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Bug #2554

write lowest energy coordinates fail with CG

Added by Carlo Camilloni 4 days ago. Updated 3 days ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Step 405, Epot=-8.872469e+04, Fnorm=7.410e+00, Fmax=7.881e+01 (atom 3770)

writing lowest energy coordinates.

-------------------------------------------------------
Program: gmx mdrun, version 2018.2
Source file: src/gromacs/mdlib/minimize.cpp (line 582)
Function: void write_em_traj(FILE *, t_commrec *, gmx_mdoutf_t, gmx_bool, gmx_bool, const char *, gmx_mtop_t *, t_inputrec *, gmx_int64_t, em_state_t *, t_state *, ObservablesHistory *)

Assertion failed:
Condition: bX
The code below assumes that (with domain decomposition), x is collected to
state_global in the call above.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

topol.tpr (219 KB) topol.tpr Carlo Camilloni, 06/15/2018 08:43 AM

History

#1 Updated by Carlo Camilloni 3 days ago

More info: this happened on my Mac with native clang compilers and open-mpi 2.1.3
running it with or without -nb cpu and in scalar

gmx_mpi mdrun -v

GROMACS version: 2018.1
Precision: single
Memory model: 64 bit
MPI library: MPI
OpenMP support: disabled
GPU support: OpenCL
SIMD instructions: AVX2_256
FFT library: fftw-3.3.7-sse2-avx
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: hwloc-1.11.0
Tracing support: disabled
Built on: 2018-03-22 13:43:21
Built by: _biodip.unimi.it [CMAKE]
Build OS/arch: Darwin 17.4.0 x86_64
Build CPU vendor: Intel
Build CPU brand: Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz
Build CPU family: 6 Model: 94 Stepping: 3
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc AppleClang 9.0.0.9000039
C compiler flags: -march=core-avx2 -Wno-unknown-pragmas -O3 -DNDEBUG
C++ compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ AppleClang 9.0.0.9000039
C++ compiler flags: -march=core-avx2 -std=c++11 -Wno-unknown-pragmas -O3 -DNDEBUG
OpenCL include dir: /System/Library/Frameworks/OpenCL.framework
OpenCL library: /System/Library/Frameworks/OPENCL.framework
OpenCL version: 1.2

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