From: Nicholus Bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Thu Aug 27 2015 - 03:00:31 CDT
Hello Peter,
Thank you foe the suggestion. Yes it worked with namd 2.10 and your
suggested command options. With this shorted out I would like to know the
answer to second part of my initial question as repeated below.
How do we use AMBER topology file in REMD of namd.
For running normal simulation we change in the configuration file
"structure XXX.psf" by
amber yes
parmfile XXX.top"
Now in REMD configuration file what we change for the following line
set psf_file "XXX.psf"
Thank you again.
On Wed, Aug 26, 2015 at 3:28 PM, Peter Freddolino <petefred_at_umich.edu>
wrote:
> Hi Nicholus,
> The error message suggests something wrong with your charmrun binary. Did
> you try running the test programs with it?
>
> Also, you should be using an lrts-enabled namd 2.10 build; I’m not sure
> why you’re still on NAMD 2.9.
>
> Also, you did not precisely copy the command line that I suggested. The
> numbers of plusses and spaces matter…
> Best,
> Peter
>
> > On Aug 26, 2015, at 8:00 AM, Nicholus Bhattacharjee <
> nicholusbhattacharjee_at_gmail.com> wrote:
> >
> > Hell Jeff and Peter,
> >
> > Thank you for the suggestions.
> >
> > Jeff,
> >
> > I tried to compile as suggested by you. After the compilation I tried to
> do the test run as follows and got the following result
> >
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > NAMD_CVS-2015-08-25_Source/Linux-x86_64-g++$ ./namd2 src/alanin
> >
> > [crim1:08977] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required
> executable either could not be found or was not executable by this user in
> file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at
> line 357
> > [crim1:08977] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required
> executable either could not be found or was not executable by this user in
> file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at
> line 230
> > [crim1:08977] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required
> executable either could not be found or was not executable by this user in
> file ../../../orte/runtime/orte_init.c at line 132
> >
> --------------------------------------------------------------------------
> > It looks like orte_init failed for some reason; your parallel process is
> > likely to abort. There are many reasons that a parallel process can
> > fail during orte_init; some of which are due to configuration or
> > environment problems. This failure appears to be an internal failure;
> > here's some additional information (which may only be relevant to an
> > Open MPI developer):
> >
> > orte_ess_set_name failed
> > --> Returned value A system-required executable either could not be
> found or was not executable by this user (-127) instead of ORTE_SUCCESS
> >
> --------------------------------------------------------------------------
> >
> --------------------------------------------------------------------------
> > It looks like MPI_INIT failed for some reason; your parallel process is
> > likely to abort. There are many reasons that a parallel process can
> > fail during MPI_INIT; some of which are due to configuration or
> environment
> > problems. This failure appears to be an internal failure; here's some
> > additional information (which may only be relevant to an Open MPI
> > developer):
> >
> > ompi_mpi_init: orte_init failed
> > --> Returned "A system-required executable either could not be found
> or was not executable by this user" (-127) instead of "Success" (0)
> >
> --------------------------------------------------------------------------
> > *** The MPI_Init_thread() function was called before MPI_INIT was
> invoked.
> > *** This is disallowed by the MPI standard.
> > *** Your MPI job will now abort.
> > [crim1:8977] Abort before MPI_INIT completed successfully; not able to
> guarantee that all other processes were killed!
> >
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> > Is that fine or I need to do something else. I am attaching the output
> from compilation.
> >
> > Peter,
> >
> > I tried to do as suggested by you and got the following error (normal
> NAMD is running fine in my computer)
> > nicholus_at_crim1:~/replica/example$ mpirun
> /usr/local/NAMD_2.9_Linux-x86_64-multicore/charmrun
> /usr/local/NAMD_2.9_Linux-x86_64-multicore/namd2 ++local +p8 +replicas 8
> job0.conf +stdout output/%d/job0.%d.log
> >
> --------------------------------------------------------------------------
> > Could not execute the executable
> "/usr/local/NAMD_2.9_Linux-x86_64-multicore/charmrun": Exec format error
> >
> > This could mean that your PATH or executable name is wrong, or that you
> do not
> > have the necessary permissions. Please ensure that the executable is
> able to be
> > found and executed.
> >
> >
> --------------------------------------------------------------------------
> > nicholus_at_crim1:~/replica/example$ mpirun
> /usr/local/NAMD_2.9_Linux-x86_64-multicore/charmrun
> /usr/local/NAMD_2.9_Linux-x86_64-multicore/namd2 +p8 +replicas 8 job0.conf
> +stdout output/%d/job0.%d.log
> >
> --------------------------------------------------------------------------
> > Could not execute the executable
> "/usr/local/NAMD_2.9_Linux-x86_64-multicore/charmrun": Exec format error
> >
> > This could mean that your PATH or executable name is wrong, or that you
> do not
> > have the necessary permissions. Please ensure that the executable is
> able to be
> > found and executed.
> >
> >
> --------------------------------------------------------------------------
> >
> >
> >
> > On Wed, Aug 26, 2015 at 6:25 AM, Peter Freddolino <petefred_at_umich.edu>
> wrote:
> > Hi Nicholus,
> > You ought to be running it through charmrun with this build of namd. For
> a local run on my laptop I can do the following:
> >
> > mpirun ~/src/NAMD_2.10_MacOSX-x86_64-netlrts/charmrun
> ~/src/NAMD_2.10_MacOSX-x86_64-netlrts/namd2 ++local ++p 6 +replicas 6
> aslov2_ja_metaRE_run01.namd +stdout output/rep_%d/rep%d_run01.log
> >
> > (you can change the paths accordingly)
> >
> > Omitting the charmrun portion yields the same error that you saw.
> >
> > Best,
> > Peter
> >
> > > On Aug 25, 2015, at 5:59 AM, Nicholus Bhattacharjee <
> nicholusbhattacharjee_at_gmail.com> wrote:
> > >
> > > Hello Douglas and Norman,
> > >
> > > Thanks for the reply. Douglas I have downloaded
> "NAMD_2.10_Linux-x86_64-netlrts" and tried running the same job with the
> following command
> > >
> > > $ mpirun /home/nicholus/softwares/NAMD_2.10_Linux-x86_64-netlrts/namd2
> +replicas 8 job0.conf +stdout output/%d/job0.%d.log
> > >
> > > The resultant error is
> > >
> > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > > Charm++: standalone mode (not using charmrun)
> > > Charm++> Running in non-SMP mode: numPes 1
> > > namd2: machine-common-core.c:863: create_partition_map: Assertion
> `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> > >
> --------------------------------------------------------------------------
> > > mpirun noticed that process rank 0 with PID 3679 on node crim1 exited
> on signal 6 (Aborted).
> > >
> --------------------------------------------------------------------------
> > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > >
> > > Could you please tell me what wrong I am doing. Thanks onece again.
> > >
> > >
> > > On Tue, Aug 25, 2015 at 11:16 AM, Douglas Houston <
> DouglasR.Houston_at_ed.ac.uk> wrote:
> > > Hi Nicholus,
> > >
> > > Are you using a NAMD build based on a patched MPI build of Charm++? I
> had to compile NAMD from source (by following the instructions in the
> notes.txt file).
> > >
> > > Alternatively there is a version on the NAMD download page called
> "Linux-x86_64-netlrts (Multi-copy algorithms)" which might be what you want
> (although it's hard to tell).
> > >
> > > cheers,
> > > Doug
> > >
> > >
> > >
> > > Quoting Nicholus Bhattacharjee <nicholusbhattacharjee_at_gmail.com> on
> Tue, 25 Aug 2015 10:01:36 +0200:
> > >
> > > Hello,
> > >
> > > I am reposting the query as I have not got any reply.
> > >
> > > I am trying to run REMD simulation using NAMD. I am following the
> > > suggestions given in
> > >
> > > http://www.ks.uiuc.edu/Research/namd/2.9/ug/node66.html
> > >
> > > I did the following
> > >
> > > example$ mkdir output
> > > example$ cd output
> > > output$ mkdir 0 1 2 3 4 5 6 7
> > > output$ cd ..
> > > example$ mpirun /usr/local/NAMD_2.9_Linux-x86_64-multicore/namd2
> +replicas
> > > 8 job0.conf +stdout output/%d/job0.%d.log
> > >
> > > I got the error message
> > > %%%%%%%%%%%%%%%%%%%%%%%%%%%
> > > FATAL ERROR: Unknown command-line option +replicas
> > > ------------- Processor 0 Exiting: Called CmiAbort ------------
> > > Reason: FATAL ERROR: Unknown command-line option +replicas
> > >
> > > Charm++ fatal error:
> > > FATAL ERROR: Unknown command-line option +replicas
> > > %%%%%%%%%%%%%%%%%%%%%%%%%%
> > >
> > > The second part of the question is about running REMD using AMBER
> topology
> > > file.
> > > For running normal simulation we change in the configuration file
> > > "structure XXX.psf" by
> > > amber yes
> > > parmfile XXX.top"
> > >
> > > Now in REMD configuration file what we change for the following line
> > >
> > > set psf_file "XXX.psf"
> > >
> > >
> > >
> > >
> > >
> > > _____________________________________________________
> > > Dr. Douglas R. Houston
> > > Lecturer
> > > Institute of Structural and Molecular Biology
> > > Room 3.23, Michael Swann Building
> > > King's Buildings
> > > University of Edinburgh
> > > Edinburgh, EH9 3JR, UK
> > > Tel. 0131 650 7358
> > > http://tinyurl.com/douglasrhouston
> > >
> > > --
> > > The University of Edinburgh is a charitable body, registered in
> > > Scotland, with registration number SC005336.
> > >
> > >
> > >
> >
> >
> > <error>
>
>
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