[gmx-users] PRACE benchmarks

[Mark Abraham]

Hi,

Looks like your MPI setup is broken. So far, I have only heard of people
having problems when using OpenMPI 1.10.x, even the latest patch release.

Mark

On Thu, Jul 14, 2016 at 11:52 AM Adam Huffman <adam.huffman at gmail.com>
wrote:

> 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
> --
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