From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Thu Jul 19 2018 - 09:51:25 CDT
This looks more like a problem in NAMD than in ORCA, since the memory
allocation error is coming from within NAMD.
What version of NAMD are you using?
I see you are asking for one simulation per node, but seem to have defined
two QM regions, that should not be a problem, bu could you try using two
simulations per node?
Last but not least, could you provide your test case? (PDB, PSF, and
parameter set being used)
--- Marcelo Cardoso dos Reis Melo PhD Candidate Luthey-Schulten Group University of Illinois at Urbana-Champaign crdsdsr2_at_illinois.edu +1 (217) 244-5983 On Wed, 18 Jul 2018 at 17:21, Gerard Rowe <GerardR_at_usca.edu> wrote: > I'm having trouble getting hybrid QM/MM to run properly on my Linux > machine. Every time I try to run a QM job using orca, namd dies with the > message: > > > ... > Info: Startup phase 15 took 0.000211954 s, 194.461 MB of memory in use > Info: Finished startup at 8.24108 s, 194.461 MB of memory in use > > TCL: Minimizing for 100 steps > FATAL ERROR: Memory allocation failed on processor 0. > > .. > > > The relevant part of the configuration file: > QMSimsPerNode 1 > QMBaseDir /dev/shm > qmConfigLine "! ZINDO/1 ENGRAD" > qmConfigLine "%output PrintLevel Mini Print\[P_Mulliken \] 1 > Print\[P_AtCharges_M\] end" > qmMult 1 6 > qmCharge 1 2.00 > qmMult 2 6 > qmCharge 2 2.00 > qmSoftware orca > qmExecPath /usr/local/orca/orca_4_0_0_2_linux_x86-64/orca > > I have defined two QM regions with 83 atoms each. I have no problem > running namd2 or orca by themselves. I find it hard to believe that this > semiempirical job is running out of memory on a system with 48 GB of RAM > (569 MB in use at the start of the the job). This error occurs regardless > of the number of processors > > Is there some way to find out how much memory the program is attempting to > allocate? Or is there a common reason this error may arise? > > Thanks, > Gerard > University of South Carolina Aiken > > >
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