Re: Namd can not be launched for umbrella sample

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Thu Jan 28 2021 - 10:35:45 CST

Hi,

If you read the release note, it clearly states

-- Multi-Copy Algorithm Support --

Multi-copy algorithms (such as replica exchange) require at least one
process per replica, plus a Charm++ build based on "LRTS" (low-level
run-time system). Multi-copy-capable builds include netlrts, verbs, ucx,

and mpi.

V.

On Thu, Jan 28, 2021, 6:42 AM 辛志宏 <xzhfood_at_njau.edu.cn> wrote:

> Dear NAMD,
>
> My computer setup 2 CPU, 28 cores per CPU, 56 cores in all, it works very
> well for multithreading calculation by Amber,
>
> mpirun -np 50 sander.MPI -O -i。。。。。。
>
>
> However, an error occurred when I carried out a umbrella sample example by
> Namd2 according to the tutorial, Namd is a compiled 2020 version and can
> works in a single thread, does it only works when compile a namd from a
> source code?
>
> I will be much appreciate if there is any suggesstion.
>
> mpirun -np 16 +auto-provision namd2 +replicas 16 job0.conf +stdout
> output/%d/job0.%d.log
> The error information is as follows:
>
> Charm++> No provisioning arguments specified. Running with a single PE.
>
> Use +auto-provision to fully subscribe resources or +p1 to
> silence this message.
>
> Charm++: standalone mode (not using charmrun)
>
> Charm++> Running in Multicore mode: 1 threads (PEs)
>
> ------- Partition 0 Processor 0 Exiting: Called CmiAbort ------
>
> Reason: +partitions other than 1 is not allowed for multicore build
>
>
> [0] Stack Traceback:
>
> [0:0] namd2 0x17ce9e7
>
> [0:1] namd2 0x53d375
>
> [0:2] namd2 0x52e7c2
>
> [0:3] libc.so.6 0x2b4a719cf555 __libc_start_main
>
> [0:4] namd2 0x4145f5
>
> --------------------------------------------------------------------------
>
> Primary job terminated normally, but 1 process returned
>
> a non-zero exit code. Per user-direction, the job has been aborted.
>
> --------------------------------------------------------------------------
>
> ------- Partition 0 Processor 0 Exiting: Called CmiAbort ------
>
> Reason: +partitions other than 1 is not allowed for multicore build
>
>
> Charm++> No provisioning arguments specified. Running with a single PE.
>
> Use +auto-provision to fully subscribe resources or +p1 to
> silence this message.
>
> Charm++: standalone mode (not using charmrun)
>
> Charm++> Running in Multicore mode: 1 threads (PEs)
>
> [0] Stack Traceback:
>
> [0:0] namd2 0x17ce9e7
>
> [0:1] namd2 0x53d375
>
> [0:2] namd2 0x52e7c2
>
> [0:3] libc.so.6 0x2b2104bab555 __libc_start_main
>
> [0:4] namd2 0x4145f5
>
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 0 on node bogon exited on
> signal 11 (Segmentation fault).
>
>
> Zhihong Xin,
> Nanjing Agricultural University
>
>

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:10 CST