Hi Mark,
Here you are:
:-) GROMACS - gmx, 2019.2 (-:
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Emile Apol Rossen Apostolov Paul Bauer Herman J.C.
Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu
Virolainen
Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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GROMACS: gmx, version 2019.2
Executable: redacted/gmx2019.2_gpu/gromacs-2019.2/build/bin/./gmx
Data prefix: redacted/gmx2019.2_gpu/gromacs-2019.2 (source tree)
Working dir: redacted/gmx2019.2_gpu/gromacs-2019.2/build/bin
Command line:
gmx -version
GROMACS version: 2019.2
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: CUDA
SIMD instructions: AVX2_256
FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: hwloc-1.11.0
Tracing support: disabled
C compiler: /usr/bin/cc GNU 5.4.0
C compiler flags: -mavx2 -mfma -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast
C++ compiler: /usr/bin/c++ GNU 5.4.0
C++ compiler flags: -mavx2 -mfma -std=c++11 -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast
CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda
compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on
Fri_Feb__8_19:08:17_PST_2019;Cuda compilation tools, release 10.1, V10.1.105
CUDA compiler
flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;-D_FORCE_INLINES;;
;-mavx2;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
CUDA driver: 10.10
CUDA runtime: 10.10
On 4/20/2019 12:38 PM, Mark Abraham wrote:
Hi,
Your experience looks unusual. What does gmx -version report?
Mark
On Fri., 19 Apr. 2019, 03:02 Alex, <nedoma...@gmail.com> wrote:
Can someone please confirm that my emails indeed reach this board? :)
Thank you.
On 4/16/2019 6:31 PM, Alex wrote:
Okay, more interesting things are happening.
At the end of 'make' I get a bunch of things like
.................. nbnxn_cuda.cu <http://nbnxn_cuda.cu>(373): warning:
variable "dim_grid" was declared but never referenced
-bash: syntax error near unexpected token `373'
More errors during 'make check' right after " Building NVCC (Device)
object
src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o"
then continues as if nothing happened.
Finally, fails test #42 with what appears to be sarcasm:
"...
Thanx for Using GROMACS - Have a Nice Day
Mdrun cannot use the requested (or automatic) number of ranks,
retrying with 8.
Abnormal return value for ' gmx mdrun -nb cpu -notunepme
mdrun.out 2>&1' was 1
Retrying mdrun with better settings...
Abnormal return value for ' gmx mdrun -ntmpi 1 -notunepme >mdrun.out
2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in distance_restraints for
distance_restraints
Abnormal return value for ' gmx mdrun -ntmpi 6 -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...
Abnormal return value for ' gmx mdrun -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron
Re-running orientation-restraints using CPU-based PME
Abnormal return value for ' gmx mdrun -ntmpi 1 -pme cpu -notunepme
mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in
orientation-restraints/pme-cpu for orientation-restraints-pme-cpu
Re-running pull_geometry_angle using CPU-based PME
Re-running pull_geometry_angle-axis using CPU-based PME
Re-running pull_geometry_dihedral using CPU-based PME
3 out of 55 complex tests FAILED"
Then finally quits for good. Your suggestions will be highly appreciated.
Thank you,
Alex
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