[gmx-users] Restart REMD
Hi gmx-users I had an error as followed when I restart my REMD with commands: mpirun mdrun_mpi -multi 96 -deffnm prefix_ -s prefix_.tpr -cpi -noappend -replex 250 in gromacs version 4.5.5 Error: [glenn32-3.int.private:26794] *** An error occurred in MPI_Allreduce [glenn32-3.int.private:26794] *** on communicator MPI_COMM_WORLD [glenn32-3.int.private:26794] *** MPI_ERR_COMM: invalid communicator [glenn32-3.int.private:26794] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort -- mpirun has exited due to process rank 53 with PID 17572 on node glenn26-3 exiting improperly. There are two reasons this could occur: 1. this process did not call "init" before exiting, but others in the job did. This can cause a job to hang indefinitely while it waits for all processes to call "init". By rule, if one process calls "init", then ALL processes must call "init" prior to termination. 2. this process called "init", but exited without calling "finalize". By rule, all processes that call "init" MUST call "finalize" prior to exiting or it will be considered an "abnormal termination" This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [glenn25-3.int.private:22036] 17 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal [glenn25-3.int.private:22036] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages Is this a bug? how to fix it? Best regards Min -- View this message in context: http://gromacs.5086.x6.nabble.com/Restart-REMD-tp5010542.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Restart REMD
Probably the same issue as http://redmine.gromacs.org/issues/1072, which is probably fixed if you update to 4.5.7. Mark On Fri, Aug 16, 2013 at 3:05 PM, Min Wu wrote: > Hi gmx-users > > > > I had an error as followed when I restart my REMD with commands: > > > > mpirun mdrun_mpi -multi 96 -deffnm prefix_ -s prefix_.tpr -cpi -noappend > -replex 250 in gromacs version 4.5.5 > > > > Error: > > [glenn32-3.int.private:26794] *** An error occurred in MPI_Allreduce > [glenn32-3.int.private:26794] *** on communicator MPI_COMM_WORLD > [glenn32-3.int.private:26794] *** MPI_ERR_COMM: invalid communicator > [glenn32-3.int.private:26794] *** MPI_ERRORS_ARE_FATAL: your MPI job will > now abort > -- > mpirun has exited due to process rank 53 with PID 17572 on > node glenn26-3 exiting improperly. There are two reasons this could occur: > > 1. this process did not call "init" before exiting, but others in > the job did. This can cause a job to hang indefinitely while it waits > for all processes to call "init". By rule, if one process calls "init", > then ALL processes must call "init" prior to termination. > > 2. this process called "init", but exited without calling "finalize". > By rule, all processes that call "init" MUST call "finalize" prior to > exiting or it will be considered an "abnormal termination" > > This may have caused other processes in the application to be > terminated by signals sent by mpirun (as reported here). > -- > [glenn25-3.int.private:22036] 17 more processes have sent help message > help-mpi-errors.txt / mpi_errors_are_fatal > [glenn25-3.int.private:22036] Set MCA parameter "orte_base_help_aggregate" > to 0 to see all help / error messages > > > Is this a bug? how to fix it? > > > > Best regards > > Min > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Restart REMD
Hi gmx-users I had an error as followed when I restart my REMD with commands: mpirun mdrun_mpi -multi 96 -deffnm prefix_ -s prefix_.tpr -cpi -noappend -replex 250 in gromacs version 4.5.5 Error: [glenn32-3.int.private:26794] *** An error occurred in MPI_Allreduce [glenn32-3.int.private:26794] *** on communicator MPI_COMM_WORLD [glenn32-3.int.private:26794] *** MPI_ERR_COMM: invalid communicator [glenn32-3.int.private:26794] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort -- mpirun has exited due to process rank 53 with PID 17572 on node glenn26-3 exiting improperly. There are two reasons this could occur: 1. this process did not call "init" before exiting, but others in the job did. This can cause a job to hang indefinitely while it waits for all processes to call "init". By rule, if one process calls "init", then ALL processes must call "init" prior to termination. 2. this process called "init", but exited without calling "finalize". By rule, all processes that call "init" MUST call "finalize" prior to exiting or it will be considered an "abnormal termination" This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [glenn25-3.int.private:22036] 17 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal [glenn25-3.int.private:22036] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages Is this a bug? how to fix it? Best regards Min -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] restart REMD
On 23/05/2012 1:24 AM, Tomek Wlodarski wrote:
Hi,
-s before -deffnm works, now after starting once more REMD from
the scratch I can do restart.
I use
mpirun mdrun_mpi -multi $nrepls -deffnm ${name}_sim $npme -cpi
${name}_sim -append
and it Just Works with 4.5.5.
Mark
Thanks.
Best
tomek
On Mon, May 21, 2012 at 2:39 AM, mu xiaojia > wrote:
try put -s before -deffnm
mdrun_mpi -s -deffnm file_name -multi 120 -replex 250 -cpi -append
On Sun, May 20, 2012 at 4:50 PM, Tomek Wlodarski
mailto:tomek.wlodar...@gmail.com>> wrote:
Hi Francesco,
Thanks!
However, it does not work with my case..
tomek
On Sun, May 20, 2012 at 1:47 PM, francesco oteri
mailto:francesco.ot...@gmail.com>>
wrote:
Hi,
usually I use something like:
mdrun_mpi -v -deffnm topol_ -multi 72 -replex 1000 *-cpt*
*
*
gromacs is smart enough to understand that it has to load
topol_1.cpt topol_2.cpt ecc.ecc
Anyway, you can do a small test, i.e. using 5 replicas and
stopping you simulation after a few seconds
Francesco
2012/5/20 Tomek Wlodarski mailto:tomek.wlodar...@gmail.com>>
Hi,
I am running REMD simulation:
mdrun_mpi -v -deffnm -s topol_ -multi 72 -replex 1000
I am getting files with name like -s* (for example
-s1.trr)
How now I could restart this simulation?
I know that for regular MD simulation only I need -cpi
cpt_file_name --append to add, but what with REMD
simulation (I have cpt file: for example -s1_prev.cpt?)
Something like: -cpi "-s" ??
Thanks for suggestions!
Best!
tomek
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Cordiali saluti, Dr.Oteri Francesco
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Re: [gmx-users] restart REMD
Hi, -s before -deffnm works, now after starting once more REMD from the scratch I can do restart. Thanks. Best tomek On Mon, May 21, 2012 at 2:39 AM, mu xiaojia wrote: > try put -s before -deffnm > mdrun_mpi -s -deffnm file_name -multi 120 -replex 250 -cpi -append > > > On Sun, May 20, 2012 at 4:50 PM, Tomek Wlodarski < > tomek.wlodar...@gmail.com> wrote: > >> Hi Francesco, >> >> Thanks! >> However, it does not work with my case.. >> >> tomek >> >> On Sun, May 20, 2012 at 1:47 PM, francesco oteri < >> francesco.ot...@gmail.com> wrote: >> >>> Hi, >>> usually I use something like: >>> >>> mdrun_mpi -v -deffnm topol_ -multi 72 -replex 1000 *-cpt* >>> * >>> * >>> gromacs is smart enough to understand that it has to load topol_1.cpt >>> topol_2.cpt ecc.ecc >>> >>> >>> Anyway, you can do a small test, i.e. using 5 replicas and stopping you >>> simulation after a few seconds >>> >>> >>> Francesco >>> >>> 2012/5/20 Tomek Wlodarski >>> Hi, I am running REMD simulation: mdrun_mpi -v -deffnm -s topol_ -multi 72 -replex 1000 I am getting files with name like -s* (for example -s1.trr) How now I could restart this simulation? I know that for regular MD simulation only I need -cpi cpt_file_name --append to add, but what with REMD simulation (I have cpt file: for example -s1_prev.cpt?) Something like: -cpi "-s" ?? Thanks for suggestions! Best! tomek -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >>> >>> >>> -- >>> Cordiali saluti, Dr.Oteri Francesco >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] restart REMD
try put -s before -deffnm mdrun_mpi -s -deffnm file_name -multi 120 -replex 250 -cpi -append On Sun, May 20, 2012 at 4:50 PM, Tomek Wlodarski wrote: > Hi Francesco, > > Thanks! > However, it does not work with my case.. > > tomek > > On Sun, May 20, 2012 at 1:47 PM, francesco oteri < > francesco.ot...@gmail.com> wrote: > >> Hi, >> usually I use something like: >> >> mdrun_mpi -v -deffnm topol_ -multi 72 -replex 1000 *-cpt* >> * >> * >> gromacs is smart enough to understand that it has to load topol_1.cpt >> topol_2.cpt ecc.ecc >> >> >> Anyway, you can do a small test, i.e. using 5 replicas and stopping you >> simulation after a few seconds >> >> >> Francesco >> >> 2012/5/20 Tomek Wlodarski >> >>> Hi, >>> >>> I am running REMD simulation: >>> >>> mdrun_mpi -v -deffnm -s topol_ -multi 72 -replex 1000 >>> >>> I am getting files with name like -s* (for example -s1.trr) >>> >>> How now I could restart this simulation? >>> I know that for regular MD simulation only I need -cpi cpt_file_name >>> --append to add, but what with REMD simulation (I have cpt file: for >>> example -s1_prev.cpt?) >>> >>> Something like: -cpi "-s" ?? >>> Thanks for suggestions! >>> Best! >>> >>> tomek >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >> >> >> >> -- >> Cordiali saluti, Dr.Oteri Francesco >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] restart REMD
Hi Francesco, Thanks! However, it does not work with my case.. tomek On Sun, May 20, 2012 at 1:47 PM, francesco oteri wrote: > Hi, > usually I use something like: > > mdrun_mpi -v -deffnm topol_ -multi 72 -replex 1000 *-cpt* > * > * > gromacs is smart enough to understand that it has to load topol_1.cpt > topol_2.cpt ecc.ecc > > > Anyway, you can do a small test, i.e. using 5 replicas and stopping you > simulation after a few seconds > > > Francesco > > 2012/5/20 Tomek Wlodarski > >> Hi, >> >> I am running REMD simulation: >> >> mdrun_mpi -v -deffnm -s topol_ -multi 72 -replex 1000 >> >> I am getting files with name like -s* (for example -s1.trr) >> >> How now I could restart this simulation? >> I know that for regular MD simulation only I need -cpi cpt_file_name >> --append to add, but what with REMD simulation (I have cpt file: for >> example -s1_prev.cpt?) >> >> Something like: -cpi "-s" ?? >> Thanks for suggestions! >> Best! >> >> tomek >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> > > > > -- > Cordiali saluti, Dr.Oteri Francesco > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] restart REMD
Hi, usually I use something like: mdrun_mpi -v -deffnm topol_ -multi 72 -replex 1000 *-cpt* * * gromacs is smart enough to understand that it has to load topol_1.cpt topol_2.cpt ecc.ecc Anyway, you can do a small test, i.e. using 5 replicas and stopping you simulation after a few seconds Francesco 2012/5/20 Tomek Wlodarski > Hi, > > I am running REMD simulation: > > mdrun_mpi -v -deffnm -s topol_ -multi 72 -replex 1000 > > I am getting files with name like -s* (for example -s1.trr) > > How now I could restart this simulation? > I know that for regular MD simulation only I need -cpi cpt_file_name > --append to add, but what with REMD simulation (I have cpt file: for > example -s1_prev.cpt?) > > Something like: -cpi "-s" ?? > Thanks for suggestions! > Best! > > tomek > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] restart REMD
Hi, I am running REMD simulation: mdrun_mpi -v -deffnm -s topol_ -multi 72 -replex 1000 I am getting files with name like -s* (for example -s1.trr) How now I could restart this simulation? I know that for regular MD simulation only I need -cpi cpt_file_name --append to add, but what with REMD simulation (I have cpt file: for example -s1_prev.cpt?) Something like: -cpi "-s" ?? Thanks for suggestions! Best! tomek -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
