[gmx-users] PRACE benchmarks

[Adam Huffman]

Hello

I've been trying to run the PRACE benchmarks on a new cluster:

http://www.prace-ri.eu/ueabs/#GROMACS

and this is the command-line I've been running:

mpirun --mca plm_base_verbose 10 --debug-daemons gmx_mpi mdrun -s
ion_channel.tpr -maxh 0.50 -resethway -noconfout -nsteps 10000 -g
logfile-${SLURM_JOB_ID}

This was running over several days, so I tried again, with 1000 steps,
and then even with 10 steps, but the jobs are running seemingly
without doing anything:

sstat -j 1511 --format
Nodelist,NTasks,AveCPU,AveDiskRead,AveDiskWrite,AveRSS,AvePages
            Nodelist   NTasks     AveCPU  AveDiskRead AveDiskWrite
AveRSS   AvePages
-------------------- -------- ---------- ------------ ------------
---------- ----------
         ca[127-157]        0  00:00.000            0            0
     0          0

I'm certainly no expert on GROMACS so I would appreciate it if someone
could point out any glaring errors in that mdrun invocation. (I added
the MPI debug flags for separate reasons).

The logfile shows:

Command line:
  gmx_mpi mdrun -v -s lignocellulose-rf.BGQ.tpr -maxh 0.50 -resethway
-noconfout -nsteps 10 -g logfile-B-1-1511

GROMACS version:    VERSION 5.1.2
Precision:          single
Memory model:       64 bit
MPI library:        MPI
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:        disabled
OpenCL support:     disabled
invsqrt routine:    gmx_software_invsqrt(x)
SIMD instructions:  AVX_256
FFT library:        fftw-3.3.4-sse2
RDTSCP usage:       enabled
C++11 compilation:  enabled
TNG support:        enabled
Tracing support:    disabled
Built on:           Thu 30 Jun 07:39:10 BST 2016
Built by:           huffmaa at login000.camp.thecrick.org [CMAKE]
Build OS/arch:      Linux 3.10.0-327.18.2.el7.x86_64 x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:    Intel Xeon E312xx (Sandy Bridge)
Build CPU family:   6   Model: 42   Stepping: 1
Build CPU features: aes apic avx clfsh cmov cx8 cx16 lahf_lm mmx msr
pclmuldq popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler:
/camp/apps/eb/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/bin/mpicc GNU
4.9.3
C compiler flags:    -mavx   -fopenmp -O2 -march=native -Wundef
-Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter
-O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
-Wno-array-bounds
C++ compiler:
/camp/apps/eb/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/bin/mpicxx GNU
4.9.3
C++ compiler flags:  -mavx   -std=c++0x -fopenmp -O2 -march=native
-Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall
-Wno-unused-function  -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast  -Wno-array-bounds
Boost version:      1.60.0 (external)

and nothing after that.

strace of one of the processes shows:

[pid  1374] poll([{fd=5, events=POLLIN}, {fd=12, events=POLLIN},
{fd=15, events=POLLIN}], 3, 0) = 0 (Timeout)


Cheers,
Adam