From: 辛志宏 (xzhfood_at_njau.edu.cn)
Date: Thu Jan 28 2021 - 05:41:53 CST
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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