"plumed patch -p" shows "error while loading shared libraries: libplumedKernel.so"

[Zhang Cheng]

Dear All,

I already have Gromacs 2018.1 installed on my Ubuntu 16.04. Then I successfully installed plumed:

> ./configure --prefix=/usr/local

> make -j 4

> make doc  (this did not work, but I just ignore it, is that okay?)

> sudo make install

But I got error when typing:

> plumed patch -p

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

Can I ask how to solve this? 

Is that correct that I install the Gromacs first, then install the plumed?

Thank you.

Yours sincerely

Cheng

[Zhang Cheng]

It works now after "source sourceme.sh"

I hope this solution can be added to the https://plumed.github.io/doc-v2.4/user-doc/html/_installation.html

[Giovanni Bussi]

You should add /usr/local/lib to your LD_LIBRARY_PATH (and /usr/local/bin to your PATH)

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[Giovanni Bussi]

Notice that it this way you will use the compiled plumed and not the installed one. If you now patch gromacs it will point to this plumed library.

The best solution is to set the environment so that the installed plumed is used

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[Giovanni Bussi]

See this also:

https://unix.stackexchange.com/questions/67781/use-shared-libraries-in-usr-local-lib

[Zhang Cheng]

Should I do the below?

export LD_LIBRARY_PATH=/usr/local/lib

export PATH=/usr/local/bin

When I re-open the terminal, and type "plumed patch -p", I can still get the below, does it mean it is already using the installed one not the compiled plumed??

lanselibai@ubuntu:~/Cheng/gromacs-2018.1$ plumed patch -p

PLUMED patching tool

1) amber14     4) gromacs-4.5.7 7) namd-2.9

2) gromacs-2016.5   5) lammps-6Apr13 8) qespresso-5.0.2

3) gromacs-2018.3   6) namd-2.8 9) qespresso-6.2

[Giovanni Bussi]

You should not set the variables but rather pre-pend the path to the variables 

To know which plumed you are using type:

which plumed

And to cross check that it is loading the correct plumed library type

plumed info —root

In your case it should print

/usr/local/lib/plumed

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[Zhang Cheng]

Thank you Giovanni!

Sorry, I am not familiar with it. I got:

lanselibai@ubuntu:~/Cheng/gromacs-2018.1$ which plumed

/usr/local/bin/plumed

lanselibai@ubuntu:~/Cheng/gromacs-2018.1$ plumed info --root

/usr/local/lib/plumed

But how to exactly "pre-pend the path to the variables"?

[qingh...@gmail.com]

Hello Cheng,

By setting "export LD_LIBRARY_PATH=/usr/local/lib", you will remove all the other settings to the variable of LD_LIBRARY_PATH,

For pre-pending, you have to set something like: export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

You can also have a check the file of sourceme.sh, there are the standard settings.

Best,

Qinghua

[Zhang Cheng]

Thank you Qinghua!

I can see in the sourceme.sh file, it is just as you said.

So should I type the below?

> export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

> export PATH=/usr/local/bin:$PATH

> source sourceme.sh