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
