Re: [gmx-users] Error when for gmx tune_pme on Cray
> On 10. Apr 2018, at 18:13, Viveca Lindahl wrote: > > Thanks. It's running now. I just had a typo in my gmx_mpi variable that > gave me the last error I posted. Using the non-mpi binary for tune_pme > solved it. BTW you might find the tune_pme -ntpr 1 switch useful if you are using the Verlet cutoff scheme. Since with Verlet, mdrun does automatically balance PME grid and cutoff settings, there is no need for tune_pme to provide .tpr files with various settings for grid and cutoff. Will make the tuning significantly faster! Happy tuning, Carsten > > -- > Viveca > > > On Tue, Apr 10, 2018 at 5:22 PM, Mark Abraham > wrote: > >> Hi, >> >> On Tue, Apr 10, 2018 at 4:52 PM Viveca Lindahl >> wrote: >> >>> @Carsten: thanks for the suggestions. I needed the 'aprun -n 1' to be >> able >>> to run with my mpi-binary (otherwise I get 'illegal instruction'). I now >>> tried >>> >>> >>> export MPIRUN=aprun; $gmx tune_pme -npstring n -s topol.tpr -np 16 -mdrun >>> $gmx_mpi >>> >>> where gmx/gmx_mpi are a thread-mpi/real MPI builds and get >>> >>> Fatal error: >>> Need an MPI-enabled version of mdrun. This one >>> (/cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx) >>> seems to have been compiled without MPI support. >>> >>> referring to the mpi build. >>> >> >> It's tried out what you supplied to the -mdrun flag and found it didn't >> work. Probably for the reason below. >> >> >>> @Mark: Do you mean that tune_pme expects the binaries to have exactly >> these >>> names gmx/gmx_mpi (and be in the same location)? >>> >> >> No, but checking out gmx help tune_pme regarding -mdrun would help you >> provide what is needed, e.g. "gmx_mpi mdrun" (modulo however you built and >> suffixed your gmx binaries). >> >> Mark >> -- >> 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Error when for gmx tune_pme on Cray
Thanks. It's running now. I just had a typo in my gmx_mpi variable that gave me the last error I posted. Using the non-mpi binary for tune_pme solved it. -- Viveca On Tue, Apr 10, 2018 at 5:22 PM, Mark Abraham wrote: > Hi, > > On Tue, Apr 10, 2018 at 4:52 PM Viveca Lindahl > wrote: > > > @Carsten: thanks for the suggestions. I needed the 'aprun -n 1' to be > able > > to run with my mpi-binary (otherwise I get 'illegal instruction'). I now > > tried > > > > > > export MPIRUN=aprun; $gmx tune_pme -npstring n -s topol.tpr -np 16 -mdrun > > $gmx_mpi > > > > where gmx/gmx_mpi are a thread-mpi/real MPI builds and get > > > > Fatal error: > > Need an MPI-enabled version of mdrun. This one > > (/cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx) > > seems to have been compiled without MPI support. > > > > referring to the mpi build. > > > > It's tried out what you supplied to the -mdrun flag and found it didn't > work. Probably for the reason below. > > > > @Mark: Do you mean that tune_pme expects the binaries to have exactly > these > > names gmx/gmx_mpi (and be in the same location)? > > > > No, but checking out gmx help tune_pme regarding -mdrun would help you > provide what is needed, e.g. "gmx_mpi mdrun" (modulo however you built and > suffixed your gmx binaries). > > Mark > -- > 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] Error when for gmx tune_pme on Cray
Hi, On Tue, Apr 10, 2018 at 4:52 PM Viveca Lindahl wrote: > @Carsten: thanks for the suggestions. I needed the 'aprun -n 1' to be able > to run with my mpi-binary (otherwise I get 'illegal instruction'). I now > tried > > > export MPIRUN=aprun; $gmx tune_pme -npstring n -s topol.tpr -np 16 -mdrun > $gmx_mpi > > where gmx/gmx_mpi are a thread-mpi/real MPI builds and get > > Fatal error: > Need an MPI-enabled version of mdrun. This one > (/cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx) > seems to have been compiled without MPI support. > > referring to the mpi build. > It's tried out what you supplied to the -mdrun flag and found it didn't work. Probably for the reason below. > @Mark: Do you mean that tune_pme expects the binaries to have exactly these > names gmx/gmx_mpi (and be in the same location)? > No, but checking out gmx help tune_pme regarding -mdrun would help you provide what is needed, e.g. "gmx_mpi mdrun" (modulo however you built and suffixed your gmx binaries). Mark -- 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] Error when for gmx tune_pme on Cray
@Carsten: thanks for the suggestions. I needed the 'aprun -n 1' to be able to run with my mpi-binary (otherwise I get 'illegal instruction'). I now tried export MPIRUN=aprun; $gmx tune_pme -npstring n -s topol.tpr -np 16 -mdrun $gmx_mpi where gmx/gmx_mpi are a thread-mpi/real MPI builds and get Fatal error: Need an MPI-enabled version of mdrun. This one (/cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx) seems to have been compiled without MPI support. referring to the mpi build. @Mark: Do you mean that tune_pme expects the binaries to have exactly these names gmx/gmx_mpi (and be in the same location)? -- Viveca On Tue, Apr 10, 2018 at 3:54 PM, Mark Abraham wrote: > Hi, > > Yes, Cray's MPI also does not permit such nesting. This is why it's > generally advisable that installations make both an MPI and non-MPI build, > and to let the default suffixing of the gmx binary handle itself so both > installations can go to the same place for convenience. > > Mark > > On Tue, Apr 10, 2018 at 3:50 PM Kutzner, Carsten wrote: > > > Hi Viveca, > > > > > On 10. Apr 2018, at 15:10, Viveca Lindahl > > wrote: > > > > > > Hi users, > > > > > > I never used gmx tune_pme before and thought I'd try. On a Cray > machine, > > > using aprun instead of mpirun, I did > > > > > > args="/cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx > > > mdrun -pin on -quiet -stepout 5000 -ntomp 2 -noconfout" > > > export MPIRUN=aprun; aprun -n 1 $gmx tune_pme -npstring n -s topol.tpr > > -np > > > 32 -mdrun "$args” > > You don’t need to use aprun -n 1 on $gmx tune_pme, as this is > > just a serial program that itself calls aprun on mdrun_mpi. > > Does the following work: > > > > export MPIRUN=aprun > > $gmx tune_pme -npstring n -s topol.tpr -np 32 -mdrun /path/to/mdrun_mpi > > > > I don’t know if on Cray it is allowed that one MPI executable (tune_pme) > > starts > > another MPI executable (mdrun), IBM PE e.g. does not allow it. > > There, tune_pme must be compiled without MPI, only mdrun can be linked to > > the MPI lib. > > > > Best, > > Carsten > > > > > > > > It hangs (no output) for some minutes, then I get the error > > > > > > Program: gmx tune_pme, version 2018.1-dev-20180315-3dfa11852 > > > Source file: src/gromacs/gmxana/gmx_tune_pme.cpp (line 740) > > > > > > Fatal error: > > > Cannot execute mdrun. Please check benchtest.log for problems! > > > > > > For more information and tips for troubleshooting, please check the > > GROMACS > > > website at http://www.gromacs.org/Documentation/Errors > > > --- > > > Making sure that mdrun can be executed. Trying 'aprun -n 32 > > > /cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx mdrun > > -pin > > > on -quiet -stepout 5000 -ntomp 2 -noconfout -version -maxh 0.001 1> > > > benchtest.log 2>&1' ... Rank 0 [Tue Apr 10 14:58:12 2018] [c1-0c0s4n0] > > > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > > > > > > the suggested log file to look in has > > > > > > craylog: WARNING: log tmp dir /var/spool/cray/llm is not writable > > > aprun: Unable to contact apsys > > > aprun: Exiting due to errors. Application aborted > > > > > > Am I doing something wrong or is this a bug/limitation of the system I > am > > > trying to run on? > > > > > > Thanks, > > > -- > > > Viveca > > > -- > > > 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] Error when for gmx tune_pme on Cray
Hi, Yes, Cray's MPI also does not permit such nesting. This is why it's generally advisable that installations make both an MPI and non-MPI build, and to let the default suffixing of the gmx binary handle itself so both installations can go to the same place for convenience. Mark On Tue, Apr 10, 2018 at 3:50 PM Kutzner, Carsten wrote: > Hi Viveca, > > > On 10. Apr 2018, at 15:10, Viveca Lindahl > wrote: > > > > Hi users, > > > > I never used gmx tune_pme before and thought I'd try. On a Cray machine, > > using aprun instead of mpirun, I did > > > > args="/cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx > > mdrun -pin on -quiet -stepout 5000 -ntomp 2 -noconfout" > > export MPIRUN=aprun; aprun -n 1 $gmx tune_pme -npstring n -s topol.tpr > -np > > 32 -mdrun "$args” > You don’t need to use aprun -n 1 on $gmx tune_pme, as this is > just a serial program that itself calls aprun on mdrun_mpi. > Does the following work: > > export MPIRUN=aprun > $gmx tune_pme -npstring n -s topol.tpr -np 32 -mdrun /path/to/mdrun_mpi > > I don’t know if on Cray it is allowed that one MPI executable (tune_pme) > starts > another MPI executable (mdrun), IBM PE e.g. does not allow it. > There, tune_pme must be compiled without MPI, only mdrun can be linked to > the MPI lib. > > Best, > Carsten > > > > > It hangs (no output) for some minutes, then I get the error > > > > Program: gmx tune_pme, version 2018.1-dev-20180315-3dfa11852 > > Source file: src/gromacs/gmxana/gmx_tune_pme.cpp (line 740) > > > > Fatal error: > > Cannot execute mdrun. Please check benchtest.log for problems! > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > Making sure that mdrun can be executed. Trying 'aprun -n 32 > > /cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx mdrun > -pin > > on -quiet -stepout 5000 -ntomp 2 -noconfout -version -maxh 0.001 1> > > benchtest.log 2>&1' ... Rank 0 [Tue Apr 10 14:58:12 2018] [c1-0c0s4n0] > > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > > > > the suggested log file to look in has > > > > craylog: WARNING: log tmp dir /var/spool/cray/llm is not writable > > aprun: Unable to contact apsys > > aprun: Exiting due to errors. Application aborted > > > > Am I doing something wrong or is this a bug/limitation of the system I am > > trying to run on? > > > > Thanks, > > -- > > Viveca > > -- > > 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] Error when for gmx tune_pme on Cray
Hi Viveca, > On 10. Apr 2018, at 15:10, Viveca Lindahl wrote: > > Hi users, > > I never used gmx tune_pme before and thought I'd try. On a Cray machine, > using aprun instead of mpirun, I did > > args="/cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx > mdrun -pin on -quiet -stepout 5000 -ntomp 2 -noconfout" > export MPIRUN=aprun; aprun -n 1 $gmx tune_pme -npstring n -s topol.tpr -np > 32 -mdrun "$args” You don’t need to use aprun -n 1 on $gmx tune_pme, as this is just a serial program that itself calls aprun on mdrun_mpi. Does the following work: export MPIRUN=aprun $gmx tune_pme -npstring n -s topol.tpr -np 32 -mdrun /path/to/mdrun_mpi I don’t know if on Cray it is allowed that one MPI executable (tune_pme) starts another MPI executable (mdrun), IBM PE e.g. does not allow it. There, tune_pme must be compiled without MPI, only mdrun can be linked to the MPI lib. Best, Carsten > > It hangs (no output) for some minutes, then I get the error > > Program: gmx tune_pme, version 2018.1-dev-20180315-3dfa11852 > Source file: src/gromacs/gmxana/gmx_tune_pme.cpp (line 740) > > Fatal error: > Cannot execute mdrun. Please check benchtest.log for problems! > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > Making sure that mdrun can be executed. Trying 'aprun -n 32 > /cfs/klemming/nobackup/v/vivecal/programs/gromacs/2018.1/bin/gmx mdrun -pin > on -quiet -stepout 5000 -ntomp 2 -noconfout -version -maxh 0.001 1> > benchtest.log 2>&1' ... Rank 0 [Tue Apr 10 14:58:12 2018] [c1-0c0s4n0] > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 > > the suggested log file to look in has > > craylog: WARNING: log tmp dir /var/spool/cray/llm is not writable > aprun: Unable to contact apsys > aprun: Exiting due to errors. Application aborted > > Am I doing something wrong or is this a bug/limitation of the system I am > trying to run on? > > Thanks, > -- > Viveca > -- > 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.
