From: 辛志宏 (xzhfood_at_njau.edu.cn)
Date: Thu Apr 16 2020 - 19:40:50 CDT
Thank you Josh for your reply.
Yes,this is the point you said. Is there the case for namd or openmpi installation issue or other reasons?
What should I do to solve the issue?
Thank you for your kinkly help.
Tianyou.
Nanjing Agricultural University
-----原始邮件-----
发件人:"Josh Vermaas" <joshua.vermaas_at_gmail.com>
发送时间:2020-04-17 00:33:00 (星期五)
收件人: "NAMD list" <namd-l_at_ks.uiuc.edu>, "辛志宏" <xzhfood_at_njau.edu.cn>
抄送:
主题: Re: namd-l: Issue about replica-exchangeumbrella sampling by 16 threads
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
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:08 CST