From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Tue Jul 24 2018 - 16:28:01 CDT
I am looking into the issue with the data you sent me, but nothing like
that came up over here. Like I mentioned before, it does not look like it
has anything to do with the specific QM code you are running.
I'll let you (and the list) know when I figure this out.
--- 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 Tue, 24 Jul 2018 at 11:10, Gerard Rowe <GerardR_at_usca.edu> wrote: > I'm continuing to play with the QM/MM feature trying to get it to work > correctly, and I found that I get the same memory allocation error when > invoking mopac instead of orca. NAMD also exits with the same error message > if launched with charmrun (I also built an MPI-enabled version that gave > the same error, but I'm not certain I launched it correctly). The error > persists with QMSimsPerNode=2 or if both QM regions are combined into one. > > > I'm working with a single, dual-socket node with 48 GB of memory. Has > anyone experienced this issue before? The only reference to this > particular error message I can find is from years ago when million atom MD > simulations were literally running out of memory. > > > Thanks, > > Gerard > > > ------------------------------ > *From:* Gerard Rowe > *Sent:* Wednesday, July 18, 2018 6:18 PM > *To:* namd-l_at_ks.uiuc.edu > *Subject:* QM/MM with Orca: Memory allocation failed > > > 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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