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Hi again, The program is actually using 4 threads (as from the stdout). The fact top runs at 200% means that your threads are hampered by something else. This could for example be the reading of particles from the hard disk, which can become a bottle neck. Also: how many cores does nsit-dhcp-148-090.bsd.uchicago.edu have? You're running 4 MPI slaves, each with 4 threads on it. The master also takes 1 core. Therefore, your machine should have 17 cores to do everything you ask for. If it has fewer cores, then they'll just be in each others way. HTH, Sjors On 04/27/2016 08:18 PM, Baru Reddy wrote: > Hi Sjors, > 'top' says each mpi process is running at ~200%. This is the criteria by which I say it is only using 2 threads is based on the ~200%. The command I use and initial output I get is shown below. > > mpirun -n 5 ~/Downloads/relion-1.4/bin/relion_refine_mpi --o Class3D/run1_ct5 --continue Class3D/run1_it005_optimiser.star --iter 25 --tau2_fudge 4 --solvent_mask proteasome_mask_150.mrc --oversampling 1 --healpix_order 3 --offset_range 5 --offset_step 2 --j 4 & > > [reddybg@nsit-dhcp-148-090 gauto]$ === RELION MPI setup === > + Number of MPI processes = 5 > + Number of threads per MPI process = 4 > + Total number of threads therefore = 20 > + Master (0) runs on host = nsit-dhcp-148-090.bsd.uchicago.edu > + Slave 1 runs on host = nsit-dhcp-148-090.bsd.uchicago.edu > + Slave 2 runs on host = nsit-dhcp-148-090.bsd.uchicago.edu > + Slave 3 runs on host = nsit-dhcp-148-090.bsd.uchicago.edu > + Slave 4 runs on host = nsit-dhcp-148-090.bsd.uchicago.edu > > Cheers,Bharat ReddyPost DocUniversity of Chicago > > From: Sjors Scheres <[log in to unmask]> > To: Baru Reddy <[log in to unmask]> > Cc: [log in to unmask] > Sent: Wednesday, April 27, 2016 2:08 PM > Subject: Re: [ccpem] Stuck at 2 Threads per MPI Process > > Hi Bharat, > --j N should always launch N threads. You'll only see them as 1 process in > 'top', but it may run up to ~N00%. Why do you say relion launches only 2 > threads? How do you see this? Does it say so in the stdout? > S > >> Hi Everyone, >> Currently we are trying to mobilize the power of threads as our >> refinements have become more memory intensive and we have hit a limit with >> the number of MPI processes we can deploy. The problem is that however >> many threads I tell relion_refine_mpi to use (-j X where X is >> 4,8,16,etc.), it only uses two threads. Is there a setting I am missing, a >> variable I am failing to define, or is this a limit of relion_refine_mpi . >> Cheers,Bharat ReddyPost DocUniversity of Chicago > -- Sjors Scheres MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. tel: +44 (0)1223 267061 http://www2.mrc-lmb.cam.ac.uk/groups/scheres