libplumedKernel.so: cannot open

[kimlabSchatterjee]

I am explaining the instillation steps

1. after downloading from git I extracted all the staffs and entered into the plumed folder

2. I issued the command ./configure --enable-modules=all --enable-pdfdoc=yes --enable-boost_graph=yes --enable-boost_serialization=yes --enable-fftw=yes --enable-af_cuda=yes --enable-af_cpu=yes --enable-python=no

3. make -j8

4. sudo make install#

   (however I used ./configure --prefix=$HOME/opt. certainly i did not required sudo to install. I also tried ./configure --prefix=/opt/plumed for which i need to use sudo)

I Set environmental variable export PLUMED_KERNEL=/usr/local/lib/libplumedKernel.so export PLUMED_USE_LEPTON=yes PLUMED_VIMPATH=/usr/local/lib/plumed/vim but when i call plumed it returns following error. I am unable to figure it out.

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

kindly help me to solve the issue.

once it installed I want to extract gromacs zipped file. after entering insnide the extracted gromacs folder I want to use plumed patch -p command . Then using cmake i will build gromacs

please help to resolve the issue.

[GiovanniBussi]

Can you confirm the file /usr/local/lib/libplumedKernel.so exist (with ls /usr/local/lib/libplumedKernel.so)? Maybe you should use PLUMED_KERNEL=$HOME/opt/lib/libplumedKernel.so?

[kimlabSchatterjee]

(base) kimlab@kimlab:~/Desktop$ whereis libplumedKernel.so libplumedKernel: /usr/local/lib/libplumedKernel.so (base) kimlab@kimlab:~/Desktop$ plumed plumed: error while loading shared libraries: libplumedKernel.so: cannot open shared object file: No such file or directory (base) kimlab@kimlab:~/Desktop$ ls /usr/local/lib/libplumedKernel.so /usr/local/lib/libplumedKernel.so ##exists (base) kimlab@kimlab:~/Desktop$ plumed plumed: error while loading shared libraries: libplumedKernel.so: cannot open shared object file: No such file or directory

also put this line "PLUMED_KERNEL=$HOME/opt/lib/libplumedKernel.so" in bashrc but no work :(

[GiovanniBussi]

So, if $HOME/opt/lib/libplumedKernel.so exist I guess what does not exist is one of the dependencies

Try:

ldd $HOME/opt/lib/libplumedKernel.so

It might tell you which of the dependencies is not found. You should then add its path to env var LD_LIBRARY_PATH

Giovanni

On Thu, Jun 17, 2021 at 5:32 AM kimlabSchatterjee @.***> wrote:

(base) @.:/Desktop$ whereis libplumedKernel.so libplumedKernel: /usr/local/lib/libplumedKernel.so (base) @.:/Desktop$ plumed plumed: error while loading shared libraries: libplumedKernel.so: cannot open shared object file: No such file or directory (base) @.:/Desktop$ ls /usr/local/lib/libplumedKernel.so /usr/local/lib/libplumedKernel.so (base) @.:/Desktop$ plumed plumed: error while loading shared libraries: libplumedKernel.so: cannot open shared object file: No such file or directory

also put this line "PLUMED_KERNEL=$HOME/opt/lib/libplumedKernel.so" in bashrc but no work :(

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/plumed/plumed2/issues/700#issuecomment-862892334, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBNCXUB4UQ3DRRQLVTXRSTTTFUF5ANCNFSM46YTIF4Q .

[kimlabSchatterjee]

(base) kimlab@kimlab:~/Desktop$ ls $HOME/opt/lib/libplumedKernel.so /home/kimlab/opt/lib/libplumedKernel.so (base) kimlab@kimlab:~/Desktop$ ldd $HOME/opt/lib/libplumedKernel.so linux-vdso.so.1 (0x00007ffe607dd000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f54a588e000) libboost_serialization.so.1.65.1 => /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.65.1 (0x00007f54a5650000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f54a5433000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f54a522f000) libmpi_cxx.so.20 => /usr/lib/x86_64-linux-gnu/libmpi_cxx.so.20 (0x00007f54a5015000) libmpi.so.20 => /usr/lib/x86_64-linux-gnu/libmpi.so.20 (0x00007f54a4d23000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f54a4985000) libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00007f54a4756000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f54a453e000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f54a431f000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f54a3f2e000) /lib64/ld-linux-x86-64.so.2 (0x00007f54a6b0f000) libopen-rte.so.20 => /usr/lib/x86_64-linux-gnu/libopen-rte.so.20 (0x00007f54a3ca6000) libopen-pal.so.20 => /usr/lib/x86_64-linux-gnu/libopen-pal.so.20 (0x00007f54a39f4000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f54a37ec000) libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5 (0x00007f54a35af000) libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f54a33ac000) libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1 (0x00007f54a31a1000) libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x00007f54a2f97000)

~/Desktop$ $HOME/opt/lib/libplumedKernel.so Segmentation fault (core dumped) (base) kimlab@kimlab:~/Desktop$ whereis cuda cuda: /usr/local/cuda (base) kimlab@kimlab:~/Desktop$ plumed plumed: error while loading shared libraries: libplumedKernel.so: cannot open shared object file: No such file or directory (base) kimlab@kimlab:~/Desktop$

I Think LD lib path properly exported. export CUDAROOT=/usr/local/cuda/bin/ export CUDA_HOME=/usr/local/cuda export PATH=$CUDA_HOME/bin:$PATH export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/lib:$CUDA_HOME/lib64 export LD_LIBRARY_PATH="/usr/local/cuda/lib:${LD_LIBRARY_PATH}" export GPU_INCLUDE_PATH=/usr/local/cuda/include export GPU_LIBRARY_PATH=/usr/local/cuda/lib64

[GiovanniBussi]

Did you check if the problem is solved removing some of the configured options:

./configure --enable-modules=all --enable-pdfdoc=yes --enable-boost_graph=yes --enable-boost_serialization=yes --enable-fftw=yes --enable-af_cuda=yes --enable-af_cpu=yes --enable-python=no

I would try to remove arrayfire and boost to see if some of them is causing the problem

[kimlabSchatterjee]

./configure --enable-modules=all --enable-FEATURE=yes --enable-python=n make make install

(base) kimlab@kimlab:~/Desktop$ whereis plumed plumed: /usr/local/bin/plumed /usr/local/lib/plumed (base) kimlab@kimlab:~/Desktop$

(base) kimlab@kimlab:~/Downloads/plumed-2.5.7$ plumed plumed: error while loading shared libraries: libplumedKernel.so: cannot open shared object file: No such file or directory

imlab@kimlab:~/Desktop$ whereis libplumedKernel.so libplumedKernel: /usr/local/lib/libplumedKernel.so

(base) kimlab@kimlab:~/Desktop$ whereis libplumedKernel.so libplumedKernel: /usr/local/lib/libplumedKernel.so

(base) kimlab@kimlab:~/Desktop$ export plumed=/usr/local/lib/libplumedKernel.so (base) kimlab@kimlab:~/Desktop$ plumed plumed: error while loading shared libraries: libplumedKernel.so: cannot open shared object file: No such file or directory (base) kimlab@kimlab:~/Desktop$

I am facing same issue...

I am from south Korea, Due to some other work i was bit late to reply. Kindly accept my apology. Plz help me.

[GiovanniBussi]

I don't understand. Did you install on /usr/local/ or on $HOME/opt?

Please do:

which plumed

to know where plumed is. Let's say it is in pippo/bin, do

ldd pippo/lib/libplumedKernel.so

[kimlabSchatterjee]

(base) kimlab@kimlab:~/Desktop$ which plumed /usr/local/bin/plumed (base) kimlab@kimlab:~/Desktop$ ldd pippo/lib/libplumedKernel.so ldd: pippo/lib/libplumedKernel.so: No such file or directory (base) kimlab@kimlab:~/Desktop$ whereis libplumedKernel.so libplumedKernel: /usr/local/lib/libplumedKernel.so (base) kimlab@kimlab:~/Desktop$

[GiovanniBussi]

Did you read this sentence?

Let's say it is in pippo/bin,

In your case, please type

ldd /usr/local/lib/libplumedKernel.so

[carlocamilloni]

this is for the mailing list, anyway double check your install path