From: 辛志宏 (xzhfood_at_njau.edu.cn)
Date: Thu Jan 28 2021 - 20:42:33 CST
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> 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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