installation of plumed with gromacs

[msaeed...@gmail.com]

Hi,

when i wanted to patch plumed to gromacs, I faced this error. I am thankful if you help me to solve it.

plumed patch -p runtime

plumed: error while loading shared libraries: libmpi.so.12: cannot open shared object file: No such file or directory

[jan...@gmail.com]

Hi,

Can you post the output of the following command:

ldd `which plumed`

Are you compiling on a cluster or a workstation? What operating system are you on, and what's the version of plumed?

- Jan

[msaeed...@gmail.com]

Hi Jan and all,

I was trying several times to install plumed with gromacs because I really need it, but I couldn’t successfully install it yet. I explain what I have done completely. I am thankful to help me.

 

I wanted to install it in a computer with one processor and 8 cores. It is noted that I had gromacs-4-6-7 without plumed properly in my computer. At first I have installed plumed-2-1-0 as follow:

 

cd plumed-2.1.0/

./configure --prefix=/usr/local/opt/plumed  CC=/usr/local/bin/mpicc CXX=/usr/local/bin/mpicxx

 -fPIC was added in the CFLAG of makefile.conf manually. (CFLAGS=-g -O2 –fPIC)

make VERBOSE=1 2>&1 | tee m.txt

make install VERBOSE=1 2>&1 | tee mi.txt

export PLUMED_KERNEL=/usr/local/opt/plumed/lib/libplumedKernel.so

I added the path in bashrc file:

export PATH="$PATH:/usr/local/opt/plumed/bin"

 

There is one question, should I need to install it with mpi or without mpi? By default it will be installed with mpi.

 

 

After that I patch plumed in the gromacs-4-6-7 source directory as follow:

cd gromacs-4.6.7/

plumed patch -p –runtime and select 2 for gromacs-4.6.7

After that I installed gromacs as follow:

mkdir build

cd build

cmake .. -DGMX_BUILD_OWN_FFTW=ON  –DGMX_MPI=ON   - DCMAKE_INSTALL_PREFIX=/usr/local/opt/gromacs  -DCMAKE_C_COMPILER=/usr/local/bin/mpicc  -DCMAKE_CXX_COMPILER=/usr/local/bin/mpicxx

make VERBOSE=1 2>&1 | tee m.txt

I got the following error. I also attach m.txt file. Please help me to find and solve problem.

ld: /usr/local/lib/libmpich.a(allreduce.o): relocation R_X86_64_32 against `.rodata.str1.4' can not be used when making a shared object; recompile with -fPIC

/usr/local/lib/libmpich.a: error adding symbols: Bad value

 

Thanks in advance,

Marzieh,

[jan...@gmail.com]

Ok, good effort. Here is the error

//home/msaee/gromacs-4.6.7/buildd/src/contrib/fftw/fftwBuild-prefix/lib/libfftw3f.a -lblas -llapack -lblas -ldl -lm -openmp -llapack -ldl -lm -Wl,-rpath,::::::::::::::: 
ld: /usr/local/lib/libmpich.a(allreduce.o): relocation R_X86_64_32 against `.rodata.str1.4' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libmpich.a: error adding symbols: Bad value
make[2]: *** [src/gmxlib/libgmx_mpi.so.8] Error 1
make[2]: Leaving directory `/home/msaee/gromacs-4.6.7/buildd'
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
make[1]: Leaving directory `/home/msaee/gromacs-4.6.7/buildd'
make: *** [all] Error 2

I have no idea what it means :)

To start with, did you compile gromacs-4-5-7 on your machine yourself? Did you compile it with MPI enabled? Does it work then without plumed with mpi_run -np xyz mdrun_mpi? That's one line of attack to exclude the possibility that your gromacs compilation is messed up.
Two other ideas: remove fPIC (I understand that you may need it, but this is just to dissect the problem(s)), see if that helps. Or try to compile plumed without mpi and then patch gromacs - does that work? Again, I know that you may need it but I'd like to understand which piece of this setup is causing a problem.

[msaeed...@gmail.com]

Hi Jan, 

Thanks for good suggestion. I answered to your questions:

 

1.       I had compiled gromacs-4-6-7 in my computer myself without mpi and it works properly.

2.       I just use gromcs as usual without mpirun as:  (mdrun –s md.tpr)

I have also tried to install gromacs without mpi after installation plumed as my first attemp. And it was installed well. But when I used this command : mdrun –s –plumed plumed.dat I got this error:

you are trying to use an MPI function, but PLUMED has been compiled without MPI support

after that I tried to install it with –DGMX_MPI=ON option.

 

I will try to compile plumed without mpi and inform you about the result of it.

[msaeed...@gmail.com]

Hi Jan, I have done your two suggestions and here the results:

I tried to compile plumed with ( --enbale-mpi No ) option and after that install gromacs without mpi. They are installed well, but after I run this command, I got this error:

Mdrun –s topol.tpr –plumed plumed.dat

+++ message: you are trying to use an MPI function, but PLUMED has been compiled without MPI support

I also tried to compile plumed without –fpic in CFLAG. It compiled plumed and gromacs without mpi properly in this condition, but I faced the previous error.

 

Any suggestions are welcome. Thanks in advance,

Marzieh,

On Monday, May 9, 2016 at 1:38:36 PM UTC+4:30, msaeed...@gmail.com wrote:

[msaeed...@gmail.com]

Hi Jan, 

Thanks for good suggestion. I answered to your questions:

 

1.       I had compiled gromacs-4-6-7 in my computer myself without mpi and it works properly.

2.       I just use gromcs as usual without mpirun as:  (mdrun –s md.tpr)

I have also tried to install gromacs without mpi after installation plumed as my first attemp. And it was installed well. But when I used this command : mdrun –s –plumed plumed.dat I got this error:

you are trying to use an MPI function, but PLUMED has been compiled without MPI support

.

 I have done your two suggestions and here the results:

I tried to compile plumed with ( --enbale-mpi No ) option and after that install gromacs without mpi. They are installed well, but after I run this command, I got this error:

Mdrun –s topol.tpr –plumed plumed.dat

+++ message: you are trying to use an MPI function, but PLUMED has been compiled without MPI support

I also tried to compile plumed without –fpic in CFLAG. It compiled plumed and gromacs without mpi properly in this condition, but I faced the previous error.

 

Any suggestions are welcome. Thanks in advance,

Marzieh