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 oneMol.in...
read
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from oneMol.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 oneMol.in
read
mol pqr oneMol.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 oneMol.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).
The issue was in the apbs/CMakeLists.txt file. The maloc folder was before the declaration of HAVE_MPI_H thus all maloc's preprocessor #if define were evaluating to false. See commit e3db9c1
From one of our users:
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:
My SBATCH script looks like this:
and the input file (oneMol.in) like this:
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).