problem about installing PLUMED-2.0

[Zhang Zhengqing]

Dear all,

 

I followed  the procedures to install PLUMED-2.0 .

 

The procedure as follows:

 

1.  ./configure.sh

2.  source ./sourceme.sh

3. make

 

In the third stage,  I met the problems.

 

g++ -rdynamic ../main/main.o  -o plumed-shared -ldl
../main/main.o(.text+0x37): In function `main':
: undefined reference to `plumed_create'
../main/main.o(.text+0x69): In function `main':
: undefined reference to `plumed_cmd'
../main/main.o(.text+0x7c): In function `main':
: undefined reference to `plumed_cmd'
../main/main.o(.text+0x91): In function `main':
: undefined reference to `plumed_cmd'
../main/main.o(.gnu.linkonce.t._ZN4PLMD6PlumedD0Ev+0x1d): In function `PLMD::Plumed::~Plumed()':
: undefined reference to `plumed_finalize'
../main/main.o(.gnu.linkonce.t._ZN4PLMD6PlumedD1Ev+0x1d): In function `PLMD::Plumed::~Plumed()':
: undefined reference to `plumed_finalize'
collect2: ld returned 1 exit status
make[4]: *** [plumed-shared] Error 1

 

 

Any suggestions would be much appreciated.

 

Best wishes,

Zhengqing

 

 

 

 

[Giovanni Bussi]

Dear Zhang,

which configuration did you choose among the listed ones (after ./configure.sh)?

Did you edit the Makefile.conf?

Which exact version are you using (2.0b0)?

Can you post the content of directory src/lib/? Is a file named src/lib/libplumed.so there?

Giovanni

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[Zhang Zhengqing]

Hi,

 

which configuration did you choose among the listed ones (after ./configure.sh)?

 

I chose the 1. (Linux.gcc)

 

Did you edit the Makefile.conf?

 

I didn't edit the Makefile.conf. Should i edit some part ?

 

Which exact version are you using (2.0b0)?

 

 Yes, I use the PLUMED-2.0b0

 

Can you post the content of directory src/lib/? Is a file named src/lib/libplumed.so there?

 

This is content of directory src/lib.

 

  .gitignore                    libplumed.so*          plumed*          Plumed.cmake.static           Plumed.inc.static
 libplumedKernel.so*     Makefile              Plumed.cmake           Plumed.inc                  plumed-patch*

 

 

 

Best wishes,

Zhengqing

 

 

 

 

[Giovanni Bussi]

Hi, it seems everything compiled fine, but your make program does not understand the word "realpath".

I think that static binding should work anyway, so you can already try plumed e.g. with gromacs. Just check that "plumed" should be in your execution path.

Meanwhile, can you check the version of your make program? Or try to do

cd src/lib

gmake # gnu make might be installed under this name

Thanks!

Giovanni

[Zhang Zhengqing]

Hi

 

After i update the make program, I can compile successfully.

 

Thanks for your help!

 

 

I also want to compile the PLUMED-2.0b0 with MPI (mpich).

 

1.  ./configure.sh

 

      I choice the 3. (Linux.mpi.gcc)

 

2.  source ./sourceme.sh

3. make -j 4

 

Those procedures  i followed the websit.(http://plumed2.berlios.de/v2.0b0/user-doc/html/_installation.html)

 

But it does not work. it  means  the PLUMED can not find the MPI . Should i edit some part ?

 

Which MPI should i use mpich or openmpi ?

 

Could you give me some suggestion? 

 

 

Best wishes,

Zhengqing

 

 

 

 

[Giovanni Bussi]

Hi Zhang,

if you want to combine plumed with e.g. gromacs or lammps you should use the same mpi version for both packages.

Typically, mpi c/c++ compiler is named mpicc/mpic++. In case the name of your compiler is different you might have to edit the Makefile.conf accordingly.

Do you have mpicc in your execution path?

Giovanni

[Zhang Zhengqing]

hi,

 

I compiled the PlUMED2.0b0 using mpicc.

 

1.  ./configure.sh

 

      I choice the 4. (Linux.mpi.icc)

 

2.  source ./sourceme.sh

 

3. make

 

I met the problem. I tried to solve this problem, but i failed.

 

opt/intel/cce/10.1.018/lib/libimf.so: warning: warning: feupdateenv is not implemented and will always fail
mpif90 -c  mainf.f90 -o mainf.o
mpif90 mainf.o -o plumedf /home/zhangz/test/plumed-2.0b0/src/lib/libplumed.so -ldl -rdynamic
/opt/intel/fce/10.1.018/lib/libimf.so: warning: warning: feupdateenv is not implemented and will always fail
/home/zhangz/test/plumed-2.0b0/src/lib/libplumed.so: undefined reference to `MPI_Comm_f2c'
/home/zhangz/test/plumed-2.0b0/src/lib/libplumed.so: undefined reference to `ompi_mpi_int'
/home/zhangz/test/plumed-2.0b0/src/lib/libplumed.so: undefined reference to `ompi_mpi_char'
/home/zhangz/test/plumed-2.0b0/src/lib/libplumed.so: undefined reference to `ompi_mpi_op_sum'
/home/zhangz/test/plumed-2.0b0/src/lib/libplumed.so: undefined reference to `ompi_mpi_float'
/home/zhangz/test/plumed-2.0b0/src/lib/libplumed.so: undefined reference to `ompi_mpi_comm_world'
/home/zhangz/test/plumed-2.0b0/src/lib/libplumed.so: undefined reference to `ompi_mpi_double'
/home/zhangz/test/plumed-2.0b0/src/lib/libplumed.so: undefined reference to `ompi_mpi_unsigned'
/home/zhangz/test/plumed-2.0b0/src/lib/libplumed.so: undefined reference to `ompi_mpi_comm_self'
/home/zhangz/test/plumed-2.0b0/src/lib/libplumed.so: undefined reference to `ompi_mpi_unsigned_long'

 

Best wishes,

Zhengqing

[Giovanni Bussi]

Hi Zhang,

can you try to do:

cd src/lib

make

and see if you still get errors? It seems your error depends on the libraries linked by the fortran compiler. If the problem is only with fortran, you can safely use plumed anyway.

Giovanni

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