[gmx-users] Fatal error: Invalid character in digit-only string: '�'

Du, Yu duyu at sioc.ac.cn
Thu Jul 6 16:52:46 CEST 2017

Dear Gromacs Users, 

I'm using the Gromacs 2016.3.  I'm repeating the Tutorial 5: Protein-Ligand Complex.
If I use `gmx mdrun -deffnm nvt`, Gromacs will not show any error.

If gmx mdrun -quiet -nt 8 -ntomp 2 -gpu_id “1111” -deffnm nvt, I will get the following errors.

Is this a bug or the some error with the installment.
I use gcc-4.9.4 and cuda 7.0 and part of nvt.log is at the end of this email. 
The compile I used is `cmake .. -DCMAKE_C_COMPILER=gcc-4.9.4 -DCMAKE_CXX_COMPILER=g++-4.9.4 -DCMAKE_C_FLAGS="-Wl,-rpath -Wl,/home/duyu/software/gcc-4.9.4/lib64" -DGMX_OPENMP=ON -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.0 -DCMAKE_INSTALL_PREFIX=/home/duyu/software/gromacs-2016.3 -DREGRESSIONTEST_PATH=/home/duyu/src/gromacs-2016.3suit/regressiontests-2016.3 -DGMX_FFT_LIBRARY=fftw3 -DGMX_SIMD=AVX_256 -DFFTWF_LIBRARY=/home/duyu/software/fftw-3.3.6/lib/libfftw3f.so -DFFTWF_INCLUDE_DIR=/home/duyu/software/fftw-3.3.6/include`

Thanks for any information about the error, my nvt.log file and the compile command parameters.


[duyu at gpu-new 3htb_for_gromacs]$ gmx mdrun -v -ntmpi 8 -gpu_id “1111” -deffnm nvt

Back Off! I just backed up nvt.log to ./#nvt.log.3#

Running on 1 node with total 20 cores, 40 logical cores, 4 compatible GPUs
Hardware detected:
  CPU info:
    Vendor: Intel
    Brand:  Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
    SIMD instructions most likely to fit this hardware: AVX2_256
    SIMD instructions selected at GROMACS compile time: AVX_256

  Hardware topology: Basic
  GPU info:
    Number of GPUs detected: 4
    #0: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
    #1: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
    #2: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible
    #3: NVIDIA Tesla K40m, compute cap.: 3.5, ECC:  no, stat: compatible

Compiled SIMD instructions: AVX_256, GROMACS could use AVX2_256 on this machine, which is better.

Reading file nvt.tpr, VERSION 2016.3 (single precision)
Changing nstlist from 10 to 40, rlist from 1.4 to 1.472

Program:     gmx mdrun, version 2016.3
Source file: src/gromacs/utility/cstringutil.cpp (line 583)

Fatal error:
Invalid character in digit-only string: '�'

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

GROMACS version:    2016.3
Precision:          single
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:        CUDA
SIMD instructions:  AVX_256
FFT library:        fftw-3.3.6-pl2-sse2-avx
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
Built on:           Tue Jul  4 17:23:23 CST 2017
Built by:           duyu at gpu-new [CMAKE]
Build OS/arch:      Linux 2.6.32-431.el6.x86_64 x86_64
Build CPU vendor:   Intel
Build CPU brand:    Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
Build CPU family:   6   Model: 63   Stepping: 2
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler:         /home/duyu/software/gcc-4.9.4/bin/gcc-4.9.4 GNU 4.9.4
C compiler flags:    -mavx   -Wl,-rpath -Wl,/home/duyu/software/gcc-4.9.4/lib64  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
C++ compiler:       /home/duyu/software/gcc-4.9.4/bin/g++-4.9.4 GNU 4.9.4
C++ compiler flags:  -mavx    -std=c++0x   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  
CUDA compiler:      /usr/local/cuda-7.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2015 NVIDIA Corporation;Built on Mon_Feb_16_22:59:02_CST_2015;Cuda compilation tools, release 7.0, V7.0.27
CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-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_52,code=compute_52;-use_fast_math;-ccbin=/home/duyu/software/gcc-4.9.4/bin/gcc-4.9.4;;;-Xcompiler;,-mavx,,,,,,;-Xcompiler;-O3,-DNDEBUG,-funroll-all-loops,-fexcess-precision=fast,,; 
CUDA driver:        7.0
CUDA runtime:       7.0

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