RE: [gmx-users] Gromacs in Parallel

[Jim Kress]

Yes, many people have encountered this problem with mpich 1.2.7  Use a
version of MPICH2 (like OpenMPI) v1.3

Jim 

> -Original Message-
> From: gmx-users-boun...@gromacs.org 
> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Andrew Paluch
> Sent: Monday, August 10, 2009 10:53 AM
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Gromacs in Parallel
> 
> To whom this may concern,
> 
> I am receiving the following errors when attempting to run 
> Gromacs in parallel:
> 
> Making 1D domain decomposition 4 x 1 x 1
> p2_21562:  p4_error: Timeout in establishing connection to 
> remote process: 0
> p2_21562: (302.964844) net_send: could not write to fd=5, errno = 32
> 
> 
> where I am using mpich 1.2.7 for 64 bit processors.  From 
> what I can find, it seems as if this is a mpich issue and not 
> an issue of Gromacs.  Has anyone else encountered such a 
> problem?  Also, does anyone have any suggestions for a solution?
> 
> Thank you,
> 
> Andrew 
> 

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Re: [gmx-users] Gromacs in Parallel

[TJ Piggot]

I agree. Mpich 1 is very old, you should try mpich 2 or lam or openmpi.

Tom

--On Tuesday, August 11, 2009 09:16:54 +1000 Mark Abraham 
 wrote:



Andrew Paluch wrote:

To whom this may concern,

I am receiving the following errors when attempting to run Gromacs in
parallel:

Making 1D domain decomposition 4 x 1 x 1
p2_21562:  p4_error: Timeout in establishing connection to remote
process: 0 p2_21562: (302.964844) net_send: could not write to fd=5,
errno = 32


where I am using mpich 1.2.7 for 64 bit processors.  From what I can
find, it seems as if this is a mpich issue and not an issue of Gromacs.
Has anyone else encountered such a problem?  Also, does anyone have any
suggestions for a solution?


Indeed, this is not a problem intrinsic to GROMACS. I'm not aware of
problems with particular MPI libraries, but you might try compiling
GROMACS with another such library. Whoever configured this machine should
probably look into the problem.

Mark
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--
TJ Piggot
t.pig...@bristol.ac.uk
University of Bristol, UK.

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Re: [gmx-users] Gromacs in Parallel

[Mark Abraham]

Andrew Paluch wrote:

To whom this may concern,

I am receiving the following errors when attempting to run Gromacs in
parallel:

Making 1D domain decomposition 4 x 1 x 1
p2_21562:  p4_error: Timeout in establishing connection to remote process: 0
p2_21562: (302.964844) net_send: could not write to fd=5, errno = 32


where I am using mpich 1.2.7 for 64 bit processors.  From what I can find,
it seems as if this is a mpich issue and not an issue of Gromacs.  Has
anyone else encountered such a problem?  Also, does anyone have any
suggestions for a solution?


Indeed, this is not a problem intrinsic to GROMACS. I'm not aware of 
problems with particular MPI libraries, but you might try compiling 
GROMACS with another such library. Whoever configured this machine 
should probably look into the problem.


Mark
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[gmx-users] Gromacs in Parallel

[Andrew Paluch]

To whom this may concern,

I am receiving the following errors when attempting to run Gromacs in
parallel:

Making 1D domain decomposition 4 x 1 x 1
p2_21562:  p4_error: Timeout in establishing connection to remote process: 0
p2_21562: (302.964844) net_send: could not write to fd=5, errno = 32


where I am using mpich 1.2.7 for 64 bit processors.  From what I can find,
it seems as if this is a mpich issue and not an issue of Gromacs.  Has
anyone else encountered such a problem?  Also, does anyone have any
suggestions for a solution?

Thank you,

Andrew
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Re: [gmx-users] gromacs in parallel version

[Diego Enry Gomes]

Looks like you are using MPICH2 as "mpi" software.
Try including "mpirun" before mdrun_mpi.

mpirun -n 4 mdun_mpi -v -s topol.tpr


If that doesn't work you shoud run start the MPI DAEMON ( MPD ) before  
mpirun:


mpdboot
mpirun -n 2 mdun_mpi -v -s topol.tpr

after you job finishes you might want to stop the mpi daemon by running:
mpdallexit

Diego.

--
=
Diego Enry B Gomes | PhD Student @ UFRJ - Brazil
/tmp/home/@ Pacific Northwest National Laboratory
Richland, WA.  +1 (509) 372.6363
diegoenry.go...@pnl.gov
=


On Mar 6, 2009, at 5:13 AM, ANINDITA GAYEN wrote:


Dear all,
Sorry for the former post without any subject.
I want to install gromacs in parallel version. I already  
have the normal version of gromacs and i want an MPI version of  
mdrun. The commands i have used are as followed.

make distclean
./configure --enable-float --enable-mpi --prefix=/home/x --program- 
suffix=_mpi

make mdrun -j 4
make install-mdrun
[ i have installed fftw with --prefix=/home/x/fftw-3.2.1 and  
in .bashrc include ...

   export CPPFLAGS=-I/home/x/fftw-3.2.1/include
   export LDFFLAGS=-L/home/x/fftw-3.2.1/lib]
grmmacs installation run successfully.
But when i run
mdrun_mpi ..i got the message  "Can't read  
MPIRUN_MPD" and the mdrun_mpi program does not run.

Any suggestion regarding this problem will be highly acceptable.
thanks in advance,

Ms. Anindita Gayen
C/O Dr. Chaitali Mukhopadhyay
Senior Research Fellow
Department of Chemistry
University of Calcutta
92, A. P. C. Road
Kolkata-700 009
India

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Re: [gmx-users] gromacs in parallel version

[Justin A. Lemkul]

ANINDITA GAYEN wrote:

Dear all,

Sorry for the former post without any subject.
I want to install gromacs in parallel version. I already 
have the normal version of gromacs and i want an MPI version of mdrun. 
The commands i have used are as followed.

*make distclean*
*./configure --enable-float --enable-mpi --prefix=/home/x 
--program-suffix=_mpi*

*make mdrun -j 4*
*make install-mdrun*
[ i have installed fftw with --prefix=/home/x/fftw-3.2.1 and in .bashrc 
include ...

   export CPPFLAGS=-I/home/x/fftw-3.2.1/include
   export LDFFLAGS=-L/home/x/fftw-3.2.1/lib]
grmmacs installation run successfully.
But when i run
mdrun_mpi ..i got the message  "Can't read MPIRUN_MPD" 
and the mdrun_mpi program does not run.


What command are you actually issuing to run mdrun_mpi?  This sounds like more 
of an MPI environment problem, not a Gromacs problem.


-Justin


Any suggestion regarding this problem will be highly acceptable.
thanks in advance,

Ms. Anindita Gayen
C/O Dr. Chaitali Mukhopadhyay
Senior Research Fellow
Department of Chemistry
University of Calcutta
92, A. P. C. Road
Kolkata-700 009
India



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--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] gromacs in parallel version

[ANINDITA GAYEN]

Dear all,
    Sorry for the former post without any subject.
    I want to install gromacs in parallel version. I already have the 
normal version of gromacs and i want an MPI version of mdrun. The commands i 
have used are as followed.
make distclean
../configure --enable-float --enable-mpi --prefix=/home/x --program-suffix=_mpi
make mdrun -j 4
make install-mdrun
[ i have installed fftw with --prefix=/home/x/fftw-3.2.1 and in .bashrc include 
...
   export CPPFLAGS=-I/home/x/fftw-3.2.1/include
   export LDFFLAGS=-L/home/x/fftw-3.2.1/lib]
grmmacs installation run successfully.
But when i run 
mdrun_mpi ..i got the message  "Can't read MPIRUN_MPD" and the 
mdrun_mpi program does not run.
Any suggestion regarding this problem will be highly acceptable.
thanks in advance,

Ms. Anindita Gayen
C/O Dr. Chaitali Mukhopadhyay
Senior Research Fellow
Department of Chemistry
University of Calcutta
92, A. P. C. Road
Kolkata-700 009
India


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Re: [gmx-users] GROMACS in parallel on a multicore PC?

[Yang Ye]

On 11/21/2007 7:33 PM, Vasilii Artyukhov wrote:


Hi everybody,

Sorry for a somewhat technical question, but I'd like to know which is 
the best way to run GROMACS on a SMP machine (in particular, a 
multicore PC). The (known) points of interest are:


- Does GROMACS support multithreaded execution & how efficient is it?


No.


- Should I rather use some kind of MPI & which (LAM/Open/MPICH) is 
better & why?



Yes. This is the only way.


Surely, there's always the option to run two serial jobs instead with 
a greater efficiency, but having some means to boost the single job 
performance by something like 1.9x would be very useful...


Thanks in advance,

Vasilii



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Re: [gmx-users] GROMACS in parallel on a multicore PC?

[David van der Spoel]

Vasilii Artyukhov wrote:

Thanks for the quick response :)
2007/11/21, Carsten Kutzner <[EMAIL PROTECTED] >:

Hi Vasilii,


 > - Does GROMACS support multithreaded execution & how efficient is it?
As far as I know this is planned, but not supported yet.

Ok, but what about the underlying math libs? Would using threaded libs 
boost performance to any noticeable extent?

No. We're not using any.






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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] GROMACS in parallel on a multicore PC?

[Vasilii Artyukhov]

Thanks for the quick response :)
2007/11/21, Carsten Kutzner <[EMAIL PROTECTED] >:
>
> Hi Vasilii,
>
>
> > - Does GROMACS support multithreaded execution & how efficient is it?
> As far as I know this is planned, but not supported yet.

Ok, but what about the underlying math libs? Would using threaded libs boost
performance to any noticeable extent?
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Re: [gmx-users] GROMACS in parallel on a multicore PC?

[Carsten Kutzner]

Hi Vasilii,


Vasilii Artyukhov wrote:
> Hi everybody,
> 
> Sorry for a somewhat technical question, but I'd like to know which is
> the best way to run GROMACS on a SMP machine (in particular, a multicore
> PC). The (known) points of interest are:
> 
> - Does GROMACS support multithreaded execution & how efficient is it?
As far as I know this is planned, but not supported yet.

> 
> - Should I rather use some kind of MPI & which (LAM/Open/MPICH) is
> better & why?
Yes. This is the way to go. On an SMP box you will probably not see
large differences between the different MPI implementations, but why not
try a few? My own experience is that LAM tends to be the fastest, partly
due to the memory mangager it uses.

Carsten

> Surely, there's always the option to run two serial jobs instead with a
> greater efficiency, but having some means to boost the single job
> performance by something like 1.9x would be very useful...
> 
> Thanks in advance,
> 
> Vasilii
> 
> 
> 
> 
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-- 
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/research/dep/grubmueller/
http://www.gwdg.de/~ckutzne
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[gmx-users] GROMACS in parallel on a multicore PC?

[Vasilii Artyukhov]

Hi everybody,

Sorry for a somewhat technical question, but I'd like to know which is the
best way to run GROMACS on a SMP machine (in particular, a multicore PC).
The (known) points of interest are:

- Does GROMACS support multithreaded execution & how efficient is it?

- Should I rather use some kind of MPI & which (LAM/Open/MPICH) is better &
why?

Surely, there's always the option to run two serial jobs instead with a
greater efficiency, but having some means to boost the single job
performance by something like 1.9x would be very useful...

Thanks in advance,

Vasilii
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Re: [gmx-users] GROMACS in parallel

[Mark Abraham]

Akshay Patny wrote:

Dear Sir

 

I am trying to install GROMACS. I have tried to install program and it 
goes through okay. However, when I try to compile the program in 
parallel using the –enable-mpi option, it gives me an error: “Cannot 
compile and link MPI code with cc”


 


See below for the command and the error.

 


Can you suggest what I can do to fix the same?


Use an MPI compiler. Find out what it is called on your system and take 
steps to use it - see ./configure --help for some options that can help 
here.


Mark
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[gmx-users] GROMACS in parallel

[Akshay Patny]

Dear Sir

 

I am trying to install GROMACS. I have tried to install
program and it goes through okay. However, when I try to compile the program in
parallel using the –enable-mpi option, it gives me an error:
“Cannot compile and link MPI code with cc”

 

See below for the command and the error.

 

Can you suggest what I can do to fix the same?

_

redwood r0914/gromacs-3.3.1> ./configure
--prefix=/ptmp/r0914/gromacsp --enable-mpi

 

checking build system type... ia64-unknown-linux-gnu

checking host system type... ia64-unknown-linux-gnu

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for gawk... gawk

checking whether make sets $(MAKE)... yes

checking how to create a ustar tar archive... cpio

checking for cc... cc

checking for C compiler default output file name... a.out

checking whether the C compiler works... yes

checking whether we are cross compiling... no

checking for suffix of executables... 

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether cc accepts -g... yes

checking for cc option to accept ANSI C... none needed

checking for style of include used by make... GNU

checking dependency style of cc... gcc3

checking for mpxlc... no

checking for mpicc... no

checking for mpcc... no

checking for hcc... no

checking whether the MPI cc command works... configure:
error: Cannot compile and link MPI code with cc

_

 

Regards

Akshay

 

 

Akshay Patny

Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry

Research Institute of Pharmaceutical
Sciences
University
 of Mississippi
University,
 MS 38677
E-mail: [EMAIL PROTECTED]
Tel: 662-915-1286 (office); Web: www.olemiss.edu 

 






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