installing as root with user anaconda cython

[Ben Harland]

I am having a similar problem to:

https://groups.google.com/g/plumed-users/c/woUu4F1FC4k/m/q8-66dOkFwAJ

My cython is from user-installed anaconda and isn't found by 'sudo make install'.  I tried 'sudo pip install cython' but this makes me nervous, and in any case I now have:

     plumed.cpp:34:10: fatal error: Python.h: No such file or directory

I see in the install instructions that 'make install' is not strictly required, but when I try to patch to gromacs, I get:

     plumed: error while loading shared libraries: libplumedKernel.so: cannot open shared object file: No such file or directory

What is the "best practise" for getting a working plumed/gromacs?

Many thanks! 

[Giovanni Bussi]

Hi,

first, for a working plumed + gromacs you do not need python, so just configure with --disable-python if this is creating problems on your installation.

Second, if libplumedKernel.so is not found it might be because you installed it in a non standard path. E.g., if you install it in

/home/opt/lib/libplumedKernel.so

you should add path /home/opt/lib to LD_LIBRARY_PATH

Let us know if this fixes your problem

Giovanni

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[Ben Harland]

Thanks!  Ok, I've done

     ./configure --prefix=/usr/local —disable-python

I'm still getting `libplumedKernel.so: cannot open shared object file` when I run `plumed patch -p` in the gromacs directory.  Is there a way to tell plumed where to find it's shared library files?

[Ben Harland]

Sorry -- that wasn't as clear as I'd like.  I did:

      ./configure --prefix=/usr/local —disable-python

     make -j 4

which gave me:

     ...

Building python interface for PLUMED
unset CXX && unset CC && unset CFLAGS && unset CXXFLAGS && unset LDSHARED && \
         plumed_program_name=plumed \
         plumed_force_cython=yes \
         plumed_version=2.7.2 \
         plumed_include_dir=../src/wrapper \
         plumed_default_kernel="$PWD/../src/lib/libplumedKernel.so" \
         python setup.py build_ext -i
Module name plumed
Version number 2.7.2
Hardcoded PLUMED_KERNEL /home/bharland/plumed-2.7.2/src/lib/libplumedKernel.so
plumed_force_cython=yes
importing cython
running build_ext

And then:

     [... gromacs-2021.4]$ plumed patch -p

gives:

plumed: error while loading shared libraries: libplumedKernel.so: cannot open sh
ared object file: No such file or directory

[Giovanni Bussi]

Did you set ld_lbrary_path as I wrote below?

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/929f900f-c298-436d-a74e-a74a9a8639d1n%40googlegroups.com.

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[Ben Harland]

Whoops -- sorry!  I've now added the path to my libplumedKernel.so to LD_LIBRARY_PATH.  Patching gives 'detecting previous patch' warnings and appears to have skipped doing anything.  Doing:

     plumed patch -p -f

gets me further, but trying to run still gives:

     gmx mdrun -s topol.tpr -nsteps 5000 -plumed plumed.dat

Error in user input: Invalid command-line options Unknown command-line option -plumed

[Giovanni Bussi]

You are using a non-patched version of plumed.

Please follow the instructions on how to patch gromacs and then compile it. I suggest you to start from a clean gromacs copy

Giovanni

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/d6cbad9f-8211-4676-8a9a-ed167ebea5acn%40googlegroups.com.

[Ben Harland]

Thanks for all your help.  Patching before evoking gromacs' cmake was the key.