Re: RE : RE : [gmx-users] segmentation fault in mdrun when using PME
Hi Diane, On May 3, 2006, at 5:45 PM, Diane Fournier wrote: It seems that in my case this is a bug (see Bugzilla, bug # 74) related to using the Intel Math Kernel Library (MKL) v. 8.0.1 for Fourier transforms. The team managing the Altix are trying different FFT libraries. Eric Lindahl says that using a FFT library that is not optimized for Itanium 2 shouldn't hamper the perfomance very much since FT doesn't represent a very big part of the computation. For reference, that bug probably isn't in Gromacs, but the ia64 (not i386 or x86-64) version of MKL. Still haven't been able to confirm it, though. Cheers, Erik ___ 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 : RE : [gmx-users] segmentation fault in mdrun when using PME
It seems that in my case this is a bug (see Bugzilla, bug # 74) related to using the Intel Math Kernel Library (MKL) v. 8.0.1 for Fourier transforms. The team managing the Altix are trying different FFT libraries. Eric Lindahl says that using a FFT library that is not optimized for Itanium 2 shouldn't hamper the perfomance very much since FT doesn't represent a very big part of the computation. I think the error I get with the version compiled without Fortran is boggus, because this tutorial (John Kerrigan's) was tried sucessfully by many people, so there shouldn't be any mistakes in the .mdp file. Also, the runs I do with that version have strange output and anyway, I don't get that error with the Fortran-enabled version. Segmentation fault has been documented in the position restrained dynamics stage of this tutorial with gromacs 3.3.0 though, and was solved when upgrading to 3.3.1. An exploding system is often caused by extreme forces due to bad contacts, which can be relieved by a minimization step. Have you used a steepest descents minimization step on your system before doing the pr ? De: [EMAIL PROTECTED] de la part de Arneh Babakhani Date: mar. 2006-05-02 23:21 À: Discussion list for GROMACS users Objet : Re: RE : [gmx-users] segmentation fault in mdrun when using PME Hello, I'm experiencing the exact same problem, when trying to do some restrained molecular dynamics of a small peptide in a water box. Have you had any luck in trouble-shooting this? (I've pasted my mdp file below, for your reference). Also running Gromacs 3.3.1 Arneh title = ResMD warnings = 10 cpp = /usr/bin/cpp ; location of cpp on SGI define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 25000 ; total 50.0 ps. nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein sol ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Diane Fournier wrote: De: [EMAIL PROTECTED] de la part de David van der Spoel Date: lun. 2006-05-01 13:33 À: Discussion list for GROMACS users Objet : Re: [gmx-users] segmentation fault in mdrun when using PME Have you enabled fortran at the compilation stage? In that case try it without, otherwise please file a bugzilla, such that we can document this problem (and try to fix it of course). Still doesn't work. logfile ends in the usual way. Except this time, I get this output: Reading file trp_em.tpr, VERSION 3.3.1 (single precision) Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 500 Warning: 1-4 interaction between 1 and 7 at distance 39513.957 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.1# Wrote pdb files with previous and current coordinates and then these files get written: step0.pdb #step0.pdb.1# step-1.pdb step1.pdb Will file a bugzilla. ___ 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: RE : [gmx-users] segmentation fault in mdrun when using PME
Hello, I'm experiencing the exact same problem, when trying to do some restrained molecular dynamics of a small peptide in a water box. Have you had any luck in trouble-shooting this? (I've pasted my mdp file below, for your reference). Also running Gromacs 3.3.1 Arneh title = ResMD warnings = 10 cpp = /usr/bin/cpp ; location of cpp on SGI define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 25000 ; total 50.0 ps. nstcomm = 1 nstxout = 500 ; output coordinates every 1.0 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein sol ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Diane Fournier wrote: De: [EMAIL PROTECTED] de la part de David van der Spoel Date: lun. 2006-05-01 13:33 À: Discussion list for GROMACS users Objet : Re: [gmx-users] segmentation fault in mdrun when using PME Have you enabled fortran at the compilation stage? In that case try it without, otherwise please file a bugzilla, such that we can document this problem (and try to fix it of course). Still doesn't work. logfile ends in the usual way. Except this time, I get this output: Reading file trp_em.tpr, VERSION 3.3.1 (single precision) Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 500 Warning: 1-4 interaction between 1 and 7 at distance 39513.957 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.1# Wrote pdb files with previous and current coordinates and then these files get written: step0.pdb #step0.pdb.1# step-1.pdb step1.pdb Will file a bugzilla. ___ 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 ___ 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 -- 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 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 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 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] segmentation fault in mdrun when using PME
De: [EMAIL PROTECTED] de la part de David van der Spoel Date: lun. 2006-05-01 13:33 À: Discussion list for GROMACS users Objet : Re: [gmx-users] segmentation fault in mdrun when using PME Have you enabled fortran at the compilation stage? In that case try it without, otherwise please file a bugzilla, such that we can document this problem (and try to fix it of course). >Still doesn't work. logfile ends in the usual way. Except this time, I get >this output: > Reading file trp_em.tpr, VERSION 3.3.1 (single precision) Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 500 Warning: 1-4 interaction between 1 and 7 at distance 39513.957 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.1# Wrote pdb files with previous and current coordinates and then these files get written: step0.pdb #step0.pdb.1# step-1.pdb step1.pdb Will file a bugzilla. >> >> >> >> >> >>___ >>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 > > > > > > > ___ > 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 -- 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 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 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] segmentation fault in mdrun when using PME
Diane Fournier wrote: -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Sat 4/29/2006 2:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] segmentation fault in mdrun when using PME Diane Fournier wrote: Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex molecular dynamics simulation. I have tried doing John Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation fault and core dump at the steepest descents minimization step. However, mdrun works fine when using cutoff instead of PME. I'm working with Gromacs v. 3.3.1 on a SGI altix 3700 with 32 Intel Itanium 2 processors (but I'm currently using a single node, so it's not a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel Math Kernel Librarary (MKL) v. 8.0.1 as FFT library (which is optimized for Itanium 2). the em.mdp file looks like: title = drg_trp cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Is it possible this could be related to insufficient memory allocation ? How demanding is this PME calculation ? Not likely a memory problem. It could be a compiler issue but we need more info! Where does it crash? Is it reproducible? DOes the same tpr file cause a crash on another architecture (e.g. your desktop)? I installed gromacs 3.3.1 on my desktop (Pentium 4 under linux fedora core 4 and using the fftw3 fourier transform library). I used the .tpr file generated on the altix in mdrun and it worked fine. When I run that same file on the altix, it crashes every time without any iteration in the .log file: Removing pbc first time Done rmpbc Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 14580 Started Steepest Descents on node 0 Mon May 1 11:47:39 2006 PLEASE READ AND CITE THE FOLLOWING REFERENCE S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 --- Thank You --- After that the file ends. There is no other error message than segmentation fault with core dump. The compilers that are used on the altix are: C++ Version 99.0-023 -> 9.0-031 C++ Version 88.1-033 -> 8.1-036 Fortran 99.0-021 -> 9.0-032 Fortran 88.1-029 -> 8.1-033 IPP 4.1 -> 5.0 Have you enabled fortran at the compilation stage? In that case try it without, otherwise please file a bugzilla, such that we can document this problem (and try to fix it of course). ___ 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 ___ 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 -- 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 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] segmentation fault in mdrun when using PME
-Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Sat 4/29/2006 2:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] segmentation fault in mdrun when using PME Diane Fournier wrote: > Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex > molecular dynamics simulation. I have tried doing John > Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation > fault and core dump at the steepest descents minimization step. However, > mdrun works fine when using cutoff instead of PME. > > I'm working with Gromacs v. 3.3.1 on a SGI altix 3700 with 32 Intel > Itanium 2 processors (but I'm currently using a single node, so it's not > a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel > Math Kernel Librarary (MKL) v. 8.0.1 as FFT library (which is optimized > for Itanium 2). > > the em.mdp file looks like: > > title = drg_trp > cpp = /usr/bin/cpp > define = -DFLEX_SPC > constraints = none > integrator = steep > dt = 0.002; ps ! > nsteps = 500 > nstlist = 10 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb= 0.9 > rvdw= 0.9 > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft= yes > ; > ; Energy minimizing stuff > ; > emtol = 1000.0 > emstep = 0.01 > Is it possible this could be related to insufficient memory allocation ? > How demanding is this PME calculation ? Not likely a memory problem. It could be a compiler issue but we need more info! Where does it crash? Is it reproducible? DOes the same tpr file cause a crash on another architecture (e.g. your desktop)? I installed gromacs 3.3.1 on my desktop (Pentium 4 under linux fedora core 4 and using the fftw3 fourier transform library). I used the .tpr file generated on the altix in mdrun and it worked fine. When I run that same file on the altix, it crashes every time without any iteration in the .log file: Removing pbc first time Done rmpbc Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 14580 Started Steepest Descents on node 0 Mon May 1 11:47:39 2006 PLEASE READ AND CITE THE FOLLOWING REFERENCE S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 --- Thank You --- After that the file ends. There is no other error message than segmentation fault with core dump. The compilers that are used on the altix are: C++ Version 99.0-023 -> 9.0-031 C++ Version 88.1-033 -> 8.1-036 Fortran 99.0-021 -> 9.0-032 Fortran 88.1-029 -> 8.1-033 IPP 4.1 -> 5.0 > > > > > > ___ > 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 -- 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 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 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] segmentation fault in mdrun when using PME
Diane Fournier wrote: Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex molecular dynamics simulation. I have tried doing John Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation fault and core dump at the steepest descents minimization step. However, mdrun works fine when using cutoff instead of PME. I'm working with Gromacs v. 3.3.1 on a SGI altix 3700 with 32 Intel Itanium 2 processors (but I'm currently using a single node, so it's not a MPI problem) under Red Hat Enterprise Linux AS release 3 with Intel Math Kernel Librarary (MKL) v. 8.0.1 as FFT library (which is optimized for Itanium 2). the em.mdp file looks like: title = drg_trp cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep dt = 0.002; ps ! nsteps = 500 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Is it possible this could be related to insufficient memory allocation ? How demanding is this PME calculation ? Not likely a memory problem. It could be a compiler issue but we need more info! Where does it crash? Is it reproducible? DOes the same tpr file cause a crash on another architecture (e.g. your desktop)? ___ 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 -- 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 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
