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Re: [ESPResSo] parallel computing

From: Mikheil Azatov
Subject: Re: [ESPResSo] parallel computing
Date: Tue, 10 Aug 2010 13:16:27 -0400

Hi, thank you for your response.
I did the way you suggested Torsten and it seems to work. But when I compile espresso file that worked without mpi i get the following error. Do you have any idea what could this possibly mean ?

[bender:12461] *** Process received signal ***
[bender:12461] Signal: Floating point exception (8)
[bender:12461] Signal code: Integer divide-by-zero (1)
[bender:12461] Failing at address: 0x442cbf
[bender:12461] [ 0] /lib/ [0x7f2edf15e190]
[bender:12461] [ 1] ./obj-Core-pc-linux/Espresso_bin(force_calc+0x19f) [0x442cbf]
[bender:12461] [ 2] ./obj-Core-pc-linux/Espresso_bin(integrate_vv+0x197e) [0x43993e]
[bender:12461] [ 3] ./obj-Core-pc-linux/Espresso_bin(mpi_integrate_slave+0xb) [0x4142cb]
[bender:12461] [ 4] ./obj-Core-pc-linux/Espresso_bin(mpi_loop+0x2d) [0x41304d]
[bender:12461] [ 5] ./obj-Core-pc-linux/Espresso_bin(main+0x40) [0x4100a0]
[bender:12461] [ 6] /lib/ [0x7f2ededfdabd]
[bender:12461] [ 7] ./obj-Core-pc-linux/Espresso_bin [0x40ff89]
[bender:12461] *** End of error message ***
mpiexec noticed that job rank 0 with PID 12460 on node bender exited on signal 15 (Terminated). 
1 additional process aborted (not shown)


On Tue, Aug 10, 2010 at 5:19 AM, Torsten Stuehn <address@hidden> wrote:
Hi Mikheil,

if you have several mpi libraries installed in your system you can
manually specify all the PATHs in the configure line.

Here is an example on how you would configure in SuSE 11.2 with openMPI:

./configure \
 CC=/usr/lib64/mpi/gcc/openmpi/bin/mpicc \
 LD_LIBRARY_PATH=/usr/lib64/mpi/gcc/openmpi/lib64 \

The summary at the end of configure will then tell you that it
found a "generic" mpi version.


PS: If you want to know what exactly the mpicc wrapper does, type "mpicc -show"
   on command line.

On 08/10/2010 03:43 AM, Ahmad A. J. Agung wrote:
> Hi Mikheil,
> Sorry I didn't notice your previous email. From the ../configure result
> in your previous email:
>>checking for mpirun... /usr/bin/mpirun
>> configure-ac: error: LAM/MPI not working
> There is an MPI inside your default path /usr. The problem is if you do
> not install MPI in a default path, (i.e. your last LAM installation:
> --prefix=/usr/local/lam), the ../configure ESPResSo will call the mpirun
> in /usr/bin/mpirun first and use it in the whole setting. You can
> install MPI with --prefix=/usr, which will replace the old MPI, but I do
> not suggest it because it is risky and you cannot do this if later you
> install in a public cluster which you do not have a root access. What I
> suggest is trying to declare your environment path in your .bashrc or
> .bash_profile file in your home directory. If you never do this, you can
> googling first. The point is making the ../configure ESPResSo call the
> mpirun and mpi library and mpi header in your MPI installation directory
> first.
> I prefer OpenMPI because I heard there is no serious development in LAM
> now. Manually installing gcc also requires much time, mostly when you
> get problem with its dependency. If you install with openMPI, try this
> in the flag:
> ../configure-ac CC=mpicc MPICC=MPICC --with-mpi=openmpi CPPFLAGS=... etc...
> FMIIW, Good Luck,
> Aang
> ----------------------------------------------------------------------
> Message: 1
> Date: Mon, 9 Aug 2010 16:29:51 -0400
> From: Mikheil Azatov <address@hidden <mailto:address@hidden>>
> Subject: Re: [ESPResSo] parallel computing
> To: address@hidden <mailto:address@hidden>
> Message-ID:
>     <address@hidden
> <mailto:address@hidden>>
> Content-Type: text/plain; charset="iso-8859-1"
> Hi Aang, sorry to bother you again. I think I figured out what is the
> problem after a long day. So when I install lam it gives me an error that
> "LAM requires a C++ compiler with support for the bool data type." I don't
> know if you ever had this problem but after looking through lam forums the
> only suggestion i found was to downgrade gcc version. before doing that i
> thought it might be better to try other mpi's. As i understand other two
> options are Open mpi and MPICH. MPICH is not recommended in Espresso manual
> (as working slower) and Open MPI is not described there at all( so i don't
> know what option would I even use in ./configure --with-mpi=???) . So I was
> wandering what would you suggest to do in my situation. Which one of these
> to try to install or maybe keep trying with lam?
> Thank you so much!!! Your help will be really appreciated!
> Mikheil Azatov
> University of Maryland

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