[gmx-users] Fatal error: Invalid character in digit-only string: '�'
Du, Yu
duyu at sioc.ac.cn
Fri Jul 7 02:26:27 CEST 2017
Yeah, Thanks for the clue.
> -----Original Messages-----
> From: "Mark Abraham" <mark.j.abraham at gmail.com>
> Sent Time: Friday, July 7, 2017
> To: gmx-users at gromacs.org
> Cc:
> Subject: Re: [gmx-users] Fatal error: Invalid character in digit-only string: '�'
>
> 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/
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users
mailing list