From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Tue Feb 02 2021 - 18:35:14 CST
Dear Zhihong,
From your output, it looks like you are running the multicore version. The multicore version supports only single-copy simulation. For running replicas, I would recommend you use the netlrts build of NAMD.
Best regards,
Dave
-- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Jan 28, 2021, at 8:42 PM, 辛志宏 <xzhfood_at_njau.edu.cn> wrote: > > Thank you for your suggestion, I try the following command, however, it fail again > > charmrun namd2 ++local +p16 +replicas 16 job0.conf +stdout output/%d/job0.%d.log > or > charmrun namd2 ++local +p32 +replicas 16 job0.conf +stdout output/%d/job0.%d.log > > Running command: namd2 +p16 +replicas 16 job0.conf +stdout output/%d/job0.%d.log > > Charm++: standalone mode (not using charmrun) > Charm++> Running in Multicore mode: 16 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 0x2aff0e324555 __libc_start_main > [0:4] namd2 0x4145f5 > Segmentation fault (core dumped) > > Zhihong XIn > > 发件人：Victor Kwan <vkwan8_at_uwo.ca> > 发送日期：2021-01-29 00:35:45 > 收件人：NAMD Listserve <namd-l_at_ks.uiuc.edu>,"辛志宏" <xzhfood_at_njau.edu.cn> > 主题：Re: namd-l: Namd can not be launched for umbrella sample > 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 <mailto: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 > >
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