Re: [gmx-users] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)
On 2/10/15 7:35 AM, Felipe Villanelo wrote: Absolutely nothing is written in the log file, just the citations That indicates that the simulation systems are totally unstable and crash immediately. Test by running each job individually (not as part of REMD) and see if you can do any diagnosis and troubleshooting based on http://www.gromacs.org/Documentation/Terminology/Blowing_Up. -Justin Felipe Villanelo Lizana Bioquímico Laboratorio de Biología Estructural y Molecular Universidad de Chile 2015-02-03 10:01 GMT-03:00 Felipe Villanelo el.maest...@gmail.com: Hi, I trying to learn REMD following the tutorial on gromacs page http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B on a 4-cores computer. However when I try to use the command: mpirun -np 4 mdrun_mpi -v -multidir equil[0123] (as the tutorial says) the program crashed with the following error: mpirun noticed that process rank 2 with PID 13013 on node debian exited on signal 11 (Segmentation fault). The mpi is running fine with the 4 cores if I run a simple gromacs simulation (NPT equil) in the same machine. So I think it is not a problem of mpi configuration (as I read in another thread) These with gromacs version is 5.0.2 If I try to run the same with an older version of gromacs (4.5.5) the error is different (previously adjusting the options on the mdp file to match changes in syntaxis betweeen versions): [debian:23526] *** An error occurred in MPI_comm_size [debian:23526] *** on communicator MPI_COMM_WORLD [debian:23526] *** MPI_ERR_COMM: invalid communicator [debian:23526] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) But this version also work fine with mpi using the 4 cores on a simple simulation Thanks Bye Felipe Villanelo Lizana Bioquímico Laboratorio de Biología Estructural y Molecular Universidad de Chile -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)
Absolutely nothing is written in the log file, just the citations Felipe Villanelo Lizana Bioquímico Laboratorio de Biología Estructural y Molecular Universidad de Chile 2015-02-03 10:01 GMT-03:00 Felipe Villanelo el.maest...@gmail.com: Hi, I trying to learn REMD following the tutorial on gromacs page http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B on a 4-cores computer. However when I try to use the command: mpirun -np 4 mdrun_mpi -v -multidir equil[0123] (as the tutorial says) the program crashed with the following error: mpirun noticed that process rank 2 with PID 13013 on node debian exited on signal 11 (Segmentation fault). The mpi is running fine with the 4 cores if I run a simple gromacs simulation (NPT equil) in the same machine. So I think it is not a problem of mpi configuration (as I read in another thread) These with gromacs version is 5.0.2 If I try to run the same with an older version of gromacs (4.5.5) the error is different (previously adjusting the options on the mdp file to match changes in syntaxis betweeen versions): [debian:23526] *** An error occurred in MPI_comm_size [debian:23526] *** on communicator MPI_COMM_WORLD [debian:23526] *** MPI_ERR_COMM: invalid communicator [debian:23526] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) But this version also work fine with mpi using the 4 cores on a simple simulation Thanks Bye Felipe Villanelo Lizana Bioquímico Laboratorio de Biología Estructural y Molecular Universidad de Chile -- 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] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)
Hi, What was the last thing written to the log files? Mark On Tue, Feb 3, 2015 at 2:01 PM, Felipe Villanelo el.maest...@gmail.com wrote: Hi, I trying to learn REMD following the tutorial on gromacs page http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B on a 4-cores computer. However when I try to use the command: mpirun -np 4 mdrun_mpi -v -multidir equil[0123] (as the tutorial says) the program crashed with the following error: mpirun noticed that process rank 2 with PID 13013 on node debian exited on signal 11 (Segmentation fault). The mpi is running fine with the 4 cores if I run a simple gromacs simulation (NPT equil) in the same machine. So I think it is not a problem of mpi configuration (as I read in another thread) These with gromacs version is 5.0.2 If I try to run the same with an older version of gromacs (4.5.5) the error is different (previously adjusting the options on the mdp file to match changes in syntaxis betweeen versions): [debian:23526] *** An error occurred in MPI_comm_size [debian:23526] *** on communicator MPI_COMM_WORLD [debian:23526] *** MPI_ERR_COMM: invalid communicator [debian:23526] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) But this version also work fine with mpi using the 4 cores on a simple simulation Thanks Bye Felipe Villanelo Lizana Bioquímico Laboratorio de Biología Estructural y Molecular Universidad de Chile -- 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] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)
Hi, I trying to learn REMD following the tutorial on gromacs page http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B on a 4-cores computer. However when I try to use the command: mpirun -np 4 mdrun_mpi -v -multidir equil[0123] (as the tutorial says) the program crashed with the following error: mpirun noticed that process rank 2 with PID 13013 on node debian exited on signal 11 (Segmentation fault). The mpi is running fine with the 4 cores if I run a simple gromacs simulation (NPT equil) in the same machine. So I think it is not a problem of mpi configuration (as I read in another thread) These with gromacs version is 5.0.2 If I try to run the same with an older version of gromacs (4.5.5) the error is different (previously adjusting the options on the mdp file to match changes in syntaxis betweeen versions): [debian:23526] *** An error occurred in MPI_comm_size [debian:23526] *** on communicator MPI_COMM_WORLD [debian:23526] *** MPI_ERR_COMM: invalid communicator [debian:23526] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) But this version also work fine with mpi using the 4 cores on a simple simulation Thanks Bye Felipe Villanelo Lizana Bioquímico Laboratorio de Biología Estructural y Molecular Universidad de Chile -- 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.
