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Hello Yun Lin-- > > > >> > >> ? ? I am using xplor-nih ( Xplor-nih version used 2.21, system RedHat > >> Linux 8.0 ) > >> for ensemble-based structure calculation of Intrinsic disordered > >> protein and I have several problems: > >> 1. Setting threads during parallel calculation > >> ? ? I had used the following command to set threads per node: > >> ? ? xplor -py ensemble.py -o 1.out -parallel -machines machinefile > >> -num_threads 2 > >> ? ? After generating the extended structure, there were always 4 > >> threads (the ensemble size is 4) threads per node, while we have only > >> two CPUs per node. How to set threads number so that there are 2 > >> threads per node? > > > > this depends on your machinefile: you need to make sure that each node > > appears only once in this file. Also, if you are using pbs you might try > > pbsxplor. > I had checked my machinefile, it was right. If a node name appears > twice, there would be 8 threads of xplor-nih in the node. And, our > cluster dose not using PBS, it is just a joint of distributed > computers, each node has its own hard-disk and memory. We can access > them using 'rsh' without password, and all the nodes share a public > disk via NFS. ok. There is a little misunderstanding. With EnsembleSimulation calculations, the number of Xplor-NIH *processes* is fixed at the ensemble size. The -num_threads argument changes how how many are run at a single time. If you have two nodes, you will want to specify - -num_threads 2: that will cause the job to get done twice as fast compared to running with -num_threads 1. Now, the machine load will not reliably report the machine's performance, i.e. uptime may report a load > 2, but with num_threads 2 only two threads are running at a single time. You might try looking at top when running num_threads=1,2. I think things are working fine for you. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkrwOCIACgkQPK2zrJwS/laoegCfcb53X4sn2d2qtm2/2vQbRDjv g/oAnRqtvtEItHpBBfVrdnVP8UOSymU5 =Gjtq -----END PGP SIGNATURE-----
