[gmx-users] parallel run error

[Lianqing Zheng]

Thanks, David! It finally works after I copies all relevant library files
to each node. An interesting thing I found, though, is it takes 18 seconds
to run with one  node, but 46 seconds with four nodes (I used the water in
tutorial). I also found the CPU usage for one node is about 99%, but
only ~20% on each node if four nodes are used. Any hints?

Thanks!

Lianqing

On Tue, 23 Nov 2004, David wrote:

>On Tue, 2004-11-23 at 12:42 -0500, Lianqing Zheng wrote:
>> Thanks, David! Do I need to recompile lam, fftw, and gromacs or just
>> gromacs? I did it for gromacs but still got the same error.
>> 
>Running 
>make distclean
>configure [OPTS]
>make install 
>
>should do it.
>
>> We actually have libxml2 at /usr/lib/libxml2.so.2. It's only on
>> the master node. Do I need to install it on all nodes?
>Yes that would be a good solution.
>
>> 
>> Thanks,
>> Lianqing
>> 
>> 
>> On Tue, 23 Nov 2004, David wrote:
>> 
>> >On Tue, 2004-11-23 at 11:46 -0500, Lianqing Zheng wrote:
>> >> Dear GMX-pals,
>> >> 
>> >> Here is what I did:
>> >> 
>> >> 1. Compile and install fftw
>> >> a) MPICC=/opt/lam-7.0/bin/mpicc
>> >> b) ./configure --prefix=/home/lzheng/fftw-2.1.3 --enable-float
>> >> --enable-type-prefix --enable-mpi 
>> >> c) make
>> >> d) make install
>> >> 
>> >> 2. Compile and install gromacs 3.2.1
>> >> a) export CPPFLAGS=-I/home/lzheng/fftw-2.1.3/include
>> >> b) export LDFLAGS=-L/home/lzheng/fftw-2.1.3/lib
>> >> c) ./configure --prefix=/home/lzheng/gromacs-3.2.1 --enable-mpi
>> >> --without-motif-libraries --without-motif-includes --without-x 
>> >> d) make
>> >> e) make install
>> >> 
>> >> 3. Run water simulation in tutorial
>> >> a) lamboot -v bhost.def
>> >> b) grompp -f grompp.mdp -p water.top -c spc216.gro -o water.tpr -np 4
>> >> c) /opt/lam-7.0/bin/mpirun n21-24
>> >> /home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun  -s water.tpr -o
>> >> water.trr -c water_out.gro -v -g water.log -np 4
>> >> 
>> >> OK, then I got the following error message:
>> >> 
>> >> ****begin****
>> >> /home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun: error while
>> >> loading shared libraries: libxml2.so.2: cannot open shared object file: No
>> >> such file or directory
>> >Your cluster does not have libxml2 installed. Either ask your sysadm to
>> >install libxml2 or configure --without-libxml2
>> >
>> >Note that xml may become obligatory in the next (4.0) release.
>> >
>> >> /home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun: error while
>> >> loading shared libraries: libxml2.so.2: cannot open shared object file: No
>> >> such file or directory
>> >> /home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun: error while
>> >> loading shared libraries: libxml2.so.2: cannot open shared object file: No
>> >> such file or directory
>> >> /home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun: error while
>> >> loading shared libraries: libxml2.so.2: cannot open shared object file: No
>> >> such file or directory
>> >> -----------------------------------------------------------------------------
>> >> It seems that [at least] one of the processes that was started with
>> >> mpirun did not invoke MPI_INIT before quitting (it is possible that
>> >> more than one process did not invoke MPI_INIT -- mpirun was only
>> >> notified of the first one, which was on node n0).
>> >> 
>> >> mpirun can *only* be used with MPI programs (i.e., programs that
>> >> invoke MPI_INIT and MPI_FINALIZE).  You can use the "lamexec" program
>> >> to run non-MPI programs over the lambooted nodes.
>> >> -----------------------------------------------------------------------------
>> >> ****end****
>> >> 
>> >> I also tried mpirun -np 4 and got the same error.
>> >> 
>> >> Thanks for your kind help!
>> >> 
>> >> Lianqing
>> >> 
>> >> _______________________________________________
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>> >-- 
>> >David.
>> >________________________________________________________________________
>> >David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> >Dept. of Cell and Molecular Biology, Uppsala University.
>> >Husargatan 3, Box 596,          75124 Uppsala, Sweden
>> >phone:  46 18 471 4205          fax: 46 18 511 755
>> >spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
>> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> >
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>> 
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>-- 
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596,          75124 Uppsala, Sweden
>phone:  46 18 471 4205          fax: 46 18 511 755
>spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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