[gmx-users] Fatal error: Invalid character in digit-only string: '�'
Mark Abraham
mark.j.abraham at gmail.com
Thu Jul 6 22:35:27 CEST 2017
Hi,
Yes. And it looks like you've copied and pasted a "smart quote" character
produced from some fancy editor. If that's a tutorial or user guide, please
ask them to fix it ;-)
Mark
On Thu, 6 Jul 2017 17:25 Hermann, Johannes <J.Hermann at lrz.tu-muenchen.de>
wrote:
> Hey Yu
>
> Try:
>
> gmx mdrun -v -ntmpi 8 -gpu_id 1111 -deffnm nvt
>
> So the same command you used, but _without_ the quotation marks. That is
> what the error tells you.
>
> Best
> Johannes
> On 06.07.2017 16:52, Du, Yu wrote:
> > 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.
> >
> >
> > Yu
> >
> >
> > =======================================================
> > [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
> > -------------------------------------------------------
> > =======================================================
> > LOG FILE:
> >
> > 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
> > =======================================================
> >
> >
>
> --
> ______________________________________
> *Technische Universität München*
> *Johannes Hermann, M.Sc.*
> Lehrstuhl für Bioverfahrenstechnik
> Boltzmannstr. 15
> D-85748 Garching
> Tel: +49 8928915730
> Fax: +49 8928915714
>
> Email: j.hermann at lrz.tum.de
> http://www.biovt.mw.tum.de/
>
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