[apbs-users] Help with SLURM and APBS

[Grant Kemp]

Hi everyone,

I was wondering if anyone has any experience with using the SLURM workload manager (https://slurm.schedmd.com/) along with APBS? I have installed an MPI-compiled APBS-1.4.2 and it works just fine for small tests when I run it with the mg-auto, but when I use mg-para I get:

Parsing input file NC_from3J00.in...

read

Parsed input file.

Got paths for 1 molecules

Reading PQR-format atom data from NC_from3J00.pqr.

NOsh_setupMGPARA:  There are too few processors (1) to satisfy requirements (4)

/var/spool/slurmd/job12336001/slurm_script: line 9:  6603 Segmentation fault  (core dumped) apbs NC_from3J00.in

My SBATCH script looks like this:

#! /bin/bash -l

#

#SBATCH -A snic2016-7-97

#SBATCH -p core -n 4 -C mem64GB

#SBATCH -t 60:00

#SBATCH -J NC_test_2016_11_29

#

module load pgi openmpi

apbs NC_from3J00.in

and the input file (NC_from3J00.in) like this:

read

    mol pqr NC_from3J00.pqr

end

elec

    mg-para

    ofrac 0.1

    pdime 2 2 1

    dime 97 129 129

    cglen 284.7058 90.9908 79.7538

    fglen 187.4740 73.5240 66.9140

    cgcent mol 1

    fgcent mol 1

    mol 1

    lpbe

    bcfl sdh

    pdie 2.0000

    ion charge 1 conc 0.150 radius 1.02

    ion charge -1 conc 0.150 radius 1.81

    sdie 78.5400

    srfm smol

    chgm spl2

    sdens 10.00

    srad 1.40

    swin 0.30

    temp 298.15

    calcenergy total

    calcforce no

    write pot dx NC_from3J00.pqr

end

print elecEnergy 1 end

quit

My current thinking is that the SLURM and APBS are not communicating properly (i.e. SLURM is supposed to be allocating 4 cores to the APBS calculations, but APBS only sees 1). Eventually I want to do calculations on the entire ribosome (with various mutations). This will obviously be very computationally heavy so I want to make sure that the calculation is being properly distributed before I submit a larger job. Thanks for the help. 

Best,

Grant Kemp

Postdoc with Gunnar von Heijne

Dept of Biochemistry and Biophysics, Stockholm University

[Baker, Nathan]

Hi Grant –

 

I’m Cc’ing Keith, Dave, and Juan for their help with this.

 

Thanks,

 

-- 

Nathan Baker

Advanced Computing, Mathematics, and Data Division — Pacific Northwest Natl Lab

Division of Applied Mathematics — Brown University

+1-509-375-3997 — http://go.usa.gov/xWY9Y