Problem in PLUMED make

[Rajorshi Chattopadhyay]

Dear All,

I am trying to run PLUMED with LAMMPS. As instructed in the LAMMPS manual, I do the following:

1. downloaded plumed source code from the git-hub repository

2. within the plumed directory I run './configure' command. It is executed without any errors

3. I then run the 'make' command. However, in this step I get the following error:

/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: warning: libz.so.1, needed by libplumedKernel.so, not found (try using -rpath or -rpath-link)
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: warning: libgomp.so.1, needed by libplumedKernel.so, not found (try using -rpath or -rpath-link)
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `GOMP_critical_start@GOMP_1.0'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `GOMP_barrier@GOMP_1.0'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `GOMP_parallel@GOMP_4.0'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `gzflush'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `GOMP_loop_end_nowait@GOMP_1.0'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `omp_get_thread_num@OMP_1.0'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `GOMP_loop_nonmonotonic_dynamic_next@GOMP_4.5'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `GOMP_loop_nonmonotonic_dynamic_start@GOMP_4.5'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `GOMP_critical_end@GOMP_1.0'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `GOMP_loop_end@GOMP_1.0'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `gzclearerr@ZLIB_1.2.0.2'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `gzwrite'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `gzopen'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `gzclose'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `gzread'
/home/rajorshi/anaconda3/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: libplumedKernel.so: undefined reference to `omp_get_num_threads@OMP_1.0'
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:497: plumed] Error 1

Both the libz.so.1 and libgomp.so.1 are installed and are within '/usr/lib/lib/x86_64-linux-gnu' directories.

4. I am working with Ubuntu 20.04 and the version of LAMMPS is 29-Sep2021

Thanking in advance for any help and suggestions.

[Rajorshi Chattopadhyay]

For further information I have attached the output from ./configure command. I have also tried installing the gxx_linux-64 package using 'conda install gxx_linux-64' command. However, that does not solve the problem.

[Julien PERRADIN]

Hi,

I am not an expert of plumed but I had the same issue and I figured it out by avoiding the c compiler from conda.

I specified the path for the c/c++ compiler such as: 

CXX=/usr/bin/g++ CC=/usr/bin/gcc 

(my version of gcc/g++:  g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0)

Here is my command for ./configure which worked for me (as an example):

./configure --prefix=$HOME/opt --disable-mpi --disable-gsl --enable-modules=opes+adjmat --enable-debug CXX=/usr/bin/g++ CC=/usr/bin/gcc PYTHON_BIN=$HOME/anaconda3/bin/python

then follow the rest of the installation instructions and it should work :)

Best,

Julien