[gmx-users] Re: problem of installing gromacs4.5.4

[Mark Abraham]

On 6/01/2012 12:37 AM, mircial at sjtu.edu.cn wrote:
> Dear Justin:
>
> Thank you very much for your reply, but I have another problem.
>
> After I install the fftw package, and remove the argument of the --enable-mpi when installing the gromacs package by using the follow commands:
>
> export CPPFLAGS=-I/my_path/
> export LDFFLAGS=-L/my_path/
>  
> ./configure --prefix=my_path --enable-shared --disable-float --enable-mpi
>
> make mdrun
>
> then I encountered the following errors:
>
> libtool: link: cannot find the library `../mdlib/libmd_mpi_d.la' or unhandled argument `../mdlib/libmd_mpi_d.la'
> make[1]: *** [libgmxpreprocess_mpi_d.la] Error 1
> make[1]: directory `/home/dw11-sg007/dying/gromacs-4.5.4/src/kernel'
>
> what does this mean? Does it mean there is some problem with the mpi I used?

Maybe. Shared libraries and MPI do not always work well together. Also,
be sure to use "make distclean" between attempts.

Mark

>
> Thanks in advance!!
>
> R-X Gu
> Message: 2
> Date: Wed, 04 Jan 2012 09:44:53 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] a installation problem of gromacs4.5.4 using
> 	mpi
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F0465E5.6090101 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> mircial at sjtu.edu.cn wrote:
>> Dear All:
>>
>> I encountered a problem when installing gromacs4.5.4 by using mpi. When 
>>
>> I finished the installation successfully, I submit a job by assigning 8 processes. However, the job was not run by 8 processes, by generate 8 same jobs each use only 1 process (I have encountered the same problem before, but it is solved by using the same mpirun path during the installation and the simulation. However, this time i am sure the path of mpirun assigned during the installation is the same of that assigned in the simulation command and this problem occures again.). The followings are the commonds used in my installation:
>>
>> ########################install fftw#######
>> ./configure --prefix=my_path --enable-thread --disable-float --enable-shared
>> make 
>> make install
>>
>> #######################install gromacs#####
>>
>> export CPPFLAGS=-I/my_path/
>> export LDFFLAGS=-L/my_path/
>>
>> ./configure --prefix=my_path --enable-shared --disable-float --enable-mpi=the_path_of_mpirun
> The --enable-mpi flag does not take any argument. It is also advisable to append 
> a suffix (e.g. _mpi) to the mdrun executable so you can unambiguously use the 
> commands.
>
>> make
>> make install
> There is no need to try to compile the entire Gromacs package with MPI support; 
> only mdrun is MPI-aware.  Instead, use:
>
> make mdrun
> make install-mdrun
>
> -Justin
>
>> ###########################################
>>
>> then I used the following command to do the simulations
>>
>> /the_path_of_mpirun/mpirun -np 8 mdrun -s myfile.tpr
>>
>> I am sure the path of mpirun assigned during the installation is the same of that assigned in the simulation command.
>>
>> Could anyone tell me how to solve this problem?
>>
>> Thanks in advance!!
>>
>> R-X Gu
>>