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
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
