[gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells
Hi, I am using gromacs-2019.4. I have been running simulations box that contains a peptide embedded in a DOPC bilayer membrane, using all atom simulations. I have been running for weeks in a TACC computer that has 4 gpu in a single node, so I usually run 4 trajectories in a single node using the -multidir option. My submission script is: #!/bin/bash #SBATCH -J sb16 # Job name #SBATCH -o test.o%j # Job name #SBATCH -e test.e%j # Job name #SBATCH -N 1 # Total number of nodes requested #SBATCH -n 4# Total number of mpi tasks requested #SBATCH -p rtx # Queue (partition) name -- normal, development, etc. #SBATCH -t 48:00:00 # Run time (hh:mm:ss) - 1.5 hours module load cuda/10.1 module use -a /home1/01247/alfredo/Software/ForGPU/plumed-2.5.3/MyInstall/lib/plumed/ModuleFile module load plumed_gpu export OMP_NUM_THREADS=4 ibrun /home1/01247/alfredo/Software/gromacs-2019.4_gpu/build-gpu-mpi-plumed/My_install/bin/mdrun_mpi -s topol.tpr -plumed plumed.dat -multidir 1 2 3 4 Because the system is going to be down for a week I want to do continuation runs in a slower computer system, also using gpus. Because the system is slower I want to run it using two nodes. A script that I have used successfully in that old machine is: #!/bin/bash #SBATCH -J SB9_pi1 # Job name #SBATCH -o test.o%j # Job name #SBATCH -N 2 # Total number of nodes requested #SBATCH -n 2# Total number of mpi tasks requested #SBATCH -p gpu # Queue (partition) name -- normal, development, etc. #SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 1.5 hours module load gcc/5.2.0 module load cray_mpich/7.7.3 module load cuda/9.0 # Launc hMPI-based executable export OMP_NUM_THREADS=6 ibrun /home1/01247/alfredo/gromacs-2019.4/build_MPI/My_install/bin/mdrun_mpi -s topol2.tpr -pin on -cpi state.cpt -noappend It works great if I setup a new simulation of the same molecular system (create a new tpr file). But if I attempt to run a continuation run coming from the other machine (that used 4 threads). I get Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: Bond of 10801 missing -5 U-B of 53187 missing 22 Proper Dih. of 89703 missing119 LJ-14 of 73729 missing 3 srun: Job step aborted: Waiting up to 32 seconds for job step to finish. And it stops. If I modified the script for the old machine to use 1 nodes, 1 task and 4 thread, it runs well but it is a lot slower. My question is if there is any way to avoid this error, so I can do a continuation run using state.cpt with a different domain decomposition. I have seen in the list that is suggested to use -rdd. The value printed in the log file is 1.595 nm. I increased to 2.0 and gave a similar error. Thanks, Alfredo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Getting a high potential energy error when using some specific gpu options. Gromacs 2019.4
Hi, I am testing a new computer system with single nodes containing four GPU’s, for a membrane containing a peptide with numerous restraints. I have read in the gmx_users list that for this kind of systems maybe the more efficient use of a node is to run several simulations on it so I have tried several input options. Anyway, what I show here is an attempt to run a single trajectory on two specific GPUs of a node and using -pme gpu. The command is: mdrun -v -deffnm topolshort -nt 8 -pin on -pinoffset 8 -pinstride 1 -ntmpi 8 -ntomp 1 -npme 1 -pme gpu -gpu_id 23 I obtained the error: Program: mdrun, version 2019.4 Source file: src/gromacs/mdlib/sim_util.cpp (line 752) MPI rank:6 (out of 8) Fatal error: Step 0: The total potential energy is 1.40845e+15, which is extremely high. The LJ and electrostatic contributions to the energy are 1.2 and -118338, respectively. A very high potential energy can be caused by overlapping interactions in bonded interactions or very large coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology. Link to see the complete log file: https://utexas.box.com/s/eofa6ocil6mp947ahbvvtstt9qhnppsg When I removed “-npme 1 -pme gpu”, the error doesn’t occur and the trajectory finish normally. What it could be the cause of the error? Thanks, Alfredo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers
Hi Roland and others gmx-users,
I am also getting a similar compilation error regarding pullutil.cpp:
icpc: error #10106: Fatal error in
/opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
terminated by floating point exception
compilation aborted for
/home1/01247/alfredo/Software/gromacs-2019.4/src/gromacs/pulling/pullutil.cpp
(code 1)
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
Error 1
make[2]: *** Waiting for unfinished jobs
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2
using optimization for AVX512. I saw this post where you suggested a
work-around adding "#pragma intel optimization_level 2" in front of
pull_calc_coms. I see the line in pullutil.cpp:
void pull_calc_coms(const t_commrec *cr,
pull_t *pull,
const t_mdatoms *md,
t_pbc *pbc,
double t,
const rvec x[], rvec *xp)
{
I tried putting the pragma before void and it gave me a bunch of errors. Where
exactly should it be added?
Thanks,
Alfredo
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Re: [gmx-users] can dynamic selection be used with gmx rdf?
Here I am posting the solution of the problem that I described in my first post: gmx rdf -f ../../../../traj_200to500.xtc -s ../../../../step7_4.tpr -o -cn -rmax 0.8 -excl -ref '(resname DPPS and name O22) and within 0.3 of name CAL' -sel 'name OH2' Alfredo From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Cardenas, Alfredo E Sent: Thursday, February 28, 2019 10:50 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] can dynamic selection be used with gmx rdf? Hi Mark, Thanks for your reply. I have tried the following run: gmx rdf -f ../../../traj_200to500.xtc -s ../../../step7_4.tpr -o -cn -rmax 0.8 -excl -ref -sf selection1.dat -sel -sf selection2.dat where the selections files are: selection1.dat: rdist = name CAL distance from name O22; name O22 and rdist <= 0.3; (for the first line I am following an example in the User guide) selection2.dat: name OH2 When attempting to run I get an error: Error in user input: Invalid command-line options In command-line option -sf Error in parsing selections from file 'selection1.dat' Invalid selection 'rdist = name CAL distance from name O22' syntax error In command-line option -sf Error in adding selections from file 'selection2.dat' Too few selections provided I guess the syntax of my selection instructions is wrong. Any help will be appreciated. Thanks, Alfredo From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Wednesday, February 27, 2019 5:27 PM To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] can dynamic selection be used with gmx rdf? Hi, One way to check that is to consult the online documentation... http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html shows options taking dynamic selections! Mark On Wed, 27 Feb 2019 at 15:08 Cardenas, Alfredo E wrote: > Hello all, > I would like to calculate the rdf between a set of oxygen atoms in a lipid > bilayer to water. But I would like to include in this calculation only a > subset of these oxygen atoms that come closer (< 0.3 nm) to Ca ions. I > wonder if such a dynamic selection is possible combined with the rdf tool. > Thanks > Alfredo Cardenas > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] can dynamic selection be used with gmx rdf?
Hi Mark, Thanks for your reply. I have tried the following run: gmx rdf -f ../../../traj_200to500.xtc -s ../../../step7_4.tpr -o -cn -rmax 0.8 -excl -ref -sf selection1.dat -sel -sf selection2.dat where the selections files are: selection1.dat: rdist = name CAL distance from name O22; name O22 and rdist <= 0.3; (for the first line I am following an example in the User guide) selection2.dat: name OH2 When attempting to run I get an error: Error in user input: Invalid command-line options In command-line option -sf Error in parsing selections from file 'selection1.dat' Invalid selection 'rdist = name CAL distance from name O22' syntax error In command-line option -sf Error in adding selections from file 'selection2.dat' Too few selections provided I guess the syntax of my selection instructions is wrong. Any help will be appreciated. Thanks, Alfredo From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Wednesday, February 27, 2019 5:27 PM To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] can dynamic selection be used with gmx rdf? Hi, One way to check that is to consult the online documentation... http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html shows options taking dynamic selections! Mark On Wed, 27 Feb 2019 at 15:08 Cardenas, Alfredo E wrote: > Hello all, > I would like to calculate the rdf between a set of oxygen atoms in a lipid > bilayer to water. But I would like to include in this calculation only a > subset of these oxygen atoms that come closer (< 0.3 nm) to Ca ions. I > wonder if such a dynamic selection is possible combined with the rdf tool. > Thanks > Alfredo Cardenas > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] can dynamic selection be used with gmx rdf?
Hello all, I would like to calculate the rdf between a set of oxygen atoms in a lipid bilayer to water. But I would like to include in this calculation only a subset of these oxygen atoms that come closer (< 0.3 nm) to Ca ions. I wonder if such a dynamic selection is possible combined with the rdf tool. Thanks Alfredo Cardenas -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
