with infinite Fmax, no matter what I do, Always on Step=0. The strangest thing is that it still attempts the minimization but the values never change except for Dmax in a steepest descent. If I change the coordinates of the atom that has the inf value another one has infinite value and so on. I use lam/mpi, with the command 'mpirun -np 5 mdrun_d -v -deffnm potd'. My double precision was configured with both --enable-mpi and --enable-double. Here is a copy of the mdp file I use: title = potd cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 0 ns_type = grid nstcomm = 1 nstlist = 10 rlist = 1.4 coulombtype = Shift vdw_type= Shift rcoulomb= 1.2 rvdw= 1.2 rcoulomb_switch = 1.0 rvdw_switch = 1.0 epsilon_r = 6.0 optimize_fft= yes emtol = 1000 emstep = 0.01 nstcgsteep = 100 It doesn't matter if it is in vaccum or water. I have minimized to an emtol of 10 and mdrun_d still does not work. I am using gromacs 3.3.1. I have tried changing or removing almost every value in the mdp file. I have tried different pdb files. Tried using grompp and grompp_d. Tried with -sort -shuffle and without. Is this another one of those compiler issues like genion? Any help would be great. Thanks, Josiah Zayner ___ 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
