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GiovanniBussi / plumed2

My own public branches for plumed2
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cannot understand line: PYTORCH_MODEL LABEL=deep FILE=model.ptc #4

Open Dong-Shiyu opened 1 year ago

Dong-Shiyu commented 1 year ago 
          :-) GROMACS - gmx mdrun, 2022.4-plumed_2.9.0_dev (-:

Executable: /home/sydong/gromacs/bin/gmx_mpi Data prefix: /home/sydong/gromacs Working dir: /home/sydong/work/plumed_data/masterclass-plumed/2_DeepTICA/1_psi/2_deeptica1 Command line: gmx_mpi mdrun -s input.tpr -deffnm alanine -plumed plumed.dat -ntomp 1 -nsteps 5000000

+++ Loading the PLUMED kernel runtime +++ +++ PLUMED_KERNEL="/home/sydong/plumed2/src/lib/libplumedKernel.so" +++ +++ Loading the PLUMED kernel runtime +++ +++ PLUMED_KERNEL="/home/sydong/plumed2/src/lib/libplumedKernel.so" +++ Reading file input.tpr, VERSION 2020.6-MODIFIED (single precision) Note: file tpx version 119, software tpx version 127 Overriding nsteps with value passed on the command line: 5000000 steps, 1e+04 ps Changing nstlist from 10 to 50, rlist from 1.034 to 1.219

Using 1 MPI process Using 1 OpenMP thread

NOTE: Thread affinity was not set. starting mdrun 'Generated by trjconv : Alanine in vacuum in water t= 0.00000' 5000000 steps, 10000.0 ps.

Program: gmx mdrun, version 2022.4-plumed_2.9.0_dev

Unknown exception: (exception type: N4PLMD6Plumed14ExceptionErrorE)

(core/PlumedMain.cpp:816) void PLMD::PlumedMain::readInputWords(const std::vector<std::__cxx11::basic_string >&) ERROR I cannot understand line: PYTORCH_MODEL LABEL=deep FILE=model.ptc ARG=d_2_5,d_2_6,d_2_7,d_2_9,d_2_11,d_2_15,d_2_16,d_2_17,d_2_19,d_5_6,d_5_7,d_5_9,d_5_11,d_5_15,d_5_16,d_5_17,d_5_19,d_6_7,d_6_9,d_6_11,d_6_15,d_6_16,d_6_17,d_6_19,d_7_9,d_7_11,d_7_15,d_7_16,d_7_17,d_7_19,d_9_11,d_9_15,d_9_16,d_9_17,d_9_19,d_11_15,d_11_16,d_11_17,d_11_19,d_15_16,d_15_17,d_15_19,d_16_17,d_16_19,d_17_19 Maybe a missing space or a typo?

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

WARNING: internal inconsistency in allocated PlumedMain instances (1

Dong-Shiyu commented 1 year ago

My configure file and its output

./configure --prefix=$HOME/temp/plumed \ --enable-rpath \ --disable-mpi \ --enable-libtorch \ --enable-modules=all \ CXXFLAGS="-O3 -D_GLIBCXX_USE_CXX11_ABI=1"\ CPPFLAGS="-I/home/sydong/libtorch/include/torch/csrc/api/include/ -I/home/sydong/libtorch/inculde/ -I/home/sydong/libtorch/include/torch"\ LDFLAGS="-L/home/sydong/libtorch/lib -ltorch_cpu -ltorch -lc10 -Wl,-rpath,/home/sydong/libtorch/lib" ~
~
~
configure: Optional modules are disabled by default configure: Enabling all optional modules checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gfortran... gfortran checking whether we are using the GNU Fortran compiler... yes checking whether gfortran accepts -g... yes configure: Initial CXX: g++ configure: Initial CXXFLAGS: -O3 -D_GLIBCXX_USE_CXX11_ABI=1 configure: Initial CPPFLAGS: -I/home/sydong/libtorch/include/torch/csrc/api/include/ -I/home/sydong/libtorch/inculde/ -I/home/sydong/libtorch/include/torch configure: Initial CFLAGS: -g -O2 configure: Initial LDFLAGS: -L/home/sydong/libtorch/lib -ltorch_cpu -ltorch -lc10 -Wl,-rpath,/home/sydong/libtorch/lib configure: Initial LIBS:
configure: Initial STATICLIBS: configure: Initial LD:
configure: Initial LDSHARED: g++ configure: Initial SOEXT:
checking whether g++ accepts -fPIC... yes checking whether gcc accepts -fPIC... yes checking whether g++ accepts -Wall... yes checking whether g++ accepts -pedantic... yes checking whether g++ accepts -std=c++11... yes checking whether g++ declares c++11 support... yes checking whether C++ library supports C++11 exceptions... yes checking whether g++ can generate dependency file with -MM -MF... yes configure: dependency tracking enabled configure: Now we will check compulsory headers and libraries checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dirent.h usability... yes checking dirent.h presence... yes checking for dirent.h... yes checking for readdir... yes checking whether dgemv can be linked with no library... no checking whether dgemv can be linked with no library... no checking for library containing dgemv... no checking for library containing dgemv... no configure: WARNING: using internal lapack and blas, could be inefficient configure: Now we will check for optional headers and libraries checking libmolfile_plugin.h usability... no checking libmolfile_plugin.h presence... no checking for libmolfile_plugin.h... no configure: WARNING: cannot enable PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS configure: WARNING: using internal molfile_plugins, which only support dcd/xtc/trr/trj/crd files checking for dlopen in -ldl... yes checking for g++ option to support OpenMP... -fopenmp checking whether architecture is X86/X64... yes checking for library containing clock_gettime... none required configure: Enabling embedded asmjit checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking for library containing regcomp... none required checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for library containing dlopen... none required checking RTLD_DEFAULT without extra libs... yes checking for unistd.h... (cached) yes checking for library containing chdir... none required checking subprocess without extra libs... yes checking for unistd.h... (cached) yes checking for library containing getcwd... none required checking cstdio usability... yes checking cstdio presence... yes checking for cstdio... yes checking for library containing popen... none required checking execinfo.h usability... yes checking execinfo.h presence... yes checking for execinfo.h... yes checking for library containing backtrace... none required checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for library containing gzopen... -lz checking for library containing cblas_dgemv... no configure: WARNING: cannot enable PLUMED_HAS_GSL checking fftw3.h usability... no checking fftw3.h presence... no checking for fftw3.h... no configure: WARNING: cannot enable __PLUMED_HAS_FFTW checking for python... python configure: Python executable is python checking support for required python modules (python3, setuptools, cython)... yes checking whether g++ accepts -std=c++14... yes checking libtorch without extra libs... no checking libtorch with -ltorch_cpu... no checking libtorch with -lc10... yes configure: Release mode, adding -DNDEBUG configure: Special settings for dynamic libraries on Linux configure: Dynamic library extension is 'so' configure: LDSHARED and LDFLAGS need special flags checking whether LDFLAGS can contain -rdynamic... yes checking whether LDFLAGS can contain -Wl,-Bsymbolic... yes configure: Using LDSHARED='g++ -shared' configure: Using LDFLAGS='-L/home/sydong/libtorch/lib -ltorch_cpu -ltorch -lc10 -Wl,-rpath,/home/sydong/libtorch/lib -rdynamic -Wl,-Bsymbolic' checking whether LDSHARED can create dynamic libraries... yes checking for readelf... found configure: Enabling RUNPATH checking for doxygen... no configure: Manuals will not be generated configure: A PDF version of the manual will not be generated checking whether a program can be run on this machine... yes configure: PLUMED seems to be configured properly! configure: ** checking whether C++ objects can be grouped with ld -r -o... yes checking whether static libraries can be created with ar cr... yes checking whether static-object constructors can be linked from a static archive... yes configure: I will now check if C++ objects can be linked by C/Fortran compilers configure: This is relevant if you want to use plumed patch --static on a non-C++ code checking whether C can link a C++ object... no checking whether C can link a C++ object with library -lstdc++... yes checking whether FORTRAN can link a C++ object... yes checking for pkg-config... /usr/bin/pkg-config configure: bash-completion is not installed or it is installed on a different prefix configure: bash completion for plumed will not be installed configure: PLUMED will be installed using the following paths: configure: prefix: /home/sydong/temp/plumed configure: exec_prefix: ${prefix} configure: bindir: ${exec_prefix}/bin configure: libdir: ${exec_prefix}/lib configure: includedir: ${prefix}/include configure: datarootdir: ${prefix}/share configure: datadir: ${datarootdir} configure: docdir: ${prefix}/share/doc/plumed configure: htmldir: ${docdir} configure: Executable will be named plumed configure: As of PLUMED 2.5, you cannot change paths anymore during "make install" configure: Please configure and make clean to change the prefix configure: WARNING: Bash completion for plumed will not be installed, please add the following two lines to your bashrc configure: WARNING: _plumed() { eval "$(plumed --no-mpi completion 2>/dev/null)";} configure: WARNING: complete -F _plumed -o default plumed configure: **** PLUMED will be compiled without MPI configure: creating ./config.status config.status: creating Makefile.conf config.status: creating sourceme.sh config.status: creating stamp-h