From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Mon Oct 26 2020 - 11:04:02 CDT
Hi Zeynab,
If you wanted two different simulations to execute independently within the
queuing system, I don't think you'd use the +replicas options at
all. +replicas 2 means that NAMD will run the .namd file twice under the
same process (so that if one crashes, the whole simulation goes down).
Based on the links you pointed to, +replicas 2 would write the same set of
files. The trick to setting up multiple replicas under the same process is
to use "myReplica" within the NAMD configuration file (
https://www.ks.uiuc.edu/Research/namd/2.14/ug/node9.html#SECTION00052300000000000000)
to say what replica you are, and use that to setup the output files
accordingly.
-Josh
On Mon, Oct 26, 2020 at 6:39 AM zeynab hosseini <hosseinizeynab93_at_gmail.com>
wrote:
> Dear all,
>
> I want to perform multiple walker/well-tempered (MWWT) metadynamics
> through several replicas. I followed the example test under this link
> <https://github.com/Colvars/colvars/tree/master/namd/tests/library/011_multiple_walker_mtd>,
> creating the namd (.namd file) and collective variable (.in file)
> configuration files for each replicas (e.g, rep1.namd, rep1.in and
> rep2.namd, rep2.in and so on ). From NAMD user guide
> <https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_meta_mr>
> I understood that there are two way to run MWWT metadynamics replicas, (1)
> as a bundle (i.e. a single job in a cluster’s queueing system) or (2) as
> fully independent runs (i.e. as separate jobs for the queueing system). I
> think I know how to run the second one (please correct me if I'm wrong):
>
> charmrun /usr/local/bin/namd2 ++local +p8 +replicas 2 test.rep1.namd >
> test.rep1.log
> charmrun /usr/local/bin/namd2 ++local +p8 +replicas 2 test.rep2.namd >
> test.rep2.log
>
> I tested the 2nd case and it worked. But I don't know how to perform the
> first one. i.e. to run a single job and to get all replicas proceed
> simultaneously. Would that be possible to guide me? (I assume that it is
> related to the common.tcl provided in the example test
> <https://github.com/Colvars/colvars/blob/master/namd/tests/library/011_multiple_walker_mtd/common.tcl> but
> I don't know the proper commands to launch it).
>
> All the best,
> Zeynab
>
>
>
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