Hi, Mark, Thank you for help. It works. But now I have new fatal error:
Fatal error: The number of nodes (1) is not a multiple of the number of simulations (2) MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. What does it mean about nodes? Thank you! Bo On Thu, Mar 1, 2012 at 7:42 PM, <[email protected]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: mdrun -multi flag (Mark Abraham) > 2. Re: dihedral distributions (Juliette N.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 02 Mar 2012 10:17:12 +1100 > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] mdrun -multi flag > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 2/03/2012 10:15 AM, bo.shuang wrote: > > Hello, all, > > > > I am trying to do REMD simulation. So I used command: > > > > mdrun -s t2T.tpr -multi 2 -replex 1000 > > > > And gromacs gives error report: > > Fatal error: > > mdrun -multi is not supported with the thread library.Please compile > > GROMACS with MPI support > > For more information and tips for troubleshooting, please check the > > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > > > Then I tried re-install mdrun: > > ./configure --enable-mpi --program-suffix=_mpiq > > make mdrun > > make install-mdrun > > > > It looks fine, but I still cannot use multi flag, and it is still the > > same error. I don't know what the problem is and what I should do > > next. Thank you for help! > > With that program suffix, you need to use mdrun_mpiq > > Mark > > > ------------------------------ > > Message: 2 > Date: Thu, 1 Mar 2012 20:42:06 -0500 > From: "Juliette N." <[email protected]> > Subject: Re: [gmx-users] dihedral distributions > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <cagdqh4os1kuuogwlncznyxrf9sra_+a8s0eku2bum6cojvz...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Skipped content of type multipart/alternative-------------- next part > -------------- > A non-text attachment was scrubbed... > Name: RB1.88.PNG > Type: image/png > Size: 9359 bytes > Desc: not available > Url : > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120301/e812dbaf/RB1.88.png > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: RB1.46.PNG > Type: image/png > Size: 9580 bytes > Desc: not available > Url : > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120301/e812dbaf/RB1.46.png > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 95, Issue 10 > ***************************************** > >
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
