From: Nicolas Martin (nicolasmartin973_at_gmail.com)
Date: Wed Sep 21 2016 - 03:26:18 CDT
Dear Giacomo,
Thanks a lot for your reply. I'll have a look at what you suggested,
especially the scripting interface of colvar that seems very promising
for my work.
Cheers,
Nicolas
On 09/19/2016 06:22 PM, Giacomo Fiorin wrote:
> Hello Nicolas, the multiple-replica infrastructure in NAMD underwent
> several revisions, particularly because its first implementation had
> to be done in pure Tcl. This was due to a limitation of Charm++,
> which unlike MPI did not support multiple communicators until recently
> (Charm++ 6.5 - NAMD 2.10).
>
> Starting version 2.10, NAMD does support replica exchange protocols
> natively, but the user interface remains Tcl for other reasons,
> primarily flexibility. There is actually support for many more
> algorithms than replica-exchange:
> http://www.ks.uiuc.edu/Research/namd/2.11/ug/node9.html#SECTION00052300000000000000
> <http://www.ks.uiuc.edu/Research/namd/2.11/ug/node9.html#SECTION00052300000000000000>
>
> This can be coupled to the scripting interface of Colvars:
> http://www.ks.uiuc.edu/Research/namd/2.11/ug/node59.html
> <http://www.ks.uiuc.edu/Research/namd/2.11/ug/node59.html>
> http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html
> <http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html>
> For example, bias exchange through Colvars can be done either by the
> specialized Tcl commands (e.g. colvarbias) or by using the
> general-purpose cv command to delete/add/swap biases. More direct
> communication mechanisms between specific biases will be supported in
> the future, to eliminate the overhead of destroying and creating biases.
>
> Lastly, keep in mind that most user tutorials only reflect the
> functionality that was current when they were written, but the only
> up-to-date documentation is a user's guide or reference manual.
>
> Giacomo
>
>
>
> On Wed, Sep 14, 2016 at 4:10 AM, Nicolas Martin
> <nicolasmartin973_at_gmail.com <mailto:nicolasmartin973_at_gmail.com>> wrote:
>
> Dear users,
>
> I am trying to run bias exchange umbrella sampling and read in
> this tutorial
> (http://www.ks.uiuc.edu/Training/Tutorials/science/umbrella/REUS-1D.pdf
> <http://www.ks.uiuc.edu/Training/Tutorials/science/umbrella/REUS-1D.pdf>)
> that there is no official NAMD command or colvar module for doing
> so. I figure out I might as well start with running temperature
> exchange and then change the script to perform bias exchange
> (BEUS) and not temperature exchange but to avoid non productive
> use of my time I wanted to know if any of you had a TCL script to
> do so or a in house tutorial that I could follow.
>
> Running the tutorial mentioned above I'm getting an error as shown
> bellow. Sorry for the super long text but I don't know what is
> relevant to shown you. I'm running on a 32 cores machine. Does any
> of you know what I am doing wrong ?
>
> XXXXX_at_nXXX:~/umbrella_1d$ mpirun -np 16
> NAMD_2.10_Linux-x86_64-netlrts/namd2 +replicas 16 job0.conf
> +stdout output/%d/job0.%d.log
> namd2: machine-common-core.c:863: create_partition_map: Assertion
> `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> namd2: machine-common-core.c:863: create_partition_map: Assertion
> `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> namd2: machine-common-core.c:863: create_partition_map: Assertion
> `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> namd2: machine-common-core.c:863: create_partition_map: Assertion
> `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> namd2: machine-common-core.c:863: create_partition_map: Assertion
> `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> namd2: machine-common-core.c:863: create_partition_map: Assertion
> `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> namd2: machine-common-core.c:863: create_partition_map: Assertion
> `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> namd2: machine-common-core.c:863: create_partition_map: Assertion
> `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> namd2: machine-common-core.c:863: create_partition_map: Assertion
> `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> namd2: machine-common-core.c:863: create_partition_map: Assertion
> `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> namd2: machine-common-core.c:863: create_partition_map: Assertion
> `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in non-SMP mode: numPes 1
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in non-SMP mode: numPes 1
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in non-SMP mode: numPes 1
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in non-SMP mode: numPes 1
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in non-SMP mode: numPes 1
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in non-SMP mode: numPes 1
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in non-SMP mode: numPes 1
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in non-SMP mode: numPes 1
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in non-SMP mode: numPes 1
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in non-SMP mode: numPes 1
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in non-SMP mode: numPes 1
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 30840 on node n304
> exited on signal 6 (Aborted).
> --------------------------------------------------------------------------
> 10 total processes killed (some possibly by mpirun during cleanup)
> namd2: machine-common-core.c:863: create_partition_map: Assertion
> `(_Cmi_numnodes_global % _partitionInfo.numPartitions) == 0' failed.
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in non-SMP mode: numPes 1
> 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.
>
> I finally, I have a more general question to the NAMD community.
> Why is replica exchange not implemented in NAMD and one has to use
> this TCL script ? Isn't it decreasing the performances ? From what
> I have seen it is implement in PLUMED and other codes such as GROMACS.
>
> Cheers, and thank you in advance for you help and advices,
>
> NM
>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213 <tel:%2B1-215-204-4213>
>
> Scholar: http://goo.gl/Q3TBQU
> Personal: http://giacomofiorin.github.io/
> <http://giacomofiorin.github.io/>
> Lab page: https://icms.cst.temple.edu/members.html
> <https://icms.cst.temple.edu/members.html>
>
> /"As computer programmers we have a responsibility to make sure that
> we run the computers instead of the computers running us."/ - Steve
> Oualline
>
>
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