From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Thu Apr 16 2020 - 11:33:00 CDT
Is the namd2 executable an MPI executable? It looks like its running
multiple independent namd instances, which is what you get when you try and
run the standard multicore with MPI.
-Josh
On Thu, Apr 16, 2020 at 3:13 AM 辛志宏 <xzhfood_at_njau.edu.cn> wrote:
> Dear all,
> I installed the NAMD in paralle according to the installation tutorial and
> tested successfully with 16 threads using the following command:
> mpirun -np 16 ./namd2 ./apoa1/apoa1.namd
> However, there was a problem in the calculation of the replica-exchange
> umbrella sampling tutorial provided by NAMD. I would like to ask how to
> solve the problem. Thank you in advanced.
>
> I also looked through the namd mailing list and find several topotic about
> the replica-exchange umbrella, but all of them failed for the error.
>
>
> mkdir output; cd output
> mkdir {0..15}; cd ..
> $ mpirun -np 16 namd2 +replicas 16 job0.conf+stdout output/%d/job0.%d.log
>
> Charm++> No provisioning argumentsspecified. Running with a single PE.
> Use +auto-provision to fully subscribe resources or +p1 to silence
> thismessage.
> Charm++: standalone mode (not using charmrun)
> ------- Partition 0 Processor 0 Exiting:Called CmiAbort ------
> Reason: +partitions other than 1 is notallowed for multicore build
> Charm++> Running in Multicore mode: 1threads (PEs)
> [0] Stack Traceback:
> [0:0]namd2 0x14fcc37
> [0:1]namd2 0x516d93
> [0:2] namd2 0x50c772
> [0:3]libc.so.6 0x2afb01d1b505 __libc_start_main
> [0:4]namd2 0x4118f5
> Charm++> No provisioning argumentsspecified. Running with a single PE.
> Use +auto-provision to fully subscribe resources or +p1 to silence
> thismessage.
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in Multicore mode: 1threads (PEs)
> ------- Partition 0 Processor 0 Exiting:Called CmiAbort ------
> Reason: +partitions other than 1 is notallowed for multicore build
> [0] Stack Traceback:
> [0:0]namd2 0x14fcc37
> [0:1]namd2 0x516d93
> [0:2]namd2 0x50c772
> [0:3]libc.so.6 0x2b28394c7505 __libc_start_main
> [0:4]namd2 0x4118f5
> Charm++> No provisioning argumentsspecified. Running with a single PE.
> Use +auto-provision to fully subscribe resources or +p1 to silence
> thismessage.
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in Multicore mode: 1threads (PEs)
> ------- Partition 0 Processor 0 Exiting:Called CmiAbort ------
> Reason: +partitions other than 1 is not allowedfor multicore build
>
>
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