problems in installing plumed-2.7 in linux Mint 20.1

[Sergio Sebastian]

Dear plumed users

 I am having problems in installing plumed 2.7 in linux mint 20.1. My pc is a Intel i7-7700 (x86_64), with a graphics cards, GeForce GTX 1080 Ti.

I need to install plumed taking advantage of the full potential of the graphics card

I am following the instructions:

......................................................................................................................................................

./configure LDFLAGS="-L/run/timeshift/backup/usr/local/include/plumed/molfile" CPPFLAGS="-I/run/timeshift/backup/usr/local/include -I/run/timeshift/backup/usr/local/include/plumed/molfile"  --prefix=$HOME/opt_plumed --enable-af_cuda=yes --enable-af_cpu=yes --enable-af_ocl=yes --enable-modules=all
configure: Optional modules are disabled by default
configure: Enabling all optional modules
checking for mpic++... mpic++
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 mpic++ 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:         mpic++
configure: Initial CXXFLAGS:    -O3
configure: Initial CPPFLAGS:    -I/run/timeshift/backup/usr/local/include -I/run/timeshift/backup/usr/local/include/plumed/molfile
configure: Initial CFLAGS:      -g -O2
configure: Initial LDFLAGS:     -L/run/timeshift/backup/usr/local/include/plumed/molfile
configure: Initial LIBS:        
configure: Initial STATIC_LIBS:
configure: Initial LD:          
configure: Initial LDSHARED:    mpic++
configure: Initial SOEXT:       
checking whether mpic++ accepts -fPIC... yes
checking whether gcc accepts -fPIC... yes
checking whether mpic++ accepts -Wall... yes
checking whether mpic++ accepts -pedantic... yes
checking whether mpic++ accepts -std=c++11... yes
checking whether mpic++ declares c++11 support... yes
checking whether C++ library supports C++11 exceptions... yes
checking whether mpic++ can generate dependency file with -MM -MF... no
configure: WARNING: dependencies tracking disabled - always make clean before make
configure: Now we will check compulsory headers and libraries
checking how to run the C++ preprocessor... mpic++ -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_... -lblas
checking for library containing dsyevr_... no
configure: WARNING: using internal lapack, could be inefficient
checking whether sdot returns float... yes
configure: Now we will check for optional headers and libraries
checking libmolfile_plugin.h usability... yes
checking libmolfile_plugin.h presence... yes
checking for libmolfile_plugin.h... yes
checking for library containing molfile_dcdplugin_init... 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 mpi.h usability... yes
checking mpi.h presence... yes
checking for mpi.h... yes
checking for library containing MPI_Init... none required
checking for mpic++ option to support OpenMP... -fopenmp
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 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... none required
checking gsl/gsl_vector.h usability... yes
checking gsl/gsl_vector.h presence... yes
checking for gsl/gsl_vector.h... yes
checking for library containing gsl_vector_alloc... -lgsl
checking xdrfile/xdrfile_xtc.h usability... yes
checking xdrfile/xdrfile_xtc.h presence... yes
checking for xdrfile/xdrfile_xtc.h... yes
checking for library containing write_xtc... -lxdrfile
checking fftw3.h usability... yes
checking fftw3.h presence... yes
checking for fftw3.h... yes
checking for library containing fftw_execute... -lfftw3
checking for python... python
configure: Python executable is python
checking support for required python modules (python3, setuptools, cython, subprocess, os, shutil)... yes
checking arrayfire.h usability... yes
checking arrayfire.h presence... yes
checking for arrayfire.h... yes
checking for library containing af_is_double... no
configure: WARNING: cannot enable __PLUMED_HAS_ARRAYFIRE
checking for arrayfire.h... (cached) yes
checking for library containing af_is_double... (cached) no
configure: WARNING: cannot enable __PLUMED_HAS_ARRAYFIRE
checking for arrayfire.h... (cached) yes
checking for library containing af_is_double... (cached) no
configure: WARNING: cannot enable __PLUMED_HAS_ARRAYFIRE
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='mpic++ -shared'
configure: Using LDFLAGS='-L/run/timeshift/backup/usr/local/include/plumed/molfile -rdynamic -Wl,-Bsymbolic'
checking whether LDSHARED can create dynamic libraries... yes
checking for doxygen... found
configure: Doxygen version is fine
checking for dot... found
configure: Manuals will be generated
configure: A PDF version of the manual will not be generated
checking for xxd... found
checking whether a program can be run on this machine... yes
checking whether a program compiled with mpi can be run on this machine... no
configure: Regtest suite will use env var PLUMED_MPIRUN to run MPI tests (default: mpirun)
configure: PLUMED seems to be configured properly!
configure: **************************
nvc++-Error-Unknown switch: --print-prog-name=ld
checking whether C++ objects can be grouped with  -r -o... no
checking whether C++ objects can be grouped with mpic++ -Wl,-r -o... no
checking whether C++ objects can be grouped with ld -r -o... yes
nvc++-Error-Unknown switch: --print-prog-name=ar
checking whether static libraries can be created with  cr... no
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/ssebast/opt_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 using MPI
configure: WARNING: plumed executable will not run on this machine
configure: WARNING: unless you invoke it as 'plumed --no-mpi'
configure: WARNING: all command line tools are thus available as 'plumed --no-mpi name-of-the-tool'
configure: WARNING: e.g. 'plumed --no-mpi driver'
configure: WARNING: to patch an MD code use 'plumed --no-mpi patch'
configure: WARNING: (notice that MPI will be available anyway in the patched code)
configure: creating ./config.status
config.status: creating Makefile.conf
config.status: creating sourceme.sh
config.status: creating stamp-h

........................................................................................................................................

and following I made: make -j 8

the last lines show error:

/usr/bin/ld: ../core/PlumedMain.o: en la función `PLMD::PlumedMain::readInputLines(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
/home/ssebast/plumed2/src/core/PlumedMain.cpp:665: aviso: the use of `tmpnam' is dangerous, better use `mkstemp'
/usr/bin/ld: ../core/PlumedMain.o: en la función `PLMD::PlumedMain::readInputLines(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
/home/ssebast/plumed2/src/core/PlumedMain.cpp:665: aviso: the use of `tmpnam' is dangerous, better use `mkstemp'
/usr/bin/ld: /usr/local/lib/libxdrfile.a(xdrfile.o): relocation R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5' can not be used when making a shared object; recompile con -fPIC
/usr/bin/ld: falló el enlace final: bad value
pgacclnk: child process exit status 1: /usr/bin/ld
make[4]: *** [Makefile:463: libplumedKernel.so] Error 2
make[4]: *** Se espera a que terminen otras tareas....
make[4]: se sale del directorio '/home/ssebast/plumed2/src/lib'
make[3]: *** [Makefile:112: all] Error 2
make[3]: se sale del directorio '/home/ssebast/plumed2/src/lib'
make[2]: *** [Makefile:8: lib] Error 2
make[2]: se sale del directorio '/home/ssebast/plumed2/src'
make[1]: *** [Makefile:32: lib] Error 2
make[1]: se sale del directorio '/home/ssebast/plumed2'
make: *** [Makefile:21: all] Error 2

.....................................................................................................................................

for me plumed is an essential tool, can anybody help me
thanks for everything

[Bhanu Priya bt21d012]

Dear Users,

I'm also facing similar error during installation of PLUMED2.6 with MPI in the cluster. After installation by ignoring warnings, the 'plumed' executable is not working with the following error:

-----------------------------------------------------------------------------------------------------------------------------------------------------------------

$ plumed
Abort(2140047) on node 0 (rank 0 in comm 0): Fatal error in PMPI_Init: Other MPI error, error stack:
MPIR_Init_thread(703)........:
MPID_Init(958)...............:
MPIDI_OFI_mpi_init_hook(1334):
MPIDU_bc_table_create(444)...:

---------------------------------------------------------------------------------------------------------------------------------------------------------------

Any help in this regard is highly appreciated. The output of the configuration step is given below

------------------------------------------------------------------------------------------------------------------------------------------------------

$   ./configure --prefix=/lfs/usrhome/phd/bt21d012/plumed2.6/ CXX="$MPICXX"

configure: Optional modules are disabled by default

checking for mpic++... no
checking for mpicxx... mpicxx

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 mpicxx accepts -g... yes

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 whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes

configure: Initial CXX:         mpicxx

configure: Initial CXXFLAGS:    -O3
configure: Initial CPPFLAGS:    

configure: Initial CFLAGS:      -g -O2
configure: Initial LDFLAGS:    

configure: Initial LIBS:        
configure: Initial STATIC_LIBS:
configure: Initial LD:          

configure: Initial LDSHARED:    mpicxx
configure: Initial SOEXT:      
checking whether mpicxx accepts -fPIC... yes

checking whether gcc accepts -fPIC... yes

checking whether mpicxx accepts -Wall... yes
checking whether mpicxx accepts -pedantic... yes
checking whether mpicxx accepts -std=c++11... yes
checking whether mpicxx declares c++11 support... yes

checking whether C++ library supports C++11 exceptions... yes

checking whether mpicxx 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... mpicxx -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_... -lblas

checking for library containing dsyevr_... -llapack

checking whether sdot returns float... yes
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 mpi.h usability... yes
checking mpi.h presence... yes
checking for mpi.h... yes
checking for library containing MPI_Init... none required

checking for mpicxx option to support OpenMP... -fopenmp

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 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... -lgslcblas

checking gsl/gsl_vector.h usability... yes
checking gsl/gsl_vector.h presence... yes
checking for gsl/gsl_vector.h... yes
checking for library containing gsl_vector_alloc... -lgsl

checking xdrfile/xdrfile_xtc.h usability... no
checking xdrfile/xdrfile_xtc.h presence... no
checking for xdrfile/xdrfile_xtc.h... no
configure: WARNING: cannot enable __PLUMED_HAS_XDRFILE
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, subprocess, os, shutil)... no
configure: WARNING: cannot enable python interface

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='mpicxx -shared'
configure: Using LDFLAGS=' -rdynamic -Wl,-Bsymbolic'

checking whether LDSHARED can create dynamic libraries... yes
checking for doxygen... found
configure: Doxygen version is fine

checking for dot... no
configure: WARNING: You will not be able to see diagrams in the manual

configure: Manuals will be generated
configure: A PDF version of the manual will not be generated
checking for xxd... found
checking whether a program can be run on this machine... yes
checking whether a program compiled with mpi can be run on this machine... no
configure: Regtest suite will use env var PLUMED_MPIRUN to run MPI tests (default: mpirun)
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: /lfs/usrhome/phd/bt21d012/plumed2.6